Annual/Termination Reports:

[03/15/2011] [03/29/2010] [05/02/2011] [03/26/2012] [02/28/2013]

Report Information

Participants

Brief Summary of Minutes

The NRSP-8 business meeting was preceded by workshops for all species and area subcommittees as well as a combined Animal Genome Workshop, which contained four plenary presentations. Professor Morris Soller gave the 2011 NRSP-8 Distinguished Lecture. The business meeting was called to order by Chris Bidwell, the 2011 NRSP-8 Chair and recorded by Geoff Waldbieser, Secretary, with 43 members and guests in attendance. The 2009 minutes were approved unanimously. Noelle Cockett, who presented the 2010 Distinguished Lecture, was honored with a commemorative plaque to recognize her efforts in small ruminant genomics. Species/area coordinator reports were given for Aquaculture, Bioinformatics, Cattle, Equine, Poultry, Sheep/Goat, and Swine. Colin Kaltenbach and Muquarrab Qureshi provided administrative reports. Geoff Waldbieser, USDA-ARS assumed the NRSP-8 Chair for 2011-2012. Tom Porter, University of Maryland was elected as Secretary for 2011-2012. A motion to hold the 2012 meeting in conjunction with the Plant and Animal Genome conference was approved unanimously. The meeting was adjourned.

Accomplishments

Overview<br /> <br /> The NRSP-8 participants and their collaborators have far reaching national and international impact on basic discovery and application of genomics to animal agriculture with over 220 peer-reviewed publications in 2010. The community has rapidly adopted new genomics technologies including high-throughput short read sequencing, high density SNP detection and several types of microarrays to sequence genomes, generate high quality genetic maps and analyze gene expression of a rapidly increasing number of species. The NRSP-8 has facilitated the transfer of experience from the earliest species with sequenced genomes to the current efforts to produce higher quality integrated genetic maps and genome sequences. The NRSP-8 participants and their collaborators are using genomics technology, bioinformatics resources and diverse animal models to investigate fundamental mechanisms affecting production efficiency, product quality, animal health, disease resistance and food safety. Genomics technology has been successfully adopted for genetic selection programs for some sectors of animal agriculture. Some species pose unique challenges for the application of genomics technology due to the complex structures of brood stock development. NRSP-8 participants are also working to solve those challenges as genomics technologies and capabilities to predict genetic merit are evolving. The NRSP-8 has fostered the development of critical technical and information resources for animal genomics in the USA and throughout the world. The annual NRSP-8 workshops have become an essential component for development of collaborations, training and dissemination of new information to government, academic and industry stakeholders in animal agriculture.<br /> <br /> The annual NRSP-8 meetings comprised of Aquaculture, Cattle/Sheep/Goat, Equine, Poultry and Swine workshops was held in conjunction with the XIX International Plant and Animal Genome conference in San Diego, CA on January 15-16, 2011. There were 572 registered participants with specific interests in animal genomics. Attendance in the various NRSP-8 workshops ranged from 60 to 250 people from 10-15 different countries. The following report summarizes 2010 reports from the species/area technical reports from subcommittee/workshop chairs based on experiment station reports of the participants. <br /> <br /> Annual reports from the species/area coordinators can be found under the project description for NRSP008: National Animal Genome Research Program on the NIMSS website under ATTACHMENTS.<br /> <br /> <br /> Aquaculture Technical Report <br /> <br /> Genome Sequencing: The Oyster Genome Consortium was successful in establishing a whole genome sequencing project for the Pacific oyster (Crassostrea gigas). Sequencing and assembly of a catfish reference genome is also underway with participants from ARS Catfish Genetics Research Unit, Auburn U., USDA-ARS Bovine Functional Genomics Laboratory, and U. of British Columbia. Gene transcripts from various tissues of multiple individual catfish with diverse genetic background were also sequenced. Projects to identify EST and define the transcriptomes of various tissues were conducted in catfish, rainbow trout, brook trout and striped bass.<br /> <br /> Genome Mapping: The USDA-ARS National Center for Cool & Cold Water Aquaculture (NCCCWA) rainbow trout map was used for producing a first generation integrated physical and genetic map. A high density RAD (restricted site associated DNA) genetic map of Swanson x Whale Rock recombinant double haploids is being constructed using approximately 7,600 SNPs to aid in future assembly of a reference genome sequence for trout. The 2nd generation NCCCWA rainbow trout genetic map is now available through G-browser at the Animal Genome website of the NRSP-8 bioinformatics group. A first SNP genetic map for Pacific white shrimp was built with 418 SNP markers mapped onto 45 sex-averaged linkage groups. This SNP genetic map lays the foundation for future shrimp genomics studies. Scientists from the USDA-ARS NCCCWA, VIMS and N. Carolina State U. (NCSU) developed a linkage map for striped bass by genotyping two half-sib families at 289 microsatellite DNA markers and assembled a map with 26 linkage groups. <br /> <br /> The USDA-ARS SNARC generated 192 crosses of Morone using National Breeding Program foundation stocks and completed studies evaluating heritability of phenotypic variation growth of hybrid striped bass as tank-reared fingerlings. Scientists from SNARC and the U. Arkansas at Pine Bluff evaluated the genetic and phenotypic influence of parental traits on hybrid striped basslarval size and quality, and the influence of genetic factors on metabolic and stress-related traits, discovering that female phenotype does not significantly affect larval traits (e.g. growth) but that genotype does have a significant affect. This finding is significant because any increase in larval size at hatch resulting from selection would reduce the need for live feeds, which could make year-round tank production of fry and fingerlings economically viable for industry. SNARC and NCSU researchers also distributed advanced fingerlings and mature broodfish from National Breeding Program stocks to HSB producers engaged in propagation of commercial domesticated broodstocks.<br /> <br /> Database Activities: Many useful links for aquaculture can be found at http://www.animalgenome.org/aquaculture/. In collaboration with John Liu, Auburn U., a Catfish SNP Project web site (http://www.animalgenome.org/catfish/cbarbel/), a Teleost Alternative Splicing Database (http://www.animalgenome.org/tasd), and a Catfish COI DNA Barcode Database (http://www.animalgenome.org/fishid/) have been established. The bioinformatics coordinators have helped Moh Salem of West Virginia U. to set up web blast and data download of the rainbow trout transcriptome data characterized using Sanger and Next GENeration sequencing data (http://www.animalgenome.org/aquaculture/salmonids/rainbowtrout/EST_WV.html).<br /> <br /> Cattle Technical Report <br /> <br /> The U. of California-Davis Station (J.F. Medrano and collaborators) has utilized next-generation RNA sequencing to examine expression patterns in the bovine mammary gland and in milk somatic cells The results show that milk somatic cells are representative of the mammary gland transcriptome and can be used as an alternative tissue to study gene expression of milk related traits. RNA expression was also examined in cows at day 15 (transition) and day 250 (late) lactation. Genes encoding milk proteins had the most abundant transcripts in transition milk and genes involved in immune regulation and cell defense had the most abundant transcripts in late lactation. The accuracy of RNA-Seq SNP discovery was tested by comparing SNP detected in a set of 42 candidate genes expressed in milk that had been resequenced earlier using Sanger sequencing technology. The results confirmed that analyzing the transcriptome using RNA-Seq technology is an efficient and cost effective method to identify SNP in transcribed regions. The study provided guidelines to maximize the accuracy of SNP discovery and the prevention of false-positive SNP detection, and provided more than 33,000 SNP in Holsteins, that are located in coding regions of genes expressed during lactation.<br /> <br /> The Pennsylvania Station (W. Liu) has analyzed the transcriptome of the bovine Y-chromosome (BTAY) using a direct testis cDNA selection and Next-Generation sequencing approach using Illumina GA2. Their results suggest an extensive transcriptional activity on BTAY. Examining the lineage specific gene families temporal and spatial expression patterns of ZNF280BYs in testis suggest a role in spermatogenesis. The study provides insights into the genomic organization of the bovine Y chromosome and gene regulation in spermatogenesis, and provides a model for studying evolution of multi-copy gene families in mammals.<br /> <br /> At the Massachusetts Station (C. Baldwin, J. Telfer and collaborators), bovine T cell receptor delta chains of the ³´ high species have been characterized. By annotating the bovine genome Btau_3.1 assembly the presence of 56 distinct variable (V) genes was found, 52 of which belong to the TRDV1 subfamily and were co-mingled with the TCR± V genes. In addition two genes belonging to the TRDV2 subfamily and a single TRDV3 and TRDV4 gene were found. The organization of the TRD locus was described, together with a system by which to classify the TRDV1 genes based on their phylogenetic grouping. On a similar line of work, this station annotated and performed evolutionary analysis in WC1/CD163 co-receptors. Annotation in the bovine genome identified genes coding for bovine CD163A and CD163c-± but found no evidence for CD163b. Bovine CD163A is widely expressed in immune cells, whereas CD163c-± transcripts are enriched in the WC1+ ³´ T cell population. Phylogenetic analyses of the CD163 family genes and WC1 showed that CD163c-± is most closely related to WC1 and that chicken and platypus have WC1 orthologous genes, previously classified as among their CD163 genes.<br /> <br /> At the Washington Station (Z. Jiang and collaborators) the reverse cholesterol transport pathway (RCT) were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population. Among 36 SNPs detected in 11 of 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F2 progeny. Single-marker analysis for 19 of 36 SNP had significant associations with nine phenotypes (P<0.05). Combining these results with previously reported genetic networks derived from 71 known functional genes, genetic networks related to the RCT pathway were identified. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production. Holly Neibergs and collaborators have continued to do fine mapping on regions that have been identified as associated with Johnes disease. Illumina custom veracode assays were utilized to place markers about every 3 kb around a 200-300 kb regions previously identified as harboring positional candidates. This provided information to proceed with re-sequencing of the significant areas in collaboration with Dr. Van Tassell and Dr. Matukumali. An initial association analysis was conducted on bovine viral diarrhea-persistently infected (BVD-PI) cattle. Samples were obtained after testing over 10,000 animals for BVD-PI. To refine these loci, the density of markers on BTA2 and BTA26 was increased in order to determine if the loci associated with BVD-PI calves differed from the loci associated with the dams of BVD-PI calves or animals with bovine respiratory disease. Bovine viral diarrhea virus is one of the viral pathogens that comprise the bovine respiratory disease complex. In relation to bovine respiratory disease (BRD) an initial genome-wide study identified two chromosomal regions on BTA2 and BTA26 that were linked with BRD in four Bos taurus x Bos indicus crossbred cattle.<br /> <br /> At the U. of Wisconsin-Madison Station (B. Kirkpatrick and collaborators) further validation of SNP associations with twinning rate are being conducted. In collaboration with scientists at USMARC (L. Kuehn, G. Bennett), 66 SNPs previously identified as associated with twinning rate in the US Holstein population have been genotyped on 731 animals from the USMARC twinning population. A second validation analysis is being conducted in collaboration with a commercial twinner herd in which ovulation and twinning rate data have been collected. A total of 299 animals from this herd have been genotyped with the same 66 SNPs. Four of the 66 SNPs were successfully validated at a nominal p<0.01 in the USMARC herd. The most significant (p<1.8x10-4) was a SNP previously discovered in the IGF1 gene and associated with twinning rate in two Holstein populations. Creation of a resource family to map the location of a major gene for ovulation rate continued. The first 88 daughters of a bull believed to possess a major gene for ovulation rate have been evaluated and the gene has been fine-mapped. Analysis of a candidate gene is ongoing. An additional 33 daughters were born in 2010.<br /> <br /> The Oklahoma Station (R.G. Mateescu) has worked on the effect of breed and muscle type on fatty acid composition. Steers from two different breeds known for high (Angus) and low (Charolais) marbling scores are used in the study. Two extreme muscle types are being analyzed: longissimus dorsi (more oxidative) and semitendinosus (more glycolytic). Fatty acid profile of the two muscles were significantly different, with longissimus having a greater percentage SFA (P < 0.0001), a lower percentage of MUFA (P < 0.0001), and tended to have a lower percent PUFA (P = 0.06) than semitendinosus. Gene expression profiles were analyzed using a bovine whole-genome 70-mer oligo array with 24,000 long oligonucleotide probes was used. Ingenuity Pathways Analysis was used to identify the most relevant biological mechanisms, pathways, and functions of these genes. Thirty-five array elements were found to be differentially (P < 0.01) expressed between longissimus and semitendinosus muscles, with at least a 2-fold change in expression, with 32 elements up-regulated and 3 down-regulated.<br /> <br /> The Texas Station (C. Gill and collaborators) has continued to collect phenotypes from the Cycle 1 (F2 Nellore-Angus cows), Cycle 2 (reciprocal F2 steers and heifers) and Cycle 3 (F3 Nellore-Angus steers and heifers) McGregor Genomics populations. They have continued work on a pilot study to investigate the genetic basis of variation in immunological response to vaccination for BVDV using steers from Cycle 2 and Cycle 3. They are investigating the genetic mechanisms behind variation in growth, disposition, nutrient utilization, feed efficiency, carcass and meat traits in the steers as well as female reproductive efficiency traits in the heifers. Penny Riggs, P. Holman and J. Womack have examined gene expression related to tick resistance in cattle. Differentially expressed genes associated with the site of tick attachment have been identified, and further investigation will be conducted. They continue to collaborate with Dr. E. Amaral of Brazil, J. Womack and L. Skow to refine the genetic map of the river buffalo, focusing on river buffalo genes in the MHC region. Jim Womack and S. Dindot are also examining copy number variants (CNVs) in innate immune genes, particularly cathelicidins and defensins. Polymorphisms of copy number for bovine cathelicidin genes have been demonstrated and current experiments are designed to test the effect of copy number on gene function. Through collaborations they have begun comparative genetic studies of bovids using the cattle genome as a reference. <br /> <br /> Equine Technical Report<br /> <br /> Illumina 74K SNP genotyping Chip: A new Illumina Infinium array containing ~74,500 SNP markers in 2011. The marker list submitted for assay design of the second generation Beadchip has an average of 1.5 SNPs per 50 kb bin and therefore represents a substantial increase in the number of markers across the genome. SNP markers included on this new genotyping array include ~53,000 markers that were validated on the Equine SNP50 Beadchip which had a minimum minor allele frequency of e 0.005 across the 354 samples analyzed in the Gentrain dataset. The ~21,500 additional markers included in the new assay design were chosen to address as many gaps in coverage from the Equine SNP50 Beadchip as possible, and to globally improve coverage across the genome. As there were insufficient SNPs from the seven discovery breeds alone to achieve these goals, ~ 3,900 Twilight SNPs, and ~ 2,800 SNPs from RNAseq data were used, and increased numbers of SNPs were included in bins that flank many of the larger gaps. In addition, the new SNP panel includes enhanced coverage of the MHC region on ECA20 and the X chromosome, as well as several SNPs from coat color loci to use for sample validation purposes.<br /> <br /> Equine Whole Genome Tiling Array: In order to enable comprehensive studies of Equine copy number variation (CNV), a whole genome tiling array was designed based on the EquCab2 (Sep. 2007) assembly by researchers at University of Adelaide and Texsas A&M. The array contains design a total of 418,577 probes, 305,416 of which were tiled into repeat-masked EquCab2 with an average resolution of 7.5 Kb. In addition to genome wide high resolution, there are three other significant features of this tiling array: 1) a subset of 85,852 probes for almost all Equine RefSeqs (18,427 out of 18,763), mainly from exons; 2) 519 chromosome Y specific probes, designed from 362 available STSs (BAC end tags) and 3) the inclusion of 26,790 probes for 3 Mb long sub-telomeric regions of all chromosomes except chromosome Y. This array is the first comprehensive equine high resolution resource for CNV mapping.<br /> <br /> The Equine breed diversity consortium was developed to facilitate large scale population genetic analysis in the domestic horse. This is an international collaboration of scientists from 22 different intuitions and represents genetic data from approximately 40 horse breeds. Many groups continue to focus on the collection of samples for mapping of simple and complex traits of interest, with a major focus on disease and athletic performance phenotypes<br /> <br /> Poultry Technical Report<br /> <br /> Telomere/telomerase dysregulation and Mareks Disease virus (MDV): MDV is a major cause of mortality leading to substantial economic losses to the poultry industry. Interestingly, the oncogenic MDV genome (which is circular and has no need for a telomere-maintenance system) contains two copies of the chicken telomerase RNA gene as well as several sets of telomere repeats. We hypothesize the MDV is utilizing aspects of the telomere-telomerase system to integrate into the chicken genome at the site of telomeres, and that this contributes to aspects of the disease state  pathology, persistence and/or oncogenesis.<br /> <br /> Iowa State University maintains 13 unique chicken research lines [including highly inbred; MHCcongenic; closed populations; and advanced intercross lines (AIL)] that serve as resources for identifying genes and QTL of economic importance. The continued production of AIL (now at generation F18) facilitates the opportunity to narrow the confidence intervals (fine-map) around QTL and to conduct detailed studies on gene expression. Financial constraints resulted in the termination of 11 of the 24 lines in the past two years (2009-2010). Lines are maintained in minimal numbers, so collaborative studies or requests for genetic material must be arranged well in advance. Genetic material (chicks, fertile eggs, blood, tissue, DNA or RNA) has been shared with cooperating investigators to expand studies on the chicken genome, in addition to the studies conducted at Iowa State University. Current studies utilizing ISU chicken lines include collaborations with Huaijun Zhou of Texas A & M University (copy-number variation, avian influenza response) Andrew Clark of Cornell University (embryonic tissues for imprinting studies), Shane Burgess of Mississippi State University (F8 tissues for proteomic analysis of host response to Salmonella), Calvin Keeler of University of Delaware (F8 cDNA for microarray analysis of host response to Salmonella), and Hyun Lillehoj of USDA-ARS (Fayoumi chicks for analysis of response to Eimeria infection).<br /> <br /> AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. GOModeler, a tool that enables researchers to conduct hypothesis-based testing of high throughput datasets using the GO. GOModeler summarizes the overall effect of a user defined gene/protein differential expression dataset on specific GO hypothesis terms selected by the user to describe a biological experiment. The design of the tool allows the user to complement the functional information in the GO with his/her domain specific expertise for comprehensive hypothesis testing. GOModeler allows hypothesis driven analysis of high throughput datasets using the GO. Using this tool, researchers can quickly evaluate the overall effect of quantitative expression changes of gene set on specific biological processes of interest. The results are provided in both tabular and graphical formats. <br /> <br /> Sheep/Goat Technical Report<br /> <br /> Sheep Radiation Hybrid Map: Utah State University has added around 300 new markers to the ovine whole-genome RH map, in order to close gaps between adjacent RH groups and to extend the telomeric ends of the chromosomes. The addition of these markers increased marker density from 1.51 Mb/marker to 1.13 Mb/marker and the total map size increased ~37% in comparison to the previous version of the RH map. In addition, cross-species comparative maps based on marker-dense maps and high-coverage genome sequences were used to identify homologous synteny blocks (HSBs) and chromosome evolutionary breakpoint (EBRs) between sheep and other mammalian species. The number of homologous synteny blocks and chromosomal breakpoints between sheep and the human, cattle, horse and dog genomes were 216/54, 95/39, 122/61 and 135/75, respectively. Of the 229 conserved chromosomal segments, seventeen on human chromosomes (HSA1, 2, 3, 4, 6 and 21) and three on bovine chromosomes (BTA19, 27 and 28) had not been previously identified. This whole-genome RH map for sheep is a resource that can be used for fine-mapping economically important QTLs and will contribute to the assembly of the ovine reference sequence. It also contributes to a better understanding of the evolutionary history of ruminant species. A detailed review of the role of chromosome rearrangements in mammal evolutionary history is now possible.<br /> <br /> Goat Radiation Hybrid Map: Virginia State University has developed a radiation hybrid (RH) map for stronger comparative genomic analyses. A collaboration of VSU, Huazhong Agricultural University, Texas A & M, DNA Landmarks, INRA and IAEA. A RH panel of 92 clones has been established and used for initial mapping projects. DNA Landmarks has subjected the panel to the bovine and ovine 50K SNP panels. Data from the bovine panel has been developed into the initial goat RH map by Bertrand Servin at INRA.<br /> <br /> Goat Genome Sequencing: Two sequencing projects have begun for the goat, one public and one private, in association with the international goat consortium. The public project was undertaken by the research group at BGI in China as part of their 1000 genomes project. The initial sequencing has been completed on Illumina GX sequencers and the sequences are currently in the assembly process. NRSP-8 members have contributed to this project by providing virtual and RH maps for the assembly team and have discussed VSU working on aspects of the assembly and annotation. <br /> <br /> A sheep flock segregating for genes controlling parasite resistance has been created at Louisiana State University. The flock includes 378 F2 offspring of five F1 sires produced from Gulf Coast Native (resistant) and Suffolk (susceptible) crosses. Fecal egg counts (FEC) for Haemonchus contortus and packed cell volume (PCV) measurements were taken on all lambs at three time-points (at weaning, after 5 weeks on pasture, and 6 weeks after experimental challenge). In addition, all offspring, as well as their parents and grandparents, were genotyped with the Illumina Ovine SNP50 BeadChip. Preliminary analysis of a select group of 25 lambs (resistant = 19 and susceptible = 6) using PLINK software revealed significant associations (P < 1.31E - 06) for PCV1, PCV2 and FEC2 on 9 chromosomes. Using R/qtl, significant associations (LOD > 6.0) were found for PCV1, PCV2 and FEC2 on 10 chromosomes.<br /> <br /> Ovine progressive pneumonia virus (OPPV), a lentivirus of sheep, infects 66% of ewes at USSES. Scientists at the Animal Disease Research Unit and U.S. Sheep Experiment Station initiated a study to identify genetic factors influencing host control of OPPV and disease progression. OPPV cELISA antibody status and provirus concentrations were measured for 1000 ewes of 3 breeds, Rambouillet, Polypay, and Columbia for whole genome association using the Illumina OvineSNP50 marker set. Initial results indicate genes with logical roles in both cELISA status and provirus concentration. Further, some of these genes have no prior association with HIV (human immunodeficiency virus). Since both OPPV and HIV are macrophage-tropic lentiviruses with similar genomic structure, these genes may contribute to human medicine as well as animal agriculture. A molecular genetic study on transmission of OPPV unexpectedly found maternal transmission events accounted for the small minority of cases in one flock. This is contrary to the situation in caprine arthritis encephalitis virus (CAEV) in goats, and counter to previous expectation for OPPV in sheep. These results may suggest a broader range of possible explanations for mechanisms underlying genomic regions associated with OPPV.<br /> <br /> Swine Technical Report<br /> <br /> At PSU, an integrated genetic, RH, BAC-FP, RNASeq and comparative map has been created for SSC4 with 573 loci mapped to this chromosome. A similar integrated map for the remainder of the genome is being created with 11 chromosomes finished through 2010; the rest of the genome will be finished during 2011. Average map resolution is an improved 250 kb/marker for SSC4. <br /> <br /> At BARC, the nomenclature for the swine leukocyte antigen (SLA) complex, was updated and is posted on the Immuno Polymorphism Database-MHC (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla). BARC also reported on development of a polymerase chain reaction (PCR)-sequence-specific primer (PCR-SSP) typing method for detecting SLA class I and class II alleles, and this method was used for typing of PHGC pigs to determine the influence of SLA diversity on genetic resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection in outbred pigs. BARC also reported on a fluorescent microsphere immunoassay (FMIA) developed with South Dakota State University to detect innate inflammatory, regulatory, Th1, and Th2 cytokines. BARC, through the US Veterinary Immune Reagent Network www.vetimm.org continues to develop and distribute immune molecule detection resources to the research community. At WSU, SNP marker development for 15 candidate genes for PRRSV resistance is ongoing.<br /> <br /> At ISU, a DNA bank of pigs with Salmonella fecal shedding data was created and made available. ISU provided sequence data and annotations to scientists at Roslin Institute and Affymetrix to develop a second-generation custom Genechip, which is now available for genome-wide transcriptional profiling using the Affymetrix platform.<br /> <br /> At MSU, scientists added 20 additional markers on 9 chromosomes across 954 animals and added an additional 444 animals to their pQTL/eQTL resource population. A QTL scan found 26-29 QTL for growth (depending on model used), as well as 38-51 QTL for carcass and meat quality traits. Using the new NRSP-8 supported oligo array to find gene expression differences during muscle development, they found nearly 500 probes had signals indicating differential expression for the corresponding transcripts in Piau or York-Landrace pigs, and signals for 1,300 probes were different between breeds. An eQTL study was reported on selected animals from this population, and 62 eQTLs and three gene networks for loin muscle expression were found. Thirteen regions had oeverlapping pQTL and eQTL locations, indicating a significant number of cis-acting QTLs were found.<br /> <br /> At UNL, a population to study sow longevity genetics was initiated, samples are being collected through 2011 using the Nebraska growth/reproduction selection lines. The SNP chip was used to find association to development, reproduction and lifetime productivity traits for the first four replicates of animals. SNPs associated with these traits were found for many chromosomes, depending on trait of interest. <br /> <br /> At NCSU, a project to investigate porcine patellar gene expression patterns during impact injury as a human model is ongoing; 11 genes have been tested by q-PCR for response to different modalities of injury, of which many showed differential responses. A second project, investigating the copper metabolism on iron has been initiated. The effect of differing levels of dietary iron or source of copper ion on the expression of several genes relevant to copper metabolism as well as on copper levels was performed on young male pigs. Gene expression for a number of genes was shown to be affected by iron deficiency or by the level and/or source of copper.<br /> <br /> At BARC, continued progress in the PRRS host Genetics Consortium (PHGC) project, a large consortia with many collaborating groups, was reported. Eight trials of 200 pigs each have been completed, and blood samples for viral titer and RNA expression work, as well as growth data, have been collected. Genomic DNA has been prepared for trials 1-6 and provided to collaborators for SNP chip analysis, which is ongoing. In collaboration with MSU and NCSU, measurement of expression using the pigoligoarray for a number of tissues from pigs infected with two different PRRSV isolated have been performed, and the data is being analyzed.<br /> At ISU, results using the SNP chip to find SNPs associated with traits measured on several populations were described. Commercial populations with traits including sow productive life and other reproductive traits recorded were analyzed and a number of SNPs were found for several traits. Feet and leg soundness traits were also tested, and SNPs associated with these traits were found. The SNP chip was also used to find SNPs associated with a number of traits associated with production efficiency in the ISU Residual Feed Intake (RFI) selection lines. For 716 pigs tested (387 select and 329 control animals), many associated SNPS were found, and pathway analysis of genes mapping near these SNPs showed two pathways of functional relevance (fatty acid metabolism and cellular energy production).<br /> <br /> At ISU, the PHGC database is continuing to be developed. The ANEXdb database on gene expression and expressed sequence annotation has been used by many groups world-wide and cited in over 6 publications reporting gene expression profiling of porcine tissues. ANXdb has been migrated to www.animalgenome.org under the NRSP-8 Bioinformatics Coordinator. The Pig QTLDB is now part of an expanded AnimalQTLDB.<br /> <br /> PUBLICATIONS<br /> <br /> <br /> Peer Reviewed Publications 221 (SEE FOLLOWING);<br /> Abstracts and Proceedings 134;<br /> Book Chapters 6;<br /> Dissertations and Thesis 15;<br /> Other Publications 5<br /> <br />

