Brief Summary of Minutes of Annual Meeting

I. Call to order at 4:30 pm by Caird Rexroad, Chair. Minutes taken by David Adelson (standing for Clare Gill). Sue Lamont moved to approve minutes from January 16, 2005 meeting. Motion was unanimously affirmed. II. Old Business 1. Species Reports: a. Cattle/Sheep/Goat i. Noelle Cockett, Sheep Genome Coordinator Progress on sheep RH panel: distributed to 4 labs (see coordinators report). Significant typing efforts in Cockett lab include: 257 markers screened so far, about 50% of which are scoreable, with about 2/3 of those results duplicated. Efforts now are aimed at scaling up to type large numbers of markers. There will soon be a need for a data repository and infrastructure for the analysis of typing data. A Tools and reagents proposal was funded for BAC end sequencing and construction of a physical map from the CHORI sheep library. Kellye Eversole negotiated a very favorable price with TIGR to end sequence the full 200,000 clones from the library. Related statistics are in the coordinators report, but a key feature is that ~6% of the ovine genome is represented. A whole genome physical map is being constructed by Brian Dalrymple (CSIRO Australia) using end sequences. International Scientists linkage program. A large scale SNP discovery project (30,000 total sheep SNPS to create a 20,000 SNP chip) was initiated with Frank Nicholas (Sydney University). Dr. Cockett invited scientists to attend the meeting of International Sheep Genome Consortium to be held at PAG Jan. 16. ii. James Womack, Cattle Genome Coordinator The Cattle genome sequencing project has consumed most of the resources and attention of the coordinator. At present there are efforts to develop a cell culture repository to immortalize DNA from the animals used in the sequencing project and first phase of SNP detection. Live cell lines will be provided to investigators upon request. The 5000RH panel is still available and results can be mapped automatically via web site supported by Womack lab. Web site is being updated to the 3rd generation IL/TX RH map, skipping the 2nd generation map. Water buffalo RH panel made in collaboration with Brazilian investigator. iii. Colin Kaltenbach, Administrative Advisor Very positive comments about progress in the Bovine Genome Sequencing Project. NRSP8 was praised for its role. iv. No Industry Representative comments. v. No discussion. b. Equine i. Ernest Bailey, Equine Genome Coordinator: not present ii. William Trumble, Administrative Advisor Administrative Advisor (William Trumble) spoke in lieu of Ernie Bailey. Next year Jamie MacLeod will be the equine chair, Terje Raudsepp secretary. He praised the equine research community within NRSP8. iii. Industry Representatives not present. iv. No discussion. c. Poultry i. Jerry Dodgson / Hans Cheng, Poultry Genome Co-Coordinators Jerry Dodgson: A draft genome sequence is out, described in a Nature paper. Many investigators are now finding the sequence very useful. To rectify some flaws in the sequence, NHGRI has approved funds to finish the chicken genome to the quality of the mouse genome. The second build is due out imminently. Efforts are expanding to improve the linkage map and enhance the physical map between turkey and chicken. Biggest event: a huge expansion in SNP mapping with tremendous engagement of the poultry industry. Coordinator funds were used to add birds to the group for SNP typing. This is a work in progress which will provide insights into evolution. Animals used represent birds from 75% of commercial populations world wide (Hans Cheng). ii. Administrative Advisor not present. iii. Industry Representatives not present. iv. No discussion. d. Swine i. Max Rothschild, Swine Genome Coordinator $10M (USDA) granted over the next two years for sequencing the pig genome. Industry money has gone to Sanger with sequencing under way. Larry Schook was thanked for efforts. Affymetrix chips have been made available to investigators, still have some to distribute. Oligonucleotide microarray efforts continue. Final clustering work is to be done by Christine Elsik, array to be ready for printing/distribution perhaps in May. ii. Administrative Advisor Bert Stromberg Positive endorsements of sequencing efforts. iii. Industry Representatives not present. iv. No discussion. e. Aquaculture i. Caird Rexroad (organizer) and John Liu (interim coordinator) Caird Rexroad: Reported on aquaculture workshop. This year the workshop broke into finfish and shell fish groups in the afternoon. Named next years chair (Dennis Hedgecock) and chair elect (Geoff Waldbieser). John Liu: Aquaculture is not a species, covers ~20 species of 200 cultured world wide, ~60 species in USA. Current report lacks shrimp and striped bass, which will be added later. Joint Genome Institute sequencing support: 1) Catfish - 300,000 bidirectional ESTs. 2) Tilapia - 0.1x coverage of 5 species of cichlid fishes. 