Brief Summary of Minutes of Annual Meeting

Aquaculture, Bioinformatics, Cattle, Equine, Pig, Poultry, Sheep/Goat Species Groups (80-100 attendees in workshop/business meeting) The Business meeting was preceded by the joint Animal Genome Workshop session with presentations by: Randall Prather, University of Missouri, Utility of Genetically Modified Swine; Noelle Cockett, Utah State University, Recent Advancements in Sheep Genomics, James MacLeod, University of Kentucky, "Analyses of the equine mRNA transcriptome using RNA-seq data" and Larisa Rudenko, Senior Advisor for Biotechnology, Food and Drug Administration, Genetically Engineered Animals: Regulation, Research, and Opportunities for Collaboration Business Meeting: A. Old Business: Call to order 4:50 PM, Cecilia Penedo, NRSP8 2009 Chair, Motion to approve minutes from January 11, 2009, approved by acclamation. B. Species Coordinator Reports: 1. Aquaculture  John Liu, Caird Rexroad, Co-coordinators. Coordinator funds were used to support travel, the aquaculture genome workshop, and two community based projects (oyster genome workshop, rainbow trout PCR pool construction). The Aquaculture Workshop was well attended with 85 signed in participants representing 13 countries. Whole genome sequencing (WGS) projects using Sanger or next-generation sequencing methods are underway for catfish, Pacific oyster and tilapia, with rainbow trout and Atlantic salmon to follow in 2010. The International Shrimp Genome Consortium (China, USA and Thailand) is organizing a WGS initiative for June 2010. Linkage maps for shrimp (SNP-based) and striped bass (microsatellite-based) were constructed. Understanding of reproductive behavior of channel catfish has improved through molecular individual identification and pedigree analyses. Research efforts to improve reproduction traits of hybrid catfish have been successful; hybrid catfish have superior production traits and commercial farms (currently 47 involved) can realize significant increase in income. Work is underway in salmonids to investigate QTLs that impact handling stress and pathogen resistance. Several databases are being developed (teleost alternative splicing, oyster EST and BAC contig annotation, rainbow trout genetic map, striped bass ovarian contigs, multi-tissue transcriptome of white perch). Many of these resources can be accessed through http://www.animalgenome.org. 2. Bioinformatics  James Reecy, Coordinator. In collaboration with Chris Tuggles group, a public open-source database and website (www.ANEXdb.org) was developed for storage and analysis of functional genomics data in livestock. The Database Coordination team has started to migrate this database into http://www.animalgenome.org for long-term maintenance and to expand its capabilities, which currently consist of: a) tools to facilitate storage of Affymetrix-based gene expression data from any species with an available GeneChipÒ; b) submission of user data to NCBI Gene Expression Omnibus; and c) a comprehensive annotation of all porcine expressed sequences. The current efforts will expand the data storage capabilities to all widely used livestock gene expression profiling tools, as well as create comparative annotation of the sequence elements on these profiling tools. In partnership with KSU, MSU and USDA, relational databases to store and disseminate phenotypic and genotypic information from large genomic studies in farm animals are being developed to support research labs, share information among collaborators and facilitate data analysis. One example is the development of the relational database for the PRRS CAP Host Genome consortium (http://www.animalgenome.org/lunney/index.php). The coordinator actively communicated with curators and compiled information of other relevant genome databases for poultry, cattle, pig, sheep and aquaculture. Many of the resources are accessible through http://www.animalgenome.org. Another focused effort was to integrate the Animal Trait Ontology into the Vertebrate Trait Ontology to provide researchers an online resource of standardized trait terms and improve communication among different groups within the livestock, rat, mouse and human research communities. Other activities included software development for sequence assembly using a seed sequence, visualization tools for whole genome association data and the Virtual Comparative Map (VCMap), expansion of Animal QTLdb functionality and providing bioinformatics expertise to assist research groups with data assembly and analysis. 3. Cattle  Juan Medrano, Coordinator. Funds supported student award and speakers for PAG XVIII, 2010. Publications of the bovine WGS, SNP variation, and other features of the bovine genome were released in 2009. Current bovine WGS assemblies are represented by Btau_4.2 (from Baylor) and the University of Maryland (UMD2 and UMD3.1). Improvements in the assembly algorithms, manual curation and annotation of the genome are continuing. This work illustrates the value of the support and collaboration through NRSP8 and many contributions from the bovine community. Several projects are underway in the USA to resequence individual animals to increase SNP density, improve assembly and understanding of genome structure and variation. Development of the BovineSNP50 genotyping assay has been implemented for whole genome selection in dairy cattle by the USDA-AIPL and adopted globally by the dairy industry. A joint effort by NRSP8 investigators to produce new high density genotyping chip resources (600K+) in Illumina and Affimetrix platforms has the potential of truly refining QTL position for fine mapping and expanding the application of targeted genome selection to a large group of cattle breeds. Coordination is being provided for the development of a new bovine Affymetrix gene sampling array. This array will include ~550k probes representing most exons for increased sensitivity to measure gene expression. The creation of this array platform is being coordinated with the input of US investigators and a German group that will support the development costs. Also, plans are in progress to develop shared tools for enhanced cDNA library construction (NSR primers) to improve representation and selection of transcripts for gene expression arrays and high throughput sequencing (RNASeq). Database and bioinformatics activities are led by the NRSP8 Bioinformatics Coordinator, Jim Reecy. 