Publications

REFEREED PAPERS<br /> <br /> Abel, E.L., J. M. Angel, P. K. Riggs, L. Langfield, H.-H. Lo, M. D. Person, Y. C. Awasthi, L. E. Wang, S. S. Strom, Q. Wei, and J. DiGiovanni. 2010. Gsta4, a modifier of susceptibility to skin tumor development in mice and humans. J. Natl Cancer Inst. 102:1663-1675.<br /> <br /> Adelson DL, Rayson, Edgar RC (2010) Characterization and Distribution of Retrotransposons and Simple Sequence Repeats Animal Genetics 41 (Suppl. 2):9199. <br /> <br /> Alexander, L.S., A. Qu, S.A. Cutler, A. Mahajan, M.F. Rothschild, W. Cai, J.C. Dekkers, and C.H. Stahl. 2010. A calcitonin receptor (CALCR) single nucleotide polymorphism is associated with growth performance and bone integrity in response to dietary phosphorus deficiency. J Anim Sci. 88:1009-1016.<br /> <br /> Ankra-Badu GA, Bihan-Duval EL, Mignon-Grasteau S, Pitel F, Beaumont C, Duclos MJ, Simon J, Carré W, Porter TE, Vignal A, Cogburn LA, Aggrey SE (2010) Mapping QTL for growth and shank traits in chickens divergently selected for high or low body weight. nim Genet 41:400-405<br /> <br /> Ankra-Badu GA, Shriner D, Le Bihan-Duval E, Mignon-Grasteau S, Pitel F, Beaumont C, Duclos MJ, Simon J, Porter TE, Vignal A, Cogburn LA, Allison DB, Yi N, Aggrey SE (2010) Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate. BMC Genomics 11:107<br /> <br /> Archibald, A.L., L. Bolund, C. Churcher, M. Fredholm, M.A. Groenen, B. Harlizius, K.T. Lee, D. Milan, J. Rogers, M.F. Rothschild, H. Uenishi, J. Wang, and L.B. Schook. 2010. Swine Genome Sequencing Consortium. Pig genome sequence--analysis and publication strategy. BMC Genomics. 11:438.<br /> <br /> Ashworth, M.D., Ross, J.W., Stein, D.R., White, F.J., DeSilva, U., and Geisert, R.D. 2010. Endometrial caspase 1 and interleukin-18 expression during the estrous cycle and periimplantation period of porcine pregnancy and response to early exogenous estrogen administration. Reproductive Biology and Endocrinology 8:33<br /> <br /> Aston, K.I., G.P Li, B.A. Hicks, B.R. Sessions, T.D. Bunch, L.F. Rickords, B. Weimer, and K.L. White (2010) Aberrant expression of developmentally important genes in various stages of preimplantation bovine somatic cell nuclear transfer embryos. Cloning Stem Cells 12:23-32.<br /> <br /> Bailey, D.W., M.G. Thomas, J.W. Walker, B.K. Witmore, and D. Tolleson. 2010. Effect of previous experience on grazing patterns and diet selection of Brangus cows in the Chihuahuan Desert. Range Ecol. Manage. 62:223-232.<br /> <br /> Baird JD, Valberg SJ, Anderson SM, McCue ME, Mickelson JR. Presence of the glycogen synthase 1 (GYS1) mutation causing type 1 polysaccharide storage myopathy in continental European draught horse breeds. Vet Rec. 2010 Nov 13;167(20):781-4.<br /> <br /> Barb, C.R., Hausman, G.J., Rekaya, R. Lents, C.A., Lkhagvadorj, S., Qu, L., Cai, W., Couture, O.P., Anderson, L.L., Dekkers, J.C.M., Tuggle. C.K. 2010. Gene expression in hypothalamus, liver and adipose tissues and feed intake response to melanocortin-4 receptor (MC4R) agonist in pigs expressing MC4R mutations. Physiological Genomics 41: 254-268.<br /> <br /> Bierman, C.D., E.-S. Kim, K. Weigel, P.J. Berger and B.W. Kirkpatrick. 2010. Fine-mapping quantitative trait loci for twinning rate on BTA14 in North American Holsteins. J Animal Science 88:2556-2564.<br /> <br /> Bierman, C.D., E.-S. Kim, X. Shi, K. Weigel, P.J. Berger and B.W. Kirkpatrick. 2010. Validation of twinning rate whole genome association study results. Animal Genetics 41:406-416.<br /> <br /> Bellone RB, Forsyth G., Leeb T, Archer S, Sigurdsson S, Mauceli E., Enquensteiner M., Bailey E., Sandmeyer L, Grahn, B (2010) Fine mapping and mutation analysis of TRPM1, a candidate gene for Leopard Complex (LP) spotting and congential stationary Night Blindness (CNSB) in horses. and Fine Mapping the Leopard Complex (LP) Spotting Gene and Congenital Stationary Night Blindness (CSNB) in Horses. Briefings in Functional Genomics and Proteomics Advance Access doi:10.1093/bfgp/elq002<br /> <br /> Bellone R.R., S. Archer S., Wade, C.M., Cuka-Lawson, C., Haase, B., Leeb,T., Forsyth, G., Sandmeyer, L., and Grahn, B. (2010) Association analysis of candidate SNPs in TRPM1 with leopard complex spotting (LP) and congenital stationary night blindness (CSNB) in horses. Animal Genetics 41(Suppl. 2): 207.<br /> <br /> Bellone, R.R. (2010) Pleiotropic effects of pigmentation genes in horses. Animal Genetics 41(Suppl. 2): 100110.<br /> <br /> Bower MA, Campana MG, Whitten M, Edwards CJ, Jones H, Barrett E, Cassidy R, Nisbet RE, Hill EW, Howe CJ, Binns M. 2010 The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares. Biol Lett. PMID 20926431.<br /> <br /> Boyd, P. E. Hudgens, J.P.Loftus, D. Tompkins, J. Labresh, M. Wysocki, C.L. Baldwin and J. Lunney. 2010. Expressed gene sequence and bioactivity of the IFN³-response chemokine CXCL11 of cattle and swine. Veterinary Immunology and Immunopathology 136: 170-175.<br /> <br /> Brooks SA & Bailey E (2010) RT-qPCR Comparison of Mast Cell Populations in Whole Blood from Healthy Horses and those with Laminitis. Animal Genetics 41 (supl 2): 16-22.<br /> <br /> Brooks, S., Gabreski, N., Miller, D., Brisbin, A., Brown, H., Streeter, C., Mezey, J. G., Cook, D., Antczak, D. (2010). Whole Genome SNP Association in the Horse: Identification of a Deletion in Myosin Va Responsible for Lavender Foal Syndrome. PLoS Genetics, 6 (4), e1000909.<br /> <br /> Brooks, S., Makvandi-Nejad, S., Chu, E., Allen, J., Streeter, C., Gu, E., McCleery, B., Murphy, B., Bellone, R., Sutter, N. (2010). Morphological variation in the horse: defining complex traits of size and shape.. Animal Genetics, 41, 159-165.<br /> <br /> Brosnahan, M. M., Brooks, S., Antczak, D. F. (2010). Equine Clinical Genomics: A clinician's primer. Equine Veterinary Journal, 42 (7), 658-670.<br /> <br /> Broughton-Neiswanger, L.E., S. N. White, D. P. Knowles, M. R. Mousel, G. S. Lewis, D. R. Herndon, and L. M. Herrmann-Hoesing (2010) Non-maternal transmission is the major mode of ovine lentivirus transmission in a ewe flock: A molecular epidemiology study. Infection, Genetics and Evolution. 10(7):998-1007. <br /> <br /> Brunelli, J.P,, C.A. Steele and G. H. Thorgaard, 2010. Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout. Mol. Phylo. Evol. 56: 983-990.<br /> <br /> Byerly MS, Simon J, Cogburn LA, Le Bihan-Duval E, Duclos MJ, Aggrey SE, Porter TE (2010) Transcriptional profiling of the hypothalamus during development of adiposity in genetically selected fat and lean chickens. Physiol Genomics 42:157-167<br /> <br /> Byrne, K., M. Colgrave, T. Vuocolo, R. Pearson, C. Bidwell, N. Cockett, D. Lynn, J. Waddell, and R. Tellam (2010) The imprinted retrotransposon-like gene Peg11 is expressed as a full length protein in skeletal muscle from callipyge sheep. PLoS ONE 5(1): e8638.<br /> <br /> Byrne, K., T. Vuocolo, C. Gondro, J. White, N. E. Cockett, T. Hadfield, C. A. Bidwell, J. N. Waddell, and R. T. Tellam (2010) A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development. BMC Genomics 11:378.<br /> <br /> Cánovas, A, G. Rincón, A.D. Islas, S. Wickramasinghe, and J. F. Medrano 2010. SNP Discovery in the bovine milk transcriptome using RNA-Seq technology. Mammalian Genome 21:592-598<br /> <br /> Casellas, J., C.R. Farber, R.A. Verdugo and J.F.Medrano 2010. Segregation analysis of a sex ratio distortion locus in congenic mice. J Heredity 101:351-359 <br /> <br /> Chang, Shuang, Dunn, J.R., Heidari, M., Lee, L., Song, J.Z., Ernst, C.W., Ding, Z., Bacon, L.D., and Zhang, H.M. 2010. Genetics and Vaccine Efficacy: Host genetic variation affecting Mareks disease vaccine efficacy in White Leghorn chickens. Poultry Sci. 89:2083-2091.<br /> <br /> Chang, T.-C, Liu, W.-S. (2010) The molecular evolution of PL10 homologs. BMC Evol Biol 10, 127. <br /> <br /> Chen F, Lee Y, Jiang Y, Wang S, Peatman E, Abernathy J, Liu H, Liu S, Kucuktas H, Ke C, Liu ZJ. 2010. Identification and characterization of full-length cDNAs in catfish (Ictalurus spp.). PLoS One 12, e11546.<br /> <br /> Chen J, Dodson MV, Jiang Z. 2010. Cellular and molecular comparison of redifferentiation of intramuscular- and subcutaneous- adipocyte derived progeny cells. International Journal of Biological Science 6:80-88.<br /> <br /> Choi, I., J.P. Steibel, R.O. Bates, N.E. Raney, J.M. Rumph and C.W. Ernst. 2010. Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population. BMC Genetics. 11:97.<br /> <br /> Ciraci, C., C.K. Tuggle, M. Wannemuehler, D. Nettleton, S.J. Lamont. 2010. Unique Genome-wide Transcriptome Profiles of Chicken Macrophages upon exposure to Salmonella-derived Endotoxin. BMC Genomics 11:545.<br /> <br /> Coleman SJ, Zeng Z, Wang K, Luo S, Khrebtukova I, Mienaltowski MJ, Schroth GP, Liu, J., MacLeod JN. Structural annotation of equine protein-coding genes determined by mRNA sequencing. Animal Genetics, 41 (Suppl. 2):121130, 2010.<br /> <br /> Cook D, Gallagher PC and Bailey E (2010) Genetics of Swayback in American Saddlebred Horses. Animal Genetics 41 (supl 2): 64-71.<br /> <br /> Corbin LJ, Blott SC, Swinburne JE, Vaudin M, Bishop SC, Woolliams JA. (2010) Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Animal Genetics 41 (Supp. 2): 8-15. <br /> <br /> Costa de Melo, A. G., E. S. Varela, C. R. Beasley, H. Schneider, I. Sampaio, P. M. Gaffney, K. S. Reece, and C. H. Tagliaro. 2010. Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea). Genetics and Molecular Biology 33:564-572.<br /> <br /> Cothran, G., PhD. 2010. XX/XY Blood Lymphocyte Chimerism in Heterosexual Dizygotic Twins from an American Bashkir Curly Horse. Case Report. J.Equine Vet. Sci. 30:575-580.<br /> <br /> Curole, J. P., Meyer, E., Manahan, D. T., Hedgecock, D. (2010). Expression of the Pacific oyster mitochondrial genome: Variation among loci and evidence for regulation by nuclear-cytoplasmic interaction. Biological Bulletin. Vol. 218 (2), pp. 122-131.<br /> <br /> Dalloul RA et al., 2010. Multiplatform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology 8(9):e1000475.<br /> <br /> Daniels TF, Wu X-L, Pan ZX, Michal JJ, Wright Jr. RW, Killinger KM, MacNeil MD, Jiang Z. 2010. The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth. PLoS ONE 5(12): e15203.<br /> <br /> Dawes, M.J., R.O. Bates, N.E. Raney, J.P. Steibel and Ernst, C.W. 2010. Evaluation of single nucleotide polymorphism markers on pig chromosomes 3 and 6 for potential associations with meat quality traits. J. Anim. Sci. 88(E-Suppl. 3):143-4.<br /> <br /> Dégremont L, Bédier E, Boudry P (2010a). Summer mortality of hatchery-produced Pacific oyster spat (Crassostrea gigas). II. Response to selection for survival and its influence on growth and yield. Aquaculture 299: 21-29.<br /> <br /> Dégremont L, Boudry P, Ropert M, Samain JF, Bédier E, Soletchnik P (2010b). Effects of age and environment on survival of summer mortality by two selected lines of the Pacific oyster Crassostrea gigas. Aquaculture 299: 44-50.<br /> <br /> De los Campos, G., Gianola, D., Rosa, G. J. M., Weigel, K. A. and Crossa J. 2010. Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods. Genetics Research 92: 295-308.<br /> <br /> Dierks C, Komm K, Lampe V, Distl O. Fine mapping of a quantitative trait locus for osteochondrosis on horse chromosome 2. Anim Genet. 2010 41 Suppl 2:87-90. <br /> Dodson MV, Guan LL, Fernyhough ME, Mir PS, Bucci L, McFarland DC, Novakofski J, Reecy JM, Ajuwon KS, Thompson DP, Hausman GJ, Benson ME, Bergen WG, Jiang Z. 2010. Perspectives on the formation of an interdisciplinary research team. Biochem Biophysical Res Comm 391:155-1157.<br /> <br /> Dodson MV, Hausman GJ, Guan LL, Du M, Rasmussen TP, Poulos SP, Mir P, Bergen WG, Fernyhough ME, McFarland DC, Rhoads RP, Soret B, Reecy JM, Velleman SG, Jiang Z. 2010. Lipid metabolism, adipocyte depot physiology and utilization of meat animals as experimental models for metabolic research. International Journal of Biological Science 6:691-699. <br /> <br /> Dodson MV, Hausman GJ, Guan LL, Du M, Rasmussen TP, Poulos SP, Mir P, Bergen WG, Fernyhough ME, McFarland DC, Rhoads RP, Soret B, Reecy JM, Velleman SG, Jiang Z. 2010. Skeletal muscle stem cells from animals I. Basic cell biology. International Journal of Biological Science 6: 465-474.<br /> <br /> Dodson MV, Jiang Z, Chen J, Hausman GJ, Guan LL, Novakofski J, Thompson DP, Lorenzen CL, Fernyhough ME, Mir P, Reecy JM. 2010. Allied industry approaches to alter intramuscular fat content and composition in beef animals. Journal of Food Science 75:R1-8.<br /> <br /> Dodson MV, Vierck JL, Hausman GJ, Guan LL, Fernyhough ME, Poulos SP, Mir P, Jiang Z. 2010. Examination of adipose depot-specific PPAR moieties. Biochem Biophysical Res Comm 394:241-242.<br /> <br /> Dorshorst, B.J., Okimoto, R., Ashwell, C.M. 2010. Genomic Regions Associated with Dermal Hyperpigmentation, Polydactyly and Other Morphological Traits in the Silkie Chicken. J. Heredity. 101:339-50.<br /> <br /> Du ZQ, Ciobanu DC, Onteru SK, Gorbach D, Mileham AJ, Jaramillo G, Rothschild MF. 2010. A gene-based SNP linkage map for pacific white shrimp, L. vannamei. Animal Genetics 41(3):286-294.<br /> <br /> Edholm, E.-S., Hudgens, E.D., Tompkins, D., Sahoo, M., Burkhalter, B., Miller, N.W., Bengtén, E., Wilson, M., 2010.Characterization of anti-channel catfish IgL Ã monoclonal antibodies. Veterinary Immunology and Immunopathology. 135(3-4) 325-328.<br /> <br /> Edholm, E.S., Bengtén, E., Stafford, J.L., Sahoo, M., Taylor, E.B., Miller, N.W., Wilson, M. 2010. Identification of two IgD+ B cell populations in channel catfish, Ictalurus punctatus. Journal of immunology, 185 (7), pp. 4082-4094.<br /> <br /> Fahrenkrug, S. C., A. Blake, D. F. Carlson, T. Doran, A. L. Van Eenennaam, D. Faber, C. Galli, P. B. Hackett, N. Li, E. A. Maga, J. D. Murray, R. Stotish, E. Sullivan, J. F. Taylor, M. Walton, M. Wheeler, B. Whitelaw, B. P. Glenn. 2010. Precision Genetics for Complex Objectives in Animal Agriculture. Journal of Animal Science. 88:2530-9<br /> <br /> Fan, B., Z.-Q. Du, D.M. Gorbach, and M.F. Rothschild. 2010. Development and application of high-density SNP arrays in genomic studies of domestic animals. Asian-Australasian Journal of Animal Science. 23:833-847.<br /> <br /> Fan, B., S. Lkhagvadorj, W. Cai, J. Young, R.M. Smith, J.C. Dekkers, E. Huff-Lonergan, S.M. Lonergan, and M.F. Rothschild. 2010. Identification of genetic markers associated with residual feed intake and meat quality traits in the pig. Meat Sci. 84:645-650.<br /> <br /> Felicetti M, Lopes MS, Verini-Supplizi A, Machado Ada C, Silvestrelli M, Mendonça D, Distl O. Genetic diversity in the Maremmano horse and its relationship with other European horse breeds. Anim Genet. 2010. 41 Suppl 2:53-5. <br /> <br /> Fernando, S.C., Purvis II, H.T., Najar, F.Z., Sukharnikov, L.O., Krehbiel, C.R., Nagaraja, T.G., Roe, B.A., and DeSilva, U. (2010) Rumen Microbial Population Dynamics during Adaptation to a High Grain Diet. Applied and Environmental Microbiology 76, 7482-90.<br /> <br /> Fleury E, Moal J, Boulo V, Daniel J-Y, Mazurais D, Hénaut A, Boudry P, Favrel P, Huvet A (2010). Identification of new genes associated with summer mortality in the oyster Crassostrea gigas. Marine Biotechnology 12: 326-339.<br /> <br /> Fry, R.S., Spears, J.W., Hansen, S.L., and Ashwell, M.S. (2010) Dietary iron affects mRNA expression of porcine copper transporters. FASEB J 24:229-7.<br /> <br /> Fuller, S.A., McEntire, M.E., and Ludwig, G.M. 2010. Development and testing of a pedigree marking system using visible implant elastomer tags for selective improvement in Morone breeding programs. Aquaculture Research 41(8): 1250-1254.<br /> <br /> Waddell, J. N., P. Zhang, Y. Wen, S.K. Gupta, A. Yevtodiyenko, J.V. Schmidt, C.A. Bidwell, A. Kumar, and S. Kuang. (2010) DLK1 is necessary for proper skeletal muscle development and regeneration. PLoS ONE. 5: e15055.<br /> <br /> Gaffney, P. M., C. E. Pascal, J. P. Barnhart, W. S. Grant, and J. E. Seeb. 2010. Genetic homogeneity of weathervane scallops in the Northeastern Pacific. Can. J. Fish. Aquat. Sci. 67:1827-1839.<br /> <br /> Gonzalez-Recio, O., Weigel, K. A., Gianola, D., Naya, H. and Rosa, G. J. M. L2-Boosting algorithm applied to high-dimensional problems in genomic selection. Genetics Research 92: 227-237, 2010.<br /> <br /> Gorbach, D., B. Mote, L. Totir, R. Fernando, and M.F. Rothschild. 2010. Polydactyl inheritance in the pig. J Hered 101:469-475.<br /> <br /> Gorbach DM, Hu ZL, Du ZQ, Rothschild MF. 2011. Mining ESTs to determine the usefulness of SNPs across shrimp species. Animal Biotechnology 21(2):100-103.<br /> <br /> <br /> Gao, Yu, Laurence Flori, Jerome Lecardonnel, Diane Esquerre, Zhi-Liang Hu, Angelique Teillaud, Gaetan Lemonnier, Francois Lefevre, Isabelle P Oswald and Claire Rogel-Gaillard (2010). Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response. BMC Genomics 2010, 11:292.<br /> <br /> Hansen, S.L., Ashwell, M.S., Moeser, A.J., Fry, R.S., Knutson, M.D., and Spears, J.W. (2010) High dietary iron reduces transporters involved in iron and manganese metabolism and increases intestinal permeability in calves. Journal of Dairy Science. 93:656-65.<br /> <br /> Hansen, S.L., Trakooljul, N., Liu, H.-C.S., Hicks, J.A., Ashwell, M.S., and Spears, J.W. (2010) Proteins involved in iron metabolism in beef cattle are affected by copper deficiency in combination with high dietary manganese, but not by copper deficiency alone. Journal of Animal Science. 88:275-83.<br /> <br /> Hawkridge, A.M., Wysocky, R.B., Petitte, J.N., Anderson, K.E., Mozdziak, P.E., Fletcher, O.J., Horowitz, J.M., Muddiman, D.C,.2010. Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma. Anal Bioanal Chem. 398(2):737-49.<br /> <br /> He, W., R.L. Fernando, J.C.M. Dekkers, and H. Gilbert. 2010. A gene frequency model for QTL mapping using Bayesian inference. Genet. Sel. Evol. 42: 21.<br /> <br /> Hedgecock, D. (2010). Determining parentage and relatedness from genetic markers sheds light on patterns of marine larval dispersal. Molecular Ecology. 19 (5), 845-847.<br /> <br /> Hee CS, Gao S, Loll B, Miller MM, Uchanska-Ziegler B, Daumke O, Ziegler A. 2010. Structure of a classical MHC class I molecule that binds "non-classical" ligands. PLoS Biol 8:e1000557.<br /> <br /> Heidari M., A. Lopes, M. Huebner, S. Sharif, D. Kireev and H. Zhou. 2010. Mareks disease virus-induced immunosuppression: array analysis of chicken immune response genes expression profiling. Viral Immunology 23(3):309-19.<br /> <br /> Herrmann-Hoesing, L.M., S. M. Noh, K. R. Snekvik, S. N. White, D. A. Schneider, T. C. Truscott, and D. P Knowles (2010) Ovine progressive pneumonia virus capsid is found in CD163 and CD172a positive alveolar macrophages of persistently infected sheep. Veterinary Pathology. 47(3):518-528.<br /> <br /> Herrmann-Hoesing, L.M., L.E. Broughton-Neiswanger, K. C. Gouine, S. N. White, M. R. Mousel, G. S. Lewis, K. L. Marshall, and D. P. Knowles (2010) Evaluation of a CAEV/MVV indirect ELISA in the serological diagnosis of ovine progressive pneumonia virus in U.S. sheep. Clin. Vaccine Immunol. 17(2):307-310. 2010.<br /> <br /> Herzig, C.T.A., R.W. Waters, C.L. Baldwin and J.C. Telfer. 2010. Evolution of the CD163 family and its relationship to the bovine gamma delta T cell co-receptor WC1. BMC Evolutionary Biology. 10: 181.<br /> <br /> Herzig, C.T.A.H., M. P. Lafranc and C.L. Baldwin. 2010. Genomic organization of the bovine T cell receptor delta locus, BMC Genomics 11:100 (19 pages).<br /> <br /> Higgins SE, Ellestad LE, Trakooljul N, McCarthy F, Saliba J, Cogburn LA, Porter TE (2010) Transcriptional and Pathway Analysis in the Hypothalamus of Newly Hatched Chicks during Fasting and Delayed Feeding. BMC Genomics 11:162<br /> <br /> Hill EW, Gu J, Eivers SS, Fonseca RG, McGivney BA, Govindarajan P, Orr N, Katz LM, MacHugh DE. A sequence polymorphism in MSTN predicts sprinting ability and racing stamina in thoroughbred horses. PLoS One. 2010 5 ;e8645. <br /> <br /> Hill EW, Gu J, McGivney BA, MacHugh DE. Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance. Anim Genet. 2010 Dec;41 Suppl 2:56-63. <br /> <br /> Hill, EW, McGivney BA, Gu J, Whiston R, Machugh DE. A genome-wide SNP-association study confirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses. BMC Genomics. 2010;11:552. <br /> <br /> Hill EW. Livestock issue. Brief Funct Genomics. 2010 May;9(3):191-2. <br /> <br /> Hirota, K., Kakoi, H., Gawahara, H., Hasegawa, T., and Tozaki, T. Construction and Validation of Parentage Testing for Thoroughbred Horses by 53 Single Nucleotide Polymorphisms. J. Vet Med. Sci. 72 (6): 719-726, 2010.<br /> <br /> Holl H., Brooks S & Bailey E. (2010) De novo mutation of KIT discovered as a result of non-hereditary white coat color pattern. Animal Genetics 41(supl2): 196-198.<br /> <br /> Huang, W., Kirkpatrick, B. W., Rosa, G. J. M. and Khatib, H. 2010. A genome wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle. Animal Genetics 41, 570578.<br /> <br /> Huvet A, Normand J, Fleury E, Quillien V, Fabioux C, Boudry P (2010). Reproductive effort of Pacific oysters: a trait associated with susceptibility to summer mortality. Aquaculture, 304: 95-99.<br /> <br /> Jhingory S, Wu CY, and Taneyhill LA. 2010. Novel insight into the function and regulation of aN-catenin by Snail2 during chick neural crest cell migration. Dev Biol 344: 896-910.<br /> <br /> Jiang Y, Abernathy J, Peatman E, Liu H, Wang S, Xu D-H, Kucuktas H, Klesius P, Liu Z.J. 2010. Identification and characterization of matrix metalloproteinase-13 sequence structure and expression during embryogenesis and infection in channel catfish (Ictalurus punctatus). Developmental and Comparative Immunology 34:590-597.<br /> <br /> Jordan, L.G., C.A. Steele and G.H. Thorgaard, 2010. Universal mtDNA primers for species identification of degraded bony fish samples. Molecular Ecology Resources 10: 225-228.<br /> <br /> Juras, R., DVM, PhD, T. Raudsepp, PhD, P.J. Das, DVM, PhD, E. Conant, PhD, and E. Kim, T., Hunt, H.D., and Cheng, H.H. 2010. Mareks disease viruses lacking either RLORF10 or LORF4 have altered virulence in chickens. Virus Genes 40:410-420.<br /> <br /> Kirkpatrick, B.W., X. Shi, G.E. Shook and M.T. Collins. 2010. Whole genome association study of susceptibility to infection by Mycobacterium avium subsp. paratuberculosis in Holstein cattle. Animal Genetics, DOI: 10.1111/j.1365- 2052.2010.02097.<br /> <br /> Klukowska-Rötzler J, Marti E, Bugno M, Leeb T, Janda J. Molecular cloning and characterization of equine thymic stromal lymphopoietin. Vet Immunol Immunopathol. 2010 136(3-4):346-9. <br /> <br /> Kubosaki A, Lindgren G, Tagami M, Simon C, Tomaru Y, Miura H, Suzuki T, Arner E, Forrest AR, Irvine KM, Schroder K, Hasegawa Y, Kanamori-Katayama M, Rehli M, Hume DA, Kawai J, Suzuki M, Suzuki H, Hayashizaki Y. 2010. The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. Mol Immunol. 47(14):2295-302.<br /> <br /> Lallias D, Boudry P, Lapègue S, King JW, Beaumont AR (2010). Strategies for the retention of high genetic variability in European flat oyster (Ostrea edulis) restoration programmes. Conservation Genetics 11: 1899-1910.<br /> <br /> Lallias D, Taris N, Boudry P, Bonhomme F, Lapègue S (2010). Variance in reproductive success of flat oyster Ostrea edulis L. assessed by parentage analyses in natural and experimental conditions. Genetics Research 92(3): 175-187.<br /> <br /> Lawson S, Lunney JK, Zuckermann F, Osorio F, Nelson EA, Welbon C, Clement T, Fang Y, Wong S, Kulas, K, Christopher-Hennings J. 2010. Development of an 8-plex Luminex assay to detect swine cytokines for vaccine development: Assessment of immunity after porcine reproductive and respiratory syndrome virus (PRRSV) Vaccine. 32: 5383-5391.<br /> <br /> Lee JY, Song JJ, Wooming A. Li XY, HJ Zhou, Bottje W. Kong BW. 2010 Transcriptional profiling of host gene expression in chicken embryo lung cells infected with laryngotracheitis virus. BMC Genomics 2010, 11:445.<br /> <br /> Lee, Lucy F., Kreager, K.S., Arango, J., Paraguassu, A., Beckman, B., Zhang, H.M., Fadly, A.M., Lupiani, B., and Reddy, S. 2010. Comparative evaluation of vaccine efficacy of recombinant Mareks disease virus vaccine lacking Meqoncogene in commercial chickens. Vaccine 28:1294-1299.<br /> <br /> Leeds, T.D., Silverstein, J.T., Weber, G.M., Vallejo, R.L., Palti, Y., Rexroad, C.E., Iii, Evenhuis, J., Hadidi, S., Welch, T.J. & Wiens, G.D. (2010). Response to selection for bacterial cold water disease resistance in rainbow trout. J Anim Sci, 88: 1936-46.<br /> <br /> Li X., C. L. Swaggerty, M. H. Kogut, H. Chiang, Y. Wang, K. J. Genovese, H. He, H. Zhou. 2010. Gene expression profiling of the local cecal response of genetic chicken lines that differ in their susceptibility to Campylobacter jejuni colonization. PLoS ONE 5(7): e11827. <br /> <br /> Liu H, Tomokazu T, Abernathy J, Wang S, Sha Z, Terhune J, Kucuktas H, Jiang Y, Liu ZJ. 2010. Structure and expression of transferrin gene of channel catfish, Ictalurus punctatus. Fish and Shellfish Immunology 28:159-166.<br /> <br /> Liu H, Takano T, Peatman E, Abernathy J, Wang S, Sha Z, Kucuktas H, Liu ZJ. 2010. Molecular characterization and gene expression of the channel catfish ferritin H subunit after bacterial infection and iron treatment. Journal of Experimental Zoology, Part A: Ecological Genetics and Physiology 313:359-368.<br /> <br /> Lkhagvadorj, S., L. Qu, W. Cai, O. P. Couture, C. R. Barb, G. J. Hausman, D. Nettleton, L.L. Anderson, J.C.M. Dekkers, C. K. Tuggle. 2010. Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency. American Journal of Physiology: Regulatory, Integrative and Comparative Physiology 298:494-507.<br /> <br /> Long, N. M., Prado-Cooper, M. J., Krehbiel, C. R., DeSilva, U., and Wettemann, R. P. (2010) Effects of nutrient restriction of calves during early gestation on postnatal growth, carcass and organ characteristics and regulation of plasma glucose. Journal of Animal Science, 88, 3251-61.<br /> <br /> Long, N., Gianola, D., Rosa, G. J. M., Weigel, K. A., Kranis, A. and Gonzalez-Recio. O. 2010. Radial basis function regression methods for predicting quantitative traits using SNP markers. Genetics Research 92, 209-225.<br /> <br /> Lopes MS, Diesterbeck U, Machado Ada C, Distl O. Refinement of quantitative trait loci on equine chromosome 10 for radiological signs of navicular disease in Hanoverian warmblood horses. Anim Genet. 2010 41, Suppl 2:36-40. <br /> <br /> Lu J, Peatman E, Wang W, Yang Q, Abernathy J, Wang S, Kucuktas H, Liu ZJ. 2010. Alternative splicing in teleost fish genomes: Same-species and cross-species analysis and comparisons. Molecular Genetics and Genomics 283:531539.<br /> <br /> Luna-Nevarez, P., D.W. Bailey, C.C. Bailey, D.M. VanLeeuwen, R.M. Enns, G.A. Silver, K.L. DeAtley, and M.G. Thomas. 2010. Growth characteristics, reproductive performance, and evaluation of their associative relationship in Brangus cattle managed in a Chihuahuan Desert production system. J. Anim. Sci. 88:1891-1904.<br /> <br /> <br /> Lunney JK, Chen H. 2010. Genetic control of porcine reproductive and respiratory syndrome virus responses. Virus Research. 154: 161-169.<br /> <br /> Lunney JK, Fritz ER, Reecy JM, Kuhar D, Prucnal E, Molina R, Christopher-Hennings J, Zimmerman J, Rowland RRR. 2010. Interleukin-8, interleukin-1² and interferon-³ levels are linked to PRRS virus clearance. Viral Immunology. 23: 127-134.<br /> <br /> Lunney JK Benfield DA, Rowland RRR. 2010. Porcine Reproductive and Respiratory Syndrome Virus: An update on an emerging and re-emerging viral disease of swine. Virus Research. 154: 1-6.<br /> <br /> Lunney JK and Rowland RRR. (CoEditors). 2010. Progress in porcine respiratory and reproductive syndrome virus biology and control. Virus Research. 154 (1-2): 1-192.<br /> <br /> Lykkjen S, Dolvik NI, McCue ME, Rendahl AK, Mickelson JR, Roed KH. Genome-wide association analysis of osteochondrosis of the tibiotarsal joint in Norwegian Standardbred trotters. Anim Genet. 2010 41 Suppl 2:111-20. <br /> <br /> Manda, P., M. G. Freeman, S. M. Bridges, T. J. Jankun-Kelly, B. Nanduri, F. M. McCarthy, and S. C. Burgess. 2010. GOModeler--a tool for hypothesis-testing of functional genomics datasets. BMC Bioinformatics 11 Suppl 6:S29.<br /> <br /> Mao, W., Hunt, H.D., and Cheng, H.H. 2010. Cloning and functional characterization of chicken stem cell antigen 2. Devel. Comp. Immunol. 34:360-368.<br /> <br /> Martin AM, Elliott JA, Duffy P, Blake CM, Ben Attia S, Katz LM, Browne JA, Gath V, McGivney BA, Hill EW, Murphy BA. Circadian regulation of locomotor activity and skeletal muscle gene expression in the horse. J Appl Physiol. 2010 109(5):1328-36. <br /> <br /> Martin, K.E., C.A. Steele, J.P. Brunelli and G.H. Thorgaard, 2010. Mitochondrial variation and biogeographic history of Chinook salmon. Trans. Amer. Fish. Soc. 139: 792-802.<br /> <br /> Mateescu, R.G. and M. L. Thonney (2010) Genetic mapping of quantitative trait loci for milk production in sheep. Anim Genet. 41:460-466.<br /> <br /> Maturana, E. L., de los Campos, G., Wu, X.-L., Gianola, D., Weigel, K. A. and Rosa, G. J. M. Modeling relationships between calving traits: a comparison between standard and recursive mixed models. Genetics Selection Evolution 42(1), 2010.<br /> <br /> McCarthy, F. M., C. R. Gresham, T. J. Buza, P. Chouvarine, L. R. Pillai, R. Kumar, S. Ozkan, H. Wang, P. Manda, T. Arick, S. M. Bridges, and S. C. Burgess. 2010. AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Res 39:D497-506.<br /> <br /> McCue ME, Anderson SM, Valberg SJ, Piercy RJ, Barakzai SZ, Binns MM, Distl O, Penedo MC, Wagner ML, Mickelson JR. Estimated prevalence of the Type 1 Polysaccharide Storage Myopathy mutation in selected North American and European breeds. Anim Genet. 2010 41 Suppl 2:145-9.<br /> <br /> McGivney BA, McGettigan PA, Browne JA, Evans AC, Fonseca RG, Loftus BJ, Lohan A MacHugh DE, Murphy BA, Katz LM, Hill EW. Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training. BMC Genomics. 2010 23;11:398. <br /> <br /> McGlynn OF, Browne JA, Blake CM, Murphy BA (2010) Time of day influences cytokine and clock gene response to immune stimulation in equine whole blood. Animal Genetics. Volume 41, Issue Supplement s2, pages 202204. <br /> <br /> Medrano, J.F. and G. Rincón 2010. Genes involucrados en la determinación de la composición y rendimiento de la leche. In: Genética de Animales Domésticos, Editores G. Giovambattista and P. Peral-García, Editorial Inter-Medica S.A., Argentina.<br /> <br /> Medrano, J.F., A. Ahmadi and J. Casellas 2010. Dairy Cattle Breeding Simulation Program (DCBSP v.4.9), a simulation program to teach animal breeding principles and practices. J Dairy Sci 93:2816-2826.<br /> <br /> <br /> Mienaltowski MJ, Huang L, Bathke A, Stromberg AJ, MacLeod JN. Transcriptional comparisons between articular repair tissue, neonatal cartilage, cultured chondrocytes, and mesenchymal stromal cells. Briefings in Functional Genomics & Proteomics, 9:238-250, 2010.<br /> <br /> Milbury, C. A., J. C. Lee, J. J. Cannone, P. M. Gaffney, and R. R. Gutell. 2010. Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes. BMC Genomics 11:485.<br /> <br /> Meng, Q., C. Bai Y.L. Chunling, L. Ying, W. Xia, T.D. Bunch, and G-P. Li (2010) In vitro development and chromosomal configuration of bovine somatic cloned embryos with no-enucleated metaphase ii oocytes. Cell. Reprogram. 12:481-490.<br /> <br /> Michelizzi VN, Dodson MV, Pan ZX, Amaral ME, Michal JJ, McLean DJ, Womack JE, Jiang Z. 2010. Water buffalo genome science comes of age. International Journal of Biological Sciences 6: 333-349.<br /> <br /> Michelizzi VN, Wu X-L, Dodson MV, Michal JJ, Zambrano-Varon J, McLean DJ, Jiang Z. 2011. A global view of 54,001 single nucleotide polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and their transferability to water buffalo. Int. Journal of Biological Science 7:18-27.<br /> <br /> Mittmann EH, Mömke S, Distl O. Whole-genome scan identifies quantitative trait loci for chronic pastern dermatitis in German draft horses. Mamm Genome. 2010 21(1-2):95-103. <br /> <br /> Mohan, S., Davis, R. L., DeSilva, U., and Stevens, C. W. (2010) Dual regulation of ¼ opioid receptors in SK-N-SH neuroblastoma cells by morphine and interleukin-1 ²: Evidence for opioid-immune crosstalk. Journal of Neuroimmunology 227, 26-34.<br /> <br /> Morris, C.A., M. Wheeler, G. L. Levet, and B.W. Kirkpatrick. 2010. A cattle family in New Zealand with triplet calving ability. Livestock Science 128:193-196.<br /> <br /> Nanduri, B., N. Wang, M. L. Lawrence, S. M. Bridges, and S. C. Burgess. 2010. Gene model detection using mass spectrometry. Methods Mol Biol 604:137-44.<br /> <br /> Neibergs, H.L., M.L. Settles, R.H. Whitlock, J.F. Taylor. GSEA-SNP identifies genes associated with Johne's disease in cattle. 2010. Mammalian Genome 21(7): 419.<br /> <br /> Onteru, S.K., A. Ampaire, M.F. Rothschild. 2010. Biotechnology developments in developing countries. Biotechnol. Genet. Eng. Rev. 27: 1-12.<br /> <br /> Orr N, Back W, Gu J, Leegwater P, Govindarajan P, Conroy J, Ducro B, Van Arendonk JA, MacHugh DE, Ennis S, Hill EW, Brama PA. Genome-wide SNP association-based localization of a dwarfism gene in Friesian dwarf horses. Anim Genet. 2010 41 Suppl 2:2-7. <br /> <br /> Ozden, O., Black, B.L., Ashwell, C.M., Tipsmark, C.K., Borski, R.J., Grubb, B.J. 2010. Developmental profile of claudin-3, -5, and -16 proteins in the epithelium of chick intestine. Anat Rec (Hoboken). 293(7):1175-83.<br /> <br /> Palti, Y., Gahr, S.A., Purcell, M.K., Hadidi, S., Rexroad III, C.E. & Wiens, G.D. (2010). Identification, characterization and genetic mapping of TLR7, TLR8a1 and TLR8a2 genes in rainbow trout (Oncorhynchus mykiss). Developmental & Comparative Immunology, 34: 219-233.<br /> <br /> Palti, Y., Rodriguez, M.F., Gahr, S.A., Purcell, M.K., Rexroad Iii, C.E. & Wiens, G.D. (2010). Identification, characterization and genetic mapping of TLR1 loci in rainbow trout (Oncorhynchus mykiss). Fish & Shellfish Immunology, 28: 918-926.<br /> <br /> <br /> Phillips, R.B. & Devlin R.H. (2010). Integration of growth hormone gene constructs in transgenic strains of coho salmon (Oncorhynchus kisutch) at centromeric or telomeric sites. Genome, 53:79-82.<br /> <br /> Proszkowiec-Weglarz M, Porter TE (2010) Functional characterization of chicken glucocorticoid and mineralocorticoid receptors. Am J Physiol Regul Integrative Comp Physiol 298:1257-1268.<br /> <br /> Qiu, H., X. Xu, B. Fan, M.F. Rothschild, Y. Martin, and B. Liu. 2010. Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2. Mol Biol Rep. 37:629-636.<br /> <br /> Quinn, N., Boroevich, K., Lubieniecki, K., Chow, W., Davidson, E., Phillips, R., Koop, B. & Davidson, W. (2010). Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire. BMC Genomics, 11: 539.<br /> <br /> Raudsepp T, Durkin K, Lear TL, Das PJ, Avila F, Kachroo P, Chowdhary BP (2010). Molecular heterogeneity of XY sex reversal in horses. Animal Genetics 41 (suppl 2):41-52.<br /> <br /> Redmond, S.B., Tell, R.M., Coble, D., Mueller, C., Palic, D., Andreasen, C.B., and Lamont, S.J. 2010. Differential splenic cytokine responses to dietary immune modulation by diverse chicken lines. Poultry Sci. 89: 1635-1641.<br /> <br /> Ren, J., X. Liu, F. Jiang, X. Guo and B Liu. 2010. Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia. BMC Evolutionary Biology, 10:394.<br /> <br /> Renaville, B., E. Piasentier, B. Fan, M. Vitale, A. Prandi, and M.F. Rothschild. 2010. Candidate gene markers involved in San Daniele ham quality. Meat Sci. 85:441-445.<br /> <br /> Rijnkels,M., C. Freeman-Zadrowski, J. Hernandez, V. Potluri, A. Lin, G. Rincon, A.D. Islas, L. Wang, W. Li, J.F. Medrano 2010. Insight in development and functional differentiation of the mammary gland; a chromatin perspective. 9th World Congress of Genetics Applied to Livestock Production (WCGALP), Leipzig-Germany, No. 0976.<br /> <br /> Rios JJ, Fleming JG, Bryant UK, Carter CN, Huber JC, Long MT, Spencer TE, Adelson DL (2010) OAS1 and RNASEL Polymorphisms Are Associated With Susceptibility To West Nile Encephalitis In Horses. PLoS ONE 5(5): e10537.<br /> Robinson, C.M., Hunt, H.D., Cheng, H., and Delany, M. 2010. Mapping of Mareks disease herpesvirus integrations into chicken chromosomes indicates positional preference for telomeres and clonal relationships among tumors. Herpesviridae 1:5.<br /> <br /> Robinson, C.M., H. Hunt, H. Cheng and M.E. Delany. 2010. Chromosomal integration of an avian oncogenic herpesvirus reveals telomeric preferences and evidence for lymphoma clonality. Herpesviridae 1:5 http://www.herpesviridae.org/content/1/1/5.<br /> <br /> Roe, B.A., and DeSilva, U. (2010) Rumen Microbial Population Dynamics during Adaptation to a High Grain Diet. Applied and Environmental Microbiology 76, 7482-90.<br /> <br /> Rosa, G. J. M. and Vazquez, A. I. Integrating biological information into the statistical analysis and design of microarray experiments. Animal 4(2): 165172, 2010.<br /> <br /> Salem, M., Kenney, P.B., Rexroad Iii, C.E. & Yao, J. (2010). Proteomic signature of muscle atrophy in rainbow trout. Journal of Proteomics, 73: 778-789.<br /> <br /> Salem M, Rexroad C, Wang J, Thorgaard G, Yao J (2010). Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 11(1): 564.<br /> <br /> Salem, M., Xiao, C., Womack, J., Rexroad, C. & Yao, J. (2010). A MicroRNA Repertoire for Functional Genome Research in Rainbow Trout. Marine Biotechnology, 12: 410-429.<br /> <br /> Salger, S.A., Reading, B.J., Baltzegar, D.A., Sullivan, C.V., and E.J. Noga. 2011. Molecular characterization of two isoforms of piscidin 4 from the hybrid striped bass (Morone chrysops X Morone saxatilis). Fish and Shellfish Immunology 30: 420-424.<br /> <br /> Sauvage C, Boudry P, de Koning DJ, Haley CS, Heurtebise S, Lapègue S (2010). Quantitative Trait Loci for resistance to summer mortality and OsHV1 load in the Pacific oyster (Crassostrea gigas). Animal Genetics: 41(4): 390-399.<br /> <br /> Scharrenberg A, Gerber V, Swinburne JE, Wilson AD, Klukowska-Rotzler J, Laumen E, Marti E. (2010) IgE, IgGa, IgGb and IgG(T) serum antibody levels in offspring of two sires affected with equine recurrent airway obstruction. Animal Genetics 41 (Suppl. 2): 131-137.<br /> <br /> Schmitz A, Demmel S, Peters LM, Leeb T, Mevissen M, Haase B. Comparative human-horse sequence analysis of the CYP3A subfamily gene cluster. Anim Genet. 2010 41 Suppl 2:72-9. <br /> <br /> Seabury, C. M., P. M. Seabury, J. E. Decker, R. D. Schnabel, and J. E. Womack. 2010. Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle. PNAS 107:151-156.<br /> <br /> Shakhsi-Niaei M, Klukowska-Rötzler J, Drögemüller C, Swinburne JE, Gerber V, Leeb T. Characterization of the equine ITGAX gene and its association with recurrent airway obstruction in European Warmblood horses. Anim Genet. 2010 41(5):559-60. <br /> <br /> Silva, R.F., Dunn, J.R., Cheng, H.H., and Niikura, M. 2010. A MEQ deleted Mareks disease virus cloned as a bacterial artificial chromosome is a highly efficacious vaccine. Avian Diseases 54:862-869.<br /> <br /> Staiger, E. A., M. L. Thonney, J. W. Buchanan, E. R. Rogers, P. A. Oltenacu, and R. G. Mateescu (2010) Effect of prolactin, ß-lactoglobulin and º-casein genotype on estimated breeding values for milk production in East Friesian sheep. J. Dairy Sci. 93(4):1736-1742.<br /> <br /> Suo, L., Q. Meng, Y. Pei, X-W. Fu, Y-P. Wang, T.D. Bunch, and S-E. Zhu (2010) Effect of cryopreservation on acetylation patterns of lysine 12 of histone H4 (acH4K12) in mouse oocytes and zygotes. J. Assisted Repro. Genet. 27:735-741.<br /> <br /> Swanberg, S.E., T.H. OHare, E.A. Robb, C.M. Robinson, H. Chang, and M.E. Delany. 2010. Telomere biology of the chicken: A model for aging research. Exptl Gerontology. 45:647-654.<br /> <br /> Tai, S.H.S., Niikura, M., Cheng, H.H., Kruger, J.M., Wise, A.G., and Maes, R.K. 2010. Complete genomic sequence and an infectious BAC clone of feline herpesvirus-1 (FHV-1). Virology 401:215-227.<br /> <br /> Thanthrige-Don, N., P. Parvizi, A. J. Sarson, ,L. A. Shack, S. C. Burgess, and S. Sharif. 2010. Proteomic analysis of host responses to Marek's disease virus infection in spleens of genetically resistant and susceptible chickens. Dev Comp Immunol 34:699-704.<br /> <br /> Toosi, A., R.L. Fernando, and J.C.M. Dekkers. 2010. Genomic Selection in admixed and crossbred populations. J. Anim. Sci. 88: 32-46.<br /> <br /> Tozaki, T., Hirota, K., Sugita, S., Ishida, N., Miyake, T., Oki, H., and Hasegawa, T. A genome-wide scan for tying-up sundrome in Japanese thoroughbreds. Anim. Genet. 41 (suppl. 2): 80-86, 2010.<br /> <br /> Tozaki, T., Miyake, T., Kakoi, H., Gawahara, H., Sugita, S., Hasegawa, T., Ishida, N., Hirota, K., and Nakano, N. A genome-wide association study for racing performance in Thoroughbreds clarifies a candidate region near the MSTN gene. Anim. Genet. 41 (suppl. 2): 28-35, 2010.<br /> <br /> Towfic, F., VanderPlas, S., Oliver, C.A., Couture, O., Tuggle, C.K., Greenlee, M.H.W., and V. Honavar. 2010. Detection of Gene Orthology Based On Biomolecular Networks. BMC Bioinformatics 11:S7.<br /> <br /> Tuggle CK. Bearson SMD, Uthe JJ, Huang TH, Qu L, Couture O, Wang YF, Kuhar D, Lunney JK, Nettleton D, Honavar V, Dekkers JCM. 2010. Updated methods for transcriptomic analyses of the porcine host immune response: Application to Salmonella infection. Vet. Immunol. Immunopathol. 138: 280-91.<br /> <br /> Tseng CT, D. Miller D, Cassano J, Bailey E and Antczak DF (2010) Molecular Identification of Equine Major Histocompatibility Complex Haplotypes using Polymorphic Microsatellites. Animal Genetics 41 (supl 2): 150-153.<br /> <br /> Valente, B. D., Rosa, G. J. M., de los Campos, G., Gianola, D. and Silva, M. A. Searching for recursive causal structures in multivariate quantitative genetics mixed models. Genetics 185: 633-644, 2010.<br /> <br /> Vallejo, R.L., Wiens, G.D., Rexroad, C.E., III, Welch, T.J., Evenhuis, J.P., Leeds, T.D., Janss, L.L.G. & Palti, Y. (2010). Evidence of major genes affecting resistance to bacterial cold water disease in rainbow trout using Bayesian methods of segregation analysis. J Anim Sci, 88: 3814-32.<br /> <br /> Van den Berg, B. H., F. M. McCarthy, S. J. Lamont, and S. C. Burgess. 2010. Re-annotation is an essential step in systems biology modeling of functional genomics data. PLoS One 5:e10642.<br /> <br /> Van Eenennaam, A. L., K. L. Weber, K. Cooprider and D. J. Drake. 2010. Development and implementation of a vertically-integrated beef cattle data collection system. California Agri 64:94-100.<br /> <br /> Van Melis, M. H., Eler, J. P., Rosa, G. J. M., Ferrz, J. B. S., Figueiredo, L. G. G., Mattos, E. C. And Oliveira, H. N. 2010. Additive genetic relationships between scrotal circumference, heifer pregnancy, and stayability in Nellore cattle. J. Anim. Sci. 88: 38093813.<br /> <br /> Varian, A. & Nichols, K.M. (2010). Heritability of Morphology in Brook Trout with Variable Life Histories. PLoS ONE, 5: e12950.<br /> <br /> Vazquez, A. I., Bates, D., Rosa, G. J. M., Gianola, D. and Weigel, K. A. 2010. Technical Note: An R package for fitting generalized linear mixed models in animal. J. Anim. Sci. 88: 497504.<br /> <br /> Vazquez, A. I., Rosa, G. J. M., Weigel, K. A., de los Campos, G., Gianola, D. and Allison, D. B. 2010. Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins. J. Dairy Sci. 93: 5942-5949.<br /> <br /> Verdugo, R.A., C.R. Farber, C.H. Warden and J.F. Medrano 2010. Serious limitations of the QTL/Microarray approach for QTL gene discovery. BMC Biology 8:96 <br /> Waldbieser, Geoffrey; Bosworth, Brian; Quiniou, Sylvie . 2010. Production of Viable Homozygous, Doubled Haploid Channel Catfish (Ictalurus punctatus) Marine Biotechnology, 12(4) 380-385.<br /> <br /> Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, Xiaping H, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Research, 38(18):e178, 2010.<br /> <br /> Wang S, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock C, Small B, Wilson M, Liu H, Jiang Y, Lee Y, Chen F, Lu J, Wang W, Peatman E, Xu P, Somridhivej B, Baoprasertkul P, Quilang J, Sha Z, Bao B, Wang Y, Wang Q, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rokhsar D, Liu ZJ., and Catfish Genome Consortium. 2010. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biology 11 (1):R8.<br /> <br /> Wang S, Peatman E, Liu H, Bushek D, Ford SE, Kucuktas H, Quilang J, Li P, Wallace R, Wang Y, Guo X, Liu Z. 2010. Microarray analysis of gene expression in eastern oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge. Fish Shellfish Immunol., 29: 921-929.<br /> <br /> Wang, Y., X. Wang, A. Wang and X. Guo. 2010. A 16-microsatellite multiplex assay for parentage assignment in the eastern oyster (Crassostrea virginica). Aquaculture, 308:S28-S33.<br /> <br /> Weigel, K. A., de los Campos, G., Vazquez, A. I., Rosa, G. J. M., Gianola, D. and Van Tassel, C. P. Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle. J. Dairy Sci. 93: 54235435, 2010.<br /> <br /> Wu, X.-L., Gianola, D., Rosa, G. J. M. and Weigel, K. A. Bayesian model averaging for evaluation of candidate gene effects. Genetica 138:395-407, 2010.<br /> <br /> Yamashita, J., Oki, H., Hasegawa, T., Honda T., and Nomura T. Demographic Analysis of Breeding Structure in Japanese Thoroughbred Population. J. Equine Sci. 21(2): 11-16, 2010.<br /> <br /> Yamashita, J., Oki, H., Hasegawa, T., Honda, T., and Nomura, T. Gene Dropping Analysis of Ancestral Contributions and Allele Survival in Japanese Thoroughbred Population. J. Equine Sci. 21(3): 39-45, 2010.<br /> <br /> Yeh, H.-Y., Klesius, P.H., 2010. Sequence analysis, characterization and mRNA distribution of channel catfish (Ictalurus punctatus Rafinesque, 1818) chemokine (C-X-C motif) receptor 4 (CXCR4) cDNA. Veterinary Immunology and Immunopathology, 134 (3-4), pp. 289-295.<br /> <br /> Yeh, H.-Y., Klesius, P.H., 2010. Characterization and tissue expression of channel catfish (Ictalurus punctatus Rafinesque, 1818) ubiquitin carboxyl-terminal hydrolase L5 (UCHL5) cDNA, 2010. Molecular Biology Reports, 37 (3), 1229-1234.<br /> <br /> Yeh, H.-Y., Klesius, P.H., 2010. Sequence analysis, characterization and tissue distribution of channel catfish (Ictalurus punctatus Rafinesque, 1818) myeloperoxidase cDNA, Fish and Shellfish Immunology, 28 (3), pp. 504-509.<br /> <br /> Yeh, H.-Y., Klesius, P.H., 2010. Channel catfish (Ictalurus punctatus Rafinesque, 1818) tetraspanin membrane protein family: Identification, characterization and expression analysis of CD63 cDNA, 2010. Veterinary Immunology and Immunopathology, 133 (2-4), 302-308.<br /> <br /> Xie X, Yu Y, Liu G, Yuan Z, Song JZ. (2010) Complexity and Entropy Analysis of DNA Methyltransferase. J Data Mining in Genom Proteomics 1:105. <br /> <br /> Xu, X., H. Qiu, Z.Q. Du, B. Fan, M.F. Rothschild, F. Yuan, and B. Liu. 2010. Porcine CSRP3: polymorphism and association analyses with meat quality traits and comparative analyses with CSRP1 and CSRP2. Mol Biol Rep. 37:451-459. <br /> <br /> Zaitoun, I., Downs, K. M., Rosa, G. J. M. and Khatib, H. Upregulation of imprinted genes in mice: an insight into the intensity of gene expression and the evolution of genomic imprinting. Epigenetics 5(2): 1-10, 2010.<br /> <br /> Zhang, L. and X. Guo. 2010. Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing. Aquaculture, 302:124-129.<br /> <br /> Zhang, X.M., X.P. Yue, W.-S. Liu, T.C. Chang, X.Y. Lan, H. Chen and C.Z. Lei (2010) Y-chromosome haplotype analysis revealing two major haplogroups in Chinese swamp buffaloes. Submitted to J. of Animal Breeding and Genetics (Nov 2010).<br /> <br /> Zimmerman J, Rowland RRR. 2010. Interleukin-8, interleukin-1² and interferon-³ levels are linked to PRRS virus clearance. Viral Immunology. 23: 127-134.<br />