3) Oysters - 300,000 ESTs and 50 BACs Tilapia, salmonids and catfish are making good progress, shell fish are lagging behind a bit most likely due to a late start. The Tilapia map has been increased by new markers and a BAC physical map. QTLs for color and sex determination are being mapped and investigators are close to identifying genes responsible. Catfish physical mapping has 6x coverage using BAC fingerprinting. An additional 57,000 BAC end sequences have been done and a microarray is now available. ii. No comments from advisor. iii. No discussion. f. Database i. James Reecy, Database Lead Coordinator Significant progress this year. Pig QTL db to be moved into other species. Support of EST clustering in various species to support microarray efforts. NRI now has RFA targeting bioinformatics. This is welcomed. Database use logged 2.5 million hits last year. Efforts continue to improve resources from a QTL centric view. Next year focus on supporting and facilitating dialog between investigators to develop and use bioinformatics tools. 2. Administrators Reports a. Colin Kaltenbach, Lead Administrative Advisor Flat funding at 99% expected this year. Stressed the importance of getting final report in on time, 60 days from PAG. There is more and more demand for impact statements; these should be included in reports submitted to coordinators/chairs. NRSP8 is held up as the model for such multi-state projects. b. Muquarrab Qureshi, Program Leader Very positive about animal genome research and the contribution of NRSP8, in particular for feedback at the federal level. Joe Jens leadership is acknowledged by and appreciated for bringing NRSP8 and CSREES to this point in terms of funding and genome sequencing in chicken, cow and pig. Thanks to Ronnie Green for his sterling efforts with the interagency working group. To NRSP8, keep up the good work and send in those impact statements. c. Peter Burfening, NRI Animal Genomics Update for NRI efforts and team. Last year Peter Burfening took over Animal Genome in CSREES. The PART program (program assessment and rating tool) was used to evaluate NRI. Review of the program has stressed accountability as the key. The logic model was used to evaluate and provide new (current) priorities and goals for the program. Funding is flat, making it difficult to fund at high levels. ~22% of proposals get funded. A recommendation from National Academy of Sciences to increase award sizes has led to a decrease in funding success rates for investigators. Now awards (when made) are not significantly cut, but fewer awards are made. Over the last 6 years 139 awards were made for $53M. This is more per project than for NRI as a whole. Peter Burfening discussed the breakdown of success rate in funding by species/group as delineated in the report. Peter Burfening is very concerned about the low success rate. Comments about panel composition: it is very difficult to find ~15 individuals that meet all the diversity requirements for panel composition. Peter Burfening discussed the process and mechanics of proposal ranking. 8% ranked outstanding in the last few years. Only 95% of these outstanding proposals were funded indicating how tight the funding situation is. To fund all outstanding and high priority proposals an additional $6.6M would be needed. To fund at a 40% level would entail a doubling of the budget (additional ~$12.6M). Taking input from NRSP8 to help prioritize funding, one example is the tools and reagents program which is now split to separate out bioinformatics. As a result of internal deliberations and not in response to species lobbying, this year only proposals from species with 5x genome sequence coverage or better will be considered. This is done to focus the program and narrow down the number of proposals. The due date is June 15; the panel manager has not yet been officially named. d. Discussion followed. Question from Noelle Cockett who questioned the effective limitation of species that can apply for funding by using sequencing data as the metric for funding. NC urged a re-visitation of the effective moratorium this imposes. Members of the audience endorsed this. Peter Burfening replied to reaffirm that the door is not shut to other species, but that the significant expense on genome sequences is a priority maker. Dissent for this view from the audience who questioned the wisdom of this approach. Peter Burfening acknowledged this objection and said that one item that is being considered is prioritizing high risk research. Max Rothschild commented that the current rule to consider applications only from 5x genome sequence organisms makes haves and have nots. He said that this is a very dangerous road that marginalizes other species. Anna Palmisano commented on success rates. She is concerned that many young scientists are not submitting to NRI. But the flat budget is a limiting factor that leads to hard choices. She solicited advice and guidance from the community. Jerry Dodgson commented that while disappointing, this (22%) funding is not worse than NIH RO1 success rate. He also endorsed the view that there should not in the future be a restriction on species restrictions as imposed by 5x rule. Anna Palmisano said that current success rate this last year is 14% compared to NSF and NIH at ~30%. James Reecy commented that the problem is not the success rate but rather the lack of sufficient funding. There were suggestions to lobby congress to change the situation. John Liu commented about the ethics of urging students and young researchers to enter a field that has no funding. He thanked CSREES for their responsiveness to the community in the past and endorsed that restrictions for grant applications based on species of >5x genome coverage should not be continued. Colin Kaltenbach suggested writing to ones congress person. 