4. Equine  Ernie Bailey, Coordinator. Funds were used to support administration of the SNP chip resource, support for students and post-docs to participate in scientific meetings (PAG 2009, The Equine Science Society meeting in Colorado and the Dorothy Russell Havemeyer Meeting in the United Kingdom in July 2009), and for the coordinator and workshop committee members to attend industry meetings to explain and promote the use of horse genomics in research. The assembled Horse Whole Genome Sequence has accelerated research of health-related traits, e.g. developmental bone diseases (osteochondrosis and related diseases), muscle diseases (polysaccharide storage myopathy), neurological disease, growth and stature, dwarfism, bone fracture and aspects of performance, and infectious disease. The 55K Equine SNP chip developed by Illumina with grant support from Morris Animal Foundation, USDA and other independent sources (University of Kentucky, University of Berne, Animal Health Trust (Newmarket, England) and Royal Veterinary College (London, England). The SNP chip has been very effective and subject of research presentations at several meetings during the past year. Use of that assay by researchers is facilitated and coordinated by scientists at the University of Minnesota in connection with grants from the Morris Animal Foundation and the USDA. Efforts are underway to develop tools for investigation of gene expression including hybridization and sequencing methods. 5. Pig  Max Rothschild, Coordinator. New gene markers continue to be identified and mapped. Integration of maps continues to take place as QTL maps are expanded. Maps are being developed based on the pig sequencing efforts and the 60K SNP chip. QTL and trait associations have continued to be reported on all chromosomes for many traits. Candidate gene analyses have proven successful with several gene tests being recently released and used in the industry for many traits including, fat, feed intake, growth, meat quality, litter size and coat color. The PigQTLdb (http://www.animalgenome.org/QTLdb/pig.html) is an excellent repository for all of these results. The Swine Genome Sequencing Consortium (SGSC) continued its efforts this past year and considerable advances have been made. A total of 160 attendees came to this historic meeting where speakers presented updates on several subjects related to the sequencing effort and plans for the future. The deadline has passed for new clones to enter the sequencing pipeline. However, some new clones (~150) are being identified using physical map and sequence information as a possible resource for future sequence gap closure. All chromosomes are over 90% sequenced taking the genome to 95.72% from 16,974 sequenced clones. About 94% of the genome is at the Improved status (15720 clones). There is 123Mb of finished quality data within the 2.994Gb currently available. Sanger will continue with chromosome X/Y sequencing  chromosome X clones sequenced in the genome project will be finished and the map will continue to be refined using a fosmid library too. Sanger has produced a chromosome Y fosmid library which is currently being fingerprinted. This will be used to select up to 1100 fosmid clones for sequencing and finishing. This work is funded by BBSRC. In collaboration with TGAC (Norwich, UK) the remaining BAC clones which have been selected from the fingerprint map will be pooled and sequenced on the Illumina platform. A further 10X coverage of Duroc sow DNA will be produced on the Illumina platform to be combined with the BGI data and assembled (also in collaboration with TGAC). Automatic annotation will continue to be provided by Ensembl. Another annotation jamboree is to be organized in 2010. The Pig Genome Database continues to be updated to report the genome sequencing progress (http://www.animalgenome.org/pigs/genomesequence/). New QTL continue to be curated into the Pig QTL Database (http://www.animalgenome.org/QTLdb/pig.html) currently with 4,928 QTLs representing 499 pig traits and another 200 QTLs undergoing a quality control process before their release. New functions have been added to the PigQTLdb tools to align pig RH map-human comparative maps, pig BAC physical maps, new microsatellite markers from Sino-Danish genome project, pig SNPs from dbSNP, Affy and Oligo microarray elements against pig QTL. A new function allows users to download all curated QTL data when browsing the QTL chromosome map views. Efforts are being made to align the current genome assembly against pig QTL, among other genome features, (http://www.animalgenome.org/gbrowse/). Database activities were transferred to the Bioinformatics Coordinator. 6. Poultry  Jerry Dodgson and Hans Chang, Co-coordinators. Chicken linkage mapping has transitioned almost solely into high throughput SNP assays (60K SNP Illumina iSelect genotyping array) which have greatly enhanced the reference map and are also essential components for trait mapping and genome-wide marker assisted selection (GMAS). Coordination funding was used to enhance the SNP linkage map by genotyping the Wageningen reference panel and supported SNP genotyping of 100 samples by NRSP-8 members. Efforts are underway to evaluate the latest map and to compare it with the latest genome sequence assembly and to develop a denser SNP map specifically useful for the East Lansing reference linkage map population. Reduced representation and high throughput sequencing of the UCD003 genome will be employed to generate additional SNPs between the UCD001 and UCD003 parents of that population. Physical mapping