Impact Statements

1. This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken and now the turkey genome. Industries have begun to apply the sequence and SNP we generated to characterizing and improving production lines using genome-wide marker-assisted selection. Since publication of the first draft of the chicken genome sequence, a shift has been made from providing and supporting physical genomics resources to those focused on gene expression and function.

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Brief Summary of Minutes

Aquaculture, Bioinformatics, Cattle, Equine, Pig, Poultry, Sheep/Goat Species Groups (80-100 attendees in workshop/business meeting)


The Business meeting was preceded by the joint Animal Genome Workshop session with presentations by: Randall Prather, University of Missouri, Utility of Genetically Modified Swine; Noelle Cockett, Utah State University, Recent Advancements in Sheep Genomics, James MacLeod, University of Kentucky, "Analyses of the equine mRNA transcriptome using RNA-seq data" and Larisa Rudenko, Senior Advisor for Biotechnology, Food and Drug Administration, Genetically Engineered Animals: Regulation, Research, and Opportunities for Collaboration

Business Meeting:
A. Old Business: Call to order 4:50 PM, Cecilia Penedo, NRSP8 2009 Chair, Motion to approve minutes from January 11, 2009, approved by acclamation.

B. Species Coordinator Reports:
1. Aquaculture  John Liu, Caird Rexroad, Co-coordinators. Coordinator funds were used to support travel, the aquaculture genome workshop, and two community based projects (oyster genome workshop, rainbow trout PCR pool construction). The Aquaculture Workshop was well attended with 85 signed in participants representing 13 countries. Whole genome sequencing (WGS) projects using Sanger or next-generation sequencing methods are underway for catfish, Pacific oyster and tilapia, with rainbow trout and Atlantic salmon to follow in 2010. The International Shrimp Genome Consortium (China, USA and Thailand) is organizing a WGS initiative for June 2010. Linkage maps for shrimp (SNP-based) and striped bass (microsatellite-based) were constructed. Understanding of reproductive behavior of channel catfish has improved through molecular individual identification and pedigree analyses. Research efforts to improve reproduction traits of hybrid catfish have been successful; hybrid catfish have superior production traits and commercial farms (currently 47 involved) can realize significant increase in income. Work is underway in salmonids to investigate QTLs that impact handling stress and pathogen resistance. Several databases are being developed (teleost alternative splicing, oyster EST and BAC contig annotation, rainbow trout genetic map, striped bass ovarian contigs, multi-tissue transcriptome of white perch). Many of these resources can be accessed through http://www.animalgenome.org.

2. Bioinformatics  James Reecy, Coordinator. In collaboration with Chris Tuggles group, a public open-source database and website (www.ANEXdb.org) was developed for storage and analysis of functional genomics data in livestock. The Database Coordination team has started to migrate this database into http://www.animalgenome.org for long-term maintenance and to expand its capabilities, which currently consist of: a) tools to facilitate storage of Affymetrix-based gene expression data from any species with an available GeneChipÒ; b) submission of user data to NCBI Gene Expression Omnibus; and c) a comprehensive annotation of all porcine expressed sequences. The current efforts will expand the data storage capabilities to all widely used livestock gene expression profiling tools, as well as create comparative annotation of the sequence elements on these profiling tools. In partnership with KSU, MSU and USDA, relational databases to store and disseminate phenotypic and genotypic information from large genomic studies in farm animals are being developed to support research labs, share information among collaborators and facilitate data analysis. One example is the development of the relational database for the PRRS CAP Host Genome consortium (http://www.animalgenome.org/lunney/index.php). The coordinator actively communicated with curators and compiled information of other relevant genome databases for poultry, cattle, pig, sheep and aquaculture. Many of the resources are accessible through http://www.animalgenome.org. Another focused effort was to integrate the Animal Trait Ontology into the Vertebrate Trait Ontology to provide researchers an online resource of standardized trait terms and improve communication among different groups within the livestock, rat, mouse and human research communities. Other activities included software development for sequence assembly using a seed sequence, visualization tools for whole genome association data and the Virtual Comparative Map (VCMap), expansion of Animal QTLdb functionality and providing bioinformatics expertise to assist research groups with data assembly and analysis.

3. Cattle  Juan Medrano, Coordinator. Funds supported student award and speakers for PAG XVIII, 2010. Publications of the bovine WGS, SNP variation, and other features of the bovine genome were released in 2009. Current bovine WGS assemblies are represented by Btau_4.2 (from Baylor) and the University of Maryland (UMD2 and UMD3.1). Improvements in the assembly algorithms, manual curation and annotation of the genome are continuing. This work illustrates the value of the support and collaboration through NRSP8 and many contributions from the bovine community. Several projects are underway in the USA to resequence individual animals to increase SNP density, improve assembly and understanding of genome structure and variation. Development of the BovineSNP50 genotyping assay has been implemented for whole genome selection in dairy cattle by the USDA-AIPL and adopted globally by the dairy industry. A joint effort by NRSP8 investigators to produce new high density genotyping chip resources (600K+) in Illumina and Affimetrix platforms has the potential of truly refining QTL position for fine mapping and expanding the application of targeted genome selection to a large group of cattle breeds. Coordination is being provided for the development of a new bovine Affymetrix gene sampling array. This array will include ~550k probes representing most exons for increased sensitivity to measure gene expression. The creation of this array platform is being coordinated with the input of US investigators and a German group that will support the development costs. Also, plans are in progress to develop shared tools for enhanced cDNA library construction (NSR primers) to improve representation and selection of transcripts for gene expression arrays and high throughput sequencing (RNASeq). Database and bioinformatics activities are led by the NRSP8 Bioinformatics Coordinator, Jim Reecy.
4. Equine  Ernie Bailey, Coordinator. Funds were used to support administration of the SNP chip resource, support for students and post-docs to participate in scientific meetings (PAG 2009, The Equine Science Society meeting in Colorado and the Dorothy Russell Havemeyer Meeting in the United Kingdom in July 2009), and for the coordinator and workshop committee members to attend industry meetings to explain and promote the use of horse genomics in research. The assembled Horse Whole Genome Sequence has accelerated research of health-related traits, e.g. developmental bone diseases (osteochondrosis and related diseases), muscle diseases (polysaccharide storage myopathy), neurological disease, growth and stature, dwarfism, bone fracture and aspects of performance, and infectious disease. The 55K Equine SNP chip developed by Illumina with grant support from Morris Animal Foundation, USDA and other independent sources (University of Kentucky, University of Berne, Animal Health Trust (Newmarket, England) and Royal Veterinary College (London, England). The SNP chip has been very effective and subject of research presentations at several meetings during the past year. Use of that assay by researchers is facilitated and coordinated by scientists at the University of Minnesota in connection with grants from the Morris Animal Foundation and the USDA. Efforts are underway to develop tools for investigation of gene expression including hybridization and sequencing methods.
5. Pig  Max Rothschild, Coordinator. New gene markers continue to be identified and mapped. Integration of maps continues to take place as QTL maps are expanded. Maps are being developed based on the pig sequencing efforts and the 60K SNP chip. QTL and trait associations have continued to be reported on all chromosomes for many traits. Candidate gene analyses have proven successful with several gene tests being recently released and used in the industry for many traits including, fat, feed intake, growth, meat quality, litter size and coat color. The PigQTLdb (http://www.animalgenome.org/QTLdb/pig.html) is an excellent repository for all of these results. The Swine Genome Sequencing Consortium (SGSC) continued its efforts this past year and considerable advances have been made. A total of 160 attendees came to this historic meeting where speakers presented updates on several subjects related to the sequencing effort and plans for the future. The deadline has passed for new clones to enter the sequencing pipeline. However, some new clones (~150) are being identified using physical map and sequence information as a possible resource for future sequence gap closure. All chromosomes are over 90% sequenced taking the genome to 95.72% from 16,974 sequenced clones. About 94% of the genome is at the Improved status (15720 clones). There is 123Mb of finished quality data within the 2.994Gb currently available. Sanger will continue with chromosome X/Y sequencing  chromosome X clones sequenced in the genome project will be finished and the map will continue to be refined using a fosmid library too. Sanger has produced a chromosome Y fosmid library which is currently being fingerprinted. This will be used to select up to 1100 fosmid clones for sequencing and finishing. This work is funded by BBSRC. In collaboration with TGAC (Norwich, UK) the remaining BAC clones which have been selected from the fingerprint map will be pooled and sequenced on the Illumina platform. A further 10X coverage of Duroc sow DNA will be produced on the Illumina platform to be combined with the BGI data and assembled (also in collaboration with TGAC). Automatic annotation will continue to be provided by Ensembl. Another annotation jamboree is to be organized in 2010. The Pig Genome Database continues to be updated to report the genome sequencing progress (http://www.animalgenome.org/pigs/genomesequence/). New QTL continue to be curated into the Pig QTL Database (http://www.animalgenome.org/QTLdb/pig.html) currently with 4,928 QTLs representing 499 pig traits and another 200 QTLs undergoing a quality control process before their release. New functions have been added to the PigQTLdb tools to align pig RH map-human comparative maps, pig BAC physical maps, new microsatellite markers from Sino-Danish genome project, pig SNPs from dbSNP, Affy and Oligo microarray elements against pig QTL. A new function allows users to download all curated QTL data when browsing the QTL chromosome map views. Efforts are being made to align the current genome assembly against pig QTL, among other genome features, (http://www.animalgenome.org/gbrowse/). Database activities were transferred to the Bioinformatics Coordinator.
6. Poultry  Jerry Dodgson and Hans Chang, Co-coordinators. Chicken linkage mapping has transitioned almost solely into high throughput SNP assays (60K SNP Illumina iSelect genotyping array) which have greatly enhanced the reference map and are also essential components for trait mapping and genome-wide marker assisted selection (GMAS). Coordination funding was used to enhance the SNP linkage map by genotyping the Wageningen reference panel and supported SNP genotyping of 100 samples by NRSP-8 members. Efforts are underway to evaluate the latest map and to compare it with the latest genome sequence assembly and to develop a denser SNP map specifically useful for the East Lansing reference linkage map population. Reduced representation and high throughput sequencing of the UCD003 genome will be employed to generate additional SNPs between the UCD001 and UCD003 parents of that population. Physical mapping of the turkey genome is nearly complete, along with construction of a detailed chicken-turkey BAC contig-based comparative map that was essential for the assembly of the first draft turkey genome sequence (see below). The regularly updated comparative BAC contig map is available at http://poultry.mph.msu.edu/resources/resources.htm#TurkeyBACChicken. Improvement of the second assembly of the chicken genome (May 2006 build) is underway with high throughput next generation sequencing being used at WUGSC and also in an effort to obtain the ~5% of missing sequence (predominantly on the microchromosomes). The third build of the chicken genome was released in November, 2009, based on 12x 454-Roche reads, but this is not yet on the major genome browsers. Efforts to map SNPs in the 60K chip chosen from unassigned sequence contigs were generally unsuccessful, suggesting that much of chr_Un derives from small unplaced microchromosomes, chromosome W, and repetitive elements or CNV regions. The Turkey Genome Sequencing Consortium generated a first draft genome sequence using a combination of Next Generation sequencing platforms, along with the turkey BAC contig-based comparative map alignments. The project was led by Otto Folkerts and Rami Dalloul of VaTech, Julie Long of USDA-ARS-BARC and Kent Reed, UMN. Coordination funds were committed to aid in this effort which also enjoyed support from VaTech, BARC and UMN, among others. The effort also garnered support to both VaTech and BARC from USDA-NIFA-AFRI. Sequence assembly was led by researchers at the UMD Center for Bioinformatics and Computational Biology. Sequences have been submitted to Genbank and browser support will be available through Birdbase at http://birdbase.net/cgi-bin/gbrowse/turkeygenome/ (thanks to Carl Schmidt, U. of Del.). Efforts are on-going to improve the annotation of genes and fill gaps in the turkey sequence. Coordination funds have been used provide samples of the 44K element long oligonucleotide chicken microarray made by Agilent Corp. to several NRSP-8 participants, along with a new 244K whole genome long oligo array that can be used for comparative genome hybridization and whole genome transcriptional profiles. Some participants chose to be provided GeneChip® Chicken Genome arrays from Affymetrix, Inc. (http://www.affymetrix.com/products/arrays/specific/chicken.affx). Further support for transcriptomics is anticipated in future years.
7. Sheep/Goat. Noelle Cockett, Coordinator. Periodical updates of the sheep linkage map continues with current version 4.6 (ca. 1400 markers spanning over 3,500 cM) available on the Australian Gene Mapping Web Site (http://rubens.its.unimelb.edu.au/~jillm/jill.htm), maintained by Jill Maddox, University of Melbourne, Australia. Coordinator funds were used to a) support production of paired-end sequences from clones in the CHORI-243 ovine BAC library to create a virtual sheep genome through comparative analysis with sequenced genomes of other species. Detailed information can be obtained through the virtual sheep genome website (http://www.livestockgenomics.csiro.au/vsheep/); b) development of an ovine radiation hybrid (RH) panel (USUoRH5000) and map with 2104 loci and average spacing of 1.5 Mb/locus. By identifying the locations of mapped loci within the whole genome sequences of human and other closely related mammalian species, ovinemammalian comparative maps were developed. The ovine RH map will provide a unique opportunity for determining chromosomal synteny at the molecular level. The identification and positional cloning of genes governing traits significant to the ovine industry will be enhanced and the RH map can be used as a scaffold for assembling the ovine whole genome sequence. The NRSP-8 sheep coordinator is a participant in the International Sheep Genome Consortium (ISGC), a multi-institutional group developing sheep resources needed for genomic research (http://www.sheephapmap.org/). These resources include a high coverage BAC library with complete end-sequencing, high and moderate resolution RH panels, full coverage linkage maps, an integrated ovine genetic map, a whole genome BAC physical map, the virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep/), a 1536 SNP pilot chip and a high density 60K SNP array, released in January, 2009, as the Ovine SNP50 BeadChip. To date, 3064 sheep from 64 breeds and strains, seven species of wild sheep and nine outgroup species were typed with the BeadChip for the world-wide ovine HapMap project, as well as two ovine RH panels and the International Mapping Flock. The ISGC is using next-generation sequencing technologies to complete a whole genome reference sequence (7X coverage equivalence) with DNA from the Texel male used to create the CHORI-243 BAC library. The reference sequence will have low error rate (< one base pair in 10,000) and minimal number of gaps. Assembly of the sequences will be iterative, starting with de novo assembly into high quality contigs and continuing with information from syntenic alignments to the human, bovine, dog and horse whole genome sequences. Information from the ovine linkage, RH and cytogenetic maps and positional information from the ovine consensus genome assembly will also be utilized to support the assembly. Problem areas will be finished by sequencing BAC clones that cover large gaps and array-based hybridization enrichment across short gaps. Substantial leveraging of funds and expertise from the ISGC, combined with technological and computational advances in the area of de novo sequence assembly, will contribute significantly to the success of the project.

