Brief Summary of Minutes of Annual Meeting

Brief Summary of Minutes of the Annual Meeting: OLD BUSINESS A. Call to Order 3:40 pm - Mary Delany, NRSP-8 2007 Chair. Motion to approve minutes from January 14, 2007 meeting by C Ashwell, NCSU; 2nd J Reecy, ISU; approval by acclimation. B. Species Coordinator Reports 1. Sheep/Goat Report - Noelle Cockett, Sheep Genome Coordinator. NRSP8 funds have been used to leverage other funding for the International Sheep Genome Consortium. BAC end sequencing of the CHORI-243 ovine BAC library was completed under a USDA-NRICGP project, and the BAC end sequences were used to develop a sheep whole genome physical map. Combined data was compared to reference genomes, including human, cattle and horse, to give the final product, the virtual sheep genome map. A 1536 SNP array has been used for typing multiple populations, including the sheep reference population used for linkage map and the USU RH panel. New sets of primers have been generated for 1800 genes and are being typed across the RH panel. The RH and linkage maps are used to confirm the virtual sheep genome map. These primers may be useful for the planned goat RH panel. The push for a whole genome sequence for sheep will be discussed at the ISGC meeting on Monday, 1/14/08 at PAG. Several new members have been added to the NRSP8 sheep and goat committee. NRSP-8 coordinator funds are an important incentive for travel to the meeting. 2. Cattle - James Womack, Cattle Genome Coordinator. NRSP8 funds were used for travel for workshop speakers and students. Primers originally developed for RH panel are now being used successfully for RH map in other bovids. Bovine sequencing assembly is still continuing, much more effort will be required for full sequence assembly. 3. Equine - Ernest Bailey, Equine Genome Coordinator. Whole genome sequencing has already been completed for horse in 2007 at Broad Institute, MIT, MA. Plans are underway for development of new Illumina 60K SNP chip with support by Morris Animal Foundation. A major update of the horse genome webpage has been completed. It includes added information for scientists as well as for members of the horse industry. Ernie urged all species to evaluate their websites for utility by the general public and stakeholders. 4. Poultry - Jerry Dodgson / Hans Cheng, Poultry Genome Co-Coordinators. Chicken genome sequencing has been accomplished, two iterations, 2004 and 2006, even though not representative of a truly completed assembly nor fully annotated. However, the sequence availability has opened up major areas for future work including SNP efforts, comparative studies in turkeys, copy number variant investigations. There are currently no funds, but clear need and hope, for developing more comprehensive SNP chips for chickens. It is now much more evident that breeding companies have invested in genomics and are actively using tools developed by NRSP-8 scientists for their chicken work. 5. Swine - Max Rothschild, Swine Genome Coordinator. NRSP-8 funds have been used to support development and use of new expression arrays using long oligos. Slides printed at Univ. AZ are being validated at MSU, UMN and BARC in 2008 with NRSP-8 support. Swine genome sequencing is continuing at Sanger; it is coming together but not expected to be finished until mid-2009. It is currently at 2x coverage with 4-6x final coverage expected. A new swine SNP chip with 40-60K SNPs is being developed. Purchase of 700-1000 chips is planned for US labs using specifically stockpiled funds from the NRSP8 Swine Coordinator. 6. Aquaculture - John Liu, Aquaculture Genomes Coordinator. Currently 6 aquaculture species are covered under NRSP-8; at PAG 30 aquaculture species reported their research results. WGS of tilapia is scheduled by the Broad Institute. Genome BC is planning WGS for Atlantic salmon; the community is working on funding for that. New Co-Coordinator for Aquaculture is Caird Rexroad, ARS, Leetown, WV. 7. Database - James Reecy, Database Lead Coordinator. There has been recent funding for animal bioinformatics projects, e.g., Shane Burgess for GO annotation, Carl Schmidt for GallusGBrowse; Chris Elsik for bovine annotation, and Jim Reecy for expanding the web viewer to be used for many species. Jim Reecy is working with rat and mouse genome groups to develop comparative