Brief Summary of Minutes of Annual Meeting

Brief summary of minutes of annual meeting: Saturday, January 10, 2004 Diane Moody, Chair NRSP008 Swine Committee, organized the joint program with NC1004 Swine Genome Committee Chair, Brad Freking. The morning session of 3 invited speakers and afternoon combined station reports was chaired by Dr. Moody. Dr. Moody thanked Dr. Max Rothschild and the National Swine Genome Coordinators office for supporting the registration fee of the invited speakers. The morning presentations were as follows: Tosso Leeb, School of Veterinary Medicine Hannover, Germany A 5.5 MB BAC/PAC CONTIG OF PIG CHROMOSOME 6Q1.2 AND ITS INTEGRATION WITH EXISTING RH, GENETIC AND COMPARATIVE MAPS Lawrence Schook, University of Illinois RECOMBINEERING: A TOOL FOR HARVESTING GENOMIC INFORMATION Archie Clutter, Monsanto Company IMPLEMENTATION OF MARKER-ASSISTED SELECTION IN COMMERCIAL POPULATIONS After Lunch, Administrative reports were given by Margaret Dentine, NRSP008 Administrative Advisor and Burt Stromberg, NC1004 Administrative Advisor, followed by Max Rothschild, the Swine Genome Coordinator, and Jim Reecy, the new NRSP008 Bioinformatics Coordinator. Joint NRSP-8/NC1004 Station Reports were presented by BARC, ISU, IL, MSU, MN, Purdue, NCSU, NV, OK, and WSU. A written NC1004 report was supplied by OSU. No formal reports were provided by MARC, NE, KSU or VT during the meeting. The NC1004 Business meeting was called to order by Cathy Ernst at 8:00 am Jan. 11, 2004. Minutes from the previous meeting were approved. Cathy reminded every one about the NC1004 written reports. 1. The bioinformatics sub-committee. Dr. Jack Dekkers suggest that the bioinformatics sub-committee provide recommendations to Dr. James Reecy regarding the bioinformatics needs of the swine community. 2. Meeting location was discussed. Two options were proposed. Option I  rotate meeting locations between NSIF and PAG. Option II  Meet at research stations during the summer. Location would rotate among member research stations. 3. Administrative advisor comments. Bert Stromberg commented on annual reports, publications, and out reach. Max Rothschild suggested that we indicate which publications include cooperation among stations when that is not evident from authorship. Steve Moeller suggest distinguishing between journal articles and extension publications in order to highlight out reach efforts. Several examples of collaboration were discussed by the group. It was clear that efforts need to be made to better document those interactions. 4. Larry Schook suggested working more closely with NCBI with regard to bioinformatics. An effort should be made to identify bioinformatic needs and express those to James Reecy (bioinformatics coordinator). 5. There were extensive discussions of results with current microarrays and a potential plan for a joint analysis of data collected by the Fahrenkrug, MN, Tuggle, ISU, and Beever, IL, labs. Additionally members decided to have another committee to develop plans for the next set of swine arrays. 6. A joint NRSP008/NC1004 Swine Arrays committee was selected: Scott Fahrenkrug, MN, will chair the committee. Members: Chris Tuggle, ISU, Jon Beever, IL, Diane Moody, Purdue, Cathy Ernst, MI and, ex-officio, Max Rothschild, ISU. The committee will address 3 issues: 1) bioinformatic needs for analyzing and jointly storing array data; 2) companies and platforms for the next generation of swine arrays; and 3) updated criteria for selecting genes and oligo design for next generation arrays. 7. Chris Tuggle was elected secretary. 8. The meeting was adjourned at 9:15

Accomplishments: Members of the NC1004 Regional project (Genetic and functional genomic approaches to improve production and quality of pork) met on Jan 10-11, 2004 in conjunction with the NRSP8 swine meeting at PAGXII in San Diego, CA. This was the second meeting since approval of the project, and covered the period of June 1, 2003  January 10, 2004. The short interval was due to the desire to combine location and meeting time NRSP8. Continued development of genomic resources for the pig research community has been a major accomplishment of this group. The January 6, 2004 release of the TIGR porcine gene index listed a total of 170,000 