C. New Business:
1. Election of officers for 2010. John Liu nominated Geoff Waldbieser, USDA-ARS for Secretary of NRSP8 2010; approved by acclamation. 2. Selection of next meeting location and date. Jerry Dodgson suggested the meeting be held next year at PAG on Sunday; approved by acclamation. Meeting adjourned at 5:50 PM.

Accomplishments

Progress toward Objective 1.<br /> 1. Aquaculture: Catfish: Whole-genome sequencing was funded by the USDA through an AFRI grant awarded in 2009 to John Liu and Geoff Waldbieser, co-PIs, and Steven Salzburg (UMD). Research includes production and assembly of sequence contigs from a homozygous channel catfish using single and paired reads (Illumina and 454 technologies). Paired reads from a homozygous blue catfish will be mapped to the channel catfish assembly. Existing genomic resources (physical maps, genetic maps, polymorphisms, BAC end sequences, cDNA sequences) will be incorporated into the assembly. Oyster: Whole genome sequencing of the Pacific oyster (Crassostrea gigas) is in progress as collaboration among the Institute of Oceanology of Chinese Academy of Sciences (IOCAS), the Beijing Genomics Institute (BGI), and international Oyster Genome Consortium (OGC). The OGC will provide information from genetic and physical maps to BGI to assist the assembly process. Contigs assembled to date by BGI will be used to designing exon-based SNP assays, in order to provide Type I marker loci for the USDA-sponsored GigaSNP project. Salmonids: Integration of the genetic and chromosome maps of rainbow trout and Atlantic salmon was published this year. Information will be used for assembly of the Atlantic salmon (Sanger sequencing) and rainbow trout (French Genoscope group, 454 sequencing) genomes which will begin in 2010. Both genomes are large and have many duplicate genes. A BAC physical map has been generated and is being integrated with genetic maps. Shrimp: A SNP-based linkage map was constructed in Rothschild lab (ISU). International Shrimp Genome Consortium, with major players from China, US, and Thailand, is organizing the initiation of whole genome sequencing project in 2010. Striped Bass: development of a medium density linkage map for striped bass (Morone saxatilis) based on 498 microsatellite markers produced at NCSU (C.V. Sullivan, C.R. Crouch), at Kent SeaTech Corporation (M. Westerman and J. Stannard), and at the USDA/ARS NCCCWA in Kearneysville, WV (C. Rexroad III). The mapping effort was funded by the NOAA Marine Aquaculture Initiative grant program. Tilapia: Whole genome sequencing slowly progressing at the Broad Institute Sequencing Center; large number of BAC end sequences (110,880) have been generated at Genoscope (France) and comparatively mapped in silico by Kochers lab to stickleback genome sequence assembly. Working with Co-Factor Genomics, Kochers lab is also generating the whole genome sequences of the tilapia genome using the next generation sequencing.<br /> <br /> 2. Bioinformatics: Initiated migration of the www.AXEXdb.org database into www.animalgenome.org for long-term maintenance, to expand its storage capabilities to all widely used livestock gene expression profiling tools, and create comparative annotation of the sequence elements on these profiling tools.<br /> <br /> 3. Cattle: Identification of SNP markers in candidate genes associated with milk fat composition, milk and protein in yield in BTA4, milk oligosaccharide content (sialyal and fucosyl transferases), BTA6 regulators of the casein gene cluster, growth traits in beef cattle (GHR promoter), carcass traits in beef cattle (Stat6) and growth and milk traits (BTA5 GH/IGFI pathway genes). Validation of these markers for association studies in large beef cattle populations in Argentina (Brangus) and Uruguay (Hereford). Identification and validation in three beef cattle populations of 3 SNPs in the STAT6 gene significantly associated with back fat, calculated yield grade, cutability, hot carcass weight, dry matter intake, days on feed, back fat rate and average daily gain. Resequencing of 40 genes related to the GH/IGF signaling pathway in 52 samples from Bos taurus (beef and dairy) and Bos indicus origin; selection of 250 tag SNP for genotyping and marker-trait association studies. RNASeq and microarray analyses to examine mammary transcriptome in relation to oligosaccharide composition of milk, annotation of the bovine milk glycome and a study of the expression of key glycosylation genes in Holstein, Jersey and Brown Swiss cows at different stages of lactation (1, 15, 90 and 250 days). Outcomes will define the means to genetically enrich bovine milk with beneficial oligosaccharides. Analysis of the bovine toll-like receptor, cathelicidin, and defensin gene families in taurine and indicine cattle and identification of SNPs, indels and CNVs to investigate differential resistance/susceptibility to infectious diseases. Analysis of genetic mechanisms behind variation in growth, disposition, nutrient utilization, feed efficiency, carcass and meat traits in steers, and female reproductive efficiency traits in heifers from Nellore-Angus crosses. Fetal developmental time-course analyses to identify expressed genes from the polled interval on BTA1 to characterize horn/poll/scurs phenotypes. Use of genome, SNP and transcriptome information to identify of markers for QTL and QTN for economically important traits in dairy, beef and swine and use in marker-assisted selection to optimize production, quality, nutritional value and resistance to diseases in farm animals. Identification and validation of SNP markers which can be used to predict genetic merit for twinning rate in the Holstein population and facilitate selection against twinning rate where it is deemed undesirable. A similar tool has been developed for predicting genetics of susceptibility to infection by Mycobacterium avium subsp. paraturberculosis (Johness disease) in Holstein cattle. Analysis of a major gene for ovulation rate is underway. Two loci were identified that were linked with bovine respiratory disease (BRD) and found to be also associated with persistent infection of the BVD virus. Identification of Y-chromosome haplotypes (SNPs/indels) associated with fertility that can improve marker assisted selection, eliminate potential genetic defects and reduce maintenance costs prior to breeding. Genetic network analysis in beef cattle (Wagyu x Limousine reference population) indicating that carcass, eating quality and fatty acid composition traits rarely share networks. Marker-assisted selection for improvement of one category of these traits would not interfere with improvement of another. Development of a NimbleGen 12plex gene expression array for all known genes including mtDNA to evaluate the role of mitochondrial function and energy use in cattle with extreme differences in residual feed intake. Development of a RH panel and refinement of genetic map, with focus in the MHC region, for river buffalo in collaboration with E. Amaral and Brazilian agencies.<br /> <br /> 4. Horse. Fine mapping using SNP50 chip of economically important traits including Osteochondrosis, swayback in American Saddlebred horses, dwarfism in Miniature horses, Neuroaxonal Dystrophy (NAD) in the American Quarter Horse, Chronic Progressive Lymphedema (CPL) in draft horses, and Lavendar Foal Syndrome (LFS) in Arabian horses. Identification of causative mutations for dwarfism and LFS. Refinement of MHC genetic structure, function and polymorphism.<br /> <br /> 5. Pig. SNP60 BeadChip used to evaluate residual feed intake and reproductive traits, and in a population with phenotypes for backfat, loin muscle area, and feet and leg structure; to identify markers associated with sow longevity in two maternal lines; to study the genetics and porcine reproductive and respiratory syndrome (PRRS) in nursery pigs and identify associations with various PRRS response phenotypes, in a multi-agency collaborative effort led by USDA-BARC station. Improvement of the swine genome sequence assembly using high-resolution radiation hybrid mapping and pig-human comparative mapping, as well as transcriptome sequencing. Update of the SLA complex nomenclature and development of a cytokine multiplex assay. Use of transcriptional profiling being done to study PRRS-infected tissues and pig skeletal muscle, gene expression in backfat and liver in response to fasting, in MC4R genotypes in the IA feed intake selection lines, in salmonella-challenged pigs, and in two lines of boars divergently selected for testosterone levels with comparisons between lines and across ages. Transcription and proteomic approaches are also being used to examine porcine patellae as a biomedical model for osteoarthritis. <br /> <br /> 6. Poultry. Chicken linkage mapping transitioned to being almost solely based on high-throughput SNP assays. A 60K SNP Illumina iSelect genotyping array was developed and used to enhance the SNP linkage map of the Wageningen reference panel. In addition, coordination funds supported genotyping of 100 samples by NRSP-8 members. High throughput next-generation sequencing being used to generate denser SNP arrays (~ 600K) specifically useful for the East Lansing reference linkage map population (UCD001 and UCD003 parental lines). Physical mapping of the turkey genome is nearly complete. A regularly updated, detailed comparative chicken-turkey BAC contig-based comparative map is available at http://poultry.mph.msu.edu/resources/resources.htm#TurkeyBACChicken. A third, improved build of the chicken genome was released in November, 2009, based on 12x 454-Roche reads, but this is not yet on the major genome browsers. A first draft sequence of the turkey genome using next-gen sequencing was produced by the Turkey Genome Sequencing Consortium. Sequences were submitted to Genbank and browser support will be available through Birdbase at http://birdbase.net/cgi-bin/gbrowse/turkeygenome/. Chicken microarrays available to NRSP8 participants include 44K element long oligonucleotide (Agilent), the GeneChip® Chicken Genome array (Affimetrix) and the new 244K whole genome long oligo array for comparative genome hybridization and whole genome transcriptional profiles.<br /> 7. Sheep/Goat. Sheep: Development of a high resolution ovine RH map (USUoRH5000 panel, 2,754 markers, average marker interval of ~ 1 Mb or 1.26 cM) containing SNPs from a recently developed sheep 1.5K SNP chip, and selected markers to cover autosomal chromosome ends and the regions flanking interspecies chromosomal breakpoints. Integration of various sheep maps (RH, linkage, cytogenetic) and virtual sheep genome assembly. Improvement of human-sheep chromosome homology with an additional 12 new homologous identified. Development of a high-density ovine SNP array (Illumina Ovine SNP50 BeadChip) by the International Sheep Genome Consortium (ISGC). The world-wide ovine HapMap project includes 3064 sheep from 74 breeds and strains, seven species of wild sheep and nine outgroup species. These samples, including 200 submitted from Utah State University and Louisiana State University, were typed with the BeadChip. The BeadChip was also typed on the USUo5000RH panel and the International Mapping Flock. The ISGC is now working on the completion of a whole genome reference sequence, which will be produced using DNA from the Texel male used to generate the CHORI-243 BAC library. Goat: Development of goat RH panel (90 clones) from a male Boer goat as collaboration between Texas A&M, VSU and Huazhong Agricultural University. Development of a predicted map of goat ESTs with 3190 elements using comparisons with the goat and sheep genetic maps, and the bovine map as a backbone; genome conservation analysis of ESTs relative to sheep, cow, human, mouse and rat. Investigation of alternative splicing events conserved in the cow and goat is being done through comparison of mRNA, EST and whole genome data. These resources will be crucial for development of goat genome information.<br /> Progress toward Objective 2:<br /> 1. Aquaculture. Catfish. Establishment of microsatellite pedigrees for individual identification of channel catfish. Analysis confirmed multiple spawning (up to 9) by males in one season, demonstrated that females could spawn more than once per season (usually separated by 1 month) in earthen ponds, and identified full-sib families produced by multiple same-pair matings separated by 28-65 days. Reproduction problems of hybrid channel x blue catfish are being overcome through research, with steady increase of fry production; commercial hybrid catfish farms are becoming viable. Superior growth, feed conversion efficiency, survival, seinability and processing yield of hybrid catfish resulted in an increase of income of $390 to $5,340 per acre depending on the management of the farm. Salmonids. Major QTL loci identified in the NCCCWA broodstock for a) response to handling stress (measured by cortisol concentrations in the blood) which impacts growth, feed efficiency, immune response, and reproductive characteristics, b) resistance to F. psychrophilum. <br /> <br /> 2. Bioinformatics. Collaborative development of relational databases to store and disseminate phenotypic and genotypic data from large genomic studies in farm animal, such as being done with the PRRS CAP Host Genome consortium to facilitate sharing of information and data analysis among members (http://www.animalgenome.org/lunney/index.php). <br /> 3. Cattle: Development of animal resources, genomic, functional and proteomic data for identification of genes and markers for growth, fertility, feed efficiency and meat tenderness in beef cattle. Establishment of a database to house DNA, genotypes, phenotypes and herd data for evaluation and assessment of different DNA-enabled approaches for predicting the genetic merit of herd sires on commercial beef ranches.<br /> 4. Horse. mRNA resequencing of several diverse horse tissues is being used to elucidate the equine transcriptome and to identify candidate mutations for traits including Congenital Stationary Night blindness in the Appaloosa. Gene expression studies are enabling understanding of chronobiology, exercise-induced stress and complex diseases such as laminitis, among others. <br /> 5. Pig. Continued sharing, and collaborative work among NRSP8 members, of pig populations for reproduction (NE), feed intake (IA), testosterone levels (NC) and meat quality (IA and MI). The newest and most collaboratively studied population is the PRRS Host Genomic Consortium population derived from pigs contributed by several industry partners, and raised and phenotyped at KSU. The USDA-BARC station leads a large collaborative effort for genotyping and gene expression analyses of PRRS-infected pigs.<br /> <br /> 6. Poultry. Distribution of DNA from the East Lansing international reference population to many laboratories throughout the world. Virtual sharing of populations by the SNP consortium described above which involved the collection of DNA samples from several populations from Federal, state and industry locations and the coordination of a common high density genotyping effort, the results of which are then correlated with phenotypic information.<br /> <br /> 7. Sheep/Goat: Mapping for aseasonal reproduction and milk production traits in a resource Dorset population selected for aseasonality and prolificacy (Cornell University Sheep Farm) identified significant QTL in ovine chromosomes 12, 17, 19 and 24, and potential candidate regions in 3, 20, and 1 for aseasonal reproduction traits. Chromosomes 2, 12, 18, 20, and 24 had putative QTL for various measures of milk production; regions were syntenic with bovine chromosomal segments containing QTL for milk production traits. New regions associated with parasite burden of Haemonchus contortus found on OAR9 and OAR19 in a segregating sheep population, adding to a total of 54 QTL for parasite resistance identified in sheep. Comparative approaches using cattle and human genomes are being used to identify potential positional candidate genes. A systems approach and combination of data from multiple species QTL projects, is also being used to identify common pathways and candidate genes associated with the parasite resistance. Gene expression analyses used to study muscle growth in callipyge lambs and to identify pathways involved in the muscle hypertrophy phenotype. Genetic factors influencing host control of ovine progressive pneumonia virus (OPPV) are being identified. A deletion of the chemokine receptor gene CCR5 has been found to be associated with reduced OPPV concentrations and will be further evaluated in additional populations. Since both OPPV and HIV are macrophage-tropic lentiviruses with similar genomic structure, findings from this work may also contribute to human medicine. Signatures of selection with emphasis in regions common to sheep and cattle are being analyzed in the HapMap project. Expression of genes that metabolize terpenoids will be examined in two goat herds selected for propensity to eat juniper. Studies to characterize the fungal and viral community within the rumen are being carried out to expand understanding of microbial diversity and impact on animals efficiency and performance.<br /> Progress toward objective 3:<br /> In addition to information available in traditional browsers (UCSC, NCBI, Ensembl), each species groups has developed public databases to deposit various categories of genomic and functional information. The Bioinformatics coordination program expanded the capabilities of the portal www.animalgenome.org to integrate resources, tools, services, news and updates for each of the 6 species groups (aquaculture, cattle, horse, poultry, pig, sheep/goat). Additional functionalities implemented for standardized trait terms across species, Animal and Vertebrate Trait Ontology ((http://www.animalgenome.org/cgi-bin/amion/browse.cgi), virtual comparative map (http://bioneos.com/VCMap/) and multiple dataset comparisons. Development of minimal standards for publication of QTL and gene association data (http://miqas.sourceforge.net/).<br /> <br /> <br /> <br /> <br /> <br /> <br />

Publications

Impact Statements

1. 1. Cutting edge tools continue to be generated for the community in the form of genomic sequence and genome variation data, high-throughput sequencing and genotyping technologies, and bioinformatics resources for all designated species groups. These tools serve national and international researches at very economical terms.
2. 2. Research focus on identification of genetic mechanism underlying production, reproduction and health-related traits of economic value has been productive with clear benefits realized by agricultural industry. E.g., catfish farming, dairy cattle, pig, horse.
3. 3. Productive research on molecular pathways and networks is increasing in momentum and will inform discoveries of underlying processes that impact economic and health-related traits for all agricultural species.
4. 4. Genomic and expressed sequence analyses and comparisons across species has significantly enhanced the understanding of vertebrate genome organization and evolution in the context of production animal systems, model organisms and humans

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Brief Summary of Minutes

The NRSP-8 business meeting was preceded by workshops for all species and area subcommittees as well as a combined Animal Genome Workshop, which contained four plenary presentations. Professor Morris Soller gave the 2011 NRSP-8 Distinguished Lecture. The business meeting was called to order by Chris Bidwell, the 2011 NRSP-8 Chair and recorded by Geoff Waldbieser, Secretary, with 43 members and guests in attendance. The 2009 minutes were approved unanimously. Noelle Cockett, who presented the 2010 Distinguished Lecture, was honored with a commemorative plaque to recognize her efforts in small ruminant genomics. Species/area coordinator reports were given for Aquaculture, Bioinformatics, Cattle, Equine, Poultry, Sheep/Goat, and Swine. Colin Kaltenbach and Muquarrab Qureshi provided administrative reports. Geoff Waldbieser, USDA-ARS assumed the NRSP-8 Chair for 2011-2012. Tom Porter, University of Maryland was elected as Secretary for 2011-2012. A motion to hold the 2012 meeting in conjunction with the Plant and Animal Genome conference was approved unanimously. The meeting was adjourned.

Accomplishments

Overview<br /> <br /> The NRSP-8 participants and their collaborators have far reaching national and international impact on basic discovery and application of genomics to animal agriculture with over 220 peer-reviewed publications in 2010. The community has rapidly adopted new genomics technologies including high-throughput short read sequencing, high density SNP detection and several types of microarrays to sequence genomes, generate high quality genetic maps and analyze gene expression of a rapidly increasing number of species. The NRSP-8 has facilitated the transfer of experience from the earliest species with sequenced genomes to the current efforts to produce higher quality integrated genetic maps and genome sequences. The NRSP-8 participants and their collaborators are using genomics technology, bioinformatics resources and diverse animal models to investigate fundamental mechanisms affecting production efficiency, product quality, animal health, disease resistance and food safety. Genomics technology has been successfully adopted for genetic selection programs for some sectors of animal agriculture. Some species pose unique challenges for the application of genomics technology due to the complex structures of brood stock development. NRSP-8 participants are also working to solve those challenges as genomics technologies and capabilities to predict genetic merit are evolving. The NRSP-8 has fostered the development of critical technical and information resources for animal genomics in the USA and throughout the world. The annual NRSP-8 workshops have become an essential component for development of collaborations, training and dissemination of new information to government, academic and industry stakeholders in animal agriculture.<br /> <br /> The annual NRSP-8 meetings comprised of Aquaculture, Cattle/Sheep/Goat, Equine, Poultry and Swine workshops was held in conjunction with the XIX International Plant and Animal Genome conference in San Diego, CA on January 15-16, 2011. There were 572 registered participants with specific interests in animal genomics. Attendance in the various NRSP-8 workshops ranged from 60 to 250 people from 10-15 different countries. The following report summarizes 2010 reports from the species/area technical reports from subcommittee/workshop chairs based on experiment station reports of the participants. Annual reports from the species/area coordinators can be found (NIMSS site here) &<br /> <br /> Aquaculture Technical Report <br /> <br /> Genome Sequencing: The Oyster Genome Consortium was successful in establishing a whole genome sequencing project for the Pacific oyster (Crassostrea gigas). Sequencing and assembly of a catfish reference genome is also underway with participants from ARS Catfish Genetics Research Unit, Auburn U., USDA-ARS Bovine Functional Genomics Laboratory, and U. of British Columbia. Gene transcripts from various tissues of multiple individual catfish with diverse genetic background were also sequenced. Projects to identify EST and define the transcriptomes of various tissues were conducted in catfish, rainbow trout, brook trout and striped bass.<br /> <br /> Genome Mapping: The USDA-ARS National Center for Cool & Cold Water Aquaculture (NCCCWA) rainbow trout map was used for producing a first generation integrated physical and genetic map. A high density RAD (restricted site associated DNA) genetic map of Swanson x Whale Rock recombinant double haploids is being constructed using approximately 7,600 SNPs to aid in future assembly of a reference genome sequence for trout. The 2nd generation NCCCWA rainbow trout genetic map is now available through G-browser at the Animal Genome website of the NRSP-8 bioinformatics group. A first SNP genetic map for Pacific white shrimp was built with 418 SNP markers mapped onto 45 sex-averaged linkage groups. This SNP genetic map lays the foundation for future shrimp genomics studies. Scientists from the USDA-ARS NCCCWA, VIMS and N. Carolina State U. (NCSU) developed a linkage map for striped bass by genotyping two half-sib families at 289 microsatellite DNA markers and assembled a map with 26 linkage groups. <br /> <br /> The USDA-ARS SNARC generated 192 crosses of Morone using National Breeding Program foundation stocks and completed studies evaluating heritability of phenotypic variation growth of hybrid striped bass as tank-reared fingerlings. Scientists from SNARC and the U. Arkansas at Pine Bluff evaluated the genetic and phenotypic influence of parental traits on hybrid striped basslarval size and quality, and the influence of genetic factors on metabolic and stress-related traits, discovering that female phenotype does not significantly affect larval traits (e.g. growth) but that genotype does have a significant affect. This finding is significant because any increase in larval size at hatch resulting from selection would reduce the need for live feeds, which could make year-round tank production of fry and fingerlings economically viable for industry. SNARC and NCSU researchers also distributed advanced fingerlings and mature broodfish from National Breeding Program stocks to HSB producers engaged in propagation of commercial domesticated broodstocks.<br /> <br /> Database Activities: Many useful links for aquaculture can be found at http://www.animalgenome.org/aquaculture/. In collaboration with John Liu, Auburn U., a Catfish SNP Project web site (http://www.animalgenome.org/catfish/cbarbel/), a Teleost Alternative Splicing Database (http://www.animalgenome.org/tasd), and a Catfish COI DNA Barcode Database (http://www.animalgenome.org/fishid/) have been established. The bioinformatics coordinators have helped Moh Salem of West Virginia U. to set up web blast and data download of the rainbow trout transcriptome data characterized using Sanger and Next GENeration sequencing data (http://www.animalgenome.org/aquaculture/salmonids/rainbowtrout/EST_WV.html).<br /> <br /> Cattle Technical Report <br /> <br /> The U. of California-Davis Station (J.F. Medrano and collaborators) has utilized next-generation RNA sequencing to examine expression patterns in the bovine mammary gland and in milk somatic cells The results show that milk somatic cells are representative of the mammary gland transcriptome and can be used as an alternative tissue to study gene expression of milk related traits. RNA expression was also examined in cows at day 15 (transition) and day 250 (late) lactation. Genes encoding milk proteins had the most abundant transcripts in transition milk and genes involved in immune regulation and cell defense had the most abundant transcripts in late lactation. The accuracy of RNA-Seq SNP discovery was tested by comparing SNP detected in a set of 42 candidate genes expressed in milk that had been resequenced earlier using Sanger sequencing technology. The results confirmed that analyzing the transcriptome using RNA-Seq technology is an efficient and cost effective method to identify SNP in transcribed regions. The study provided guidelines to maximize the accuracy of SNP discovery and the prevention of false-positive SNP detection, and provided more than 33,000 SNP in Holsteins, that are located in coding regions of genes expressed during lactation.<br /> <br /> The Pennsylvania Station (W. Liu) has analyzed the transcriptome of the bovine Y-chromosome (BTAY) using a direct testis cDNA selection and Next-Generation sequencing approach using Illumina GA2. Their results suggest an extensive transcriptional activity on BTAY. Examining the lineage specific gene families temporal and spatial expression patterns of ZNF280BYs in testis suggest a role in spermatogenesis. The study provides insights into the genomic organization of the bovine Y chromosome and gene regulation in spermatogenesis, and provides a model for studying evolution of multi-copy gene families in mammals.<br /> <br /> At the Massachusetts Station (C. Baldwin, J. Telfer and collaborators), bovine T cell receptor delta chains of the ³´ high species have been characterized. By annotating the bovine genome Btau_3.1 assembly the presence of 56 distinct variable (V) genes was found, 52 of which belong to the TRDV1 subfamily and were co-mingled with the TCR± V genes. In addition two genes belonging to the TRDV2 subfamily and a single TRDV3 and TRDV4 gene were found. The organization of the TRD locus was described, together with a system by which to classify the TRDV1 genes based on their phylogenetic grouping. On a similar line of work, this station annotated and performed evolutionary analysis in WC1/CD163 co-receptors. Annotation in the bovine genome identified genes coding for bovine CD163A and CD163c-± but found no evidence for CD163b. Bovine CD163A is widely expressed in immune cells, whereas CD163c-± transcripts are enriched in the WC1+ ³´ T cell population. Phylogenetic analyses of the CD163 family genes and WC1 showed that CD163c-± is most closely related to WC1 and that chicken and platypus have WC1 orthologous genes, previously classified as among their CD163 genes.<br /> <br /> At the Washington Station (Z. Jiang and collaborators) the reverse cholesterol transport pathway (RCT) were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population. Among 36 SNPs detected in 11 of 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F2 progeny. Single-marker analysis for 19 of 36 SNP had significant associations with nine phenotypes (P<0.05). Combining these results with previously reported genetic networks derived from 71 known functional genes, genetic networks related to the RCT pathway were identified. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production. Holly Neibergs and collaborators have continued to do fine mapping on regions that have been identified as associated with Johnes disease. Illumina custom veracode assays were utilized to place markers about every 3 kb around a 200-300 kb regions previously identified as harboring positional candidates. This provided information to proceed with re-sequencing of the significant areas in collaboration with Dr. Van Tassell and Dr. Matukumali. An initial association analysis was conducted on bovine viral diarrhea-persistently infected (BVD-PI) cattle. Samples were obtained after testing over 10,000 animals for BVD-PI. To refine these loci, the density of markers on BTA2 and BTA26 was increased in order to determine if the loci associated with BVD-PI calves differed from the loci associated with the dams of BVD-PI calves or animals with bovine respiratory disease. Bovine viral diarrhea virus is one of the viral pathogens that comprise the bovine respiratory disease complex. In relation to bovine respiratory disease (BRD) an initial genome-wide study identified two chromosomal regions on BTA2 and BTA26 that were linked with BRD in four Bos taurus x Bos indicus crossbred cattle.<br /> <br /> At the U. of Wisconsin-Madison Station (B. Kirkpatrick and collaborators) further validation of SNP associations with twinning rate are being conducted. In collaboration with scientists at USMARC (L. Kuehn, G. Bennett), 66 SNPs previously identified as associated with twinning rate in the US Holstein population have been genotyped on 731 animals from the USMARC twinning population. A second validation analysis is being conducted in collaboration with a commercial twinner herd in which ovulation and twinning rate data have been collected. A total of 299 animals from this herd have been genotyped with the same 66 SNPs. Four of the 66 SNPs were successfully validated at a nominal p<0.01 in the USMARC herd. The most significant (p<1.8x10-4) was a SNP previously discovered in the IGF1 gene and associated with twinning rate in two Holstein populations. Creation of a resource family to map the location of a major gene for ovulation rate continued. The first 88 daughters of a bull believed to possess a major gene for ovulation rate have been evaluated and the gene has been fine-mapped. Analysis of a candidate gene is ongoing. An additional 33 daughters were born in 2010.<br /> <br /> The Oklahoma Station (R.G. Mateescu) has worked on the effect of breed and muscle type on fatty acid composition. Steers from two different breeds known for high (Angus) and low (Charolais) marbling scores are used in the study. Two extreme muscle types are being analyzed: longissimus dorsi (more oxidative) and semitendinosus (more glycolytic). Fatty acid profile of the two muscles were significantly different, with longissimus having a greater percentage SFA (P < 0.0001), a lower percentage of MUFA (P < 0.0001), and tended to have a lower percent PUFA (P = 0.06) than semitendinosus. Gene expression profiles were analyzed using a bovine whole-genome 70-mer oligo array with 24,000 long oligonucleotide probes was used. Ingenuity Pathways Analysis was used to identify the most relevant biological mechanisms, pathways, and functions of these genes. Thirty-five array elements were found to be differentially (P < 0.01) expressed between longissimus and semitendinosus muscles, with at least a 2-fold change in expression, with 32 elements up-regulated and 3 down-regulated.<br /> <br /> The Texas Station (C. Gill and collaborators) has continued to collect phenotypes from the Cycle 1 (F2 Nellore-Angus cows), Cycle 2 (reciprocal F2 steers and heifers) and Cycle 3 (F3 Nellore-Angus steers and heifers) McGregor Genomics populations. They have continued work on a pilot study to investigate the genetic basis of variation in immunological response to vaccination for BVDV using steers from Cycle 2 and Cycle 3. They are investigating the genetic mechanisms behind variation in growth, disposition, nutrient utilization, feed efficiency, carcass and meat traits in the steers as well as female reproductive efficiency traits in the heifers. Penny Riggs, P. Holman and J. Womack have examined gene expression related to tick resistance in cattle. Differentially expressed genes associated with the site of tick attachment have been identified, and further investigation will be conducted. They continue to collaborate with Dr. E. Amaral of Brazil, J. Womack and L. Skow to refine the genetic map of the river buffalo, focusing on river buffalo genes in the MHC region. Jim Womack and S. Dindot are also examining copy number variants (CNVs) in innate immune genes, particularly cathelicidins and defensins. Polymorphisms of copy number for bovine cathelicidin genes have been demonstrated and current experiments are designed to test the effect of copy number on gene function. Through collaborations they have begun comparative genetic studies of bovids using the cattle genome as a reference. <br /> <br /> Equine Technical Report<br /> <br /> Illumina 74K SNP genotyping Chip: A new Illumina Infinium array containing ~74,500 SNP markers in 2011. The marker list submitted for assay design of the second generation Beadchip has an average of 1.5 SNPs per 50 kb bin and therefore represents a substantial increase in the number of markers across the genome. SNP markers included on this new genotyping array include ~53,000 markers that were validated on the Equine SNP50 Beadchip which had a minimum minor allele frequency of e 0.005 across the 354 samples analyzed in the Gentrain dataset. The ~21,500 additional markers included in the new assay design were chosen to address as many gaps in coverage from the Equine SNP50 Beadchip as possible, and to globally improve coverage across the genome. As there were insufficient SNPs from the seven discovery breeds alone to achieve these goals, ~ 3,900 Twilight SNPs, and ~ 2,800 SNPs from RNAseq data were used, and increased numbers of SNPs were included in bins that flank many of the larger gaps. In addition, the new SNP panel includes enhanced coverage of the MHC region on ECA20 and the X chromosome, as well as several SNPs from coat color loci to use for sample validation purposes.<br /> <br /> Equine Whole Genome Tiling Array: In order to enable comprehensive studies of Equine copy number variation (CNV), a whole genome tiling array was designed based on the EquCab2 (Sep. 2007) assembly by researchers at University of Adelaide and Texas A&M. The array contains design a total of 418,577 probes, 305,416 of which were tiled into repeat-masked EquCab2 with an average resolution of 7.5 Kb. In addition to genome wide high resolution, there are three other significant features of this tiling array: 1) a subset of 85,852 probes for almost all Equine RefSeqs (18,427 out of 18,763), mainly from exons; 2) 519 chromosome Y specific probes, designed from 362 available STSs (BAC end tags) and 3) the inclusion of 26,790 probes for 3 Mb long sub-telomeric regions of all chromosomes except chromosome Y. This array is the first comprehensive equine high resolution resource for CNV mapping.<br /> <br /> The Equine breed diversity consortium was developed to facilitate large scale population genetic analysis in the domestic horse. This is an international collaboration of scientists from 22 different intuitions and represents genetic data from approximately 40 horse breeds. Many groups continue to focus on the collection of samples for mapping of simple and complex traits of interest, with a major focus on disease and athletic performance phenotypes<br /> <br /> Poultry Technical Report<br /> <br /> Telomere/telomerase dysregulation and Marek's Disease virus (MDV): MDV is a major cause of mortality leading to substantial economic losses to the poultry industry. Interestingly, the oncogenic MDV genome (which is circular and has no need for a telomere-maintenance system) contains two copies of the chicken telomerase RNA gene as well as several sets of telomere repeats. We hypothesize the MDV is utilizing aspects of the telomere-telomerase system to integrate into the chicken genome at the site of telomeres, and that this contributes to aspects of the disease state pathology, persistence and/or oncogenesis.<br /> <br /> Iowa State University maintains 13 unique chicken research lines [including highly inbred; MHCcongenic; closed populations; and advanced intercross lines (AIL)] that serve as resources for identifying genes and QTL of economic importance. The continued production of AIL (now at generation F18) facilitates the opportunity to narrow the confidence intervals (fine-map) around QTL and to conduct detailed studies on gene expression. Financial constraints resulted in the termination of 11 of the 24 lines in the past two years (2009-2010). Lines are maintained in minimal numbers, so collaborative studies or requests for genetic material must be arranged well in advance. Genetic material (chicks, fertile eggs, blood, tissue, DNA or RNA) has been shared with cooperating investigators to expand studies on the chicken genome, in addition to the studies conducted at Iowa State University. Current studies utilizing ISU chicken lines include collaborations with Huaijun Zhou of Texas A & M University (copy-number variation, avian influenza response) Andrew Clark of Cornell University (embryonic tissues for imprinting studies), Shane Burgess of Mississippi State University (F8 tissues for proteomic analysis of host response to Salmonella), Calvin Keeler of University of Delaware (F8 cDNA for microarray analysis of host response to Salmonella), and Hyun Lillehoj of USDA-ARS (Fayoumi chicks for analysis of response to Eimeria infection).<br /> <br /> AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. GOModeler, a tool that enables researchers to conduct hypothesis-based testing of high throughput datasets using the GO. GOModeler summarizes the overall effect of a user defined gene/protein differential expression dataset on specific GO hypothesis terms selected by the user to describe a biological experiment. The design of the tool allows the user to complement the functional information in the GO with his/her domain specific expertise for comprehensive hypothesis testing. GOModeler allows hypothesis driven analysis of high throughput datasets using the GO. Using this tool, researchers can quickly evaluate the overall effect of quantitative expression changes of gene set on specific biological processes of interest. The results are provided in both tabular and graphical formats. <br /> <br /> Sheep/Goat Technical Report<br /> <br /> Sheep Radiation Hybrid Map: Utah State University has added around 300 new markers to the ovine whole-genome RH map, in order to close gaps between adjacent RH groups and to extend the telomeric ends of the chromosomes. The addition of these markers increased marker density from 1.51 Mb/marker to 1.13 Mb/marker and the total map size increased ~37% in comparison to the previous version of the RH map. In addition, cross-species comparative maps based on marker-dense maps and high-coverage genome sequences were used to identify homologous synteny blocks (HSBs) and chromosome evolutionary breakpoint (EBRs) between sheep and other mammalian species. The number of homologous synteny blocks and chromosomal breakpoints between sheep and the human, cattle, horse and dog genomes were 216/54, 95/39, 122/61 and 135/75, respectively. Of the 229 conserved chromosomal segments, seventeen on human chromosomes (HSA1, 2, 3, 4, 6 and 21) and three on bovine chromosomes (BTA19, 27 and 28) had not been previously identified. This whole-genome RH map for sheep is a resource that can be used for fine-mapping economically important QTLs and will contribute to the assembly of the ovine reference sequence. It also contributes to a better understanding of the evolutionary history of ruminant species. A detailed review of the role of chromosome rearrangements in mammal evolutionary history is now possible.<br /> <br /> Goat Radiation Hybrid Map: Virginia State University has developed a radiation hybrid (RH) map for stronger comparative genomic analyses. A collaboration of VSU, Huazhong Agricultural University, Texas A & M, DNA Landmarks, INRA and IAEA. A RH panel of 92 clones has been established and used for initial mapping projects. DNA Landmarks has subjected the panel to the bovine and ovine 50K SNP panels. Data from the bovine panel has been developed into the initial goat RH map by Bertrand Servin at INRA.<br /> <br /> Goat Genome Sequencing: Two sequencing projects have begun for the goat, one public and one private, in association with the international goat consortium. The public project was undertaken by the research group at BGI in China as part of their 1000 genomes project. The initial sequencing has been completed on Illumina GX sequencers and the sequences are currently in the assembly process. NRSP-8 members have contributed to this project by providing virtual and RH maps for the assembly team and have discussed VSU working on aspects of the assembly and annotation. <br /> <br /> A sheep flock segregating for genes controlling parasite resistance has been created at Louisiana State University. The flock includes 378 F2 offspring of five F1 sires produced from Gulf Coast Native (resistant) and Suffolk (susceptible) crosses. Fecal egg counts (FEC) for Haemonchus contortus and packed cell volume (PCV) measurements were taken on all lambs at three time-points (at weaning, after 5 weeks on pasture, and 6 weeks after experimental challenge). In addition, all offspring, as well as their parents and grandparents, were genotyped with the Illumina Ovine SNP50 BeadChip. Preliminary analysis of a select group of 25 lambs (resistant = 19 and susceptible = 6) using PLINK software revealed significant associations (P < 1.31E - 06) for PCV1, PCV2 and FEC2 on 9 chromosomes. Using R/qtl, significant associations (LOD > 6.0) were found for PCV1, PCV2 and FEC2 on 10 chromosomes.<br /> <br /> Ovine progressive pneumonia virus (OPPV), a lentivirus of sheep, infects 66% of ewes at USSES. Scientists at the Animal Disease Research Unit and U.S. Sheep Experiment Station initiated a study to identify genetic factors influencing host control of OPPV and disease progression. OPPV cELISA antibody status and provirus concentrations were measured for 1000 ewes of 3 breeds, Rambouillet, Polypay, and Columbia for whole genome association using the Illumina OvineSNP50 marker set. Initial results indicate genes with logical roles in both cELISA status and provirus concentration. Further, some of these genes have no prior association with HIV (human immunodeficiency virus). Since both OPPV and HIV are macrophage-tropic lentiviruses with similar genomic structure, these genes may contribute to human medicine as well as animal agriculture. A molecular genetic study on transmission of OPPV unexpectedly found maternal transmission events accounted for the small minority of cases in one flock. This is contrary to the situation in caprine arthritis encephalitis virus (CAEV) in goats, and counter to previous expectation for OPPV in sheep. These results may suggest a broader range of possible explanations for mechanisms underlying genomic regions associated with OPPV.<br /> <br /> Swine Technical Report<br /> <br /> At PSU, an integrated genetic, RH, BAC-FP, RNASeq and comparative map has been created for SSC4 with 573 loci mapped to this chromosome. A similar integrated map for the remainder of the genome is being created with 11 chromosomes finished through 2010; the rest of the genome will be finished during 2011. Average map resolution is an improved 250 kb/marker for SSC4. <br /> <br /> At BARC, the nomenclature for the swine leukocyte antigen (SLA) complex, was updated and is posted on the Immuno Polymorphism Database-MHC (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla). BARC also reported on development of a polymerase chain reaction (PCR)-sequence-specific primer (PCR-SSP) typing method for detecting SLA class I and class II alleles, and this method was used for typing of PHGC pigs to determine the influence of SLA diversity on genetic resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection in outbred pigs. BARC also reported on a fluorescent microsphere immunoassay (FMIA) developed with South Dakota State University to detect innate inflammatory, regulatory, Th1, and Th2 cytokines. BARC, through the US Veterinary Immune Reagent Network www.vetimm.org continues to develop and distribute immune molecule detection resources to the research community. At WSU, SNP marker development for 15 candidate genes for PRRSV resistance is ongoing.<br /> <br /> At ISU, a DNA bank of pigs with Salmonella fecal shedding data was created and made available. ISU provided sequence data and annotations to scientists at Roslin Institute and Affymetrix to develop a second-generation custom Genechip, which is now available for genome-wide transcriptional profiling using the Affymetrix platform.<br /> <br /> At MSU, scientists added 20 additional markers on 9 chromosomes across 954 animals and added an additional 444 animals to their pQTL/eQTL resource population. A QTL scan found 26-29 QTL for growth (depending on model used), as well as 38-51 QTL for carcass and meat quality traits. Using the new NRSP-8 supported oligo array to find gene expression differences during muscle development, they found nearly 500 probes had signals indicating differential expression for the corresponding transcripts in Piau or York-Landrace pigs, and signals for 1,300 probes were different between breeds. An eQTL study was reported on selected animals from this population, and 62 eQTLs and three gene networks for loin muscle expression were found. Thirteen regions had oeverlapping pQTL and eQTL locations, indicating a significant number of cis-acting QTLs were found.<br /> <br /> At UNL, a population to study sow longevity genetics was initiated, samples are being collected through 2011 using the Nebraska growth/reproduction selection lines. The SNP chip was used to find association to development, reproduction and lifetime productivity traits for the first four replicates of animals. SNPs associated with these traits were found for many chromosomes, depending on trait of interest. <br /> <br /> At NCSU, a project to investigate porcine patellar gene expression patterns during impact injury as a human model is ongoing; 11 genes have been tested by q-PCR for response to different modalities of injury, of which many showed differential responses. A second project, investigating the copper metabolism on iron has been initiated. The effect of differing levels of dietary iron or source of copper ion on the expression of several genes relevant to copper metabolism as well as on copper levels was performed on young male pigs. Gene expression for a number of genes was shown to be affected by iron deficiency or by the level and/or source of copper.<br /> <br /> At BARC, continued progress in the PRRS host Genetics Consortium (PHGC) project, a large consortia with many collaborating groups, was reported. Eight trials of 200 pigs each have been completed, and blood samples for viral titer and RNA expression work, as well as growth data, have been collected. Genomic DNA has been prepared for trials 1-6 and provided to collaborators for SNP chip analysis, which is ongoing. In collaboration with MSU and NCSU, measurement of expression using the pigoligoarray for a number of tissues from pigs infected with two different PRRSV isolated have been performed, and the data is being analyzed.<br /> At ISU, results using the SNP chip to find SNPs associated with traits measured on several populations were described. Commercial populations with traits including sow productive life and other reproductive traits recorded were analyzed and a number of SNPs were found for several traits. Feet and leg soundness traits were also tested, and SNPs associated with these traits were found. The SNP chip was also used to find SNPs associated with a number of traits associated with production efficiency in the ISU Residual Feed Intake (RFI) selection lines. For 716 pigs tested (387 select and 329 control animals), many associated SNPS were found, and pathway analysis of genes mapping near these SNPs showed two pathways of functional relevance (fatty acid metabolism and cellular energy production).<br /> <br /> At ISU, the PHGC database is continuing to be developed. The ANEXdb database on gene expression and expressed sequence annotation has been used by many groups world-wide and cited in over 6 publications reporting gene expression profiling of porcine tissues. ANXdb has been migrated to www.animalgenome.org under the NRSP-8 Bioinformatics Coordinator. The Pig QTLDB is now part of an expanded AnimalQTLDB.<br />