applications. Expertise and computer structure is available for developing needed relational databases; if want to pursue could take advantage of ISU supercomputers for different applications. There was a general email message with 2 surveys for NRSP-8 web tools. Please respond to provide input. C. Administrator Reports 1. Lead Administrative Advisor - Colin Kaltenbach. There has been good progress by all the species Coordinators with improvements at both basic plus applied levels. The most important current issue is the NRSP-8 renewal. Note that the annual report must be submitted within 60 days. The writing for the new project has progressed very well, thanks to the leadership of NRSP-8 Chair, Mary Delany. Reviews to date have been very good. New species Coordinators are expected to be selected before Oct.1 2008, the start date for a new project. All scientists should remember to sign up for the new NRSP-8 project. Participation does not role over. Please contact your Experiment Station Director to add members for the new project (Appendix E form). All levels of participants are welcome, PIs, postdocs, and students. 2. Other Administrative Advisors - Eric Young and Bert Stromberg. Each affirmed the impact of the current NRSP-8 project and the importance of the efforts to renew it. It was noted that industry partners are allowed; contact Colin Kaltenbach for further information. Scientists from other countries are also welcome to participate in NRSP-8. 3. USDA-CSREES National Program Leader - Muquarrab Qureshi. NRSP-8 is a high impact project. It is impressive how many species sequencing have been completed since 2003. In 2008 numerous species sequencing are underway or being completed. These efforts are viewed as very important to the US government and its PMA and OSTP. This is viewed nationally as one of the best NRSP programs. The revised project has paid attention to USDA Animal Genome Blueprint www.csrees.usda.gov/nea/animals/pdfs/animal_genomics_blueprint.pdf Animal genomics are valued at CSREES as evidenced by NRI grant rfps. Thanks to the bioinformatics efforts, to the QTL group, for its impact for industry. Approval of the NRS-P8 rewrite is underway. Once completed CSREES will expedite Coordinators selection. The aim is for a mid-June deadline. Remember to email species leadership changes to NRSP-8 Secretary, Joan Lunney so she can send the updates to Muquarrab Qureshi. D. NRSP-8 Project Re-write  Mary Delany The new NRSP8 project objectives were each reviewed and approved. NEW BUSINESS 1. Election of officers for 2008. Jerry Dodgson nominated Joan Lunney, USDA BARC, for chair and Ernie Bailey nominated Cecilia Penedo, UC Davis, for secretary. Both nominations were 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. 3. Meeting format. Jerry Dodgson noted that the Poultry group suggested a modification of the format of the NRSP-8 PAG meeting stating a need for joint species sessions at PAG for common animal genome related topics. Its difficult to move between the separate species meetings. The suggestion is for the species meetings to end by lunch on Sunday. This would open up time for a common scientific meeting for general topics for all species, e.g., SNPs would have been good this year. Motion: Jerry Dodgson moved that NRSP-8 scientists consider a Sunday afternoon joint animal session; 2nd by Sue Lamont. Discussion: Qureshi noted that this would improve cross-species communication. Liu said many scientists only stay the weekend so a larger session on Sunday is a good idea. Reecy asked why not go for earlier Sunday for this NRSP-8 plenary session? Cassady noted that now it is difficult to go to other species sessions; it is important particularly for people working on multiple species. There had been a previous agreement for swine meeting on Saturday and cattle on Sunday. This year cattle had a 2 day meeting Saturday and Sunday. Change in meeting schedule will depend on room availability; Cheng will check possibilities and ask Scherago for options. Species chairs will plan this session with the NRSP8 leadership and with Coordinators. All present approved the motion that NRSP-8 scientists consider a Sunday afternoon joint animal session. Motion was made by Qureshi to thank Mary Delany and Joan Lunney (2007 Secretary) for a good job with this NRSP8 meeting. Meeting adjourned at 5:30 pm.

