Brief Summary of Minutes of Annual Meeting

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. OBJECTIVES Objective 1: Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. Objective 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. Objective 3: Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest. Aquaculture Technical Report Objective 1: Catfish: 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. 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. 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. An Agilent 8x60K microarray is publicly available and has been utilized for profiling channel and blue catfish skin responses to Aeromonas hydrophila infection. Oyster: International efforts to develop BAC physical maps, large volumes of SNPs and integrated cytogenetic maps culminated in the acquisition of an oyster genome sequence. Salmonids: 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. 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%. Shrimp: 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. 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. A large scale RNA-seq project was initiated to characterize disease resistance mechanisms in shrimp. Striped bass: 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. 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. Objective 2: Catfish: 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. Salmonids: 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. Shrimp: 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. Striped bass: 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. Objective 3: Catfish: 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. Salmonids: 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. Shrimp: 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. Cattle Technical Report Objective 1: 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. 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. 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. 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. 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.  Sheep/Goat Technical Report Objective 1: 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. 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. 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. Objective 2: 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. 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. 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. 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. 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. 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. 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. 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. 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. Swine Technical Report Objective 1: 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. 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. 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. 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. 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. Objective 3: 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 . Communication: The bimonthly Pig Genome Update has now published 115 issues and has been distributed electronically to over 2000 people worldwide. 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. Equine Technical Report Objective 1: 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. Objective 2: 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. Objective 3: 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. 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. Database Activities: 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; 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. A SNP database is available: http://www.broad.mit.edu/mammals/horse/. A RNAseq database: http://macleod.uky.edu/equinebrowser/ (Coleman, et al, 2010). 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. Poultry Technical Report Objective 1: 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. Physical and comparative maps: Physical mapping of the turkey genome is complete, involving construction of a detailed comparative chicken-turkey BAC contig comparative map. 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. 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. 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. Objective 2: 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. Objective 3: 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. Bioinformatics Technical Report Objective 2: 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. Objective 3: Poultry: 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/). 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. Cattle: 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 (http://www.animalgenome.org/tools/snplotz/). Swine: 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. Sheep: 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. Aquaculture: 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). Multi-species: 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. Ontology development: 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. Software development: 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. Minimal standards development: 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/). Expanded Animal QTLdb functionality: 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. Facilitating research: 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).