Publications

Abel, E.L., J. M. Angel, P. K. Riggs, L. Langfield, H.-H. Lo, M. D. Person, Y. C. Awasthi, L. E. Wang, S. S. Strom, Q. Wei, and J. DiGiovanni. 2010. Gsta4, a modifier of susceptibility to skin tumor development in mice and humans. J. Natl Cancer Inst. 102:1663-1675.<br /> <br /> Adelson DL, Rayson, Edgar RC (2010) Characterization and Distribution of Retrotransposons and Simple Sequence Repeats Animal Genetics 41 (Suppl. 2):9199. <br /> <br /> Alexander, L.S., A. Qu, S.A. Cutler, A. Mahajan, M.F. Rothschild, W. Cai, J.C. Dekkers, and C.H. Stahl. 2010. A calcitonin receptor (CALCR) single nucleotide polymorphism is associated with growth performance and bone integrity in response to dietary phosphorus deficiency. J Anim Sci. 88:1009-1016.<br /> <br /> Ankra-Badu GA, Bihan-Duval EL, Mignon-Grasteau S, Pitel F, Beaumont C, Duclos MJ, Simon J, Carré W, Porter TE, Vignal A, Cogburn LA, Aggrey SE (2010) Mapping QTL for growth and shank traits in chickens divergently selected for high or low body weight. nim Genet 41:400-405<br /> <br /> Ankra-Badu GA, Shriner D, Le Bihan-Duval E, Mignon-Grasteau S, Pitel F, Beaumont C, Duclos MJ, Simon J, Porter TE, Vignal A, Cogburn LA, Allison DB, Yi N, Aggrey SE (2010) Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate. BMC Genomics 11:107<br /> <br /> Archibald, A.L., L. Bolund, C. Churcher, M. Fredholm, M.A. Groenen, B. Harlizius, K.T. Lee, D. Milan, J. Rogers, M.F. Rothschild, H. Uenishi, J. Wang, and L.B. Schook. 2010. Swine Genome Sequencing Consortium. Pig genome sequence--analysis and publication strategy. BMC Genomics. 11:438.<br /> <br /> Ashworth, M.D., Ross, J.W., Stein, D.R., White, F.J., DeSilva, U., and Geisert, R.D. 2010. Endometrial caspase 1 and interleukin-18 expression during the estrous cycle and periimplantation period of porcine pregnancy and response to early exogenous estrogen administration. Reproductive Biology and Endocrinology 8:33<br /> <br /> Aston, K.I., G.P Li, B.A. Hicks, B.R. Sessions, T.D. Bunch, L.F. Rickords, B. Weimer, and K.L. White (2010) Aberrant expression of developmentally important genes in various stages of preimplantation bovine somatic cell nuclear transfer embryos. Cloning Stem Cells 12:23-32.<br /> <br /> Bailey, D.W., M.G. Thomas, J.W. Walker, B.K. Witmore, and D. Tolleson. 2010. Effect of previous experience on grazing patterns and diet selection of Brangus cows in the Chihuahuan Desert. Range Ecol. Manage. 62:223-232.<br /> <br /> Baird JD, Valberg SJ, Anderson SM, McCue ME, Mickelson JR. Presence of the glycogen synthase 1 (GYS1) mutation causing type 1 polysaccharide storage myopathy in continental European draught horse breeds. Vet Rec. 2010 Nov 13;167(20):781-4.<br /> <br /> Barb, C.R., Hausman, G.J., Rekaya, R. Lents, C.A., Lkhagvadorj, S., Qu, L., Cai, W., Couture, O.P., Anderson, L.L., Dekkers, J.C.M., Tuggle. C.K. 2010. Gene expression in hypothalamus, liver and adipose tissues and feed intake response to melanocortin-4 receptor (MC4R) agonist in pigs expressing MC4R mutations. Physiological Genomics 41: 254-268.<br /> <br /> Bierman, C.D., E.-S. Kim, K. Weigel, P.J. Berger and B.W. Kirkpatrick. 2010. Fine-mapping quantitative trait loci for twinning rate on BTA14 in North American Holsteins. J Animal Science 88:2556-2564.<br /> <br /> Bierman, C.D., E.-S. Kim, X. Shi, K. Weigel, P.J. Berger and B.W. Kirkpatrick. 2010. Validation of twinning rate whole genome association study results. Animal Genetics 41:406-416.<br /> <br /> Bellone RB, Forsyth G., Leeb T, Archer S, Sigurdsson S, Mauceli E., Enquensteiner M., Bailey E., Sandmeyer L, Grahn, B (2010) Fine mapping and mutation analysis of TRPM1, a candidate gene for Leopard Complex (LP) spotting and congential stationary Night Blindness (CNSB) in horses. and Fine Mapping the Leopard Complex (LP) Spotting Gene and Congenital Stationary Night Blindness (CSNB) in Horses. Briefings in Functional Genomics and Proteomics Advance Access doi:10.1093/bfgp/elq002<br /> <br /> Bellone R.R., S. Archer S., Wade, C.M., Cuka-Lawson, C., Haase, B., Leeb,T., Forsyth, G., Sandmeyer, L., and Grahn, B. (2010) Association analysis of candidate SNPs in TRPM1 with leopard complex spotting (LP) and congenital stationary night blindness (CSNB) in horses. Animal Genetics 41(Suppl. 2): 207.<br /> Bellone, R.R. (2010) Pleiotropic effects of pigmentation genes in horses. Animal Genetics 41(Suppl. 2): 100110.<br /> <br /> Bower MA, Campana MG, Whitten M, Edwards CJ, Jones H, Barrett E, Cassidy R, Nisbet RE, Hill EW, Howe CJ, Binns M. 2010 The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares. Biol Lett. PMID 20926431.<br /> <br /> Boyd, P. E. Hudgens, J.P.Loftus, D. Tompkins, J. Labresh, M. Wysocki, C.L. Baldwin and J. Lunney. 2010. Expressed gene sequence and bioactivity of the IFN³-response chemokine CXCL11 of cattle and swine. Veterinary Immunology and Immunopathology 136: 170-175.<br /> <br /> Brooks SA & Bailey E (2010) RT-qPCR Comparison of Mast Cell Populations in Whole Blood from Healthy Horses and those with Laminitis. Animal Genetics 41 (supl 2): 16-22.<br /> <br /> Brooks, S., Gabreski, N., Miller, D., Brisbin, A., Brown, H., Streeter, C., Mezey, J. G., Cook, D., Antczak, D. (2010). Whole Genome SNP Association in the Horse: Identification of a Deletion in Myosin Va Responsible for Lavender Foal Syndrome. PLoS Genetics, 6 (4), e1000909.<br /> <br /> Brooks, S., Makvandi-Nejad, S., Chu, E., Allen, J., Streeter, C., Gu, E., McCleery, B., Murphy, B., Bellone, R., Sutter, N. (2010). Morphological variation in the horse: defining complex traits of size and shape.. Animal Genetics, 41, 159-165.<br /> <br /> Brosnahan, M. M., Brooks, S., Antczak, D. F. (2010). Equine Clinical Genomics: A clinician's primer. Equine Veterinary Journal, 42 (7), 658-670.<br /> <br /> Broughton-Neiswanger, L.E., S. N. White, D. P. Knowles, M. R. Mousel, G. S. Lewis, D. R. Herndon, and L. M. Herrmann-Hoesing (2010) Non-maternal transmission is the major mode of ovine lentivirus transmission in a ewe flock: A molecular epidemiology study. Infection, Genetics and Evolution. 10(7):998-1007. <br /> <br /> Brunelli, J.P,, C.A. Steele and G. H. Thorgaard, 2010. Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout. Mol. Phylo. Evol. 56: 983-990.<br /> <br /> Byerly MS, Simon J, Cogburn LA, Le Bihan-Duval E, Duclos MJ, Aggrey SE, Porter TE (2010) Transcriptional profiling of the hypothalamus during development of adiposity in genetically selected fat and lean chickens. Physiol Genomics 42:157-167.<br /> <br /> Byrne, K., M. Colgrave, T. Vuocolo, R. Pearson, C. Bidwell, N. Cockett, D. Lynn, J. Waddell, and R. Tellam (2010) The imprinted retrotransposon-like gene Peg11 is expressed as a full length protein in skeletal muscle from callipyge sheep. PLoS ONE 5(1): e8638.<br /> <br /> Byrne, K., T. Vuocolo, C. Gondro, J. White, N. E. Cockett, T. Hadfield, C. A. Bidwell, J. N. Waddell, and R. T. Tellam (2010) A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development. BMC Genomics 11:378.<br /> Cánovas, A, G. Rincón, A.D. Islas, S. Wickramasinghe, and J. F. Medrano 2010. SNP Discovery in the bovine milk transcriptome using RNA-Seq technology. Mammalian Genome 21:592-598.<br /> <br /> Casellas, J., C.R. Farber, R.A. Verdugo and J.F.Medrano 2010. Segregation analysis of a sex ratio distortion locus in congenic mice. J Heredity 101:351-359 <br /> Chang, Shuang, Dunn, J.R., Heidari, M., Lee, L., Song, J.Z., Ernst, C.W., Ding, Z., Bacon, L.D., and Zhang, H.M. 2010. Genetics and Vaccine Efficacy: Host genetic variation affecting Mareks disease vaccine efficacy in White Leghorn chickens. Poultry Sci. 89:2083-2091.<br /> <br /> Chang, T.-C, Liu, W.-S. (2010) The molecular evolution of PL10 homologs. BMC Evol Biol 10, 127. <br /> <br /> Chen F, Lee Y, Jiang Y, Wang S, Peatman E, Abernathy J, Liu H, Liu S, Kucuktas H, Ke C, Liu ZJ. 2010. Identification and characterization of full-length cDNAs in catfish (Ictalurus spp.). PLoS One 12, e11546.<br /> <br /> Chen J, Dodson MV, Jiang Z. 2010. Cellular and molecular comparison of redifferentiation of intramuscular- and subcutaneous- adipocyte derived progeny cells. International Journal of Biological Science 6:80-88.<br /> <br /> Choi, I., J.P. Steibel, R.O. Bates, N.E. Raney, J.M. Rumph and C.W. Ernst. 2010. Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population. BMC Genetics. 11:97.<br /> <br /> Ciraci, C., C.K. Tuggle, M. Wannemuehler, D. Nettleton, S.J. Lamont. 2010. Unique Genome-wide Transcriptome Profiles of Chicken Macrophages upon exposure to Salmonella-derived Endotoxin. BMC Genomics 11:545.<br /> <br /> Coleman SJ, Zeng Z, Wang K, Luo S, Khrebtukova I, Mienaltowski MJ, Schroth GP, Liu, J., MacLeod JN. Structural annotation of equine protein-coding genes determined by mRNA sequencing. Animal Genetics, 41 (Suppl. 2):121130, 2010.<br /> <br /> Cook D, Gallagher PC and Bailey E (2010) Genetics of Swayback in American Saddlebred Horses. Animal Genetics 41 (supl 2): 64-71.<br /> <br /> Corbin LJ, Blott SC, Swinburne JE, Vaudin M, Bishop SC, Woolliams JA. (2010) Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Animal Genetics 41 (Supp. 2): 8-15.<br /> <br /> Costa de Melo, A. G., E. S. Varela, C. R. Beasley, H. Schneider, I. Sampaio, P. M. Gaffney, K. S. Reece, and C. H. Tagliaro. 2010. Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea). Genetics and Molecular Biology 33:564-572.<br /> <br /> Cothran, G., PhD. 2010. XX/XY Blood Lymphocyte Chimerism in Heterosexual Dizygotic Twins from an American Bashkir Curly Horse. Case Report. J.Equine Vet. Sci. 30:575-580.<br /> <br /> Curole, J. P., Meyer, E., Manahan, D. T., Hedgecock, D. (2010). Expression of the Pacific oyster mitochondrial genome: Variation among loci and evidence for regulation by nuclear-cytoplasmic interaction. Biological Bulletin. Vol. 218 (2), pp. 122-131.<br /> <br /> Dalloul RA et al., 2010. Multiplatform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology 8(9):e1000475.<br /> <br /> Daniels TF, Wu X-L, Pan ZX, Michal JJ, Wright Jr. RW, Killinger KM, MacNeil MD, Jiang Z. 2010. The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth. PLoS ONE 5(12): e15203.<br /> <br /> Dawes, M.J., R.O. Bates, N.E. Raney, J.P. Steibel and Ernst, C.W. 2010. Evaluation of single nucleotide polymorphism markers on pig chromosomes 3 and 6 for potential associations with meat quality traits. J. Anim. Sci. 88(E-Suppl. 3):143-4.<br /> <br /> Dégremont L, Bédier E, Boudry P (2010a). Summer mortality of hatchery-produced Pacific oyster spat (Crassostrea gigas). II. Response to selection for survival and its influence on growth and yield. Aquaculture 299: 21-29.<br /> <br /> Dégremont L, Boudry P, Ropert M, Samain JF, Bédier E, Soletchnik P (2010b). Effects of age and environment on survival of summer mortality by two selected lines of the Pacific oyster Crassostrea gigas. Aquaculture 299: 44-50.<br /> <br /> De los Campos, G., Gianola, D., Rosa, G. J. M., Weigel, K. A. and Crossa J. 2010. Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods. Genetics Research 92: 295-308.<br /> <br /> Dierks C, Komm K, Lampe V, Distl O. Fine mapping of a quantitative trait locus for osteochondrosis on horse chromosome 2. Anim Genet. 2010 41 Suppl 2:87-90.<br /> <br /> Dodson MV, Guan LL, Fernyhough ME, Mir PS, Bucci L, McFarland DC, Novakofski J, Reecy JM, Ajuwon KS, Thompson DP, Hausman GJ, Benson ME, Bergen WG, Jiang Z. 2010. Perspectives on the formation of an interdisciplinary research team. Biochem Biophysical Res Comm 391:155-1157.<br /> <br /> Dodson MV, Hausman GJ, Guan LL, Du M, Rasmussen TP, Poulos SP, Mir P, Bergen WG, Fernyhough ME, McFarland DC, Rhoads RP, Soret B, Reecy JM, Velleman SG, Jiang Z. 2010. Lipid metabolism, adipocyte depot physiology and utilization of meat animals as experimental models for metabolic research. International Journal of Biological Science 6:691-699. <br /> <br /> Dodson MV, Hausman GJ, Guan LL, Du M, Rasmussen TP, Poulos SP, Mir P, Bergen WG, Fernyhough ME, McFarland DC, Rhoads RP, Soret B, Reecy JM, Velleman SG, Jiang Z. 2010. Skeletal muscle stem cells from animals I. Basic cell biology. International Journal of Biological Science 6: 465-474.<br /> <br /> Dodson MV, Jiang Z, Chen J, Hausman GJ, Guan LL, Novakofski J, Thompson DP, Lorenzen CL, Fernyhough ME, Mir P, Reecy JM. 2010. Allied industry approaches to alter intramuscular fat content and composition in beef animals. Journal of Food Science 75:R1-8.<br /> <br /> Dodson MV, Vierck JL, Hausman GJ, Guan LL, Fernyhough ME, Poulos SP, Mir P, Jiang Z. 2010. Examination of adipose depot-specific PPAR moieties. Biochem Biophysical Res Comm 394:241-242.<br /> <br /> Dorshorst, B.J., Okimoto, R., Ashwell, C.M. 2010. Genomic Regions Associated with Dermal Hyperpigmentation, Polydactyly and Other Morphological Traits in the Silkie Chicken. J. Heredity. 101:339-50.<br /> <br /> Du ZQ, Ciobanu DC, Onteru SK, Gorbach D, Mileham AJ, Jaramillo G, Rothschild MF. 2010. A gene-based SNP linkage map for pacific white shrimp, L. vannamei. Animal Genetics 41(3):286-294. <br /> <br /> Edholm, E.-S., Hudgens, E.D., Tompkins, D., Sahoo, M., Burkhalter, B., Miller, N.W., Bengtén, E., Wilson, M., 2010.Characterization of anti-channel catfish IgL Ã monoclonal antibodies. Veterinary Immunology and Immunopathology. 135(3-4) 325-328.<br /> <br /> Edholm, E.S., Bengtén, E., Stafford, J.L., Sahoo, M., Taylor, E.B., Miller, N.W., Wilson, M. 2010. Identification of two IgD+ B cell populations in channel catfish, Ictalurus punctatus. Journal of immunology, 185 (7), pp. 4082-4094.<br /> <br /> Fahrenkrug, S. C., A. Blake, D. F. Carlson, T. Doran, A. L. Van Eenennaam, D. Faber, C. Galli, P. B. Hackett, N. Li, E. A. Maga, J. D. Murray, R. Stotish, E. Sullivan, J. F. Taylor, M. Walton, M. Wheeler, B. Whitelaw, B. P. Glenn. 2010. Precision Genetics for Complex Objectives in Animal Agriculture. Journal of Animal Science. 88:2530-9.<br /> <br /> Fan, B., Z.-Q. Du, D.M. Gorbach, and M.F. Rothschild. 2010. Development and application of high-density SNP arrays in genomic studies of domestic animals. Asian-Australasian Journal of Animal Science. 23:833-847.<br /> <br /> Fan, B., S. Lkhagvadorj, W. Cai, J. Young, R.M. Smith, J.C. Dekkers, E. Huff-Lonergan, S.M. Lonergan, and M.F. Rothschild. 2010. Identification of genetic markers associated with residual feed intake and meat quality traits in the pig. Meat Sci. 84:645-650.<br /> <br /> Felicetti M, Lopes MS, Verini-Supplizi A, Machado Ada C, Silvestrelli M, Mendonça D, Distl O. Genetic diversity in the Maremmano horse and its relationship with other European horse breeds. Anim Genet. 2010. 41 Suppl 2:53-5. <br /> <br /> Fernando, S.C., Purvis II, H.T., Najar, F.Z., Sukharnikov, L.O., Krehbiel, C.R., Nagaraja, T.G., Roe, B.A., and DeSilva, U. (2010) Rumen Microbial Population Dynamics during Adaptation to a High Grain Diet. Applied and Environmental Microbiology 76, 7482-90.<br /> <br /> Fleury E, Moal J, Boulo V, Daniel J-Y, Mazurais D, Hénaut A, Boudry P, Favrel P, Huvet A (2010). Identification of new genes associated with summer mortality in the oyster Crassostrea gigas. Marine Biotechnology 12: 326339.<br /> <br /> Fry, R.S., Spears, J.W., Hansen, S.L., and Ashwell, M.S. (2010) Dietary iron affects mRNA expression of porcine copper transporters. FASEB J 24:229-7.<br /> Fuller, S.A., McEntire, M.E., and Ludwig, G.M. 2010. Development and testing of a pedigree marking system using visible implant elastomer tags for selective improvement in Morone breeding programs. Aquaculture Research 41(8): 1250-1254.<br /> <br /> Waddell, J. N., P. Zhang, Y. Wen, S.K. Gupta, A. Yevtodiyenko, J.V. Schmidt, C.A. Bidwell, A. Kumar, and S. Kuang. (2010) DLK1 is necessary for proper skeletal muscle development and regeneration. PLoS ONE. 5: e15055.<br /> <br /> Gaffney, P. M., C. E. Pascal, J. P. Barnhart, W. S. Grant, and J. E. Seeb. 2010. Genetic homogeneity of weathervane scallops in the Northeastern Pacific. Can. J. Fish. Aquat. Sci. 67:1827-1839.<br /> <br /> Gonzalez-Recio, O., Weigel, K. A., Gianola, D., Naya, H. and Rosa, G. J. M. L2-Boosting algorithm applied to high-dimensional problems in genomic selection. Genetics Research 92: 227-237, 2010.<br /> <br /> Gorbach, D., B. Mote, L. Totir, R. Fernando, and M.F. Rothschild. 2010. Polydactyl inheritance in the pig. J Hered 101:469-475.<br /> <br /> Gorbach DM, Hu ZL, Du ZQ, Rothschild MF. 2011. Mining ESTs to determine the usefulness of SNPs across shrimp species. Animal Biotechnology 21(2):100-103. <br /> Gao, Yu, Laurence Flori, Jerome Lecardonnel, Diane Esquerre, Zhi-Liang Hu, Angelique Teillaud, Gaetan Lemonnier, Francois Lefevre, Isabelle P Oswald and Claire Rogel-Gaillard (2010). Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response. BMC Genomics 2010, 11:292.<br /> <br /> Hansen, S.L., Ashwell, M.S., Moeser, A.J., Fry, R.S., Knutson, M.D., and Spears, J.W. (2010) High dietary iron reduces transporters involved in iron and manganese metabolism and increases intestinal permeability in calves. Journal of Dairy Science. 93:656-65.<br /> <br /> Hansen, S.L., Trakooljul, N., Liu, H.-C.S., Hicks, J.A., Ashwell, M.S., and Spears, J.W. (2010) Proteins involved in iron metabolism in beef cattle are affected by copper deficiency in combination with high dietary manganese, but not by copper deficiency alone. Journal of Animal Science. 88:275-83.<br /> <br /> Hawkridge, A.M., Wysocky, R.B., Petitte, J.N., Anderson, K.E., Mozdziak, P.E., Fletcher, O.J., Horowitz, J.M., Muddiman, D.C,.2010. Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma. Anal Bioanal Chem. 398(2):737-49.<br /> <br /> He, W., R.L. Fernando, J.C.M. Dekkers, and H. Gilbert. 2010. A gene frequency model for QTL mapping using Bayesian inference. Genet. Sel. Evol. 42: 21.<br /> <br /> Hedgecock, D. (2010). Determining parentage and relatedness from genetic markers sheds light on patterns of marine larval dispersal. Molecular Ecology. 19 (5), 845-847.<br /> <br /> Hee CS, Gao S, Loll B, Miller MM, Uchanska-Ziegler B, Daumke O, Ziegler A. 2010. Structure of a classical MHC class I molecule that binds "non-classical" ligands. PLoS Biol 8:e1000557.<br /> <br /> Heidari M., A. Lopes, M. Huebner, S. Sharif, D. Kireev and H. Zhou. 2010. Mareks disease virus-induced immunosuppression: array analysis of chicken immune response genes expression profiling. Viral Immunology 23(3):309-19.<br /> <br /> Herrmann-Hoesing, L.M., S. M. Noh, K. R. Snekvik, S. N. White, D. A. Schneider, T. C. Truscott, and D. P Knowles (2010) Ovine progressive pneumonia virus capsid is found in CD163 and CD172a positive alveolar macrophages of persistently infected sheep. Veterinary Pathology. 47(3):518-528.<br /> <br /> Herrmann-Hoesing, L.M., L.E. Broughton-Neiswanger, K. C. Gouine, S. N. White, M. R. Mousel, G. S. Lewis, K. L. Marshall, and D. P. Knowles (2010) Evaluation of a CAEV/MVV indirect ELISA in the serological diagnosis of ovine progressive pneumonia virus in U.S. sheep. Clin. Vaccine Immunol. 17(2):307-310.<br /> <br /> Herzig, C.T.A., R.W. Waters, C.L. Baldwin and J.C. Telfer. 2010. Evolution of the CD163 family and its relationship to the bovine gamma delta T cell co-receptor WC1. BMC Evolutionary Biology. 10: 181.<br /> <br /> Herzig, C.T.A.H., M. P. Lafranc and C.L. Baldwin. 2010. Genomic organization of the bovine T cell receptor delta locus, BMC Genomics 11:100 (19 pages).<br /> Higgins SE, Ellestad LE, Trakooljul N, McCarthy F, Saliba J, Cogburn LA, Porter TE (2010) Transcriptional and Pathway Analysis in the Hypothalamus of Newly Hatched Chicks during Fasting and Delayed Feeding. BMC Genomics 11:162.<br /> <br /> Hill EW, Gu J, Eivers SS, Fonseca RG, McGivney BA, Govindarajan P, Orr N, Katz LM, MacHugh DE. A sequence polymorphism in MSTN predicts sprinting ability and racing stamina in thoroughbred horses. PLoS One. 2010 5 ;e8645.<br /> <br /> Hill EW, Gu J, McGivney BA, MacHugh DE. Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance. Anim Genet. 2010 Dec;41 Suppl 2:56-63. <br /> <br /> Hill, EW, McGivney BA, Gu J, Whiston R, Machugh DE. A genome-wide SNP-association study confirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses. BMC Genomics. 2010;11:552. <br /> <br /> Hill EW. Livestock issue. Brief Funct Genomics. 2010 May;9(3):191-2. <br /> Hirota, K., Kakoi, H., Gawahara, H., Hasegawa, T., and Tozaki, T. Construction and Validation of Parentage Testing for Thoroughbred Horses by 53 Single Nucleotide Polymorphisms. J. Vet Med. Sci. 72 (6): 719-726, 2010.<br /> <br /> Holl H., Brooks S & Bailey E. (2010) De novo mutation of KIT discovered as a result of non-hereditary white coat color pattern. Animal Genetics 41(supl2): 196-198.<br /> <br /> Huang, W., Kirkpatrick, B. W., Rosa, G. J. M. and Khatib, H. 2010. A genome wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle. Animal Genetics 41, 570578.<br /> <br /> Huvet A, Normand J, Fleury E, Quillien V, Fabioux C, Boudry P (2010). Reproductive effort of Pacific oysters: a trait associated with susceptibility to summer mortality. Aquaculture, 304: 95-99.<br /> <br /> Jhingory S, Wu CY, and Taneyhill LA. 2010. Novel insight into the function and regulation of aN-catenin by Snail2 during chick neural crest cell migration. Dev Biol 344: 896-910.<br /> <br /> Jiang Y, Abernathy J, Peatman E, Liu H, Wang S, Xu D-H, Kucuktas H, Klesius P, Liu Z.J. 2010. Identification and characterization of matrix metalloproteinase-13 sequence structure and expression during embryogenesis and infection in channel catfish (Ictalurus punctatus). Developmental and Comparative Immunology 34:590-597.<br /> <br /> Jordan, L.G., C.A. Steele and G.H. Thorgaard, 2010. Universal mtDNA primers for species identification of degraded bony fish samples. Molecular Ecology Resources 10: 225-228.<br /> <br /> Juras, R., DVM, PhD, T. Raudsepp, PhD, P.J. Das, DVM, PhD, E. Conant, PhD, and E. Kim, T., Hunt, H.D., and Cheng, H.H. 2010. Mareks disease viruses lacking either RLORF10 or LORF4 have altered virulence in chickens. Virus Genes 40:410-420.<br /> <br /> <br /> Kirkpatrick, B.W., X. Shi, G.E. Shook and M.T. Collins. 2010. Whole genome association study of susceptibility to infection by Mycobacterium avium subsp. paratuberculosis in Holstein cattle. Animal Genetics, DOI: 10.1111/j.1365- 2052.2010.02097.<br /> <br /> Klukowska-Rötzler J, Marti E, Bugno M, Leeb T, Janda J. Molecular cloning and characterization of equine thymic stromal lymphopoietin. Vet Immunol Immunopathol. 2010 136(3-4):346-9. <br /> <br /> Kubosaki A, Lindgren G, Tagami M, Simon C, Tomaru Y, Miura H, Suzuki T, Arner E, Forrest AR, Irvine KM, Schroder K, Hasegawa Y, Kanamori-Katayama M, Rehli M, Hume DA, Kawai J, Suzuki M, Suzuki H, Hayashizaki Y. 2010. The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. Mol Immunol. 47(14):2295-302.<br /> <br /> Lallias D, Boudry P, Lapègue S, King JW, Beaumont AR (2010). Strategies for the retention of high genetic variability in European flat oyster (Ostrea edulis) restoration programmes. Conservation Genetics 11: 1899-1910.<br /> <br /> Lallias D, Taris N, Boudry P, Bonhomme F, Lapègue S (2010). Variance in reproductive success of flat oyster Ostrea edulis L. assessed by parentage analyses in natural and experimental conditions. Genetics Research 92(3): 175-187.<br /> <br /> Lawson S, Lunney JK, Zuckermann F, Osorio F, Nelson EA, Welbon C, Clement T, Fang Y, Wong S, Kulas, K, Christopher-Hennings J. 2010. Development of an 8-plex Luminex assay to detect swine cytokines for vaccine development: Assessment of immunity after porcine reproductive and respiratory syndrome virus (PRRSV) Vaccine. 32: 5383-5391.<br /> <br /> Lee JY, Song JJ, Wooming A. Li XY, HJ Zhou, Bottje W. Kong BW. 2010 Transcriptional profiling of host gene expression in chicken embryo lung cells infected with laryngotracheitis virus. BMC Genomics 2010, 11:445.<br /> <br /> Lee, Lucy F., Kreager, K.S., Arango, J., Paraguassu, A., Beckman, B., Zhang, H.M., Fadly, A.M., Lupiani, B., and Reddy, S. 2010. Comparative evaluation of vaccine efficacy of recombinant Mareks disease virus vaccine lacking Meqoncogene in commercial chickens. Vaccine 28:1294-1299.<br /> <br /> Leeds, T.D., Silverstein, J.T., Weber, G.M., Vallejo, R.L., Palti, Y., Rexroad, C.E., Iii, Evenhuis, J., Hadidi, S., Welch, T.J. & Wiens, G.D. (2010). Response to selection for bacterial cold water disease resistance in rainbow trout. J Anim Sci, 88: 1936-46.