3. Suggestions for future plenary speakers for PAG Max Rothschild asked for suggested speakers. Discussion by audience about how speakers are selected and the timing for this activity. Frustration was expressed over crowding in the cattle session. Chairs need to make sure that expected attendance is relayed to organizers to make sure adequate sized rooms are provided. Scheduling issue: Species groups overlap, making it difficult to cross the species barrier. III. New Business 1. Election of Officers for 2006 Clare Gill to serve as chair next year (Dave Adelson filled in as secretary for meeting due to bereavement in Clare Gills family). Nomination for Mary Delany as secretary seconded and approved by acclamation. 2. Selection of next meeting location and date to be discussed with Mary Delany. IV. Adjournment. 5:45 pm

Progress toward Objective 1: Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation. Aquaculture Catfish: Progress in mapping the catfish genome has focused on the addition of Type I loci to genetic maps and BAC fingerprinting and end sequencing. A total of 54 genes and 26 BACs have been added to the channel catfish intraspecific genetic map at the USDA/ARS Catfish Genetics Research Unit and 350 Type I loci to the channel catfish x blue catfish interspecific map at Auburn University. An NRI Genome Tools and Resource Program was awarded to Auburn University which has resulted in 20,366 BAC end sequences (BES). BLAST analyses has identified homology to 1130 genes revealing 23 regions of conserved synteny among the catfish, zebrafish, and tetraodon genomes. Microsatellites were identified in 17% of these sequences, which will facilitate the integration of the BAC physical map with the genetic maps. At the USDA/ARS Catfish Genetics Research Unit 6X genome coverage of the CCBL1 BAC library constructed from a gynogenetic female has been fingerprinted resulting in a preliminary assembly generating 2000 contigs. Progress has also been made in the sequencing of BAC ends with 3X coverage completed to date. Oysters: Researchers at the University of Delaware and the University of Southern California are cooperating on the development of a linkage-mapping family for the Pacific oyster (Crassostrea gigas), which will be made available to the oyster community as a resource. The current focus is on mapping Type I loci using SNPs. More than 90% of the primer sets developed for C. gigas amplify in the related oyster species C. ariakensis which is an important cultured species in Asia and is currently being considered for introduction into U.S. waters owing to its resistance to the two major diseases affecting the native eastern oyster. Researchers at Rutgers University have developed 16 SNP and 53 microsatellite markers from eastern oyster (C. virginica) ESTs for use in genetic mapping. They have also constructed a preliminary genetic map for the bay scallop (Argopecten irradians) using primarily AFLP markers. Salmonids: This year a collaboration led by Washington State University at Vancouver has integrated the cytogenetic with the Nichols et. al 2003 genetic maps. The USDA/ARS National Center for Cool and Cold Water Aquaculture and the University of Guelph have developed microsatellite markers for ESTs. A BAC physical mapping project was initiated by NCCCWA, West Virgniai University, and UC Davis. Members of NRSP8 participated in two workshops discussing sequencing a salmonid genome. The first Workshop was held in Oslo, Norway during October 24-26, 2005 to discuss sequencing the Atlantic salmon genome, while the second Workshop, a Tri-lateral Workshop (US/Canada/Norway) hosted by the Royal Norwegian Embassy in Washington DC November 2 - 3, 2006 was entitled "Marine Fish Aquaculture: Genomics. Striped Bass: Collaboration between researchers at North Carolina State University, Kent SeaTech Corporation, and the USDA National Center for Cool and Coldwater Aquaculture in Kearneysville, WV has resulted in the development of 498 microsatellites markers for use in genome mapping and selective breeding of striped bass (Morone saxatilis). The majority (90%) of these markers were successfully t amplified in the white bass (Morone chrysops), which is important to the industry in the production of the hybrid. Tilapia: A second generation genetic linkage map was produced in at University of New Hampshire containing 550 markers (Lee et al., 2005). A physical map has been constructed by BAC fingerprinting resulting in a tilapia physical map with 3,000 contigs (Katagiri et al., 2005). Cattle Texas A&M University continues to lead an international effort to build bovine radiation hybrid maps. RH panels