Brief Summary of Minutes of Annual Meeting

I. Call to order at 4:30 pm by Dr. Bhanu Chowdhary, NRSP8 Technical Committee Chair a. Dr. Max Rothschild made a motion to approve the last meetings minutes, second by Dr. Joe Cassidy and approved by a voice vote II. Old Business a. Summary of the Executive Committee Meeting i. In 2006 the committee meeting must return to an early Sunday morning breakfast meeting at 7:00am ii. All species workshops must finish by 4:00 pm Sunday so participants may attend the General Membership Business Meeting from 4:30 to 6:00 pm b. Species Reports i. Equine-Dr. Ernest Bailey 1. NRSP8 Objective 1. Most efforts have focused on adding to linkage and radiation hybrid maps 2. NRSP8 Objective 2. Limited activity in this area, four institutions are working on a plan 3. NRSP8 Objective 3. Genome Viewer at UC Davis integrates linkage information 4. Workshop participants will meet in Dublin in July 2006 to discuss mapping, functional genomics, and their applications. ii. Poultry-Dr. Jerry Dodgson 1. This year the chicken genome sequence was published in Nature 2. This was the first post sequence workshop, topics included: a. Draft sequence has some miss-assemblies and places that require further annotation b. Use of sequence to improve genetic analyses c. Application of chicken sequence to other poultry iii. Cattle -Dr. James Womack 1. Draft sequence of 3.3X coverage was completed this fall 2. Now focus is on adding animals other than the original Hereford 3. Will keep fibroblast cell lines for these animals and others 4. The ArkDB server is no longer maintained at TAMU, moved to ISU 5. Online radiation hybrid mapping at TAMU using first generation RH map, will soon update to a more recent version 6. Somatic Cell hybrid panel still available 7. IBRP usage has dropped off significantly iv. Sheep-Dr. Noelle Cockett 1. An NRI Tools and Reagents Grant was awarded to Dr. Cockett and Dr. Womack to construct an ovine radiation hybrid panel, now using coordinators funds to distribute 2. this will strengthen comparative maps between species, Dr. Harris Lewin will map markers 3. CHORI 243 BAC library constructed by Pieter DeJong available since last year, also gridded filters, Dr. Cockett purchased some with Coordinators funds for distribution 4. BAC end sequencing project is a collaborative effort, USDA has also funded through NRI Tools and Reagents. Dr. Cockett can do .5X of the library, she leveraged funding for the rest through other international sources which will result in full library, work to be done at TIGR 5. collaboration with national animal germplasm group has been set up to collect/conserve germplasm in US. Attended meeting in Cheyenne, great info for genetic diversity study, will supply this group with primers to study their collections and use this germplasm for SNP validation v. Swine-Dr. Max Rothschild 1. design oligos for a 13K oligo array, sent to 35 labs, primarily in US, also Europe and Asia 2. Discussed a second generation oligo microarray 3. PigQTLdb on angenmap website 4. Expeditor primer design tools, other database tools 5. Swine Genome Sequencing Consortium, worked with industry to raise funds, big news is that USDA/CSREES will issue an RFA in the ball park of $10 million, possibly $1 million more from ARS, matching funds from Sanger, puts them much closer to goal of $30 million, hope to start sequencing in summer 2005 6. Industry was well represented at the workshop by Sygen and Monsanto, who are actively using molecular genetic tools from this effort vi. Aquaculture-Dr. John Liu 1. The Aquaculture group is very complex, with 6 primary species and additional sub species, includes an executive committee. 2. This year 3 species coordinators Program Chair and Chair Elect changed 3. Four proposals for sequencing project were submitted to the JGI Community Sequencing Program (trout, catfish, oyster, tilapia) oyster and tilapia scored well. 4. Aquaculture species need to set priorities 5. Two white papers were developed, one to addressed to save the NRI Tools and Reagents Program, a second distributed to other funding agencies concerning the genomic enablement of these species 6. The Aquaculture Genome website was developed and moved to ISU this year. 7. Dr. Caird Rexroad summarized the workshop report including plenary speakers, student presentations, and evening poster session vii. Database-Dr. James Reecy 1. work on objective to centralize resources for all species with bioinformatic expertise to ISU 2. team involves Dr. Chris Tuggle, Dr. Max Rothschild, Dr. Sue Lamont, and Dr. Zhiliang Hu 3. The species coordinators serve as a consulting board 4. The ISU database is a place to put programs used by all, also resources like maps, etc& 5. PigQTLdb-a database for pig QTL information, can do other species 6. Expeditor-primer design software for SNP discovery 7. in-house blast server 8. The website and Angenmap both continue to increase in number of hits and usage 9. This year the group will assist in pig oligo microarray construction, would like to make pipeline for other species c. Administrators Reports i. Margaret Dentine, Lead Administrative Advisor 1. NRSP8 is a model of how support program should work a. Democratic process, funding spread around, successful workshops 2. New review for NRSPs in experiment station system, NRSP8 received a good review and did get the budget requested. This is significant as funding comes from directors budgets 3. We all bear responsibilities to work with coordinators 4. Project will be up for review again, it is important to do a good job ii. Dr. Dr. Muquarrab Qureshi, USDA/CSREES National Program Leader 1. Thank species coordinators and executive committee for good job, help to accomplish mission, of advancing knowledge 2. Strategic goals-enhance efficiency of agricultural production systems, including genetics, under programs 303 and 304, genetics and genomics 3. Help meet performance based budget progress 4. High priority area for USDA 5. $15 million per year 6. pleased with updates in meeting including sequencing efforts 7. NRSP8 received excellent reviews, complemented for adding aquaculture 8. funded Shrimp Genome Consortium 9. hosted Animal Bioinformatics Workshop 10. NRI RFP 2006 planning is underway 11. 