of the turkey genome is nearly complete, along with construction of a detailed chicken-turkey BAC contig-based comparative map that was essential for the assembly of the first draft turkey genome sequence (see below). The regularly updated comparative BAC contig map is available at http://poultry.mph.msu.edu/resources/resources.htm#TurkeyBACChicken. Improvement of the second assembly of the chicken genome (May 2006 build) is underway with high throughput next generation sequencing being used at WUGSC and also in an effort to obtain the ~5% of missing sequence (predominantly on the microchromosomes). The third build of the chicken genome was released in November, 2009, based on 12x 454-Roche reads, but this is not yet on the major genome browsers. Efforts to map SNPs in the 60K chip chosen from unassigned sequence contigs were generally unsuccessful, suggesting that much of chr_Un derives from small unplaced microchromosomes, chromosome W, and repetitive elements or CNV regions. The Turkey Genome Sequencing Consortium generated a first draft genome sequence using a combination of Next Generation sequencing platforms, along with the turkey BAC contig-based comparative map alignments. The project was led by Otto Folkerts and Rami Dalloul of VaTech, Julie Long of USDA-ARS-BARC and Kent Reed, UMN. Coordination funds were committed to aid in this effort which also enjoyed support from VaTech, BARC and UMN, among others. The effort also garnered support to both VaTech and BARC from USDA-NIFA-AFRI. Sequence assembly was led by researchers at the UMD Center for Bioinformatics and Computational Biology. Sequences have been submitted to Genbank and browser support will be available through Birdbase at http://birdbase.net/cgi-bin/gbrowse/turkeygenome/ (thanks to Carl Schmidt, U. of Del.). Efforts are on-going to improve the annotation of genes and fill gaps in the turkey sequence. Coordination funds have been used provide samples of the 44K element long oligonucleotide chicken microarray made by Agilent Corp. to several NRSP-8 participants, along with a new 244K whole genome long oligo array that can be used for comparative genome hybridization and whole genome transcriptional profiles. Some participants chose to be provided GeneChip® Chicken Genome arrays from Affymetrix, Inc. (http://www.affymetrix.com/products/arrays/specific/chicken.affx). Further support for transcriptomics is anticipated in future years. 7. Sheep/Goat. Noelle Cockett, Coordinator. Periodical updates of the sheep linkage map continues with current version 4.6 (ca. 1400 markers spanning over 3,500 cM) available on the Australian Gene Mapping Web Site (http://rubens.its.unimelb.edu.au/~jillm/jill.htm), maintained by Jill Maddox, University of Melbourne, Australia. Coordinator funds were used to a) support production of paired-end sequences from clones in the CHORI-243 ovine BAC library to create a virtual sheep genome through comparative analysis with sequenced genomes of other species. Detailed information can be obtained through the virtual sheep genome website (http://www.livestockgenomics.csiro.au/vsheep/); b) development of an ovine radiation hybrid (RH) panel (USUoRH5000) and map with 2104 loci and average spacing of 1.5 Mb/locus. By identifying the locations of mapped loci within the whole genome sequences of human and other closely related mammalian species, ovinemammalian comparative maps were developed. The ovine RH map will provide a unique opportunity for determining chromosomal synteny at the molecular level. The identification and positional cloning of genes governing traits significant to the ovine industry will be enhanced and the RH map can be used as a scaffold for assembling the ovine whole genome sequence. The NRSP-8 sheep coordinator is a participant in the International Sheep Genome Consortium (ISGC), a multi-institutional group developing sheep resources needed for genomic research (http://www.sheephapmap.org/). These resources include a high coverage BAC library with complete end-sequencing, high and moderate resolution RH panels, full coverage linkage maps, an integrated ovine genetic map, a whole genome BAC physical map, the virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep/), a 1536 SNP pilot chip and a high density 60K SNP array, released in January, 2009, as the Ovine SNP50 BeadChip. To date, 3064 sheep from 64 breeds and strains, seven species of wild sheep and nine outgroup species were typed with the BeadChip for the world-wide ovine HapMap project, as well as two ovine RH panels and the International Mapping Flock. The ISGC is using next-generation sequencing technologies to complete a whole genome reference sequence (7X coverage equivalence) with DNA from the Texel male used to create the CHORI-243 BAC library. The reference sequence will have low error rate (< one base pair in 10,000) and minimal number of gaps. Assembly of the sequences will be iterative, starting with de novo assembly into high quality contigs and continuing with information from syntenic alignments to the human, bovine, dog and horse whole genome sequences. Information from the ovine linkage, RH and cytogenetic maps and positional information from the ovine consensus genome assembly will also be utilized to support the assembly. Problem areas will be finished by sequencing BAC clones that cover large gaps and array-based hybridization enrichment across short gaps. Substantial leveraging of funds and expertise from the ISGC, combined with technological and computational advances in the area of de novo sequence assembly, will contribute significantly to the success of the project. C. New Business: 1. Election of officers for 2010. John Liu nominated Geoff Waldbieser, USDA-ARS for Secretary of NRSP8 2010; approved by acclamation. 2. Selection of next meeting location and date. Jerry Dodgson suggested the meeting be held next year at PAG on Sunday; approved by acclamation. Meeting adjourned at 5:50 PM.

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