are freely distributed to investigators world wide, data can be analyzed with the first generation RH map of the cattle genome (Band et al. 2000) at . A third generation comparative map 3000 containing BAC end sequences has been published (Everts-van der Wind et al, PNAS 102:18526-18531, 2005). The BESs selected for mapping are ~1 Mbp apart on the human chromosomes as determined by BLASTn analysis. The map has 3,484 ordered markers, of which 3,204 are anchored in the human genome. Two hundred-and-one homologous synteny blocks (HSBs) were identified, of which 27 are newly discovered, 79 are extended in length, 26 were formed by newly found breakpoints in 18 previously defined HSBs, and 23 are the result of fusions. The comparative coverage relative to the human genome is ~91 percent, or 97 percent of the theoretical maximum. Efforts at TAMU have been directed towards identification, validation and analysis of variation in the 3 Mb of genomic sequence that constitutes the bovine major histocompatibility complex (BoLA). The primary goal of this research was to determine the haplotype structure of BoLA to provide a more efficient platform for analysis of inherent disease resistance in cattle. More than 400 simple sequence repeats in BoLA have been identified from the genomic sequence, 22 of which useful variation in the BoLA IIb region (~400kb). An area of high recombination in the region near the proteosome locus, PSMB9 has been identified. Equine During 2005 significant numbers of new markers were added to the half sibling linkage map (766 markers spanning 3740 cM, Penedo et al, 2005), the full sibling linkage map (742 markers spanning 2772 cM, Swinburne et al., 2006, Genomics 87: 1-29) and the RH map for the horse. In addition, significant efforts were made to integrate the existing horse genome maps. Those efforts are summarized in the Horse Map Viewer (http://www.vgl.ucdavis.edu/equine/caballus/). Poultry The University of Michigan has been generating avian BAC contig maps and integrating them with the respective linkage maps. Efforts have also recently begun to develop a BAC contig map for the turkey, along with a comparative turkey-chicken map. The University of Minnesota has continued to expand turkey genetic mapping by expanding the genetic map to include 438 linked markers representing a 39% increase in marker number and increases marker density to an estimated at 5 cM. The USDA-ARS Avian Disease and Oncology Laboratory coordinated the screening of 3072 SNPs on 2580 experimental and commercial birds resulting in new genetic markers and providing a high confirmation rate of the ~3 million in silico chicken SNPs. This generated a much higher density genetic map that has enhanced the second genome sequence assembly, and demonstrated that a high density SNP map can identify tightly linked markers for simple and complex traits. North Carolina State University further characterized the MHC B locus at the sequence level in numerous layer lines to provide a reproducible means to determine B haplotypes. The microsatellite marker LEI0258 known to be physically located within the MHC, was sequenced resulting in the identification of 28 distinct haplotypes. This information will be a useful tool to identify new MHC haplotypes in outbred populations of chickens. Sheep A joint collaboration has been established between Utah State University, The Institute for Genomic Research (TIGR), Australian Wool Innovation, Meat and Livestock Australia, AgResearch (New Zealand), and Genesis-Faraday (UK), with support of the Alliance for Animal Genome Research, to obtain and characterize end-sequences from the CHORI-243 BAC library. In addition, these sequences will be ordered against the soon-to-be-completed bovine genomic sequence, providing a whole genome physical map for sheep. The sequences will also be incorporated into the emerging ovine RH map. The sequencing portion of the project is complete, with 376,493 BAC-end sequences (BES) from 193,073 BAC clones hazving average insert size of 184 kb. A total of 258,650,691 bp sequence (approximately 6% of the genome) was produced from this project. A collaborative project between Utah State University and Texas A&M University has produced an ovine whole-genome radiation hybrid (RH) 5,000-rad panel consisting of 90 clones, with retention frequencies between 15-40%. To date, Utah State University has 257 markers selected from the autosomes have been screened against the panel; 131 (51%) of these markers produce resolvable patterns and will be typed in duplicate across the panel. Swine New gene markers continue to be identified and mapped; some integration of the maps continues as QTL maps are expanded. However, no new large-scale maps have been published recently. In total there are over 1,588 genes and 2,493 markers in the database. The physical map is also growing quickly and there are now nearly 6,000 genes and anonymous markers; thanks to a very useful somatic cell hybrid panel from INRA and two radiation hybrid panels (IMpRH7000 from INRA and the U. of Minnesota; IMNpRH12000 from INRA, U. Nevada-Reno and the U. of Minnesota). The Swine