2005 budget is flat compared to previous year III. New Business a. NRSP8 Business Meeting schedule-see above b. USDA/CSREES workshop on Animal Genomics held in September 2004, summary by Dr. Ronnie Green i. Summary report given in swine meeting, copies available ii. Workshop came about by charge by Dr. Joseph Jen, USDA Undersecretary for Research, Education and Extension. iii. Once we are passed sequencing genomes of major species, what next? iv. Dr. Green and Dr. Qureshi were asked to put workshop together to ask scientist and administrators what to do v. Asked subset to stay and brief the Interagency Working Group on the workshop, the working group was pleased to see scientists priorities of long term needs for animal genomics. vi. A summary of the workshop will be made public and published in Animal Genetics in March vii. Also charged to take out strategic planning exercise in this effort in 2005, involving all agencies in animal genomics, will do in 2nd and 3rd quarters of this year viii. Interagency report on NSTC website , have 2003 report now, 2004 soon c. Animal Genome Tools and Reagents Program-future prospects i. Discussion initiated by Dr. Anna Palmisano, USDA/CSREES Deputy Administrator 1. NRI is the largest competetive program in USDA 2. Now starting 2006 planning 3. Need help setting priorities-How can we make the greatest impact? 4. Need to develop linkages with other agencies, but limit overlaps 5. In FY06 planning we need to think long term approaches 6. Think big, think about more comprehensive approaches to animal genomics portfolio at CSREES 7. Question-Dr. Bob Chapman-We have an opportunity to think big, how about incorportative ecogenomics, as all of our species have environmental impacts. Answer-CSREES is working on a program for FY06 concerned with ecogenomics, mostly at the microbial level. Also, the Natural Resources group is thinking about ecogenomics. 8. Comment-Dr. Jerry Dodgson-on the importance of Tools and Reagents. Response-CSREES needs to know the priorities for Tools and Reagents for this group. 9. Comment-Dr. Max Rothschild-for swine SNPs are a high priority not funded in pigs, have for chicken and cattle. So we must prioritize not between species, but within. Response-to increase success rate may require a better, more focused RFP. 10. Comment-Dr. John Liu-Tools and Reagents has generated tools and science, still need tools for Aquaculture species, need to apply different criteria to different species. Response-group needs to articulate needs. 11. Comment-Dr. Bhanu Chowdhary-Species coordinators need to conduct prioritization. Response-Asked to provide input to Dr. Qureshi and Dr. Brayton. 12. Summary-to impact the planning process submit comment in next 2-3 months, remember to think long term. d. Motion by Dr. Noelle Cockett to include goats on the Cattle/Sheep committee. i. Not a request to re-allocate funds, goats would be a subcommittee of sheep ii. Second by Dr. Max Rothschild iii. Discussion-Virginia State, Valley State, and Prairie A&M, 1890s schools, want to move towards genomics to study traits iv. Passed voice vote e. Election of officers for 2005 i. Cattle/Sheep committees turn to nominate-nominate Dr. Clair Gill ii. Second by Dr. Max Rothschild iii. Passed voice vote f. Other i. suggestions for future plenary speakers for PAG on animal genome side, send to Dr. Hans Cheng or Dr. Max Rothschild IV. Adjournment 5:53 pm Respectfully submitted, Caird E. Rexroad III for Thomas Kocher, Co-Chair Overall attendance to the NRSP-8 species workshops: 65 (Aquaculture), 56(Cattle & sheep), 51 (Horse), (Poultry), 97 (Swine).

For a complete report, please see: http://www.wisc.edu/ncra/NRSP8-2004-SAES422Link.doc Progress toward Objective 1: Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation. Aquaculture. Good progress has been made toward reaching objective 1 among aquaculture species in 2004. The current state of aquaculture genomics include availability of relatively high-density genetic linkage maps from Atlantic salmon and rainbow trout (with over 1000 markers), moderate density linkage maps for tilapia and catfish (with several hundreds of markers), and framework linkage maps of for oysters and shrimps. BAC-based contigs have been established for Atlantic salmon and tilapia, but are lacking for catfish, rainbow trout, striped bass, shrimps, and oysters. In spite of the lack of one or the other maps, efforts were devoted to enhance and integrate these maps as detailed below: Cattle. Jim Womack from Texas A&M University gave a detailed presentation titled "Highlights of the bovine sequencing project. He reviewed that discussion to sequence a bovine genome occurred as early as 1993 by NRSP-8. Much of the initial sequencing effort is occurring at the Human Genome Sequencing Center at Baylor College of Medicine in Houston, TX. Richard Gibbs and George Weinstock are directing these efforts and a ~3X working draft was published in October of 2004 and is available at Genbank. The animal resources from this project were derived from the historic linebreeding Hereford project at the Fort Keogh United States Department of Agriculture  Agriculture Research Service (USDA-ARS) station in Miles City, Montana. A Bacterial Artificial Chromosome (BAC) DNA library was originally created from tissues of the bull L1 Domino 99375 and the whole genome shotgun sequences were derived from DNA extracted from the white blood cells of his daughter, L1 Dominette 01449. Dominette was selected since her sire was used to create the BAC library and because of the concept that sequence assembly could be made easier working with sequences from animals with similarities in their genetic background. Other contributions to this project now include sequencing within other breeds such as Holstein, Angus, Brahman, Jersey, Limousine and Norway Red. Some of these