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 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.

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. ACCOMPLISHMENTS AND IMPACTS: Overview 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. 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). Aquaculture Technical Report 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. 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. 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. Cattle Technical Report 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. 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. 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. Sheep/Goat Technical Report 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+. 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. 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. Objective 3: A website is under design for visualizing the goat RH map and potentially other data generated by the International Goat Genome Consortium. Swine Technical Report 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. 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. 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. 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 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. Equine Technical Report 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. 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. 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. Poultry Technical Report 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). 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. 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. Objective 2: DNA from the East Lansing international reference population has been sent to many laboratories throughout the world. 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. Bioinformatics Technical Report Objective 2: Developed a relational database to store individual animal genotype and phenotype data to support the PRRS CAP Host Genome consortium. Objective 3: Poultry - 285 new QTL were curated into the Chicken QTLdb. Chicken QTL can be 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 pages. A bird comparative genome browser is being developed via BirdBase and will initially include the chicken, turkey and zebra finch genomes. 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. Porcine  The new pig genome database is under development. 88 new QTL were added to the AnimalQTLdb. The pig gene Wishlist continued to serve the pig genome annotation activities. Sheep - 291 new sheep QTL were added to the Sheep QTLdb. Aquaculture - 27 QTL data for rainbow trout were curated into the Animal QTLdb. 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). Software development 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). 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). 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. The web site and user forum listserv for CRI-MAP user interactions in improving the CRIMAP software has been actively used.