Progress toward Objective 1. Aquaculture. Catfish. Over 300 microsatellite markers derived from ESTs were mapped. To integrate the linkage and physical maps hundreds of microsatellites derived from BAC-end sequence were genotyped. Two BAC contig-based physical maps of the channel catfish were generated using fingerprints; combined contig size was about 931 and 961 Mb. Some 48,275 BAC end sequences were generated with 12,586 microsatellites identified. Salmonids. Eighty percent of the NCCCWA Swanson 10x BAC library clones were fingerprinted and BAC end-sequencing of 100,000 clones was completed by a collaborative partnership (Genoscope and INRA). Assignments of 27 Atlantic salmon linkages groups were made to the 29 chromosomes pairs. BACs were assigned to 46 of the 50 rainbow trout chromosome arms using FISH. Centromere assignments were made to the trout genetic maps. Tilapia. About 20,000 BAC clones were sequenced (Genoscope). The sequencing project was assigned by NIH-NHGRI to the Broad Institute. Oysters. A JGI/Standford project to sequence 58 BAC clones progressed. A BAC-based physical map was constructed of the Pacific oyster genome from a single inbred male. The library was fingerprinted (Genome Sciences Ctr). A project that progressed was the deep-sequencing of Pacific oysters ESTs from tissue and age-specific libraries. Work also continued for the eastern oyster in marker development. Shrimps. First order genetic maps have been published, marker development continues. Striped bass. New microsatellite markers were developed (~500) and creation of the first genetic linkage map is underway. Bioinformatics. Work focused on linking QTL data to the human and livestock genome sequences for researchers to transfer information between maps; in addition minor allele frequencies and microarray features have been included as available. Cattle. Contributions were made to the NIHGR bovine genome sequencing project technical committee. Equine. A first assembly of the horse genome was accomplished (Broad Institute) and the sequence was analyzed by the horse genome group; this involved sharing amongst numerous national and international lab from previously completed RH maps, linkage maps, and FISH markers. Comparative genomic questions can now be addressed between equine, other sequenced animal genomes and human. Pig New gene markers were identified, mapped and map integration continued with expansion of QTL map and physical maps. The sequencing consortium continued its fund raising efforts and a review of progress was published; sequencing continues to advance with significant coverage of all chromosomes. Poultry The chicken linkage map provides a framework for QTL and other mapping research and the platform on which the sequences have been assembled and linked to chromosomes. Prior SNP research was built upon by USDA NRI support of an US and EU consortium to genotype thousands of birds and utilizing the EL and W linkage families further enhancing the linkage map. A second SNP study was supported by coordination funds re-using SNP genotyping information and reagents  combined this SNP data improve the linkage map and contributes to numerous on-going research to find causative genes involved in many chicken QTL. Sheep/Goats An ovine whole-genome RH 5,000-rad panel consisting of 88 clones was generated and used to construct map with 1306 markers. The result was 95 RH linkage groups over26 autosome. Progress continued with NRSP-8 collaboration in the International Sheep Genome Consortium to create new resources which includes a high coverage BAC library, end-sequencing, integrated ovine map, BAC physical map, development of the virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep ) and a 1,536 SNP chip. Progress toward Objective 2. Aquaculture. Catfish. About 300,000 EST clone sequences (200K from catfish, 100K from blue catfish) have been generated (project with Joint Genome Institute and NRSP-8 members). Salmonids. The community continues to identify ESTs from tissues and physiological conditions from a number of salmonids. Functional genomics involving global gene expression with respect to proteolysis and toxicological responses are producing candidate genes for further analysis. Two QTL were found in a study using clonal lines (WSU) and stress analysis with opposing effects. A growth QTL analysis found 22 QTL across 11 linkage groups with effects on numerous growth parameters. Tilapia. A major EST study was approved by the USDA-NRICGP to sequence 100,00 ESTs from a variety of tilapia libraries. Oysters. Deep sequencing of 16,000 Pacific oyster clones derived from multiple tissues and age-specific libraries has been completed and working is continuing. Shrimps. About 130,000 white shrimp EST clone sequences (from both ends) are being checked (Joint Genome Institute) against the physical library; these will be used to create a microarray. Striped bass. A new inter-disciplinary program of graduate education in aquaculture genomics was developed at NCSU with funding from the USDA  CSREES Food and Agricultural Sciences National Needs Grants Program. This group has been very active