other efforts include SNP mapping as well as ~10,000 full-length mRNA sequences to be provided by Genome Canada. A 7 to 8X coverage map is expected by late summer of 2005. Other mapping efforts were presented by H. Lewin of the University of Illinois. In brief, a second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map as well as to sparsely populated map intervals. Discussion also occurred regarding an international consortium formed to create a sequence-ready comparatively anchored bacterial artificial chromosome (BAC) map of the cattle genome. Horse. The resources now used most frequently for equine genome mapping include a 5000 rad horse x hamster whole genome radiation hybrid panel, a collection of stallion-based half-sib families comprising 500 offspring, and a pedigree in which a single stallion sired over 60 conceptuses from two sets of identical twin mares. Two new genetic linkage maps are in the publication process. The first contains 766 markers on the half-sib families (combined with previous maps from other families) with a single linkage group on all autosomes, and the second contains 745 markers on the 3 generation full-sibling family and reports a single linkage group on all autosomes plus the X. Microsatellite markers continue to be developed and mapped on both resource populations. Gene markers from individual human chromosomes, as well as markers from across the genome, are being mapped on the RH panel, frequently accompanied by FISH localization. Many microsatellites are also being mapped on the RH panel. More than 2,500 markers have been typed on this panel and the goal is to soon have a greater than 3,000 marker RH and comparative map. Dense (greater than 1 marker/Mb) maps are now in process for many of the autosomes as well as the X and the Y. The two genetic linkage maps, as well as the RH map are becoming increasingly integrated through the mapping of common markers on all three resources. In addition to the mapping efforts, over 2,000 BAC end sequences comprising 1.8 Mb of sequence have been collected and being used for prediction of gene content and comparative sequence alignment with human and other species, as well as for selected inclusion on the RH map. Poultry. High resolution poultry genome maps. The Reference Linkage Map(s). Numerous labs have cooperated in mapping DNA-based polymorphic markers by genotyping samples from the same two international reference crosses, the Compton population (Bumstead and Palyga, Genomics 13, 690-697, 1992), and the East Lansing population (Crittenden et al., Poultry Science 72, 334-348, 1993). This map has been enhanced by genotyping of a third cross, the Wageningen population, by Martien Groenen and colleagues (Groenen et al., Genomics 49, 265-274, 1998). A consensus map based on all three map populations has been published (Groenen et al., Genome Res. 10:137-147, 2000). Updates bring the number of markers on the consensus map to 2204, placed into 51 linkage groups, covering nearly 4000 cM (International Chicken Genome Sequencing Consortium, Nature 432:695-716, 2004). The East Lansing map has expanded to 1276 markers on 42 linkage groups (other evidence places E46 on GGA2 and E66 on GGA5, but there is not enough statistical support in our map alone to establish these linkages). This map includes 326 mapped genes. In connection with the genome sequence, the Beijing Genomics Institute randomly sequenced 0.25X, each, of a broiler, layer and Silkie genome, generating 2.8 million potential SNPs for future high resolution linkage mapping experiments (International Chicken Polymorphism Map Consortium, Nature 432:717-722, 2004). Sheep. (Develop high resolution comparative genome maps): NRSP-8 Sheep Coordinator funds have contributed to the development of an ovine radiation hybrid (RH) panel in a collaborative project between Utah State University and Texas A&M University. Ninety clones with retention frequencies between 15-40% have been selected for inclusion in the 5,000 rad RH panel. Large DNA preparations have been made for the 90 clones and the panel has been distributed to Dr. Tom Goldhammer, Research Institute for Biology of Farm Animals, Dummerstorf, Germany, and Dr. John Williams, Roslin Institute, Edinburgh, UK. An on-line, real-time comparative database being developed at Texas A&M University will be used for web-based transmission of mapping data on the distributed ovine RH panels. Database displays will include ovine RH maps of each chromosome that are cross-referenced to homologous human and bovine chromosome segments, with lines between orthologous markers indicating internal rearrangements. The goal is to type the ovine panel with 500 microsatellite markers that have been mapped on the ovine and bovine linkage maps, as well as 500 ESTs developed from ovine and bovine cDNA sequences with known locations on the human genome map. These data will be used to develop a framework/comprehensive RH map for sheep. Swine BARC and Baylor Univ researchers, with the ISAG SLA committee, established an internationally recognized nomenclature to identify and classify SLA class I gene polymorphisms. This will serve as a basis for determining critical genetic effects on infectious disease and vaccine responses. They have made data fully accessible at an international website, the IPD-MHC Sequence Database website: www.ebi.ac.uk/ipd/mhc/sla/nomenclature.html. A large number of genes continue to be identified and mapped by ISU researchers. An emphasis has been made (and will continue to be made) on genes that improve the comparative map as well as in connecting the genetic and physical pig genome maps. Several new genes that may be important QTL are being mapped by ISU researchers. These include genes associated with cured meat quality and sow longevity. QTL for several meat quality traits have been discovered. Additional fine mapping is underway and positional candidate genes are being considered. Mapping of over 400 comparative loci to pig chromosomes SSC1, 4, 7, 8 and X adds additional information to comparative