<br /> <br /> Li X., C. L. Swaggerty, M. H. Kogut, H. Chiang, Y. Wang, K. J. Genovese, H. He, H. Zhou. 2010. Gene expression profiling of the local cecal response of genetic chicken lines that differ in their susceptibility to Campylobacter jejuni colonization. PLoS ONE 5(7): e11827. <br /> <br /> Liu H, Tomokazu T, Abernathy J, Wang S, Sha Z, Terhune J, Kucuktas H, Jiang Y, Liu ZJ. 2010. Structure and expression of transferrin gene of channel catfish, Ictalurus punctatus. Fish and Shellfish Immunology 28:159-166.<br /> <br /> Liu H, Takano T, Peatman E, Abernathy J, Wang S, Sha Z, Kucuktas H, Liu ZJ. 2010. Molecular characterization and gene expression of the channel catfish ferritin H subunit after bacterial infection and iron treatment. Journal of Experimental Zoology, Part A: Ecological Genetics and Physiology 313:359-368.<br /> <br /> Lkhagvadorj, S., L. Qu, W. Cai, O. P. Couture, C. R. Barb, G. J. Hausman, D. Nettleton, L.L. Anderson, J.C.M. Dekkers, C. K. Tuggle. 2010. Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency. American Journal of Physiology: Regulatory, Integrative and Comparative Physiology 298:494-507.<br /> <br /> Long, N. M., Prado-Cooper, M. J., Krehbiel, C. R., DeSilva, U., and Wettemann, R. P. (2010) Effects of nutrient restriction of calves during early gestation on postnatal growth, carcass and organ characteristics and regulation of plasma glucose. Journal of Animal Science, 88, 3251-61.<br /> <br /> Long, N., Gianola, D., Rosa, G. J. M., Weigel, K. A., Kranis, A. and Gonzalez-Recio. O. 2010. Radial basis function regression methods for predicting quantitative traits using SNP markers. Genetics Research 92, 209-225.<br /> <br /> Lopes MS, Diesterbeck U, Machado Ada C, Distl O. Refinement of quantitative trait loci on equine chromosome 10 for radiological signs of navicular disease in Hanoverian warmblood horses. Anim Genet. 2010 41, Suppl 2:36-40. <br /> <br /> Lu J, Peatman E, Wang W, Yang Q, Abernathy J, Wang S, Kucuktas H, Liu ZJ. 2010. Alternative splicing in teleost fish genomes: Same-species and cross-species analysis and comparisons. Molecular Genetics and Genomics 283:531539.<br /> <br /> Luna-Nevarez, P., D.W. Bailey, C.C. Bailey, D.M. VanLeeuwen, R.M. Enns, G.A. Silver, K.L. DeAtley, and M.G. Thomas. 2010. Growth characteristics, reproductive performance, and evaluation of their associative relationship in Brangus cattle managed in a Chihuahuan Desert production system. J. Anim. Sci. 88:1891-1904. <br /> <br /> Lunney JK, Chen H. 2010. Genetic control of porcine reproductive and respiratory syndrome virus responses. Virus Research. 154: 161-169.<br /> <br /> Lunney JK, Fritz ER, Reecy JM, Kuhar D, Prucnal E, Molina R, Christopher-Hennings J, Zimmerman J, Rowland RRR. 2010. Interleukin-8, interleukin-1² and interferon-³ levels are linked to PRRS virus clearance. Viral Immunology. 23: 127-134.<br /> <br /> Lunney JK Benfield DA, Rowland RRR. 2010. Porcine Reproductive and Respiratory Syndrome Virus: An update on an emerging and re-emerging viral disease of swine. Virus Research. 154: 1-6.<br /> <br /> Lunney JK and Rowland RRR. (CoEditors). 2010. Progress in porcine respiratory and reproductive syndrome virus biology and control. Virus Research. 154 (1-2): 1-192.<br /> <br /> Lykkjen S, Dolvik NI, McCue ME, Rendahl AK, Mickelson JR, Roed KH. Genome-wide association analysis of osteochondrosis of the tibiotarsal joint in Norwegian Standardbred trotters. Anim Genet. 2010 41 Suppl 2:111-20. <br /> <br /> Manda, P., M. G. Freeman, S. M. Bridges, T. J. Jankun-Kelly, B. Nanduri, F. M. McCarthy, and S. C. Burgess. 2010. GOModeler--a tool for hypothesis-testing of functional genomics datasets. BMC Bioinformatics 11 Suppl 6:S29.<br /> <br /> Mao, W., Hunt, H.D., and Cheng, H.H. 2010. Cloning and functional characterization of chicken stem cell antigen 2. Devel. Comp. Immunol. 34:360-368.<br /> <br /> Martin AM, Elliott JA, Duffy P, Blake CM, Ben Attia S, Katz LM, Browne JA, Gath V, McGivney BA, Hill EW, Murphy BA. Circadian regulation of locomotor activity and skeletal muscle gene expression in the horse. J Appl Physiol. 2010 109(5):1328-36. <br /> <br /> Martin, K.E., C.A. Steele, J.P. Brunelli and G.H. Thorgaard, 2010. Mitochondrial variation and biogeographic history of Chinook salmon. Trans. Amer. Fish. Soc. 139: 792-802.<br /> <br /> Mateescu, R.G. and M. L. Thonney (2010) Genetic mapping of quantitative trait loci for milk production in sheep. Anim Genet. 41:460-466.<br /> <br /> Maturana, E. L., de los Campos, G., Wu, X.-L., Gianola, D., Weigel, K. A. and Rosa, G. J. M. Modeling relationships between calving traits: a comparison between standard and recursive mixed models. Genetics Selection Evolution 42(1), 2010.<br /> <br /> McCarthy, F. M., C. R. Gresham, T. J. Buza, P. Chouvarine, L. R. Pillai, R. Kumar, S. Ozkan, H. Wang, P. Manda, T. Arick, S. M. Bridges, and S. C. Burgess. 2010. AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Res 39:D497-506.<br /> <br /> McCue ME, Anderson SM, Valberg SJ, Piercy RJ, Barakzai SZ, Binns MM, Distl O, Penedo MC, Wagner ML, Mickelson JR. Estimated prevalence of the Type 1 Polysaccharide Storage Myopathy mutation in selected North American and European breeds. Anim Genet. 2010 41 Suppl 2:145-9. <br /> <br /> McGivney BA, McGettigan PA, Browne JA, Evans AC, Fonseca RG, Loftus BJ, Lohan A MacHugh DE, Murphy BA, Katz LM, Hill EW. Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training. BMC Genomics. 2010 23;11:398. <br /> <br /> McGlynn OF, Browne JA, Blake CM, Murphy BA (2010) Time of day influences cytokine and clock gene response to immune stimulation in equine whole blood. Animal Genetics. Volume 41, Issue Supplement s2, pages 202204. <br /> <br /> Medrano, J.F. and G. Rincón 2010. Genes involucrados en la determinación de la composición y rendimiento de la leche. In: Genética de Animales Domésticos, Editores G. Giovambattista and P. Peral-García, Editorial Inter-Medica S.A., Argentina.<br /> <br /> Medrano, J.F., A. Ahmadi and J. Casellas 2010. Dairy Cattle Breeding Simulation Program (DCBSP v.4.9), a simulation program to teach animal breeding principles and practices. J Dairy Sci 93:2816-2826.<br /> <br /> Mienaltowski MJ, Huang L, Bathke A, Stromberg AJ, MacLeod JN. Transcriptional comparisons between articular repair tissue, neonatal cartilage, cultured chondrocytes, and mesenchymal stromal cells. Briefings in Functional Genomics & Proteomics, 9:238-250, 2010.<br /> <br /> Milbury, C. A., J. C. Lee, J. J. Cannone, P. M. Gaffney, and R. R. Gutell. 2010. Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes. BMC Genomics 11:485.<br /> <br /> Meng, Q., C. Bai Y.L. Chunling, L. Ying, W. Xia, T.D. Bunch, and G-P. Li (2010) In vitro development and chromosomal configuration of bovine somatic cloned embryos with no-enucleated metaphase ii oocytes. Cell. Reprogram. 12:481-490.<br /> <br /> Michelizzi VN, Dodson MV, Pan ZX, Amaral ME, Michal JJ, McLean DJ, Womack JE, Jiang Z. 2010. Water buffalo genome science comes of age. International Journal of Biological Sciences 6: 333-349.<br /> <br /> Michelizzi VN, Wu X-L, Dodson MV, Michal JJ, Zambrano-Varon J, McLean DJ, Jiang Z. 2011. A global view of 54,001 single nucleotide polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and their transferability to water buffalo. Int. Journal of Biological Science 7:18-27.<br /> <br /> Mittmann EH, Mömke S, Distl O. Whole-genome scan identifies quantitative trait loci for chronic pastern dermatitis in German draft horses. Mamm Genome. 2010 21(1-2):95-103.<br /> <br /> Mohan, S., Davis, R. L., DeSilva, U., and Stevens, C. W. (2010) Dual regulation of ¼ opioid receptors in SK-N-SH neuroblastoma cells by morphine and interleukin-1 ²: Evidence for opioid-immune crosstalk. Journal of Neuroimmunology 227, 26-34.<br /> <br /> Morris, C.A., M. Wheeler, G. L. Levet, and B.W. Kirkpatrick. 2010. A cattle family in New Zealand with triplet calving ability. Livestock Science 128:193196.<br /> <br /> Nanduri, B., N. Wang, M. L. Lawrence, S. M. Bridges, and S. C. Burgess. 2010. Gene model detection using mass spectrometry. Methods Mol Biol 604:137-44.<br /> Neibergs, H.L., M.L. Settles, R.H. Whitlock, J.F. Taylor. GSEA-SNP identifies genes associated with Johnes disease in cattle. 2010. Mammalian Genome 21(7): 419. <br /> <br /> Onteru, S.K., A. Ampaire, M.F. Rothschild. 2010. Biotechnology developments in developing countries. Biotechnol. Genet. Eng. Rev. 27: 1-12.<br /> <br /> Orr N, Back W, Gu J, Leegwater P, Govindarajan P, Conroy J, Ducro B, Van Arendonk JA, MacHugh DE, Ennis S, Hill EW, Brama PA. Genome-wide SNP association-based localization of a dwarfism gene in Friesian dwarf horses. Anim Genet. 2010 41 Suppl 2:2-7. <br /> <br /> Ozden, O., Black, B.L., Ashwell, C.M., Tipsmark, C.K., Borski, R.J., Grubb, B.J. 2010. Developmental profile of claudin-3, -5, and -16 proteins in the epithelium of chick intestine. Anat Rec (Hoboken). 293(7):1175-83.<br /> <br /> Palti, Y., Gahr, S.A., Purcell, M.K., Hadidi, S., Rexroad III, C.E. & Wiens, G.D. (2010). Identification, characterization and genetic mapping of TLR7, TLR8a1 and TLR8a2 genes in rainbow trout (Oncorhynchus mykiss). Developmental & Comparative Immunology, 34: 219-233.<br /> <br /> Palti, Y., Rodriguez, M.F., Gahr, S.A., Purcell, M.K., Rexroad Iii, C.E. & Wiens, G.D. (2010). Identification, characterization and genetic mapping of TLR1 loci in rainbow trout (Oncorhynchus mykiss). Fish & Shellfish Immunology, 28: 918-926.<br /> <br /> Phillips, R.B. & Devlin R.H. (2010). Integration of growth hormone gene constructs in transgenic strains of coho salmon (Oncorhynchus kisutch) at centromeric or telomeric sites. Genome, 53:79-82.<br /> <br /> Proszkowiec-Weglarz M, Porter TE (2010) Functional characterization of chicken glucocorticoid and mineralocorticoid receptors. Am J Physiol Regul Integrative Comp Physiol 298:1257-1268.<br /> <br /> Qiu, H., X. Xu, B. Fan, M.F. Rothschild, Y. Martin, and B. Liu. 2010. Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2. Mol Biol Rep. 37:629-636.<br /> <br /> Quinn, N., Boroevich, K., Lubieniecki, K., Chow, W., Davidson, E., Phillips, R., Koop, B. & Davidson, W. (2010). Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire. BMC Genomics, 11: 539.<br /> <br /> Raudsepp T, Durkin K, Lear TL, Das PJ, Avila F, Kachroo P, Chowdhary BP (2010). Molecular heterogeneity of XY sex reversal in horses. Animal Genetics 41 (suppl 2):41-52.<br /> <br /> Redmond, S.B., Tell, R.M., Coble, D., Mueller, C., Palic, D., Andreasen, C.B., and Lamont, S.J. 2010. Differential splenic cytokine responses to dietary immune modulation by diverse chicken lines. Poultry Sci. 89: 1635-1641.<br /> <br /> Ren, J., X. Liu, F. Jiang, X. Guo and B Liu. 2010. Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia. BMC Evolutionary Biology, 10:394.<br /> <br /> Renaville, B., E. Piasentier, B. Fan, M. Vitale, A. Prandi, and M.F. Rothschild. 2010. Candidate gene markers involved in San Daniele ham quality. Meat Sci. 85:441-445.<br /> <br /> Rijnkels,M., C. Freeman-Zadrowski, J. Hernandez, V. Potluri, A. Lin, G. Rincon, A.D. Islas, L. Wang, W. Li, J.F. Medrano 2010. Insight in development and functional differentiation of the mammary gland; a chromatin perspective. 9th World Congress of Genetics Applied to Livestock Production (WCGALP), Leipzig-Germany, No. 0976.<br /> <br /> Rios JJ, Fleming JG, Bryant UK, Carter CN, Huber JC, Long MT, Spencer TE, Adelson DL (2010) OAS1 and RNASEL Polymorphisms Are Associated With <br /> Susceptibility To West Nile Encephalitis In Horses. PLoS ONE 5(5): e10537.<br /> <br /> Robinson, C.M., Hunt, H.D., Cheng, H., and Delany, M. 2010. Mapping of Mareks disease herpesvirus integrations into chicken chromosomes indicates positional preference for telomeres and clonal relationships among tumors. Herpesviridae 1:5.<br /> <br /> Robinson, C.M., H. Hunt, H. Cheng and M.E. Delany. 2010. Chromosomal integration of an avian oncogenic herpesvirus reveals telomeric preferences and evidence for lymphoma clonality. Herpesviridae 1:5 http://www.herpesviridae.org/content/1/1/5.<br /> <br /> Roe, B.A., and DeSilva, U. (2010) Rumen Microbial Population Dynamics during Adaptation to a High Grain Diet. Applied and Environmental Microbiology 76, 7482-90.<br /> <br /> Rosa, G. J. M. and Vazquez, A. I. Integrating biological information into the statistical analysis and design of microarray experiments. Animal 4(2): 165172, 2010.<br /> <br /> Salem, M., Kenney, P.B., Rexroad Iii, C.E. & Yao, J. (2010). Proteomic signature of muscle atrophy in rainbow trout. Journal of Proteomics, 73: 778-789.<br /> <br /> Salem M, Rexroad C, Wang J, Thorgaard G, Yao J (2010). Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 11(1): 564.<br /> <br /> Salem, M., Xiao, C., Womack, J., Rexroad, C. & Yao, J. (2010). A MicroRNA Repertoire for Functional Genome Research in Rainbow Trout. Marine Biotechnology, 12: 410-429.<br /> <br /> Salger, S.A., Reading, B.J., Baltzegar, D.A., Sullivan, C.V., and E.J. Noga. 2011. Molecular characterization of two isoforms of piscidin 4 from the hybrid striped bass (Morone chrysops X Morone saxatilis). Fish and Shellfish Immunology 30: 420-424.<br /> <br /> Sauvage C, Boudry P, de Koning DJ, Haley CS, Heurtebise S, Lapègue S (2010). Quantitative Trait Loci for resistance to summer mortality and OsHV1 load in the Pacific oyster (Crassostrea gigas). Animal Genetics: 41(4): 390-399.<br /> <br /> Scharrenberg A, Gerber V, Swinburne JE, Wilson AD, Klukowska-Rotzler J, Laumen E, Marti E. (2010) IgE, IgGa, IgGb and IgG(T) serum antibody levels in offspring of two sires affected with equine recurrent airway obstruction. Animal Genetics 41 (Suppl. 2): 131-137.<br /> <br /> Schmitz A, Demmel S, Peters LM, Leeb T, Mevissen M, Haase B. Comparative human-horse sequence analysis of the CYP3A subfamily gene cluster. Anim Genet. 2010 41 Suppl 2:72-9. <br /> <br /> Seabury, C. M., P. M. Seabury, J. E. Decker, R. D. Schnabel, and J. E. Womack. 2010. Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle. PNAS 107:151-156.<br /> <br /> Shakhsi-Niaei M, Klukowska-Rötzler J, Drögemüller C, Swinburne JE, Gerber V, Leeb T. Characterization of the equine ITGAX gene and its association with recurrent airway obstruction in European Warmblood horses. Anim Genet. 2010 41(5):559-60. <br /> <br /> Silva, R.F., Dunn, J.R., Cheng, H.H., and Niikura, M. 2010. A MEQ deleted Mareks disease virus cloned as a bacterial artificial chromosome is a highly efficacious vaccine. Avian Diseases 54:862-869.<br /> <br /> Staiger, E. A., M. L. Thonney, J. W. Buchanan, E. R. Rogers, P. A. Oltenacu, and R. G. Mateescu (2010) Effect of prolactin, ß-lactoglobulin and º-casein genotype on estimated breeding values for milk production in East Friesian sheep. J. Dairy Sci. 93(4):1736-1742.<br /> <br /> Suo, L., Q. Meng, Y. Pei, X-W. Fu, Y-P. Wang, T.D. Bunch, and S-E. Zhu (2010) Effect of cryopreservation on acetylation patterns of lysine 12 of histone H4 (acH4K12) in mouse oocytes and zygotes. J. Assisted Repro. Genet. 27:735-741.<br /> <br /> Swanberg, S.E., T.H. OHare, E.A. Robb, C.M. Robinson, H. Chang, and M.E. Delany. 2010. Telomere biology of the chicken: A model for aging research. Exptl Gerontology. 45:647-654.<br /> <br /> Tai, S.H.S., Niikura, M., Cheng, H.H., Kruger, J.M., Wise, A.G., and Maes, R.K. 2010. Complete genomic sequence and an infectious BAC clone of feline herpesvirus-1 (FHV-1). Virology 401:215-227.<br /> <br /> Thanthrige-Don, N., P. Parvizi, A. J. Sarson, L. A. Shack, S. C. Burgess, and S. Sharif. 2010. Proteomic analysis of host responses to Marek's disease virus infection in spleens of genetically resistant and susceptible chickens. Dev Comp Immunol 34:699-704.<br /> <br /> Toosi, A., R.L. Fernando, and J.C.M. Dekkers. 2010. Genomic Selection in admixed and crossbred populations. J. Anim. Sci. 88: 32-46.<br /> <br /> Tozaki, T., Hirota, K., Sugita, S., Ishida, N., Miyake, T., Oki, H., and Hasegawa, T. A genome-wide scan for tying-up sundrome in Japanese thoroughbreds. Anim. Genet. 41 (suppl. 2): 80-86, 2010.<br /> <br /> Tozaki, T., Miyake, T., Kakoi, H., Gawahara, H., Sugita, S., Hasegawa, T., Ishida, N., Hirota, K., and Nakano, N. A genome-wide association study for racing performance in Thoroughbreds clarifies a candidate region near the MSTN gene. Anim. Genet. 41 (suppl. 2): 28-35, 2010.<br /> <br /> Towfic, F., VanderPlas, S., Oliver, C.A., Couture, O., Tuggle, C.K., Greenlee, M.H.W., and V. Honavar. 2010. Detection of Gene Orthology Based On Biomolecular Networks. BMC Bioinformatics 11:S7.<br /> <br /> Tuggle CK. Bearson SMD, Uthe JJ, Huang TH, Qu L, Couture O, Wang YF, Kuhar D, Lunney JK, Nettleton D, Honavar V, Dekkers JCM. 2010. Updated methods for transcriptomic analyses of the porcine host immune response: Application to Salmonella infection. Vet. Immunol. Immunopathol. 138: 280-91.<br /> <br /> Tseng CT, D. Miller D, Cassano J, Bailey E and Antczak DF (2010) Molecular Identification of Equine Major Histocompatibility Complex Haplotypes using Polymorphic Microsatellites. Animal Genetics 41 (supl 2): 150-153.<br /> <br /> Valente, B. D., Rosa, G. J. M., de los Campos, G., Gianola, D. and Silva, M. A. Searching for recursive causal structures in multivariate quantitative genetics mixed models. Genetics 185: 633-644, 2010.<br /> <br /> Vallejo, R.L., Wiens, G.D., Rexroad, C.E., III, Welch, T.J., Evenhuis, J.P., Leeds, T.D., Janss, L.L.G. & Palti, Y. (2010). Evidence of major genes affecting resistance to bacterial cold water disease in rainbow trout using Bayesian methods of segregation analysis. J Anim Sci, 88: 3814-32.<br /> <br /> Van den Berg, B. H., F. M. McCarthy, S. J. Lamont, and S. C. Burgess. 2010. Re-annotation is an essential step in systems biology modeling of functional genomics data. PLoS One 5:e10642.<br /> <br /> Van Eenennaam, A. L., K. L. Weber, K. Cooprider and D. J. Drake. 2010. Development and implementation of a vertically-integrated beef cattle data collection system. California Agri 64:94-100.<br /> <br /> Van Melis, M. H., Eler, J. P., Rosa, G. J. M., Ferrz, J. B. S., Figueiredo, L. G. G., Mattos, E. C. And Oliveira, H. N. 2010. Additive genetic relationships between scrotal circumference, heifer pregnancy, and stayability in Nellore cattle. J. Anim. Sci. 88: 38093813.<br /> <br /> Varian, A. & Nichols, K.M. (2010). Heritability of Morphology in Brook Trout with Variable Life Histories. PLoS ONE, 5: e12950.<br /> <br /> Vazquez, A. I., Bates, D., Rosa, G. J. M., Gianola, D. and Weigel, K. A. 2010. Technical Note: An R package for fitting generalized linear mixed models in animal. J. Anim. Sci. 88: 497504.<br /> <br /> Vazquez, A. I., Rosa, G. J. M., Weigel, K. A., de los Campos, G., Gianola, D. and Allison, D. B. 2010. Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins. J. Dairy Sci. 93: 5942-5949.<br /> <br /> Verdugo, R.A., C.R. Farber, C.H. Warden and J.F. Medrano 2010. Serious limitations of the QTL/Microarray approach for QTL gene discovery. BMC Biology 8:96.<br /> <br /> Waldbieser, Geoffrey; Bosworth, Brian; Quiniou, Sylvie . 2010. Production of Viable Homozygous, Doubled Haploid Channel Catfish (Ictalurus punctatus) Marine Biotechnology, 12(4) 380-385.<br /> <br /> Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, Xiaping H, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Research, 38(18):e178, 2010.<br /> <br /> Wang S, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock C, Small B, Wilson M, Liu H, Jiang Y, Lee Y, Chen F, Lu J, Wang W, Peatman E, Xu P, Somridhivej B, Baoprasertkul P, Quilang J, Sha Z, Bao B, Wang Y, Wang Q, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rokhsar D, Liu ZJ., and Catfish Genome Consortium. 2010. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biology 11 (1):R8.<br /> <br /> Wang S, Peatman E, Liu H, Bushek D, Ford SE, Kucuktas H, Quilang J, Li P, Wallace R, Wang Y, Guo X, Liu Z. 2010. Microarray analysis of gene expression in eastern oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge. Fish Shellfish Immunol., 29: 921-929.<br /> <br /> Wang, Y., X. Wang, A. Wang and X. Guo. 2010. A 16-microsatellite multiplex assay for parentage assignment in the eastern oyster (Crassostrea virginica). Aquaculture, 308:S28-S33.<br /> <br /> Weigel, K. A., de los Campos, G., Vazquez, A. I., Rosa, G. J. M., Gianola, D. and Van Tassel, C. P. Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle. J. Dairy Sci. 93: 54235435, 2010.<br /> <br /> Wu, X.-L., Gianola, D., Rosa, G. J. M. and Weigel, K. A. Bayesian model averaging for evaluation of candidate gene effects. Genetica 138:395-407, 2010.<br /> <br /> Yamashita, J., Oki, H., Hasegawa, T., Honda T., and Nomura T. Demographic Analysis of Breeding Structure in Japanese Thoroughbred Population. J. Equine Sci. 21(2): 11-16, 2010.<br /> <br /> Yamashita, J., Oki, H., Hasegawa, T., Honda, T., and Nomura, T. Gene Dropping Analysis of Ancestral Contributions and Allele Survival in Japanese Thoroughbred Population. J. Equine Sci. 21(3): 39-45, 2010.<br /> <br /> Yeh, H.-Y., Klesius, P.H., 2010. Sequence analysis, characterization and mRNA distribution of channel catfish (Ictalurus punctatus Rafinesque, 1818) chemokine (C-X-C motif) receptor 4 (CXCR4) cDNA. Veterinary Immunology and Immunopathology, 134 (3-4), pp. 289-295.<br /> <br /> Yeh, H.-Y., Klesius, P.H., 2010. Characterization and tissue expression of channel catfish (Ictalurus punctatus Rafinesque, 1818) ubiquitin carboxyl-terminal hydrolase L5 (UCHL5) cDNA, 2010. Molecular Biology Reports, 37 (3), 1229-1234.<br /> <br /> Yeh, H.-Y., Klesius, P.H., 2010. Sequence analysis, characterization and tissue distribution of channel catfish (Ictalurus punctatus Rafinesque, 1818) myeloperoxidase cDNA, Fish and Shellfish Immunology, 28 (3), pp. 504-509.<br /> <br /> Yeh, H.-Y., Klesius, P.H., 2010. Channel catfish (Ictalurus punctatus Rafinesque, 1818) tetraspanin membrane protein family: Identification, characterization and expression analysis of CD63 cDNA, 2010. Veterinary Immunology and Immunopathology, 133 (2-4), 302-308.<br /> <br /> Xie X, Yu Y, Liu G, Yuan Z, Song JZ. (2010) Complexity and Entropy Analysis of DNA Methyltransferase. J Data Mining in Genom Proteomics 1:105. <br /> <br /> Xu, X., H. Qiu, Z.Q. Du, B. Fan, M.F. Rothschild, F. Yuan, and B. Liu. 2010. Porcine CSRP3: polymorphism and association analyses with meat quality traits and comparative analyses with CSRP1 and CSRP2. Mol Biol Rep. 37:451-459.<br /> <br /> <br /> Zaitoun, I., Downs, K. M., Rosa, G. J. M. and Khatib, H. Upregulation of imprinted genes in mice: an insight into the intensity of gene expression and the evolution of genomic imprinting. Epigenetics 5(2): 1-10, 2010.<br /> <br /> Zhang, L. and X. Guo. 2010. Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing. Aquaculture, 302:124-129.<br /> <br /> Zhang, X.M., X.P. Yue, W.-S. Liu, T.C. Chang, X.Y. Lan, H. Chen and C.Z. Lei (2010) Y-chromosome haplotype analysis revealing two major haplogroups in Chinese swamp buffaloes. Submitted to J. of Animal Breeding and Genetics (Nov 2010).<br /> <br /> Zimmerman J, Rowland RRR. 2010. Interleukin-8, interleukin-1² and interferon-³ levels are linked to PRRS virus clearance. Viral Immunology. 23: 127-134.<br />

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The NRSP-8 business meeting was preceded by two days of species workshops and area subcommittees and the combined Animal Genome Workshop. The combined workshop included four plenary presentations focused on next generation sequencing and genome assembly, salmonid genomics, and metagenomics. James Womack provided the 2012 NRSP-8 Distinguished Lecture with a historical overview of animal gene mapping and genomics. The business meeting was called to order by the Chair, Geoff Waldbieser (USDA-ARS), and was recorded by the Secretary/Chair-elect, Tom Porter (Univ. of Maryland) with 40 members in attendance. The 2010 minutes were approved unanimously. Coordinator reports were summarized by the Aquaculture, Bioinformatics, Cattle, Equine, Poultry, Sheep/Goat, and Swine chairs. Eric Young and Muquarrab Qureshi provided administrative reports and reminded members that the current project will terminate 09/30/13. Tom Porter assumed the NRSP-8 Chair for 2012-2013 and Milton Thomas (New Mexico State University) was elected Secretary/Chair-elect for 2012-2013. Both Tom and Milton agreed to co-chair the writing committee for the NRSP8 renewal. A motion to hold the 2013 meeting in conjunction with the Plant and Animal Genome conference was approved unanimously. The meeting was adjourned.
Detailed minutes are attached.