in collaborative efforts for improved breeding and development of specialized stocks, with an emphasis on enhancing genetic diversity and commercially important traits. Bioinformatics. Focus was on curation of cattle, chicken and swine QTL information generated from hundred of manuscripts describing QTL or association tests for these species. The database was expanded to include sheep QTL information. Equine Numerous studies were conducted and published related to QTL analyses and also diseases involving bone, muscle, skin as well as coat color variants and aspects of performance and infectious disease. The work involved use of the genetic marker maps previously developed by NRSP-8. Pig QTL are reports in all chromosomes for numerous traits; imprinted QTLs continue to be discovered. Candidate gene analysis was successful with several gene tests used by the industry for traits including fat, feed intake, growth, meat quality, litter size and coat color. Poultry BAC libraries were extensively fingerprinted and integrated with linkage and gene maps and used to generate a second generation contig map updated in parallel with the second build of the chicken genome sequence. Similar efforts were undertaken for the turkey CHORI-260 library to generate a BAC contig physical map of the turkey genome and a comparative chicken-turkey map. Over 21,000 BAC end sequences and 15,200 BAC overgo hybridization assignments were made to 1248 markers or genes. More tha 40,000 turkey BAC fingerprints were generated allowing a first generation physical map for turkey of about 5.6x coverage. Sheep/Goats A resource population was created by crossing Dorset ewes with East Friesian rams, with an F1 backcross to both parental populations. Phenotyping was initiated. Microsatellites will be used for genotyping. Research on the callipyge trait continued by analysis of gene expression (using bovine arrays). A QTL scan was initiated of a sheep population segregating parasite burden. A large scale EST sequencing project of 10,000 clones from a cDNA library from goat uterine/embryonic tissues was initiated. Progress toward Objective 3: Aquaculture. Catfish. Work progressed on creating chromosome-anchored ESTs with large sale informatic mining of microsatellites and SNPs Salmonids. Atlantic salmon and rainbow trout gene indices can be found at http://compbio.dfci.harvard.edu/tgi/tgipage.html Tilapia. The Gbrowse software has migrated to the University of Maryland, www.cichlidgenome.org . Shrimps. Archiving of EST and microarray can be found at www.marinegenomics.org . Bioinformatics. Extensive communication was held with curators of other relevant livestock-genomics databases, along with compilation of database information and assessment of content and function, to allow for US coordination efforts to focus on development in areas of high priority and utility. In addition alignment and display of microarray data was successful. On line tools were developed to generate PCR primers across species, a GO term counter and also graphing tools are accessible. An Animal Trait Ontology was developed. A bovine genome annotation meeting was co-hosted. Cattle Web site was maintained for on-line radiation hybrid mapping for investigators using the 5000 rad bovine RH panel available from the coordinator. Distribution of bovine reference family panel DNA (IBRP) was continued. Microsatellite primers were purchased and were distributed by the coordinator (quality tested by coordinator lab). Other tools are also available: RH panels of (5,000 and 12,000 rad)), BAC libaries, panel of 31 hybrid somatic cells. Equine Sharing of resources continued including reference families DNAs, primers, RH mapping resources, BAC clones (CHORI). Contributions were made to database develop for genetic data, BAC map data, SNP data. Pig The PigQTLdb serves as a repository for QTL related studies. There are 1,675 QTL in the database representing 246 pig trais. New functions have been added including tools to align pig RH map-human comparative maps, BAC physical maps, new microsatellite markers, pig SNPs from various sources and micro array elements  against pig QTL. News and updates are communicated to membership routinely. A second generation novel 7-mer oligo microarray for profiling expression was developed. The informational materials are available to the community (no cost); the array can be purchased via the coordination unit. Validation is ongoing through a collaborative venture. Poultry The sequence is available on three browsers (UCSC, NCBI, Ensembl). Numerous unique and resource-packed databases and browsers are available and maintained by researchers supported by USDA-NRI funds along with the NRSP-8 Bioinformatics coordination site(s), all can be accessed by the NRSP-8 poultry genome website (http://poultry.mph.msu.edu ). Sheep/Goats Sequences from the CHORI-243 BES project are available via NCBI. Matches of the ovine to bovine and human sequences and clone identity are available through CSIRO (http://www.livestockgenomics.csiro.au/SheepGenomics ). Virtual sheep genome information and mammalian comparisons are available through the site.