Genome Sequencing Consortium (SGSC) continued its efforts this past year and considerable advances have been made. Meetings have occurred at PAG and in the UK. The meetings included individuals from a number of countries including the US, France, Britain, Denmark, China, Korea, and Japan. Representatives from the USDA, the Alliance for Animal Genome Research and several of the authors of the Pig Genome Sequencing White paper participated. Funds have been committed by the National Pork Board, Iowa Pork producers Association, University of Illinois and Iowa State University, with other groups likely to follow. USDA committed a total of 10-12 million and the Sanger Institute has also participated and will commit considerable funding. Progress towards Objective 2: Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits. Aquaculture Catfish: Researchers at the University of Mississippi Medical Center have completed the sequencing of 6 BACs covering part of the catfish immunoglobulin heavy chain locus. This group has continued characterization and functional studies of catfish immune molecules, such as, T Cell Receptors and their accessory molecules CD4 and CD8, Novel Immune Type Receptors, Leukocyte Immune Type Receptors (LITR), Immunoglobulin D, FcRs and the B cell accessory molecules CD79a and 79b. Monoclonal and polyclonal antibodies specific for various LITRs, IgD, CD79b and IpFcR have been produced and are being characterized. At Auburn University much effort was made to characterize innate immune genes and analyze their expression in the resistant blue catfish as compared to the susceptible channel catfish after infection with the bacterial pathogen causing enteric septicemia of catfish (ESC). A total of 26 CC chemokine genes, 6 CXC genes, 4 antimicrobial peptide genes, interleukin-1 beta gene, 23 selenoprotein genes, 6 toll-like receptors, and a few dozens of other genes were completely sequenced, mapped to BACs, and expression analyzed. Work at the USDA/ARS Catfish Genetics Research Unit was focused on the development of a 19,000 gene (oligonucleotide) microarray developed (via Nimblegen). The microarray was tested on Lipopolysaccharide-exposed fish and initial results demonstrated good correlation between levels of hybridization to the microarray and real-time PCR expression levels for several candidate genes. Currently tests are being conducted to observe differential expression of these potentially important immune receptors in various catfish families and strains after exposure to pathogens. Also, work characterizing catfish growth hormone and the various steroidogenic factors involved in catfish growth and reproduction continues. A patent was awarded for a real-time PCR assay detecting Edwardsiella ictaluri in channel catfish. Oysters: Researchers at the University of Southern California have mapped candidate genes for growth heterosis; more samples for expression profiling and QTL-mapping from F2 populations were obtained in summer 2005. Researchers at Rutgers University have mapped twelve disease/mortality-resistance QTL in two families of the eastern oyster; at least seven of the twelve QTL are independent of each other. These results indicate that resistance to Dermo-infection or summer mortality is affected by at least seven quantitative trait loci. Salmonids: The number of ESTs for rainbow trout and Atlantic salmon increased to 239,512 and 186,364, respectively. These sequences represent transcripts from tissues and lifecycle time points not previously included in the database. Microarrays are increasingly being used to study responses to stress and chemical contaminants as well as basic biological processes. Shrimp: As a part of the USDA funded project "Shrimp gene discovery: Enlarging the EST collection for the Pacific white shrimp, Litopenaeus vannamei" (NRI Grant #2005-35205-15459), six high quality tissue specific cDNA libraries have been constructed and analyzed for depth and redundancy, with 1000 EST being collected from each library to date. Redundancy depletion and full sequencing of a minimum of 120,000 ESTs (20,000 from each library) is expected to be complete in the coming year. A first generation microarray containing in excess of 3000 unigenes has been printed and initial validation has been completed. These microarrays and are currently in use in the first round of experimental research. It has been discovered that long dsRNA of virus-specific sequence evokes a potent and specific anti-viral immune response. Continuing research in the area of antimicrobial peptides and their importance in shrimp immunity has yielded data on the structure of the Penaeidin gene family, its control elements, and specificity for microbial targets. Striped Bass: Several collaborations were established with industry members Keo Fish Farms and Kent SeaTech Corporation to extend ongoing selective breeding efforts conducted at the North Carolina State University Pamlico Aquaculture Field Laboratory. These selective breeding studies have led to the identification of broodstock showing superior growth characteristics in both extensive pond-based and intensive production