Accomplishments

OBJECTIVES<br /> <br /> Objective 1: Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest.<br /> Objective 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes.<br /> Objective 3: Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest. <br /> <br /> ACCOMPLISHMENTS AND IMPACTS:<br /> <br /> Overview<br /> <br /> The NRSP-8 participants and their collaborators have national and international impact on basic discovery and application of genomics to animal agriculture with 214 peer-reviewed publications in 2011. The community continues to adopted state of the art genomics technologies such as high-throughput DNA sequencing and transcriptional profiling (RNA-seq), and high density SNP genotyping in multiple species. These technologies are being used to produce whole genome sequence assemblies, annotate the genome assemblies, identify patterns of gene expression that correlate with phenotypes of interest, and identify genomic regions controlling economically important traits. The NRSP-8 program has excelled in the transfer of information and technology within species groups, such as the sharing of genomic tools, creation of shared bioinformatic resources, and sharing of methods and strategies for genomic analyses. The program has also excelled in the transfer of information between species groups, such as sharing experiences between researcher of genomically-enabled species with those who are still developing whole genome assemblies and tools. Genomic analyses have demonstrated the importance of the accurate and efficient measurement of phenotypes in domestic species. Also, as massive quantities of DNA and RNA sequence data become more easily obtained, NRSP8 scientists are also aimed at developing tools and platforms for the efficient storage, analysis, and sharing of genomic datasets. These efforts are aimed at more efficient selection of superior broodstock to improve animal production. <br /> <br /> The annual NRSP-8 workshops have become an essential component for development of collaborations, training and dissemination of new information to government, academic and industry stakeholders in animal agriculture. The Aquaculture, Cattle/Sheep/Goat, Equine, Poultry and Swine workshops were held in conjunction with the International Plant and Animal Genome Conference XX in San Diego, CA on January 14-15, 2012. Species workshops were attended by more than 500 U.S. and international researchers from academia, industry, and government. Attendance ranged from ~100 each in the equine and aquaculture workshops, ~150 in the swine workshop, and ~200 in the cattle/sheep/goat workshop. The following report summarizes 2012 reports from the species/area coordinators. Annual reports from the species/area coordinators can be found (NIMSS site link).<br /> <br /> Aquaculture Technical Report<br /> <br /> Objective 1: Efforts to obtain genome reference sequences for are progressing rapidly for most species, and all species focused on using SNPs to increase map densities. A significant amount of DNA fingerprinting data was used to update the rainbow trout physical map. A high density genetic map composed of approximately 5,000 single nucleotide polymorphism markers (SNPs) was produced for rainbow trout. A 1,772 SNP genetic map was produced for sockeye salmon. Efforts to obtain a genome reference sequence for the Pacific White Shrimp, Litopenaeus vannamei, have turned to finding shrimp inbred lines with relatively high homozygosity for sequencing BAC libraries due to the high heterozygosity and complexity of the shrimp genome. A deep sequencing of restriction-site associated DNA marker (RAD-seq) method was used to find genetic markers involved in disease resistance in Pacific White Shrimp. For the Pacific oyster, several groups are developing SNPs, BAC end sequences, a BAC physical map, and integrating these with genetic and cytogenetic maps. A DNA methylation-enriched Pacific oyster DNA library was produced which described functional roles of DNA methylation in oysters. The channel catfish genome assembly currently contains contigs produced from Illumina paired end libraries, and existing sequences from larger insert libraries (3 kb, 8 kb, 36 kb) have not yet been assembled. Deep sequencing of a doubled-haploid channel catfish transcriptome yielded 25,144 annotated contigs. A low density genetic map was produced for the striped bass based on 289 microsatellite DNA markers, and performance traits in the mapping populations contained ~68 QTL, many with very strong potential for predicting performance of growth and body composition. Next-generation sequencing of striped bass genomic DNA produced 14 Gb of sequence data to support initial assembly of the draft genome sequence. In addition, 5.4 Gb of sequence data for microRNAs were obtained for these striped bass. High throughput sequencing of mRNA (RNA-seq) of fast- and slow-growing hybrid striped bass revealed 1076 genes that were differentially expressed in fast- versus slow-growing fish. This analysis also identified 270,000 single nucleotide repeats (SNPs) with large numbers of SNPs being found only in fast growing or slow growing fish.<br /> <br /> Objective 2: NRSP8 members continue to maintain specialized resource populations for genome analyses, including inbred lines and designer crosses for hybrid production. However, many of these populations are derived from commercial populations, which are the focus of additional studies. Several research institutions also maintain pedigreed well-characterized breeding programs. Four multi-year pedigreed rainbow trout populations were phenotyped for plasma cortisol in response to stress, resistance to bacterial cold water disease (BCWD) and spleen size. Quantitative trait loci (QTL) with major effects were detected for these three traits in single-pair matings and are currently being evaluated and validated for potential use in germplasm improvement. Rainbow trout improved for growth and utilization of a fishmeal-free plant-based feed have been developed and are available for release. QTL mapping populations were also established to study stress tolerance (vis-a-vis) salinity tolerance in salmonids, spawning times in females and maturation timing in males/females and QTL influencing growth and its 'coupling' to determination of maturation timing in salmonids. The majority of shrimp resource populations were from commercial populations and focused on disease resistance. University/commercial cooperation continued to develop inbred oyster lines to crossbreed F1 hybrids for use in the oyster farming industry, and F2 families useful for mapping QTL for survival, growth, and sex determination. Scientists phenotyped channel, blue, and hybrid catfish that were raised in intensive raceway environments and production ponds for selective breeding. Breeding populations of striped bass and white bass continued to be maintained and selected in North Carolina and Arkansas to support the hybrid striped bass industry.<br /> <br /> Objective 3: Species-specific bioinformatics resources were developed to support efforts aimed at identifying genes of interest. Most efforts focused on database development, including development of pipelines for next-generation sequencing data processing, analyses and annotation, and in cooperation with NRSP8-supported bioinformatics capacity. The current rainbow trout WebFPC BAC physical map is continually updated with genetic markers and BACs sequence data that are being integrated onto the BAC contigs. A rainbow trout QTL database was place on the NRSP8Animal Genome website. An effort to establish a Shrimp genomics database on the NRSP8 website is underway. A pipeline was developed for identification, characterization, and selection of oyster SNPs in a mixture of Sanger and next generation cDNA sequences. Catfish RNASeq, ESTs, and related SNP information was disseminated through the Catfish Genome Database, cBARBEL, http://www.catfishgenome.org/cbarbel/. The collection of over 11,000 high-quality, annotated, striped bass transcriptome sequences was deposited in the NCBI Short Read Archive (GenBank: SRX007394) and maintained for public access on the National Animal Genome Project website.<br /> <br /> Cattle Technical Report<br /> <br /> Objective 1: The transcriptome of milk somatic cells in Holstein cows was analyzed at early, peak and late lactation. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells, most genes were ubiquitously expressed in all three stages of lactation, but a fraction of the milk transcriptome has genes devoted to specific functions unique to the lactation stage. A performance comparison of the new Illumina HighDensity Bovine BeadChip Array (777,962 SNP) and the Affymetrix Axiom GenomeWide BOS 1 Array (648,874 SNP) in DNA samples derived from 10 Holstein and 6 Jersey cattle showed both platforms were well designed and provide high quality genotypes and similar coverage of informative SNP, and the BovineHD platform measured Copy Number Variation more efficiently. A collaborative project was initiated to develop a genotyped, phenotyped population to enable the evaluation and/or assessment of different DNA-enabled approaches for predicting the genetic merit of herd sires on commercial beef ranches. Collaborative research between U.S. and Brazilian researchers continues to refine the genetic map of the river buffalo, specifically in the MHC region. In addition, comparative genetic studies of bovids are being conducted using the cattle genome as a reference. There was evidence that genes involved in heparan sulfate and heparin metabolism are also involved in regulation of lipid metabolism in bovine muscle. Whether the SNPs affected heparan sulfate proteoglycan structure is unknown and warrants further investigation. Efforts to improve the bovine genome assembly included 30x genome coverage of Illumina short and long-insert sequence reads of Dominette. In addition an optical mapping project was contracted with OpGen Inc (Maryland, USA) to generate a high-resolution, ordered, whole genome restriction maps from Dominette DNA. We expect that this resource will significantly improve the orientation of scaffolds, determination of gaps and resolve sequence challenges due to repetitive sequences. The assembly of the reference genome will be guided by the University of Maryland and by the University of Missouri.<br /> <br /> Objective 2: Phenotypes were collected from the Cycle 1 (F2 Nellore-Angus cows), Cycle 2 (reciprocal F2 steers and heifers) and Cycle 3 (F3 Nellore-Angus steers and heifers) McGregor Genomics populations to determine the genetic basis of variation in immunological response to vaccination for BVDV using steers from Cycle 2 and Cycle 3. The population is also under investigation to determine the genetic mechanisms behind variation in growth, disposition, nutrient utilization, feed efficiency, carcass and meat traits in steers as well as female reproductive efficiency traits in heifers. Collaborative research is underway to investigate genes involved in the effects of genetic polymorphism and the association of alleles specific to Bovine Respiratory Disease, differences in gene expression related to tick resistance in cattle, functional genomic and proteomic variation related to beef tenderness and other bovine traits in the McGregor Genomics populations, including a gene expression analyses of skeletal muscle samples for which accompanying sensory and carcass trait data are available. A resource family was created to map the location of a major gene for ovulation rate. A whole genome association and fine mapping studies continues correlate genotypes with susceptibility to infection by Mycobacterium avium subsp. Paratuberculosis, bovine viral diarrhea persistent infection and bovine respiratory disease. Fatty acid profiles and intramuscular expression of genes involved in fatty acid metabolism were characterized in concentrate- and forage-based finishing systems. The results suggested ADIPOQ and DGAT likely play a role in intramuscular fatty acid saturation and that significant dietary interactions with gene expression play a significant role in lipogenesis. WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR) superfamily and expression of particular WC1 genes defines functional subpopulations of WC1+ gd T cells gamma delta T cell co-receptor WC1 genes in cattle. Researchers found thirteen bovine WC1 genes code for three distinct WC1 forms which may differ in either the number of extracellular SRCR domains or their intracytoplasmic tails. Other research focused on identification of genetic loci associated with heifer pregnancy rate, and is evaluating transcriptome (RNA-Seq) and proteome (LC/MS + FT-ICR) data among pre- and post-pubertal Brangus heifers, and is developing data and DNA resources from large commercial beef operations for validation and technology transfer. <br /> <br /> Objective 3: The bovine UMD 3.1 genome assembly was made available on the NRSP8 Binoinformatics site as were 8.4 million SNP loci, data on the Illumina ~770K HD SNP chip, an updated QTLdb, and access to genomic data through Biomart. High throughput computational resources, including the use of parallelized graphics processing units, were under development to solve advanced computational problems such as sophisticated models used to predict genetic merit from candidate broodstock. While prediction of genetic values under additive gene action is well handled by a variety of parametric models, computational simulations showed that nonparametric RBF regression was a useful counterpart for dealing with situations where non-additive gene action is suspected, and was robust irrespective of the mode of gene action. Another project using computer simulation showed that the accuracy of genomic estimated breeding values accuracy could decrease over generations of selection, although at high marker density both the magnitude and duration of the response to selection were larger. Selection changed quantitative trait loci (QTL) allele frequencies and generated new but unfavorable LD for prediction.<br /> <br /> Sheep/Goat Technical Report<br /> <br /> Objective 1: The International Sheep Genome Consortium (ISGC) is a multi-institutional group developing resources needed for genomic research in sheep (http://www.sheephapmap.org/). The ISGC is now contributing to development of a whole genome reference assembly. In 2010, sequence data were generated at two sequencing facilities. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds, then DNA sequences from both animals were used to fill gaps in the assembly. Version 2.0 of the ovine whole-genome reference sequence (Oar v2.0) was publicly released in February, 2011 and contains 2.71 Gb of sequence with an N50 of 1.08 Mb. It covers 93.1% of the genome, with 2.57 Gb placed onto chromosomes. This version contains 145K intra-scaffold gaps of 0-2000 bp, 13K intra-scaffold gaps of 2 kb  20 Kb, and 4,400 inter-scaffold gaps. Of particular concern are gaps in the 5 ends of ~2,000 genes (high GC-content regions). There are also ~100 split scaffolds and ~ 1% inverted contigs. Around 140 Mb of sequence is in unmapped scaffolds. Oar v3.0 will address intra-scaffold gaps, inter-scaffold gaps and unassigned scaffolds. Additional sequence will be generated, most likely using low coverage whole genome shotgun 454 FLX+.<br /> <br /> The NRSP-8 Sheep Coordinator funds have contributed to the development of an ovine radiation hybrid (RH) 5,000 rad panel (USUoRH-5,000). In 2010, the USU RH panel and the INRAoRH-12,000 panel were genotyped with the 50K SNP BeadChip. Because the genomic constitution of RH clones differs significantly from the simple diploid organization of genomic DNA, a dedicated algorithm was needed to call the RH panel SNP genotypes from the raw intensities provided by the Illumina typing platform. Using this algorithm, an RH map was constructed for each ovine chromosome and then combined into a whole genome RH map comprised of 39,856 SNPs. The RH chromosome maps were developed using a comparative mapping approach that established the virtual sheep genome (vsg) as a reference for comparing alternative orders of markers. The genetic and RH maps are contributing independent and complementary information to the ongoing assembly of the ovine whole genome reference sequence. Comparison of contig positions on the sequence scaffolds containing SNPs located in the genetic and RH maps have allowed improvement of the assemblies of scaffolds and super-scaffolds. A radiation hybrid panel for goat is being developed in collaboration with the Goat Genome Consortium organized at the 2010 PAG meeting. Another synthesis of the 50K SNP BeadChip was completed in September, 2011. A high density chip containing ~ 1M SNPs is now being considered by the ovine genomics research community, with the goal of achieving a consortium price.<br /> <br /> Objective 2: Comparative studies were conducted in sheep to determine gene copy of domain As of the gamma delta T cell WC1/T19 co-receptor gene family. Ovine gamma delta T cells also express the co-receptor known as WC1, known as T19 in sheep. Sheep had twice the number of WC1/T19 genes as cattle (26 genes vs 13 genes). Twenty-six unique sequences of ovine WC1 Domain A were obtained from genomic DNA of a single sheep. While some ovine Domain A sequences clustered with the major Domain A groups of cattle the majority did not. Those that cluster most closely between sheep and cattle include those designated as the bovine WC1.2 serological group and a second cluster contains the unique bovine WC1 sequence coded for by WC1-10. Experiments are also underway to identify patterns of gene expression associated with the differential ability of goats to consume juniper as pasture forage. A sheep flock has been created segregating for parasite resistance, and includes 378 F2 offspring of five F1 sires produced from Gulf Coast Native (resistant) and Suffolk (susceptible) crosses. Genetic association studies using SNP the Illumina Ovine SNP50 BeadChip revealed four genomic associations with parasite resistance in sheep. Other association studies identified candidate regions for the horn gene, Booroola fecundity gene, the PNRP gene, staple length, and eyelid inversion. Early immune response of Gulf Coast Native and Suffolk sheep to Heomonchus contortus infection indicated that the local mucosal level response (eosinophils and mast cells) may play a role in the self-cure expulsion of these worms in the Native breed. In vivo and in vitro assays were used to identify genes regulated or co-regulated during muscle hypertrophy in order to better understand the callipyge phenotype. <br /> <br /> Objective 3: A website is under design for visualizing the goat RH map and potentially other data generated by the International Goat Genome Consortium. <br /> <br /> Swine Technical Report<br /> <br /> Objective 1: The PorcineSNP60 BeadChip has been used for several genome-wide association studies (GWAS) to understand the genetic control of important pig traits, such as reproduction, structural soundness, residual feed intake, disease resistance, specifically the genetic control of resistance to PRRS virus infection and related growth effects. Scientists estimated linkage disequilibrium in four US breeds of pigs (Duroc, Hampshire, Landrace, and Yorkshire) and subsequently calculated persistence of phase among them using a 60K SNP panel. Their estimates confirmed earlier findings reporting lower short-range (<10 kb) LD in pigs than in cattle, but a much stronger persistence of LD at increasing marker distances (>1 Mb). Nomenclature for the swine Major Histocompatibility Complex (MHC), the swine leukocyte antigen (SLA) complex, was updated. Development continued of a high-resolution RH and comparative map for swine genome sequence assembly and QTL mapping. A high-resolution comprehensive map of pig chromosome (SSC) 4, in comparison with the human chromosome (HSA) 1 and 8, has been published (Ma et al. 2011). In addition to the completed maps of SSC 2, 4, 6, 7, 9, 10, 11, 12, 16, 17 and 18, maps for the remaining pig chromosomes are currently in progress.<br /> <br /> Transcriptional profiling of differentially expressed genes in longissimus dorsi muscle of Yorkshire x Landrace pigs at 40 and 70 d of gestation (encompassing the transition from primary to secondary fibers) showed that results from direct high- throughput sequencing and gene expression microarrays had a correlation of 0.72. Differential gene expression and functional analysis of blood RNA from pigs showing a range of response to Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) revealed 491 genes with significant viral level-growth interaction for all time-points. A population for the study of the genetics of sow longevity was expanded and all the animals that reached puberty were genotyped using Porcine SNP60K BeadArray. The genotypes obtained were used to find association to reproduction and lifetime productivity traits for the first seven replicates of the population (n=852). SNPs associated with these traits were found for many chromosomes, depending on trait of interest.<br /> <br /> SNPs were identified in candidate genes that were differentially expressed genes in pulmonary alveolar macrophages at different stages post infection with PRRSV. There were 132 mutations discovered in 19 genes and 82 of these mutations genotyped on 616 samples provided by the PRRS Host Genomic Consortium (PHGC). Statistical analysis revealed four genes that are significantly associated with virus load at different days post infection. One of genes is located on SSC4 where a major QTL for both virus load and growth was detected using the GWAS approach.<br /> <br /> Objective 2: The PRRS Host Genomic Consortium (PHGC) has been developed to determine the role of host genetics in resistance to PRRS and in effects on pig health and related growth effects. Genome wide association studies (GWAS) using the PorcineSNP60 Genotyping BeadChip have identified chromosomal regions associated with PRRS resistance and/or improved weight gain, with an area on SSC4 correlated with both lower viral load and higher weight gain. A Berkshire x Yorkshire family continues to be used to map genes associated with growth, meat quality and carcass traits. A Yorkshire research population has been selected for RFI. A DNA bank from animals with Salmonella disease phenotypes was completed as a part of a National Pork Board project <br /> <br /> Objective 3: A QTL database, Pig QTLDB, continues to be expanded as a part of the AnimalQTLDB. An open-source transcript profiling database and website that allows the user to store and submit Affymetrix profiling data to NCBI-GEO (www.anexdb.org) was refined. In addition, the database contains a novel alignment of all public porcine expressed sequences into clusters, a consensus sequence for each of these aligned clusters, and annotation of the consensus using data from the human, mouse and other annotated genomes. A PRRS database (PHGCdb) and data is being developed. The Pig Genome Database (PGD) is under development and integrates the functions of the Pig QTLdb, GBrowse, Biomart, ANEXdb, VCmap, and SNPlotz to provide a research database tool for the community. Computational curation tools (Otterlace suite of programs) from the Sanger Institute were used to to refine the currently available automated annotation of the pig genome. <br /> <br /> Equine Technical Report<br /> <br /> Objective 1: One of the major tools for investigating the horse genome has been the Illumina SNP50 chip. Illumina discontinued that chip in 2010 and a new one was designed and produced during 2011 based on collaborations between NRSP8 scientists and scientists at Geneseek, a division of Neogen, Inc. Agilent microarrays were produced and compared for investigation of gene expression in several laboratories. At least 8 horses were sequenced in private laboratories during 2011 using next-generation DNA sequencing technology and the information is being made publically available. Scientists are now discussion approaches to improving the reference sequence infrastructure that will lead to an updated genome assembly. <br /> <br /> Objective 2: Collaborations formed at conferences and workshops facilitated collaborations in which data was shared between laboratories to investigate diverse hereditary conditions, including investigations of developmental bone diseases, respiratory disease, stable vices, immunology and population analyses. Because individual collaborations and exchange of materials were so successful, the equine genome community is dissuaded from forming a formal tissue bank. However, data from testing animals with the SNP50 chip or with RNA-Seq technologies has been shared for use as control samples or in collaborations through established community databases. <br /> <br /> Objective 3: Lack of bioinformatic capacity is a major limit to the advance of horse genomics. Investigations of complex traits, understanding copy number variants, investigation of gene expression data, integration of new genome sequence data from other horses into analyses has presented challenges that tax the expertise of the horse genome workshop. Work is underway to coordinate with NRSP8 bioinformatics capacity and Agbase. <br /> <br /> Poultry Technical Report<br /> <br /> Objective 1: A new build, Galgal4.0, of the chicken genome sequence was released which combined traditional Sanger sequence with Next-generation DNA sequence (NGS). The Z chromosome sequence was published at near-finished quality. The NGS appears to not capture the 5% of missing sequence believed to be predominantly on the microchromosomes. A number of additional chicken genomes have been or are being sequenced with NGS technology. Coordination funds support a project with DNA Landmarks to sequence 20 different chicken lines of interest. NGS data for genomes from the DF1 and DT40 chicken cell lines have also been obtained and are currently being analyzed and compared to the new reference Galgal4.0 chicken genome assembly. Linkage mapping is now primarily via high throughput SNP (single nucleotide polymorphism) assays. Coordination funds have been committed to SNP chip development and distribution. Very high density SNP mapping (ca. 600,000 SNP) panels have been developed and are being employed in genome-wide association studies and genome-wide marker-assisted selection (GMAS). <br /> <br /> The Turkey Genome Sequencing Consortium generated a draft sequence of the turkey genome using a combination of NGS reads, along with a turkey BAC contig physical map. Coordination funds were committed to aid in this effort. Efforts are on-going to improve the annotation of genes and fill gaps in the turkey sequence. Physical mapping included construction of a detailed comparative chicken-turkey BAC contig comparative map. <br /> <br /> In the past, coordination funds have been used to provide samples of the 44K element long oligonucleotide chicken array made by Agilent Corp. to several NRSP-8 participants, along with a new 244K whole genome long oligo array that can be used for comparative genome hybridization and whole genome transcriptional profiles. Alternatively, other participants chose to be provided GeneChip® Chicken Genome arrays from Affymetrix, Inc. Some coordination support has also been committed to Illumina RNA-sequencing and Agilent chip-based transcriptional profiling, partly in hopes of filling in missing sequences. <br /> <br /> Objective 2: DNA from the East Lansing international reference population has been sent to many laboratories throughout the world. <br /> <br /> Objective 3: A homepage is maintained for the NRSP-8 U.S. Poultry Genome project (http://poultry.mph.msu.edu) that provides a variety of genome mapping resources, including our newsletter archive. The Poultry Genome Newsletter is published quarterly and is distributed through our Homepage and on the angenmap email discussion group. <br /> <br /> Bioinformatics Technical Report<br /> <br /> Objective 2: Developed a relational database to store individual animal genotype and phenotype data to support the PRRS CAP Host Genome consortium.<br /> <br /> Objective 3:<br /> Poultry - 285 new QTL were curated into the Chicken QTLdb. Chicken QTL can be <br /> visualized against the genome and aligned with chicken 60K SNPs along with NCBI annotated gene information. We also continue to mirror the Gallus genome browser. NRSP-8 funds were used to support the development of BirdBase resources such as the Chicken Gene Nomenclature Committee (CGNC) database which is now linked the NCBI Entrez Gene chicken gene <br /> pages. A bird comparative genome browser is being developed via BirdBase and will initially include the chicken, turkey and zebra finch genomes. <br /> <br /> Cattle - 525 new cattle QTL were added, and cattle QTL can now be viewed relative to the UMD assembly and Btau4.2 assembly. The STS Cattle 770K high density SNPs and 4.1M dbSNP data were mapped and made available both in GBrowse to align with QTL and in SNPlotz for genome analysis.<br /> <br /> Porcine  The new pig genome database is under development. 88 new QTL were added <br /> to the AnimalQTLdb. The pig gene Wishlist continued to serve the pig genome annotation activities.<br /> <br /> Sheep - 291 new sheep QTL were added to the Sheep QTLdb. <br /> <br /> Aquaculture - 27 QTL data for rainbow trout were curated into the Animal QTLdb. <br /> <br /> Multi-species - A local copy of Biomart software was installed on the AnimalGenome.ORG server to serve the cattle, chicken, pigs and horse Community. We continued to focus on the integration of the Animal Trait Ontology into the Vertebrate Trait Ontology. Traits specific to livestock products have been incorporated into a new Livestock Product Trait Ontology. As the first stage outcome, we have mapped the cattle, pig, chicken, and sheep QTL traits to Vertebrate Trait Ontology (VT), Product Trait Ontology (PT) and Clinical Measurement Ontology (CMO) to help standardize the trait nomenclature used in the QTLdb.We have developed a livestock breed ontology. Via AgBase, we were recruited by the Phenotype Ontology Research Coordination Network (NSF DBI 0956049) to develop an avian anatomy ontology with the goal of integrating this with other, existing ontologies to describe phenotypes. We have about 650 terms that cover avian musculoskeletal and integument systems. The information for these terms includes relationships, synonyms, definitions, and comments (homologies to mammalian structures; species differences). <br /> <br /> Software development <br /> The NRSP-8 Bioinformatics Online Tool Box was actively updated. Several major software upgrades were made to SNPlotz, Gene Ontology CateGOrizer, BEAP, and the Expeditor. The new addition to the tool box is an online File Sharing Platform, with which any NRSP-8 members can freely use the tool to share large data files individually or publicly (e.g. within a consortium). <br /> <br /> The Virtual Comparative Map (VCMap) tool passed its initial development stage and was transferred to AnimalGenome.ORG for more application development. To improve links between AgBase and the NRSP-8 website, AgBase now also provides a link to the Virtual Comparative Map (VCMap). <br /> <br /> Genome2Seq, an online tool that rapidly retrieves a fasta file of sequences based on genome co-ordinates generated from RNA-Seq data, was developed. Users specify either bovine, horse, chicken or pig genomes. The input file is a tab-delimited text file containing a unique ID, chromosome number, start location, and stop location in that order. The output is (a) a list of matching genes and their associated GO annotation; and (b) a fasta file of sequences for any co-ordinates that do not match any annotated genes. Genome2Seq is available via AgBase and the NRSP-8 website.<br /> <br /> The web site and user forum listserv for CRI-MAP user interactions in improving the CRIMAP software has been actively used.<br /> <br />