maps. Progress towards Objective 2: Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits. Aquaculture. In 2004, great progress has been made in the area of transcriptome analysis using ESTs. A summary of current available ESTs in various aquaculture species is listed below. These ESTs has allowed the development of microarrays in various species as detailed below. Species Current ESTs Approximate unique sequences Rainbow trout 160,816 50,773 Atlantic salmon 120,000 40,000 Catfish 45,000 30,000 Oyster Crassostrea gigas 3,300 Crassostrea virginica 9,200 5,900 Shrimps 9,400 3,300 Tilapia 1,700 Striped bass <500 The largest progress in this area was made with salmonids. A 16,000 gene array has been developed by GRASP using salmon and trout EST data sets. This array has been tested for use in various salmonid fishes. The array has been used to study developmentally regulated genes and genes induced under various environmental conditions. Cattle. Several universities reported progress in this area. In brief, these reports included advancements in understanding of genes regulating milk production traits, muscle development (i.e, callipyge), marbling, growth hormone, disposition, gastrointestinal nematode infection, and tolerance to endophyte toxicity in cattle grazing fescue grass. Invited speakers for the cattle and sheep symposium presented that a new SNP marker in CAPN-1 associated with tenderness in cattle of indicine, taurine, and admixed decent. There is tremendous interest in the trait of tenderness in the basic scientific community and in the commercial genotyping industry. A challenge in the application of some of the initially discovered polymorphisms related to tenderness was that the markers inferred variability in prediction of tenderness traits and had diversity among genotypes in Bos taurus cattle, but not in Bos indicus cattle. These studies revealed that chromosome 29 contained an important gene defined as µ-calpain (CAPN-1) which has a large role in postmortem tenderization. There are a series of SNPs within or closely linked to this gene. Two of these SNPs appear to be informative in Bos indicus and Bos taurus cattle (316 and 4753), but a SNP at 530 only appears to be informative in Bos taurus cattle. Moreover, it appears that these markers maybe more useful in predictions using analytical procedures involving haplotypes. Stephen Moore from the University Alberta-Edmonton delivered a talk on Candidate genes of feed efficiency. The trait of residual feed intake was introduced and efforts to find genetic tools to select for this trait were discussed. Data of other measure of animal efficiency were also presented which involved evaluating oxygen consumption and methane production using a respiratory calorimetry hood. The rationale for these measures were from the concept that measures of gas consumption or production could be used to estimate metabolic rate/efficiency in cattle. Efforts to use these measures to identify candidate genes were also presented, particularly their associations with hormones such as leptin. Jeremy Taylor (University of Missouri) reported results in fine quantitative trait loci (QTL) mapping in dairy cattle (in collaboration with scientists at USDA-ARS and University of Arizona) as well as results in positional cloning in beef cattle. To fine-map QTL affecting milk production traits in dairy cattle on BTA6, 3317 bulls comprising 45 half-sib families were genotyped for 38 markers. The data were analyzed using least squares regression (QTL Express), linkage disequilibrium (LDVCM) and full pedigree MCMC (LOKI) methods. A total of 19 sires were segregating for at least one QTL under a half-sib model at chromosome-wide P < 0.05. LD results across families indicated the presence of up to 7 QTL (3 within a 6 cM region) whereas LOKI revealed only 3 QTL. Positional/functional candidate genes have been identified for five of the QTL. Osteopontin (OPN or SPP1) is a strong candidate for the QTL near marker BM143. The entire OPN gene and 5kb upstream was sequenced from four segregating sires and four non-segregating sires (12.3kb per animal). A total of 15 SNPs were identified but only one SNP resulted in sire genotypes that were concordant with the segregation status of all eight sires. For position cloning in beef cattle, the strategy outlined in Taylor and Schnabel was applied and built upon the previous projects involving Bos taurus x Bos indicus crosses and study of Bos taurus autosomal (BTA) chromosome 2 and 14. A DNA Repository from semen on 1,660 registered bulls representing 14 generations of the American Angus Association was assembled. Expected progeny differences (EPD)s and reliabilities for 20 traits are available for this population. In addition, 5,300 DNA samples were collected on commercial Angus steers (36 halfsib families have at least 30 progeny) with growth and slaughter phenotypes. A total of 113,637 genotypes for 56 microsatellite loci and SNPs for thyroglobulin in exon 5 (TG5) and diacyl glycerol acyltranferase in exon 1 (DGAT1) on BTA2 and BTA14 in 1,361 Angus sires and 559 steers were scored. Results suggested TG5 had no effect on sire Marbling EPDs or steer marbling phenotypes. Three previously published marbling QTL, 1 birth weight QTL and 1 carcass weight QTL are segregating within Angus and map to identical locations to the published reports. Horse. ESTs have been collected from unstimulated and stimulated equine leukocytes, from articular cartilage, from brain, and from skeletal muscle. 