systems. Tilapia: Researchers at the University of New Hampshire have mapped the tilapia gene for red skin color leading to positional cloning of tilapia mutation to a single BAC containing 2 genes. Great progress was also made in mapping and characterization of the sex determining mechanism in several species of tilapia. Cattle Dwarfism has been a problem with American Angus cattle for decades. Dwarves are inefficient in beef production systems and are undesirable for Angus breeders. Researchers at Iowa State university have fine mapped the dwarfism locus to bovine chromosome 6 (BTA 6). On further analysis of candidate genes in the region, they have discovered a mutation in bovine PRKG2 gene that introduces a premature stop codon to the open reading frame. The mutation is in 100% concordance with dwarf, carrier and wild-type status. The detection of causal mutation or closely linked markers for dwarfism is of great use to Angus producers as this gives them the ability to detect carriers in breeding populations and the potential to eliminate dwarfism from their herds. Researchers at New Mexico State University have identified polymorphisms within the growth hormone gene that seem to be a significant source of variation in average daily gain and carcass traits in Bos Taurus or Bos TaurusX Bos indicus composit cattle. They have identified that polymorphisms in the genes of the GH axis or its transcriptional regulators differ among Angus, Brangus or Brahman cattle. A QTL on chromosome 6 affecting milk fat and protein concentration was previously localized to a 4-cM confidence interval, centered on the microsatellite BM143. In collaboration with ARO, the University of Illinois has characterized the genes and sequence variation in this region and identified common haplotypes spanning five polymorphic sites in the genes IBSP, SPP1, PKD2, and ABCG2 for two sires heterozygous for this QTL (Cohen-Zinder et al., 2005). Expression of SPP1 and ABCG2 in the bovine mammary gland increased from parturition through lactation. SPP1 and all the coding exons of ABCG2 and PKD2 were sequenced for these two sires. Equine ESTs were identified by laboratories at Cornell University, University of Kentucky and Texas A&M University and the data pooled with the objective of creating a microarray tools for investigating gene expression in horse tissues. Over 45,000 ESTs were evaluated and approximately 10,000 unique genes were identified for incorporation into a microarray chip. Poultry The USDA-ARS Avian Disease and Oncology Laboratory continues to work on genetic resistance to Mareks disease (MD). Reassessment of the ADOL 6 x 7 F2 MD resource population confirmed at least 5 of the 15 previously identified QTL, has revealed 2 new QTL, and identified 2-way epistatic interactions that shared a QTL on chr1. Efforts are underway to identify optimal MD virus challenge conditions to characterize the lines. Polymorphisms in avian leucosis virus (ALV) receptor genes tva and tvb that confer genetic resistance were confirmed, and Pyrosequencing assays developed. Iowa State University and Hy-Line International have cooperated to conduct candidate gene and genome scan analyses in an advanced (F6) intercross between two partially inbred commercial Leghorn lines that differed in resistance to Marek's disease to detect QTL for survival following challenge with highly virulent Marek's disease virus. A total of 11 putative QTL were identified including a polymorphism in the Rh-associated glycoprotein gene which was found to be associated with survival. The University of Delaware has further mapped the chromosome 1 QTL that affected oocyst shedding during coccidiosis infection of broiler chickens. An interesting candidate gene is lymphocyte activation gene 3 (LAG-3; CD223) which was simultaneously identified in DNA microarray studies to be reduced in expression after Eimeria infection of chickens. The lympocyte-specific expression of LAG-3 has been confirmed by RT-PCR and demonstrated a rapid down-regulation of LAG-3 with coccidial infection. The University of Arkansas has characterized the vasotocin II receptor (VT2R) that was recently cloned and sequenced in the chicken using immunocytochemistry (ICC) and was found predominantly in the cephalic region of the anterior pituitary, associated with cell membranes of specific pituitary cells. Research at the University of Arkansas has also been aimed at identifying the underlying genetic and physiological causes of sperm degeneration to better understand the origins of the defect and develop genetic tests that can be used to increase male fertility. Work to define the identity and function of genes within the major histocompatibility complex (MHC) in the chicken continues at the City of Hope Medical Center with progress made on three fronts. First, CD1 genes (one active and one likely a pseudogene), encoding MHCI molecules that present lipid-type antigens to T cells, were mapped to the MHC region. Second, Y MHCI molecules were shown to be alloimmunogenic and well-expressed on blood cells providing data supporting the likelihood for a role of Y MHCI in immunity. Lastly, BG1 