expressed sequence tags (EST) in public databases (Genbank). The great majority of these EST were contributed by member institutions of this committee, combined with the ARS effort. Continued data collection from several institutions will expand this basic resource. Several institutions are also contributing information to develop and integrate the EST data with the pig physical map. Sequence data has already been used to develop the first generation of oligo-based microarrays for the pig. The Qiagen produced and University of Minnesota printed 13,000 70-mer oligos have been distributed to several of the members of this committee. Members of the committee can request 20 free arrays and 50 additional slides at the cost of printing. Extensive discussion of results and a potential plan for a joint analysis of initial data collected by the Minnesota, Iowa, and Illinois stations was conducted. A joint committee (Chaired by Scott Fahrenkrug) was created with NRSP8 to develop plans for the next set of swine arrays. This committee will establish guidelines for future use, storage, analysis, and bioinformatics infrastructure for these data. The Nebraska station developed a 4, 000 element cDNA array specifically from an ovarian follicle library that is also available for collaborative mapping and expression studies. Integrated approaches to porcine gene discovery were developed further by initiation of porcine Serial Analysis of Gene Expression (SAGE) libraries for cardiac, skeletal muscle, and adipose tissues by the Indiana station. Transcriptional profiling of specific tissues is also ongoing at Michigan (skeletal muscle and myogenic satellite cells), Iowa (muscle), and Nebraska (ovary). Efforts have continued to pursue detection of quantitative trait locus (QTL) mapping, primarily focused on meat quality traits (Iowa and Michigan). Comprehensive methods were developed to analyze QTL from line-cross F2 populations to account for QTL that not only differ between the breeds but are also segregating within the contributing grandparent generation. Strategies for implementation of marker-assisted selection were also reviewed and evaluated. A workshop to facilitate technology transfer of QTL information from the Iowa and Illinois resource populations to the industry was conducted in Des Moines, IA. This workshop presented the principles of QTL mapping, results from experimental populations, and existing industry use of marker-assisted selection. Evaluation of unique genetic resources and development of selection lines has continued to evolve. Effects of selection for testosterone production were evaluated at North Carolina. Iowa is continuing two selection experiments (residual feed intake and intramuscular fat deposition) and also evaluated overall industry selection for leanness using historical semen samples to investigate impact on meat quality traits. Development of these unique genetic resources is critical to identify the underlying genes regulating traits of interest. Discovery of the genetic mechanisms controlling animal health in pork production has also been the focus of several institutions. Characterization of the antimicrobial activity of novel and existing antimicrobial peptide genes against a range of important swine and foodborne pathogens has been developed at the Oklahoma station. Additionally, immune response of pigs to different infections on the genome scale was initiated using the available 13, 000 element microarray. Gene expression assays for a panel of immune markers known to influence pig health and control vaccine and disease immunity have also been developed at the BARC station. Large phenotypic data sets using automated recording equipment are also being collected to monitor health status factors at the Nebraska station. In summary, significant progress is being made within the regional project. Several milestones have already been achieved and shared resources are being developed further. Steps have been initiated to facilitate technology transfer to the industry. Integration of new tools being developed both from the quantitative and molecular genetic fields will facilitate more rapid discovery of important genetic variation influencing animal health, production efficiency and quality of pork.