1,000 element microarray has been printed from the leukocyte EST collection and is being used to study genes involved in pathogenesis of experimentally-induced laminitis. A 9,410 element microarray is under development from the cartilage ESTs. Discussions of combining sequences from all sources and developing a larger oligo-based microarray have been initiated. It is anticipated that this resource would assist the group in defining the processes associated with many disease and economically important traits, such as laminitis, joint disease, colic, etc. A contig of 23 overlapping BAC clones comprising the equine MHC (ELA) has been assembled and subclones scheduled for an estimated 7X sequencing of the region. Description of the gene loci in this region will help to define genetic influences on disease susceptibility and resistance. In addition, studies to characterize the T-cell receptor B gene family in horses are ongoing. Recently the molecular genetic basis of glycogen storage disease type IV (GBED) in Quarter Horses and junctional epitheliosis bullosa (JEB) in Belgian horses have been described through the use of genome mapping tools. Studies to define the molecular basis polysaccharide storage myopathy (PSSM) and hyperelastosis cutis (HERDA) in Quarter Horses, and exertional rhabdomyolysis (RER) in Thoroughbreds are ongoing as are studies to identify the gene responsible for Degenerative Suspensory Ligment Disease and the grey, sabino overo, and appaloosa coat color patterns. Poultry. Physical maps and map integration. A library of over 115,000 BACs (~15X; Lee et al., Animal Genetics 34:151-152, 2003) was generated and 65,000 of these were fingerprinted at Texas A&M, leading to a first generation physical map (Ren et al., Genome Research 13:2754-2758, 2003). P. de Jong (Childrens Hospital of Oakland Research Institute, CHORI) generated a ~10X BAC library (CHORI-261) with extra large inserts using DNA we provided from the same bird used for the Texas A&M BACs and for sequence analysis. CHORI also prepared a large insert turkey BAC library (CHORI-260). The Washington U. Genome Sequencing Center (WUGSC) was provided copies of the Texas A&M and CHORI-261 chicken BAC libraries and fingerprinted over 150,000, generating over 130,000 useable BAC fingerprints. These were employed to generate a second generation BAC contig map comprised of 260 contigs, 226 of which have been anchored to the genetic linkage/chromosome map (Wallis et al., Nature 432:761-764, 2004). Several labs participated in integrating the BAC contigs and sequence with the linkage map, primarily using overgo hybridization (Romanov et al., Cytogenetics and Genome Res., 102:277-281, 2003). This research generated over 7800 BAC assignments to over 900 distinct markers or genes. Recently, similar efforts applied to the turkey CHORI-260 library have generated over 2400 BAC assignments for 176 markers/genes. Boardman et al. (Current Biology 12:1965-19-69, 2002) announced the sequencing of over 300,000 chicken ESTs from a wide variety of tissues and developmental stages. A joint project between the U. of Manchester and the Sanger Institute (Jane Rogers) sequenced full length chicken cDNA clones using both UMIST and other libraries. A world-wide consortium of investigators report 19,626 finished cDNAs and 485,337 ESTs (Hubbard et al., Genome Research advance Epub, Dec. 8, 2004). NCBIs dbEST (http://www.ncbi.nlm.nih.gov/dbEST/) presently lists 531,351 chicken ESTs. Array development will be reported below. Masabanda et al. (Genetics 166:1367-1373, 2004) generated a molecular cytogenetic analysis of the chicken, including identification of all microchromosomes, either by chromosome paints or BAC FISH probes. Radiation hybrid (RH) panels have been constructed by Vignal and colleagues at INRA (Morisson et al., Genet. Sel. Evol. 34:521-533, 2002), and a framework RH map is being constructed (e.g., Morisson et al., Mamm. Genome 15:732-739, 2004). The Washington U. Genome Sequencing Center (WUGSC) has completed 6.6X sequencing of the chicken genome (primarily whole genome shotgun) and the first assembly of the draft chicken sequence was released on March 1, 2004. The initial analysis and annotation of the sequence was recently published (International Chicken Genome Sequencing Consortium, Nature 432:695-716, 2004). In addition to the companion physical map and SNP papers mentioned above, the January, 2005 issue of Genome Research will be devoted to companion chicken sequence analysis papers (Genome Research advance Epub, Dec. 8, 2004). Sheep. (Increase marker density of existing linkage and physical maps): The ovine linkage map is continuously updated, primarily through the efforts of Dr. Jill Maddox, University of Melbourne, Australia. The linkage map now includes over 1,250 loci [http://rubens.its.unimelb.edu.au/~jillm/jill.htm ]. A collaborative project including the US, Australia, New Zealand, and the UK will soon commence with the objective of developing a whole genome physical map (see below). Swine. BARC researchers have provided means to study expression and function of additional immune genes in normal breeding populations to identify early responders which might be more disease resistant/susceptible. New work in porcine reproductive and respiratory syndrome virus (PRRSV) resistance with UNE researchers may help identify pigs which are more disease resistant and the protective mechanisms they employ to induce resistance. ISU researchers have used two molecular techniques to identify some of the genes which increase or decrease expression levels in the early response to Salmonella choleraesuis or S. typhimurium infection. These are subtractive suppression hybridization (SSH) and microarray. Genes include signal transduction and steroid biosynthesis which are involved in the embryo elongation process. ISU and NADC researchers have begun to analyze the lungs of pigs infected with S. choleraesuis by using the NRSP8 funded long oligonucleotide microarray, and find 57 genes with some statistical evidence (P <0.001) for differential expression; of the 40 genes from this group with human functional annotation, 40% are related to the immune system. The transcriptional profiling results were verified by quantitative techniques with BARC researchers. Transcriptional profiling of skeletal muscle tissue at Michigan State Univ. reveals important genes in the pathways regulating skeletal muscle growth and development. Their development of a unique pig resource population provides a novel resource for identifying QTL associated with growth and carcass merit in pigs. NCSU researchers are characterizing changes in allelic frequencies for two RFLPs associated with the follistatin gene in a line of pigs selected for increased litter size (LS). In a separate project they are working to identify genes associated with adipose metabolism. For this they are analyzing gene expression during t10c12-CLA-induced body fat reduction in a polygenic obese line of mice. In an effort to identify genes responsible for anti-microbial responses in the gut, UMN researchers isolated expressed sequence tags (EST) from an activated porcine Peyers patch cDNA library. 