has been identified as a candidate gene influencing the incidence of Mareks disease in chickens. In mammals, natural killer (NK) cell C-type lectin receptors are encoded in a gene cluster called nature killer receptor gene complex (NKC). At Texas A & M University two chicken C-type lectin-like receptors were identified in a region on Chromosome 1 that is syntenic to the mammalian NKC region. The region containing NK C-type lectin like receptors in GGA 1 has been previously identified to be associated with disease resistance in chickens. The University of Maryland has performed transcriptional profiling screens using their cDNA microarrays to identify genes that respond directly to glucocorticoids in cultures of anterior pituitary cells. Six candidate genes for mediating the effects of glucocorticoids on expression in the anterior pituitary were identified. Gene expression profiles in the anterior pituitary and hypothalamus were also compared between lines of chickens genetically selected to have high or low abdominal fat identifying the same six candidate genes. The 5'-flanking region of these candidate genes are currently being sequenced in a Fat X Lean reference population in an attempt to identify genetic markers associated with differences in body fat. Virginia Tech has been studying the transport of nutrients (amino acids, peptides and sugars) across the intestinal epithelia, which is mediated by membrane bound transporter proteins. The abundance of mRNA for these transporters was determined by real time PCR and was found to vary depending upon the intestinal segment and the time of development (embryonic day 20 to 7 days post hatch). This work has shown that nutrient transporters are differentially expressed in a temporal and spatial manner. The efficient production of germ line chimeras using PGC transfer into early embryos has been hampered by the limited availability of PGCs obtained from blood and the early germinal ridge. North Carolina State University has produced germ line chimeras by using sorted gonadal germ cells when injected into stage X, germinal crescent and stage 17. This observation taken together with the scientific literature indicates that germline chimeras can be made using any source of PGCs up to stage 27-28 as the donor cells and any stage of embryo development up to stage 17 can be used as a recipient. Iowa State University maintains many unique chicken lines (highly inbred; MHC- congenic; closed populations; advanced intercross lines) for research. These lines serve as valuable resources for identifying genes of economic importance. Semen from all of the highly inbred and partially inbred lines was collected at ISU, and the staff of the National Animal Germplasm program cryopreserved the samples on site and then transported them to Ft. Collins for long-term storage. The feasibility of detection and mapping QTL in breeding populations with a high-density marker map using population-wide linkage disequilibrium was investigated by simulation at Iowa State University. Designs that allow adequate power and mapping precision were developed. Designs and statistical models for global gene expression analysis using micro-arrays based on pools of mRNA samples from multiple individuals were also investigated. For a given total number of individuals and arrays, simulated pooling resulted in loss of power compared to arraying all samples individually but under some conditions, loss of power was small and it was possible to find a low-cost pooling design with power close to that of an individual design. North Carolina State University has continued to develop new microsatellite markers mining the genome sequence data for use in fine-mapping QTL regions. This data indicates that there is at least one usable microsatellite marker every 40,000 bp and at least one polymorphic microsatellite marker every 115,000 bp in commercial chicken populations. Sheep A collaboration including Utah State University, Purdue University, USDA/ARS, and the University of Liége has identified a core cluster of imprinted genes (DLK1, GTL2, PEG11, and MEG8) located at the distal end of ovine chromosome 18. Using quantitative PCR, they have shown that the inheritance of the callipyge (CLPG) SNP in cis alters the expression of genes with a paternal allele-specific expression (DLK1 and PEG11) and maternal allele-specific expression (GTL2 and MEG8) in muscles that undergo hypertrophy in a genotype and age specific manner. Also, the effects of age and genotype are also significant for expression of the CLPG1 RNA that is transcribed from the intergenic region between DLK1 and GTL2 and spans the CLPG SNP. Gastrointestinal parasites have a profound effect on sheep production. In a collaborative study between Utah State University and Louisiana State University, a genome-wide QTL scan was implemented to identify chromosomal regions in the ovine genome that play a role in resistance to gastrointestinal parasites. Suggestive QTLs have been identified on ovine chromosomes 1, 6, 9 and 19. A large-scale EST sequencing project for goats has been implemented at Virginia State