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Brief Summary of Minutes

Accomplishments

The NRSP-8 business meeting was preceded by two days of species workshops and area subcommittees and the combined Animal Genome Workshop. The combined workshop included four plenary presentations as follows: Leif Andersson, Uppsala University, Detecting Loci under Selection Using Whole Genome Resequencing; Trudy Mackay, North Carolina State University, Charting the Genotype-Phenotype Map: Lessons from Drosophila; Harris Lewin, University of California, Davis, Genomic Footprints of Selection after 50 Years of Dairy Cattle Breeding; and Max F. Rothschild, Iowa State University, Application of Livestock Genomics to Global Food Security Issues. Dr. Rothschild was the NRSP8 Distinguished Lecturer for 2012. The business meeting was called to order by the Chair, Tom Porter (University of Maryland), and was recorded by the Secretary, Milt Thomas (Colorado State University) with approximately 40 members in attendance. Tom Porter provided an update on the NRSP8 project renewal. Alan Archibald presented on the status of the Livestock ENCODE project and a motion of NRSP-8 support of this activity was approved. Elspeth Bruford presented an update on the HUGO Gene Nomenclature Committee. Coordinator reports were summarized by the Aquaculture, Bioinformatics, Cattle, Equine, Poultry, Sheep/Goat, and Swine chairs. Eric Young provided an administrative report. Milt Thomas assumed the NRSP-8 Chair for 2013-2014 and Stephen White (USDA-ARS/Washington State University) was elected Secretary for 2013-2014. A motion to hold the 2013 meeting in conjunction with the Plant and Animal Genome conference was approved unanimously. The meeting was adjourned.<br /> <br /> OBJECTIVES<br /> <br /> Objective 1: Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest.<br /> Objective 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes.<br /> Objective 3: Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest.<br /> <br /> Aquaculture Technical Report<br /> <br /> Objective 1:<br /> <br /> Catfish:<br /> The channel catfish genome is under assembly. To date 60X genome equivalent of Illumina sequences and mate paired reads of 3Kb, 8Kb, and 36 Kb with sequences equivalent to 3.1X, 0.5X, and 0.15X, respectively have been generated. PacBio sequences equivalent to 9.5X genome coverage with an average length of 3.5 Kb have been generated.<br /> Doubled haploid blue catfish were produced and used as template for sequencing using Moleculos Long Reads product to generate extremely long and accurate reads. A preliminary assembly with only the long reads using 99% sequence overlap identity produced 46,098 contigs with an N50 length of 12.9 kb and N80 length of 8.5 kb. A further 42,141 long reads remained singlets with an N80 length of 4.6kb and N50 length of 7.0kb.<br /> RNA-Seq of the doubled haploid catfish generated a transcriptome assembly including 25,144 unique protein encoding genes, with over 14,000 full-length transcripts. This resource has been used for expression profiling of mucosal surfaces for catfish challenged with the pathogen Flavobacterium columnare.<br /> An Agilent 8x60K microarray is publicly available and has been utilized for profiling channel and blue catfish skin responses to Aeromonas hydrophila infection.<br /> <br /> Oyster:<br /> International efforts to develop BAC physical maps, large volumes of SNPs and integrated cytogenetic maps culminated in the acquisition of an oyster genome sequence.<br /> <br /> Salmonids:<br /> The current version of the rainbow trout assembly is estimated to cover 70% of the genome.A pooling and tagging scheme was used for sequencing of the ~15,000 clones of the BAC fingerprinting physical map minimal tiling path (MTP). Sequencing is complete and the assembly is underway.<br /> Restriction-site associated DNA (RAD) technology was employed to generate a large SNPs data set from deep sequencing of a panel of 11 homozygous lines. The dataset is composed of 145,168 high-quality putative SNPs that were genotyped in at least 9 of the 11 lines, of which 71,446 (49%) had minor allele frequencies (MAF) of at least 18%.<br /> <br /> Shrimp:<br /> Due to the high levels of heterozygosity and the complexity of the shrimp genome, assembly of the short reads generated by next-generation sequencing technologies of Pacific White Shrimp, Litopenaeus vannamei, genome sequences is very difficult. Efforts have been turned to finding shrimp inbred lines with relatively high homozygosity or sequencing BAC libraries.<br /> A deep sequencing of restriction-site associated DNA marker (RAD-Seq) method was used to find genetic markers involved in disease resistance in Pacific White Shrimp.<br /> A large scale RNA-seq project was initiated to characterize disease resistance mechanisms in shrimp.<br /> <br /> Striped bass:<br /> A database (> 11,000 entries) for gene transcripts expressed by the striped bass ovary at all maturational stages was developed to provide a foundation for gene expression research on reproduction and breeding of the striped bass and its relatives.<br /> The first genetic map of the genome of the striped bass was developed. This medium-density linkage map is based on 298 microsatellite markers and is enabling detection of QTL affecting production traits.<br /> <br /> Objective 2:<br /> <br /> Catfish:<br /> Selection for improved growth and filet yield in Year 1 of the Delta Select strain F2 Generation was completed. Channel, blue, and hybrid catfish were raised in intensive raceway environments and phenotyped for selective breeding.<br /> <br /> Salmonids:<br /> Multi-year pedigreed rainbow trout populations phenotyped for plasma cortisol in response to stress, resistance to bacterial cold water disease (BCWD), spleen size, or growth on fish meal free/plant based diets have been developed and propagated for release to industry and identification of biological mechanisms underlying these traits.<br /> <br /> Shrimp:<br /> Most of the shrimp populations developed for research are from breeding companies, and mainly support disease resistance studies. Resource populations exist for public and collaborative research.<br /> <br /> Striped bass:<br /> Broodstock populations have been established in support of genetic improvement programs for Morone species. An experimental method for accelerating puberty and maturation of Morone species based on administration of the neuropeptide kisspeptin was demonstrated, opening the door to development of practical methods for application to these late-maturing species and pinpointing the proximal signal for maturation of Morone species.<br /> <br /> Objective 3:<br /> <br /> Catfish:<br /> The catfish RNASeq, ESTs, and related SNP information has been disseminated through the Catfish Genome Database, cBARBEL, http://www.catfishgenome.org/cbarbel/, that has generated tens of thousands of hits from over 30 countries.<br /> <br /> Salmonids:<br /> A rainbow trout QTL database is now available through the Animal Genome website of the NRSP-8 bioinformatics group (http://www.animalgenome.org/cgi-bin/QTLdb/index) and is being continually updated.<br /> <br /> Shrimp:<br /> A website for the shrimp genomics community will be established, and various kinds of genomics resources for shrimp research will be assembled in the database.<br /> <br /> <br /> Cattle Technical Report<br /> <br /> Objective 1:<br /> <br /> Bovine Genome sequence: Our focus has been towards improving the bovine genome assembly. There are several actively funded efforts in this directions and the expectation is to have a new updated assembly by late 2013.<br /> <br /> Currently, two genome assemblies have been produced from the sequence data generated by Baylor College of Medicine from Line 1 Hereford cattle, Btau_4.6.1 and UMD3.1. About 28,000 genes are identified on both assemblies. Genome annotation between the two assemblies is slightly different and is being supported by NCBI and Ensembl, respectively. Many problems exist related to gene structure, lost genes, gaps and scaffold ordering. An improved reference assembly is critically needed in order to facilitate the utilization of high throughput sequencing methods for transcriptome analysis, fine mapping of QTL and copy number variation.<br /> <br /> Several groups have been collaborating to improve the assembly. 1) Jared Decker and the group at the University of Missouri are working toward generating a new bovine assembly using all the BAC and shotgun sequences from the earlier assemblies, complemented by a large accumulation of approximately 40x Illumina reads from Dominette, generated at USDA Beltsville, University of Missouri, and U.C. Davis. 2) David Schwartz and collaborators at U Wisconsin will develop an optical map project of the bovine genome complemented by data commercially contracted to OpGen Inc (Maryland, USA) to generate a high-resolution, ordered, whole genome restriction map from Dominette DNA. We expect that this resource will significantly improve the orientation of scaffolds, determination of gaps and resolve sequence challenges due to repetitive sequences. 3) Baylor is submitting a proposal to produce a whole genome shotgun sequence of Dominette using PacBio technology. The longer reads of this approach will contribute to closing gaps and correct misassemblies.<br /> <br /> In terms of annotation, UCDavis has used a large gap mapping approach with a vast amount of RNA seq data to extend the annotation of UMD3.1. Chris Elsik at the University of Missouri is also working towards this end. A valuable contribution for the annotation effort is RNAseq data that has been generated from 96 different tissues of Dominette by USDA Miles City and USDA Beltsville.<br /> <br /> Multiple efforts currently exist around the world to sequence elite sires for the purpose of developing the next generation of animal evaluation tools. These include efforts by the 1000 bull genome project, USDA MARC, U of Missouri and more.<br /> <br /> <br /> Sheep/Goat Technical Report<br /> <br /> Objective 1:<br /> <br /> Members of the NRSP-8 sheep committee are participants in the International Sheep Genome Consortium (ISGC), a multi-institutional group developing resources needed for genomic research in sheep (http://www.sheephapmap.org/). These resources include a high coverage BAC library, end-sequencing of 100% of the BAC library, high and moderate resolution radiation hybrid panels, full coverage linkage maps, an integrated ovine genetic map, a whole genome BAC physical map, development of a virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep/), a 1.5K SNP pilot chip and the high density Illumina Ovine SNP50 BeadChip. The ISGC is now contributing to the development of a whole genome reference assembly. Version 2.0 of the ovine whole-genome reference sequence (Oar v2.0) was publicly released in February, 2011 and contains 2.71 Gb of sequence with an N50 of 1.08 Mb. It covers 93.1% of the genome, with 2.57 Gb placed onto chromosomes. An update, version 3.1, was released in October 2012 with over 200,000 gaps filled relative to version 2.0, and version 3.1 will be the basis for a manuscript in preparation.<br /> <br /> Pennsylvania State University has been working to extend the ovine genome assembly to include the Y chromosome. They constructed an initial sequence of the ovine MSY (oMSY) by a combination of whole genome shotgun sequence (WGS) and BAC end sequence (BES). The WGS reads (~1 million pair-ends not assigned elsewhere in the genome assembly) were assembled into 4487 ovine Y-specific contigs (258 bp - 367 Kb) using a comparative assembly method based on the bovine MSY (bMSY) draft sequence. Alignment of the ovine BESs against the bMSY identified 605 Y chromosome BACs with one or both ends matched, of which 60 mapped in the X-degenerate and 545 in the ampliconic region. These BESs were used to orient the assembled contigs which resulted in a draft oMSY contig map that spans ~39 Mb (comparable to the 41.3 Mb of bMSY). The X-degenerate region contains genes well conserved with the bovine orthologs. This framework map of the oMSY will be useful to study the genomic organization of the ovine Y chromosome.<br /> <br /> Sequence assembly of the goat genome by the Beijing Genomics Institute (BGI) was published and released in December 2012. The initial draft is available at http://goat.kiz.ac.cn/GGD/. In addition to this sequence assembly at least two other assemblies are also in the works. The sequencing of the Bezoar goat in Iran by the NextGen project and the sequencing of an highly inbred San Clemente Island goat in the U.S. A comprehensive caprine RH map, which merges data from the ovine and bovine 50K SNP arrays, has been developed.<br /> <br /> Objective 2:<br /> <br /> DNA was extracted from 123 animals in 18 sheep flocks and genotyped with the Illumina Ovine SNP50 BeadChip. Results using PLINK software showed consistency with genetic assignments reported for the horn gene (ovine chromosome 10 or OAR10), Booroola fecundity gene (OAR6), and the PRNP gene (OAR13). Other phenotypes collected on the animals included eye pigmentation, color traits, presence of spots, striped hooves, cryptorchidism, bent leg, weight measurements, average daily gain, and traits related to wool including wool variation and grade, face cover and belly wool, clean fleece weight and staple length. Significant associations were found for staple length on OAR4 (1 SNP), OAR6 (2 SNPs) and OAR22 (2 SNPs). One SNP on OAR25 was significantly associated with staple length. While these traits have been studied in other sheep populations, there have been no other reports of QTL for the significant traits in these locations.<br /> <br /> Genotypes for the Ovine SNP50 BeadChip were obtained for 85 animals from four flocks, of which 26 animals had evidence of classic footrot with necrotic tissue in at least one hoof, 31 had intermediate footrot scores with some inflammation and/or discoloration (possibly early or resolving positives), and 28 were negative based on the absence of infection/inflammation in all four hooves. Initial analyses revealed a genome-wide significant SNP on ovine chromosome 18. Ongoing analyses include a search for candidate genes in this genetic region of the emerging sheep genome assembly and additional association testing with larger animal sets.<br /> <br /> A phenomenon called self-cure occurs when animals ingest a large number of infective Haemonchus contortus larvae over a very short period of time which results in expulsion of the existing adult worms. A study was designed to elaborate the immune response during this expulsion period and whether there is a difference in response between Native and Suffolk breeds. Fifty-six (28 Native and 28 Suffolk) age-matched lambs were removed from pasture and reared in confinement under parasite-free conditions. Results show that both resistant and susceptible breeds of sheep can undergo self-cure worm expulsion and suggests a possible role of neutrophils and mast cells in the expulsion of larval nematodes while eosinophils may play a role in the expulsion of adults.<br /> <br /> Elevated postnatal expression of DLK1 and/or RTL1 is the primary inducer(s) of muscle hypertrophy in callipyge lambs. Previous microarray experiments identified several candidate genes that are either direct transcriptional targets of DLK1 and RTL1 (secondary inducers) or tertiary responses to muscle hypertrophy. PARK7 was identified as a candidate gene that has a transcriptional response to DLK1. PARK7 expression is up-regulated in hypertrophied muscles of callipyge sheep at both mRNA and protein levels. One function of PARK7 protein is to inhibit the activity of PTEN, which is a component of growth factor signaling such as IGF-I. The ability of PARK7 to have a direct role in IGF-I signal transduction and cause an increase in myosin expression in a myotube cell culture model suggests that PARK7 is part of the physiological pathway for callipyge induced muscle hypertrophy.<br /> <br /> Concerns that goats may serve as a scrapie reservoir highlight the need for effective resistance in goats. An oral challenge experiment demonstrated highly significant extended scrapie incubation in goats heterozygous for either PRNP S146 or K222. Furthermore, the extended incubation of the K222 animals is the longest reported in goats to date. At present, neither S146 nor K222 heterozygous animals have been scrapie positive by either mucosal biopsy or clinical signs.<br /> <br /> Ovine progressive pneumonia virus (OPPV), a lentivirus of sheep, infects a quarter of U.S. sheep. TMEM154 was identified as a lentiviral susceptibility gene in sheep with multiple putative mutations. A list of other genes involved in not only odds of infection but also control of OPPV once infected was identified. Since both OPPV and HIV are macrophage-tropic lentiviruses with similar genomic structure, these genes may contribute to human medicine as well as animal agriculture.<br /> <br /> Entropion is an inversion of the eyelid margin, causing lashes or external hairs to rub against the ocular surface. Entropion has been reported in up to 80% of sheep, depending on the breed composition. A genome-wide association scan for entropion was performed with 1,000 sheep that were genotyped with the Illumina OvineSNP50 chip. Entropion status was recorded within 24 hours of birth and overall prevalence was 5.65% in the three breeds of sheep (Columbia, Polypay, and Rambouillet). One genomic region on OAR6 was found to be statistically associated with entropion. Further evaluation of this region is needed to identify underlying causal mutations, which would be useful as genetic markers for sheep producers.<br /> <br /> A collaborative project involved signatures of selection in 5 popular U.S. sheep breeds (Columbia, Polypay, Rambouillet, Suffolk, and Targhee) using the Illumina OvineSNP50 marker set designed by the International Sheep Genomics Consortium. Of these breeds, Rambouillet and Targhee were genetically most similar, and Suffolk was the most inbred. Approximately 40 different genomic regions were found to be divergent between Suffolk and Rambouillet-related breeds. Four of these regions were very similar to those identified by the International Sheep Genomics Consortium evaluation of 74 worldwide sheep breeds.<br /> <br /> Copy number variants in the gamma delta T cell WC1/T19 co-receptor gene family have been studied in sheep and goats. Sheep had 26 WC1/T19 genes and goats had 18 WC1 genes, compared to 13 bovine WC1 genes. 26 unique sequences of ovine WC1 SRCR domain a1 (which is the most variable of all the eleven bovine WC1 SRCR domains) were obtained from genomic DNA of a single sheep using PCR and primers designed against the consensus region at the ends of the 13 bovine SRCR domain a1 sequences. Nine caprine WC1 SRCR domain a1 sequences were also isolated by the same method. These results serve to better characterize genes and copy number variants underpinning gd T cell-based immunity.<br /> <br /> <br /> Swine Technical Report<br /> <br /> Objective 1:<br /> <br /> Map Development Update: New gene markers were identified with the development of the 60K SNP chip. The 60KSNP chip information can now be integrated with the development of Build 10.2 as maps now are based on the pig sequencing efforts.<br /> <br /> QTL, Candidate Genes and Trait Associations: QTL and trait associations have continued to be reported on all chromosomes for many traits. Candidate gene analyses have proven successful with several gene tests being used in the industry for many traits including, fat, feed intake, growth, meat quality, litter size and coat color. The PigQTLdb (http://www.animalgenome.org/QTLdb/pig.html) is an excellent repository for all of these results. Several new genome wide association studies (GWAS) are being published in the pigs.<br /> <br /> Sequencing Efforts: The Swine Genome Sequencing Consortium (SGSC) was pleased to announce the publication of a high quality draft genome sequence for the pig (Sus scrofa). The paper entitled "Analyses of pig genomes provide insight into porcine demography and evolution" describing the sequencing, analysis and annotation of this draft genome sequence was published in Nature in the November 15 issue. In parallel a series of companion papers has been published in BMC journals. In addition, this annotation can be visualized in Gbrowse against version 10.2 of the swine genome at http://www.animalgenome.org/cgi-bin/gbrowse/pig.<br /> <br /> Shared Materials and Funding: The Pig Genome Coordinator has recently supported community activities to find associations with many different traits and has provided nearly 2,000 chips/genotyping for those several projects from 2009-2012. The coordinator is looking for new projects to support by providing SNP genotyping.<br /> <br /> Porcine SNP chip update: Illumina and the International Porcine SNP Chip Consortium developed a porcine 60K+ SNP and has shipped it to many researchers worldwide. The original publication was Ramos et al. 2009. Prices for the chip have been dropping and are reasonable. A new custom low density chip is now available for imputation work. GeneSeek, a supplier of genotyping services has announced the GeneSeek Genomic Profiler for Porcine LD (GGP-Porcine). This custom low density BeadChip utilizes Illumina Infinium chemistry and features approximately 8,500 SNPs for high density chip imputation. The GGP - Porcine BeadChip also includes gene markers from several well-known reproduction, growth, feed efficiency, and meat quality traits at no added expense. These include the following markers: EPOR, MC4R, HMGA, CCKAR, PRKAG, and CAST. Details on these markers will be available from GeneSeek. In addition, researchers can request additional markers including the HAL, Rendement Napole (RN), Resistance marker to E.coli (F4 ab/ac), a SNP parentage panel, and the Estrogen Receptor (ESR) which impacts litter size in Large White or Yorkshire by paying additional royalty fees for these optional licensed tests. The chip was developed as a result of a collaborative effort involving leading academic, USDA, and GeneSeek researchers. The price (per sample) is about 40% of the cost of the 60K chip.<br /> <br /> Objective 3:<br /> <br /> Database Activities: The Pig Genome Database continues to receive considerable updating. The Animal QTLdb included 633 new pig QTL in its recent #18 release, making the total number of pig QTL in the database 7,451. With this release, the NAGRP bioinformatics team has done a number of improvements to the Animal QTLdb, which includes a procedure to withdraw obsolete QTL data from NCBI, a new experimental search function for animal breeds associated with QTLs, a new trait hierarchy navigator, and improved QTLdb curator/editor tools. Users are encouraged to register an account to enter new QTL data. Find out more from http://www.animalgenome.org/QTLdb. In addition, the pig genome build 10.2 annotations are ported to the BioMart http://www.animalgenome.org:8181/ for customized downloads; and pig oligoArray elements are BLAST mapped to pig genome build 10.2, available for download from http://www.animalgenome.org/repository/pig/Genome_build_10.2_mappings .<br /> <br /> Communication: The bimonthly Pig Genome Update has now published 115 issues and has been distributed electronically to over 2000 people worldwide.<br /> <br /> Final considerations: The 2013 coordinators report marks the last planned yearly report that will be issued by Max F. Rothschild. After 20 years, Dr. Rothschild indicated that it is time for a change of leadership in the Swine Genome Coordination program, and he will be stepping down September 30, 2013 if a replacement can be chosen. As a community, the swine genome group should be quite proud of all we have accomplished. This work has gone from discovering microsatellite markers, genes, and initial QTL to having a pig genome sequence, gene markers used in industry and a much better understanding of the genetic control of the traits of interest in the pig. As Coordinator, Dr. Rothschild tried to help facilitate these activities and thanks his many colleagues around the US and the world who have assisted in this success. He thanked his many colleagues for their help and support and friendship in these matters. He pledged to help the next Swine Genome Coordinator continue to work with our community and wishes whoever is chosen great success.<br /> <br /> <br /> <br /> Equine Technical Report<br /> <br /> Objective 1:<br /> <br /> A SNP assay tool was designed by the community and produced by Illumina, Inc to assay 74,000 SNPs. This replaced the Equine SNP50 tool which had been produced using a technology which became redundant in 2010. This tool was used widely in 2011 to present for gene discovery. During 2012 discussion began for design of a high density SNP assay tool (670K snps) which will be available in late 2013. At least 100 horses were sequenced in private laboratories during 2012 using NextGen technology. Some of the information has been shared for SNP discovery and other research applications. A committee was formed to investigate methods for making such information publically available with permission of the scientists who created the data. Discussions at the workshop included approaches to improving the reference sequence infrastructure leading to a new build.<br /> <br /> Objective 2:<br /> <br /> Collaborations formed at conferences and workshops facilitated collaborations in which data was shared between laboratories to investigate diverse hereditary conditions. Exchanges of materials were done on a private, collaborative basis. Studies included investigations of developmental bone diseases, respiratory disease, stable vices, immunology and population studies. Data from testing animals with the SNP50 chip, SNP74 or with RNA-Seq technologies have been shared for use as control samples or in collaborations through established community databases at the University of Sydney, the University of Kentucky and elsewhere.<br /> <br /> Objective 3:<br /> <br /> This area has come to the fore as one of the major limiting factors for advance of horse genomics. Scientists made extensive use of the horse genome information following the whole genome sequence of the first horse and made a number of discoveries. However, investigations of complex traits, understanding copy number variants, investigation of gene expression data, integration of new genome sequence data from other horses into analyses has presented challenges that tax the expertise of the horse genome workshop. Scientists have collaborated with Jim Reecy, NRSP8 coordinator for bioinformatics, to create new tools for horse research.<br /> <br /> Shared Resources: DNA and relevant analyses for radiation hybrid mapping are available through NRSP8 member scientists at Texas A&M. BAC library clones are available through a commercial enterprise at the Childrens Hospital of Oakland Institute as well as through the INRA at Jouy-en-Josas, France and Texas A&M University. Samples from horses phenotyped for MHC and other hereditary traits were shared among participants. During 2012 discussions led to a decision to create a high density SNP assay tool (670K snps), supported in part with coordinator funds. In parallel, there are several efforts to develop tools for investigation of gene expression including hybridization and sequencing methods. Information about obtaining access to these resources is available at the website for the Horse Genome Workshop: http://www.uky.edu/AG/Horsemap.<br /> <br /> Database Activities: <br /> Several genome browsers have been developed at the University of California, Santa Cruz, ENSEMBL and NCBI: http://www.genome.ucsc.edu/cgi-bin/hgGateway?hgsid=95987985&clade=vertebrate& org=Horse&db=0; <br /> http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9796; http://www.equinegenome.org/Equinegenome.org.htmlhttp://pre.ensembl.org/Equus_caballus/index.html.<br /> A SNP database is available: http://www.broad.mit.edu/mammals/horse/.<br /> A RNAseq database: http://macleod.uky.edu/equinebrowser/ (Coleman, et al, 2010).<br /> A major entry point for databases and other relevant information about the horse genome workshop and participants is the workshop website: http://www.uky.ledu/AG/Horsemap.<br /> <br /> <br /> Poultry Technical Report<br /> <br /> Objective 1:<br /> <br /> Reference linkage map: Linkage mapping is now primarily via high throughput SNP assays. Very high density SNP mapping (ca. 600,000 SNP) panels have been developed and are being employed in genome-wide association studies and genome-wide marker-assisted selection (GMAS). This year, 192 Affymetrix 600K genotypes are being obtained from DNA Landmarks for various committee members using coordination funding.<br /> <br /> Physical and comparative maps: Physical mapping of the turkey genome is complete, involving construction of a detailed comparative chicken-turkey BAC contig comparative map.<br /> <br /> Chicken genome sequence: A new build, Galgal4.0, of the chicken genome sequence which combines the original reads, next generation sequencing (NGS) reads (Roche and Illumina) and the near-finished quality of the Z sequence done by Bellott et al. (Nature 466:612-616, 2010) was released late last year and is now on some browser sites. This still has not captured the roughly 5% of missing sequence (believed to be predominantly on the microchromosomes). Methods to fill gaps and obtain the missing sequence are being pursued (e.g., optical mapping, PacBio or other sequence methods, new assembly algorithms). Cobb-Vantress Inc. has already made an ~$150,000 commitment to this effort being led by The Genome Institute at Washington U., and additional support is being sought through a USDA-NIFA-AFRI grant submission. A number of additional chicken genomes have been sequenced via NGS. Coordination funds previously supported a project to sequence 20 different chicken lines of interest to NRSP-8 members. Those data and NGS data for genomes from the DF1 and DT40 chicken cell lines are currently being analyzed and/or pursued further.<br /> <br /> Turkey genome sequence: The Turkey Genome Sequencing Consortium generated a draft sequence of the turkey genome (Dalloul et al., PLoS Biology 8(9):e1000475, 2010) using a combination of NGS reads, along with the turkey BAC contig map noted above. Coordination funds were committed to aid in this effort which also enjoyed support from VaTech, BARC and U. of Minn., among others. Efforts are on-going to improve the annotation of genes and fill gaps in the turkey sequence, as funded by a subsequent AFRI grant.<br /> <br /> Chicken microarrays: Previously, coordination funds provided microarrays for transcriptional profiling and comparative genome hybridization. Some coordination support also was committed to Illumina RNA-sequencing and Agilent chip-based transcriptional profiling, partly in hopes of filling in missing sequences.<br /> <br /> Objective 2:<br /> <br /> DNA from the East Lansing international reference mapping population has been sent to many laboratories throughout the world. Similarly, DNA from the junglefowl used to generate the reference sequence assembly has been widely distributed, especially for copy number variant studies.<br /> <br /> Objective 3:<br /> <br /> Database activities are led by the NRSP-8 Bioinformatics Coordinator, Jim Reecy, and Susan Lamont, along with Shane Burgess, represent poultry interests on the advisory committee for this group. Poultry bioinformatics has also benefitted from support at several other locations. We maintain a homepage for the NRSP-8 U.S. Poultry Genome project (http://poultry.mph.msu.edu) that provides a variety of genome mapping resources, including our newsletter archive. The Poultry Genome Newsletter is published quarterly and is distributed through our Homepage and on the angenmap email discussion group.<br /> <br /> <br /> Bioinformatics Technical Report<br /> <br /> Objective 2:<br /> <br /> Over the past year, partnered with researchers at Kansas State University, Michigan State University, Iowa State University, and U.S. Department of Agriculture, we have further developed and improved the web-interfaced relational databases to store and disseminate phenotypic and genotypic information from large genomic studies in farm animals and better serve the needs of researchers. For example, we are working with the PRRS CAP Host Genome consortium to develop a relational database to house individual animal genotype and phenotype data (http://www.animalgenome.org/lunney/index.php). This will help the consortium, whose individual research labs lack expertise with relational databases, share information among consortium members, thereby facilitating data analysis.<br /> <br /> Objective 3:<br /> <br /> Poultry: <br /> A total of 706 new QTL have been curated into the Animal QTLdb (http://www.animalgenome.org/QTLdb/chicken.html). Chicken QTL can be visualized against the genome at http://www.animalgenome.org/cgi-bin/gbrowse/chicken/ and aligned with chicken 60K SNPs along with NCBI-annotated gene information (http://www.animalgenome.org/cgi-bin/gbrowse/chicken/) on genome build GG_4.0. In addition, we continue to mirror Dr. Carl Schmidts Gallus genome browser while the original site is undergoing restructuring (http://www.animalgenome.org/cgi-bin/gbrowse/gallus/).<br /> <br /> Chicken Gene Nomenclature Committee (CGNC) database was developed and it is now possible for biocurators and community experts to add nomenclature download current nomenclature. During 2012 we modified the database to implement consistency check and updates, flagging any genes that need to be manually reviewed. We currently have 1,639 manually reviewed gene names and this data is used by HGNC and NCBI. Ensembl has reviewed our fileformats and we expect to provide them with compatible files for their platform during early 2013, enabling them to display standardized gene nomenclature for chicken.<br /> <br /> Cattle:<br /> 1098 new cattle QTL have been added to the Animal QTLdb (http://www.animalgenome.org/QTLdb/cattle). In addition, cattle QTL can now be viewed relative to both the UMD3.1 assembly (http://www.animalgenome.org/cgi-bin/gbrowse/bovine/) and Btau4.2 assembly (http://www.animalgenome.org/cgi-bin/gbrowse/cattle). Cattle 770K high-density SNPs and 4.1M dbSNP data are now available in GBrowse to align with QTL and in SNPlotz for genome analysis<br /> (http://www.animalgenome.org/tools/snplotz/).<br /> <br /> Swine:<br /> The pig genome sequencing information has been updated at http://www.animalgenome.org/pigs/genome/ and a new pig genome database has been under active development (http://www.animalgenome.org/pig/genome/db/). 1883 new QTL have been added to the AnimalQTLdb (http://www.animalgenome.org/QTLdb/pig). The pig gene Wishlist (http://www.animalgenome.org/cgi-bin/host/ssc/gene2bacs) has continued to support the pig genome annotation activities throughout 2012.<br /> <br /> Sheep:<br /> 114 new sheep QTL have been added to the Animal QTLdb (http://www.animalgenome.org/QTLdb/sheep). Active updates have been continued for the NRSP-8 web site for activities in the sheep genome community (http://www.animalgenome.org/sheep/). A new mailing list Sheep Models (www.animalgenome.org/sheep/community/SheepModels) has been set up and is being actively used. Currently there are 280+ subscribers. GBrowse alignments for sheep 54K SNP and BAC clones were set up on OAR Build 3.1.<br /> <br /> Aquaculture:<br /> Many useful links for aquaculture can be found at http://www.animalgenome.org/aquaculture/. 61 new QTL data for rainbow trout have been curated into the Animal QTLdb (http://www.animalgenome.org/cgi-bin/QTLdb/OM/index).<br /> <br /> Multi-species:<br /> A local copy of Biomart software has been kept up-to-date on the AnimalGenome.ORG server to serve the cattle, chicken, pig, and horse communities (http://www.animalgenome.org:8181/). New data sources and species continue to be updated.<br /> <br /> Ontology development:<br /> This past year we continued to focus on the integration of the Animal Trait Ontology into the Vertebrate Trait Ontology (http://bioportal.bioontology.org/ontologies/1659). We have continued working with the Rat Genome Database to integrate ATO terms that are not applicable to the Vertebrate Trait Ontology into the Clinical Measurement Ontology (http://bioportal.bioontology.org/ontologies/1583). Traits specific to livestock products continue to be incorporated into a Livestock Product Trait Ontology (PT; http://animalgenome.org/cgi-bin/amido/browse.cgi). We have also continued mapping the cattle, pig, chicken, and sheep QTL traits to Vertebrate Trait Ontology (VT), Product Trait Ontology (PT) and ClinicalMeasurement Ontology (CMO) to help standardize the trait nomenclature used in the QTLdb. Anyone interested in helping to improve the ATO/VT is encouraged to contact James Reecy (jreecy@iastate.edu), Cari Park (caripark@iastate.edu) or Zhiliang Hu (zhu@iastate.edu). The chicken adult anatomy is complete, and consists of 2,284 ontology terms cross referenced with the Vetebrate and Uberon Ontologies. The information for these terms includes relationships, synonyms, definitions, and comments (homologies to mammalian structures; species differences). Collaborating with Prof. Dave Burt (Roselin Institute) and Dr Parker Antin, we are now adding terms for pre-hatch stages.<br /> <br /> Software development:<br /> The NRSP-8 Bioinformatics Online Tool Box has been actively updated (http://www.animalgenome.org/bioinfo/tools/). Software upgrades were made continually to SNPlotz, Gene Ontology CateGOrizer, BEAP, and the Expeditor. The Virtual Comparative Map (VCMap) tool has passed its initial development stage and is now transferred to AnimalGenome.ORG (http://www.animalgenome.org/VCmap/). More application development, improvement, and testing has continued. Online help materials have been added, including a written user manual and a video tutorial. To improve links between AgBase and the NRSP-8 website, AgBase now also provides a link to the Virtual Comparative Map (VCMap). The web site and user forum listserv for CRI-MAP user interactions for improvement of the CRI-MAP software (http://www.animalgenome.org/tools/share/crimap/) has been actively used.<br /> <br /> Minimal standards development:<br /> We have continued to work on the MIBBI project http://www.mibbi.org/index.php/Main_Page to help define minimal standards for publication of QTL and gene association data (http://miqas.sourceforge.net/).<br /> <br /> Expanded Animal QTLdb functionality:<br /> In 2012, a total of 3871 new QTL have been added to the database. Currently, there are 8315 curated porcine QTL, 6305 curated bovine QTL, 3442 curated poultry QTL, 753 curated sheep QTL, and 88 curated rainbow trout QTL in the database (http://www.animalgenome.org/QTLdb/). All included livestock QTL data have been ported to NCBI. Since we started to curate SNP-association data for all livestock species, there have been 5037 association data added to the database.<br /> <br /> Facilitating research:<br /> The Data Repository for the aquaculture, cattle, chicken, and pig communities to share their genome analysis data has been proven to be very useful (http://www.animalgenome.org/repository). More species data is currently being added. The online data file-sharing tool has been actively used. Newly added functions include authenticated access for small consortium groups and/or projects. Throughout the year, we have helped to reformat large datasets to meet the needs of wet lab researchers. We have helped more than 70 research groups/individuals with their research projects and questions. Our involvement has ranged from data transfer, data assembly, and data analysis, to software applications, code development, etc. Please continue to contact us as you need help with bioinformatic issues. The ANGENMAP listserv has been heavily used in the past year. Now the annual posts sent through the list have grown from about 300 to over 400 per year. We have approximately 2300 subscribers, which is 170 more than last year (on average +130 per year for the past 10 years).<br />

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