3687 ESTs, representing 2414 unique nucleotide sequences were analyzed and spotted onto a microarray for gene expression profiling. Approximately 30% of these ESTs BLAST to genes of unknown function and 20% appear to be novel, i.e., have no known homology in the public databases. To determine chromosomal location, PCR-based mapping was performed across a swine radiation hybrid panel; 125 ESTs were mapped with a lod score > 6.0. These ESTs therefore should provide insight into early immune mechanisms and processes activated in Peyers patches. Islet gene expression profiles were assessed at UMN using the NRSP8 funded porcine 70-mer oligonucleotide microarray and real-time PCR. Microarray data were analyzed by direct pairwise comparison between culture conditions and by loop design using GeneSpring and R/maanova, respectively. Cytokine treatment resulted in increased expression of genes involved in stress, immune response, apoptosis, and cellular defense. Islets cultured under conditions of elevated glucose showed increased expression of genes involved in intracellular protein transport, glucose and lipid metabolism, and stress response. Transcriptional profiling of the response of porcine islet beta cells to inflammatory and hyperglycemic conditions will help identify molecular targets that are likely to protect porcine islets during islet isolation and engraftment. Progress Toward Objective 3: Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information. Aquaculture: Overall, bioinformatic tool development is a very weak area in aquaculture genomics. Thomas Kochers group continues to build informatic tools to integrate the genetic and physical maps of the tilapia genome with with the genome sequences now available for Fugu, Tetraodon, medaka and zebrafish. The comparative genome databases and browsers are available at http://hcgs.unh.edu/. Greg Warrs group continue to maintain the website www.marinegenomics.org for the archiving of EST and microarray data, and as a resource for on-line tools that can be used in the analysis of genomic and transcriptomic data. They have developed tools for the design of microarrays from species with limited genomic information (see Chen et al., 2004). In collaboration with Dr. Lei Liu at the Keck Bioinformatics Center, an ESTIMA system has been developed that provides searchable databases for the catfish ESTs at Auburn University. As soon as it is tested, the website will be available to the research community. Cattle: Jim Reecy of Iowa State University presented information regarding database activities of NRSP-8. During the symposium, Trey Ideker of the University of California, San Diego, gave a presentation titled Modeling cells with molecular interaction networks. Molecular interaction networks are experimentally derived connections of metabolites and proteins within pathways. While these molecules may not directly interact, they likely are related through the enzymes that process them. Dr. Ideker presented evidence that overlays, the alignment of pathways according to protein sequence or other data where similarity scores are available, may be of great use. Specifically, overlays of known networks from well studied species may elucidate the function or role of unknown metabolites and proteins in less well understood organisms. The implications of this research involve an increase in the speed of which function can be ascribed to unknown compounds in bovine using information gathered in human, mouse, and rat. Christine Elsik of Texas A&M University (TAMU) spoke on the current state of the bovine long oligo array developed among a consortium of researchers at TAMU, University of Missouri, Iowa State University, and The University of Minnesota. Sequences mined from GenBank are currently undergoing a screening process to remove duplicated sequences, vector sequences, and other artifacts of the cloning process. It is expected that a first draft of the sequences to be spotted on the array will be available by Summer of 2005. Horse: This objective is not currently a major focus of the equine group. Bioinformatic tools available include a Web interface for RH panel typing data submission and mapping, a publicly available and searchable database that houses the leukocyte ESTs at the University of Georgia, and DNA marker databases maintained at INRA and Roslin. Poultry: Database and other map resources. Sequence and Map: The sequence, along with a variety of options and tools, can be accessed at three different browsers: the UCSC Chicken Genome BrowserGateway, (http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken&db=0&hgsid=30948908); the NCBI Chicken Genome Resources, (http://www.ncbi.nlm.nih.gov/genome/guide/chicken/); and the EBI's Ensembl Chicken Genome Browser, (http://www.ensembl.org/Gallus_gallus/). See also the WUGSC chicken site at http://genome.wustl.edu/projects/chicken/. SNP data can be accessed at http://chicken.genomics.org.cn/index.jsp or the UCSC or Ensembl browsers. The ChickFPC browser at http://www.bioinformatics.nl/gbrowse/cgi-bin/gbrowse/ChickFPC allows for various searches of the BAC contig map. Similarly, BAC locations denoted by BAC end sequences can be found on other sequence browsers noted above. The BAC map can also be obtained by ftp at http://genome.wustl.edu/projects/chicken/. The SNP data generated by the Beijing Genomics Institute (described above) can be accessed on the UCSC or Ensembl browsers, but more extensive