University. To date, sequences have been obtained from about 10,000 clones from a cDNA library constructed from goat uterine/embryonic tissues collected between days 5 and 8 pregnancy. Swine QTL have continued to be reported on all chromosomes for many traits, often identifying imprinted QTL. Candidate gene analyses have proved 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. Progress towards Objective 3: Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information. Researchers at universities and other research institutions are conducting multifaceted research to develop bioinformatics programs and database resources for livestock species and this research is supported in part by the NAGRP. Continued efforts to inform scientists and lay persons about genome databases have been made and many new entries are now available at www.animalgenome.org. The NAGRP genome databases were accessed over 2.2 million times by over 140,000 users world-wide. A bioinformatics program (Expeditor) was developed to design primers for livestock species. This program takes advantage of the information from the human genome and applies it to livestock cDNA. This program can be used at http://www.animalgenome.org/~hu/expeditor. With the rapid progress in genetics and genomes, there are an increasing number of genetic analysis software programs. Each program has its own pre-defined scope, assumptions, and applicability. With the large number of available programs, it can be a challenge to identify suitable options. Thus, we have created a database and related tools to effectively archive, annotate, and manage the wealth of the software information so that researchers can easily identify, locate, and retrieve appropriate software. We have also introduced ontology concepts and tools to manage the proper classification and feature annotation of this resource. To date, there are 331 software programs listed in the category of genetic analysis. We plan to add other genomics and computational biology software in the near future. As in past years the Pig Genome Database has received considerable updating. There are over 1,254 citations in the database describing 4081 loci, over 602 clone entries and 96 library entries. This last year the US Pig Genome database had over 149,600 users making more than 3 million hits. New QTL continue to be curated into the Pig QTL Database. Up to date there are 1,263 QTLs in the database representing 236 pig traits. In addition, new functions have been added to the PigQTLdb tools to align pig RH map-human comparative maps, and pig BAC physical maps, against pig QTL. It can be seen at http://www.animalgenome.org/QTLdb/. Database activities were transferred to the Bioinformatics Coordinator. The NAGRP database has a newly developed Porcine QTL database that graphically displays QTL from over 70 experiments and can be used at http://www.animalgenome.org/QTLdb/. All information has been cross-listed at NCBI and can be viewed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&term=pig+QTL. Over the past year, links have been added to the viewer allowing researchers to visualize QTL on the human genome. Texas A&M has worked to cluster and annotate porcine and bovine EST clusters. This work supports the development of a new long-oligo arrays in collaboration with the Swine Genome Coordinator and the Bovine Oligo Microarray Consortium. The marine genomics group at the Holling Marine Laboratory and MUSC maintains www.marinegenomics.org for the archiving of shrimp EST and microarray data, and as a resource for on-line tools that can be used in the analysis of genomic and transcriptomic data, which are being used to archive and analyze shrimp metagenomic and microarray data. In addition, in collaboration with IFREMER at the Universite de Montpellier, a standardized nomenclature database for Penaeidin anitmicrobial peptide has been developed. Tools for comparative mapping are available from the University of New Hampshire (www.hcgs.unh.edu/comp). They include - comparative maps among cichlids, comparative maps among fishes, mapping of cichlid ESTs onto genome sequences of Tetraodon and Fugu. Personnel at the University of California-Davis are developing a cattle genome database and browser compiling QTL and sequence information as a tool for comparative mapping and gene discovery. Currently the database contains 580 QTL entries from 109 traits and 295 molecular markers (69% mapped to human. The database is in MySQL with a Common Gateway Interfaces (CGI) front end. Sequences from the ovine BAC end sequencing project are now publicly available at http://www.ncbi.nlm.nih.gov/genome/guide/sheep/index.html. Matches of the ovine BAC-end sequences to the bovine and human sequences and identity of clones can be obtained through a database established by CSIRO (Australia) at http://www.livestockgenomics.csiro.au/SheepGenomics/. The Bovine QTL viewer (http://bovineqtl.tamu.edu/) developed by researchers at Texas A&M University has been updated and linked to the 6.2x build of the bovine genome to show existing SNPs and gene models.

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