Brief Summary of Minutes of Annual Meeting

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.

Overview 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. 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 under the project description for NRSP008: National Animal Genome Research Program on the NIMSS website under ATTACHMENTS. Aquaculture Technical Report 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. 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. 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. 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). Cattle Technical Report 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. 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. 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. 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. 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. 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. 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. Equine Technical Report 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. 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. 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 Poultry Technical Report 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. 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). 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. Sheep/Goat Technical Report 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. 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. 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. 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. 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. Swine Technical Report 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. 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. 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. 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. 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. 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. 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. 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). 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. PUBLICATIONS Peer Reviewed Publications 221 (SEE FOLLOWING); Abstracts and Proceedings 134; Book Chapters 6; Dissertations and Thesis 15; Other Publications 5

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