descriptions (including QTL information) are available at the BGI site at http://chicken.genomics.org.cn/index.jsp. ChickGBASE: The latest version of ChickGBASE is constructed in the comparative mapping Arkdb format. Arkdb was primarily developed at the Roslin Institute. ChickGBASE is available in the Arkdb format at http://www.thearkdb.org/browser?species=chicken . A mirror site for the poultry database has been mounted at the Iowa State database site, http://www.genome.iastate.edu/. James Reecy at Iowa State has taken over direction of all bioinformatics efforts for the NAGRP, including chicken. WWW Homepage: We maintain a WWW homepage (http://poultry.mph.msu.edu) for the Poultry Genome that provides a variety of genome mapping resources, including the latest EL maps and mapping data, an updated list of published microsatellites, descriptions of available resources, the latest cytogenetic map, and access to a host of other information relating to both genetic and physical maps. Sheep: (Expand species genome databases and provide other genome mapping resources): An informational database for the ovine genome map continues to be enhanced. SheepBase contains an up-to-date compilation of published data from sheep genome mapping projects, along with physical and linkage maps of the sheep genome, and information on individual loci and associated references. The information is presented using the WWW interface and can be accessed through a number of nodes including Roslin Institute (UK) and the University of Melbourne (Australia). Currently, there are 2832 map assignments in SheepBase, with 1988 derived through linkage analysis and 844 via physical mapping. Dr. Jill Maddox, University of Melbourne, Australia, has been updating the database using NRSP-8 coordinator funds to serve as the curator of SheepBase. A memorandum of understanding was established among AgResearch (New Zealand), Meat and Livestock Australia, the USDA/ARS Meat Animal Research Center (Nebraska), and the NRSP-8 Sheep Coordinator in order to fund the construction of a 10-fold redundant BAC library by BACPAC Resources. A copy of the library has been received by Utah State University. In addition, arrayed filters have been purchased and are distributed upon request. Swine: Database development is continuing at ISU. An EST database has been developed and is quite useful. ISU researchers developed a relational pig quantitative trait loci (QTL) database (PigQTLDB) to integrate all available pig QTL data in the public domain and thus facilitate the use of QTL data in further studies. PigQTLdb has been well used since its release last December (http://www.animalgenome.org/QTLdb/). They developed a trait ontology to standardize names of traits and to simplify organization of the data making it possible to compare primary data from diverse sources and methods. The database contains all pig QTL data published during the past 10+ years. The database and its peripheral tools were made to compare, confirm, and locate on pig chromosomes the most feasible location for a candidate gene responsible for quantitative trait(s) important to pig production. To date, 791 QTL from 73 publications have been curated into the database. Those QTLs cover more than 300 different traits. Contact Zhiliang Hu (zhu@iastate.edu) with any suggested improvements or additional data to add to the database. These data have been submitted to the Gene and Map Viewer resources at NCBI, where the information about markers has been matched to marker records in NCBI's UniSTS database. This allows automatic matching of markers to public sequence data by e-PCRand data retrieval from NCBI resources. Efforts at ISU and UMN have been aimed at developing better annotation of the NRSP8 funded porcine 70-mer oligonucleotides for microarray data analyses. WSU researchers have take 3 steps to collect and generate full-length cDNA sequences of orthologous genes in livestock species, i.e., puzzle sorting, puzzle retrieving and puzzle making for a final puzzle solving. They have developed a bioinformatics tool, ELF-Walking (electronic flanking walking) to facilitate large-scale in silico cloning of full-length cDNA sequences by mining the sequence databases. All sequence data and annotation information can be downloaded from our Bioinformatics website at http://www.ansci.wsu.edu/programs/bioinformatics/.

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Proc Natl Acad Sci USA 101, 2386-2391. Raudsepp T., Santani A., Wallner A., Kata S.R., Ren C., Zhang H., Womack J.E., Skow L.C. and Chowdhary B.P. (2004). A detailed map of the horse Y chromosome. PNAS (USA) 101: 9321-9326. Takahashi, T., Yawata, M., Raudsepp, T., Lear, T. L., Chowdhary, B. P., Antczak, D. F., and Kasahara, M. (2004) Natural killer cell receptors in the horse: evidence for the existence of multiple transcribed LY49 genes. European J. of Immunology 34: 773-784. Terry RB, Archer S, Brooks S, Bernoco D, Bailey E. (2004). Assignment of the appaloosa coat colour gene (LP) to equine chromosome 1. Anim Genet. 35:134-137. Tozaki T, Penedo MC, Oliveira RP, Katz JP, Millon LV, Ward T, Pettigrew DC, Brault LS, Tomita M, Kurosawa M, Hasegawa T, Hirota K. (2004). Isolation, characterization and chromosome assignment of 341 newly isolated equine TKY microsatellite markers. Anim Genet. 35:487-496. Wagner B, Miller DC, Lear TL, Antczak DF. (2004). The complete map of the Ig heavy chain constant gene region reveals evidence for seven IgG isotypes and for IgD in the horse. J Immunol. 2004 Sep 1;173(5):3230-42. Wagner ML, Goh G, Wu JT, Raudsepp T, Morrison LY, Alexander LJ, Skow LS, Chowdhary BP, Mickelson JR. (2004) Radiation hybrid mapping of 75 previously unreported equine microsatellite loci. Anim Genet. 35:68-71. Wagner ML, Goh G, Wu JT, Raudsepp T, Morrison LY, Alexander LJ, Skow LC, Chowdhary BP, Mickelson JR. (2004) Radiation hybrid mapping of 63 previously unreported equine microsatellite loci. Anim Genet. 35:159-162. Wagner ML, Goh G, Wu JT, Morrison LY, Alexander LJ, Raudsepp T, Skow LC, Chowdhary BP, and Mickelson JR. (2004). Sixty-seven new equine microsatellite loci assigned to the radiation hybrid map. Animal Genetics 35, 484-46. Ward TL, Valberg SJ, Adelson DL, Abby CA, Binns MM, and Mickelson JR (2004). Glycogen Branching Enzyme (GBE1) Mutation Causing Equine Glycogen Storage Disease IV. Mammalian Genome 15, 570-577. Poultry: Sheep: Refereed manuscripts published or accepted: 12 Agca, C., C.A. Bidwell, and S.S. Donkin (2004) Cloning of bovine pyruvate carboxylase and 5' untranslated region variants. Animal Biotechnology15:47-66. Bidwell, C. A., L. N. Kramer, A. C. Perkins, T. S. Hadfield, D. E. Moody and N. E. Cockett (2004) Expression of PEG11 and PEG11AS transcripts in normal and callipyge sheep. BMC Biology 2:17. DOI:10.1186/1741-7007-2-17. Cockett, N. E. (2004) Summary of the 2004 International Conferences for Animal Genetics, held in Tokyo, Japan. Japanese Journal of Animal Breeding (in press). Cockett, N. E., M. Smit, C. A. Bidwell, K. Sergers, T. L. Hadfield, G. D. Snowder, M. Georges and C. Charlier (2004) The callipyge mutation and other genes that affect muscle hypertrophy in sheep. Genetics Selection Evolution 37(Suppl. 1):S65-S81. The Complex Trait Consortium (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nature Genetics 36:1133-1137. Corva, P. M., N. C. Mucci, K. Evans and J. F. Medrano (2004) Diet effects on reproduction in high growth (hg/hg) female mice that are deficient in the Socs-2 gene. Reproduction, Nutrition, Development 44:303-312. Cousens, C., Bishop, J.V., Philbey, A.W., Carlson, J.O., Gill, C.A. DeMartini, J.C., and Sharp, J.M. (2004) Analysis of integration sites of Jaagsiekte sheep retrovirus in ovine pulmonary adenocarcinoma. Journal of Virology 78 (16): 8506-8512. Davis, E., C. H. Jensen, H. D. Schroder, T. Hadfield, A. Kiem, N. Cockett, M. Georges and C. Charlier (2004) Ectopic expression of DLK1 protein in skeletal muscle of padumnal heterozygotes causes the callipyge phenotype. Current Biology 14:1858-1862. Farber, C.R. and J.F. Medrano (2004) Identification of putative homology between horse microsatellite flanking sequences and cross-species ESTs, mRNAs and genomic sequences. Animal Genetics 35:28-33. Notter, D. R. and N. E. Cockett (2004) Opportunities for detection and use of QTL influencing seasonal reproduction. Genetics Selection Evolution (in press). Rodriguez, S. M., C. A. Bidwell and S. S. Donkin (2004) Cloning the genomic sequence and proximal promoter of bovine pyruvate carboxylase. Journal of Animal Sciences 82:365. Warden, C. H., S. Stone, S. Chiu, A. L. Diament, D. Shattuck, R. Riley, P. Corva, J. Easlick, J. S. Fisler and J. F. Medrano (2004) Identification of a congenic mouse line with obesity and body length phenotypes. Mammalian Genome 15:460-71. Book chapters: 2 Cockett, N. E. And F. Galibert (2004) Genome Mapping at the Molecular Level. In: Mammalian Genomics. Editor: A. Ruvinsky. CAB International, UK (in press). Brenig, B., T. E. Broad, N. E. Cockett and A. Eggen (2004) Achievements of Research in the Field of Molecular Genetics. In: The World Association for Animal Production, Book of the Year for 2003. Wageningen Academic Publishers, The Netherlands (in press). Published abstracts and proceedings: 6 Bidwell, C.A., L.N. Kramer, T.S. Hadfield, D.E. Moody C. Charlier, M. Georges and N.E. Cockett (2004) Expression of PEG11 and AntiPEG11 transcripts in normal and callipyge sheep. Keystone Symposia: Emerging Mechanisms of Epigenetic Regulation. Tahoe City CA. Cockett, N. E. (2004) Advances in Livestock Genomics. Conference on Agricultural Genomics: Who, What and Why. AAAS, Pacific Division. Eng, S. L., E. Owens, J. E. Womack and N. E. Cockett (2004) Development of an ovine-whole genome radiation hybrid panel. Proc., Plant and Animal Genome XII, poster P650, p. 233. Liu, W-S., C. W. Beattie, N. E. Cockett and F. A. Ponce de Leon (2004) Comparative analysis of 38 bovine Y-chromosome microsatellites in cattle, sheep and goats. Proc., Plant and Animal Genome XII, poster P632, p. 229. Perkins, A. C., L. N. Kramer, D. E. Moody, T. S. Hadfiled, S. Eng, N. E. Cockett and C. A. Bidwell (2004) Developmental expression of paternally expressed genes from the callipyge locus of sheep chromosome 18. Proc., 29th International Conference on Animal Genetics, p. 73. Smit, M., F. Baraldi, E. Davis, X. Tordoir, T. Hadfield, G. Gyapay, N. Cockett, M. Georges and C. Charlier (2004) Extending the boundaries of the callipyge imprinted gene cluster on ovine chromosome 18. Proc., Plant and Animal Genome XII, poster P649, p. 233. Takeda, H., X. Tordoir, M. Smit, N. Cockett, M. Georges and C. Charlier (2004) Dnase I hypersensitive sites around the ovine callipyge mutation. Proc., 29th International Conference on Animal Genetics, p. 73. Dissertations: 1 Maria Smit. PhD in Animal Science with Molecular Genetics specialization, Utah State University. Dissertation Title: Long Range Transcriptional Regulation at the Ovine Callipyge Imprinted Gene Cluster. Swine: http://www.genome.iastate.edu/community/NRSP8/2004/index.html Bertani G, Gladney C, Johnson RK, Pomp D 2004. Evaluation of gene expression in pigs selected for enhanced reproduction. II: Anterior Pituitary. J Anim Sci 82:32-40. Blowe, C. D., E. J. Eisen, O. W. Robison, and J. P. Cassady. 2004. Characterization of a line of pigs selected for increased litter size for two RFLPs identified in follistatin. Abstract. J. Anim. Sci Supplement 1. Caetano AC, JB Edeal, K Burns, RK Johnson, C Tuggle, D Pomp 2005. Physical mapping of the differentially expressed porcine ovarian transcriptome. Animal Genetics (Accepted). Caetano A, J Ford, RK Johnson, D Pomp 2004. Microarray profiling for differential gene expression in ovaries and ovarian follicles of pigs selected for increased ovulation rate. Genetics 168: 1529-37. Cao H, Robinson JA, Jiang Z, Melville JS, Golovan SP, Jones MW and Verrinder Gibbins AM. 2004. A high-resolution radiation hybrid map of porcine chromosome 6. Anim. Genet. 35:367-378. Churchill GA and 101 others including D Pomp 2004. 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