Publications: * Indicates joint publication of institutions within NC1004 project INDIANA Bidwell, C.A., M. Spurlock, and D. Moody. 2003. Serial analysis of gene expression of pig adipose and muscle tissue. Plant and Animal Genomes XI Conference, San Diego, CA. www.intl-pag.org/11/abstracts/P01_P69_XI.html. IOWA *Baas, T. J., R. N. Goodwin, L. L. Christian, R. K. Johnson, O. W. Robison, J. W. Mabry, K. Clark, M. Tokach, S. Henry, and P. J. Berger. 2003. Design and standards for genetic evaluation of swine seedstock populations. J. Anim Sci. 81:2409-2418. Chen, P., T. J. Baas, J. C. M. Dekkers, K. J. Koehler, and J. W. Mabry. 2003. Evaluation of strategies for selection for lean growth rate in pigs. J. Anim Sci. 81:1150-1157. Chen, P., T. J. Baas, J. W. Mabry and K. J. Koehler. 2003. Genetic correlations between lean growth and litter traits in U.S. Yorkshire, Duroc, Hampshire and Landrace pigs. J. Anim. Sci. J. Anim. Sci. 81:1700-1705. Chen, P., T. J. Baas, J. W. Mabry, K. J. Koehler, and J. C. M. Dekkers. 2003. Genetic parameters and trends for litter traits in U.S. Yorkshire, Duroc, Hampshire, and Landrace pigs. J. Anim Sci. 81:46-53. Dekkers, J.C.M. 2003. Commercial application of marker-assisted selection: strategies and lessons. J. Anim. Sci. 81 (Suppl. 1): 5 Dekkers, J.C.M. 2003. Commercial application of marker-assisted selection: strategies and lessons. Eur. Assoc. Anim. Prod. Lampe, J. F., T. J. Baas and J. W. Mabry. 2003. Comparison of grain sources (barley, white corn, yellow corn) for swine diets and their effect on meat and eating quality traits. J. Anim. Sci. 81: 55 (Suppl. 2). Lampe, J. F., T. J. Baas and J. W. Mabry. 2003. Comparison of grain sources (barley, white corn, yellow corn) for swine diets and their effect on fatty acid composition and fat quality. J. Anim. Sci. 81: 76 (Suppl. 1). Liviu R. Totir, R.L. Fernando, J.C.M. Dekkers, S.A. Fernandez, and B. Guldbrandtsen. 2003. A comparison of alternative methods to compute conditional genotype probabilities for genetic evaluation with finite locus models. Genet. Sel. Evol. 35:1-20 Mabry, J. W. Closed herd production systems: Genetic systems and genetic cost of production. Proceedings of the 2003 NPB Pork Academy, June 4, 2003, Des Moines, IA. N.-T. Nguyen, K.-S. Kim, H. Thomsen, J. Helm and M. F. Rothschild 2003. Investigation of candidate gene for growth and fatness QTL on the pig chromosome 7. Proceedings Plant & Animal Genome XI meeting, January 11-15 San Diego, CA. Newcom, D. W., and T. J. Baas. 2003. Comparison of two models to estimate breeding values for intramuscular fat percentage in Duroc pigs. J. Anim Sci 82 (Suppl 1). Rothschild, M.F. 2003. Advances in pig genomics and functional gene discovery. Comp. Funct. Genom. 4:266-277. Rothschild, M.F. 2003. Approaches and Challenges in Measuring Genetic Diversity in Pigs. Archivos de Zootecnia 52:129-135 Spike, P.L., R. R. Benson, R. L. Fernando, J. C. M. Dekkers, P. J. Berger, and B. R. Skaar. 2003. A simulation program using finite loci with infinite possibilities, FLIP. J. Anim. Sci. 81 (Suppl. 1): 113 *Stoller, G. M., H. N. Zerby, S. J. Moeller, T. J. Baas, C. Johnson, and L. E. Watkins. 2003. The effect of feeding ractopamine (Paylean) on muscle quality and sensory characteristics in three diverse genetic lines of swine. J. Anim Sci. 81:1508-1516. Totir, L.R., R. L. Fernando, and J.C.M. Dekkers. 2003. Response to selection by marker assisted BLUP with use of approximate gametic variance covariance matrices. J. Anim. Sci. 81 (Suppl. 1): 113 *Tuggle, C.K., J. A. Green, C. Fitzsimmons, R. Woods, R. S. Prather, S. Malchenko, M. B. Soares, D. Tack, N. Robinson, B. O'Leary, T. Scheetz, T. Casavant, D. Pomp, J. B. Edeal, Y. Zhang, M. F. Rothschild, K. Garwood, W. Beavis .2003. EST-Based Gene Discovery in Pig: Virtual Expression Patterns and Comparative Mapping to Human, Mammal. Genome 14:565-579 Zhao, H., M. F. Rothschild, R. L. Fernando, J. C.M. Dekkers 2003. Tests of candidate genes in QTL mapping resource populations. Mammal. Genome 14:472-482. *Zhao, S.-H., D. Nettleton, W. Liu, C. Fitzsimmons, C.W. Ernst, N.E. Raney, and C.K. Tuggle. 2003. Complementary DNA macroarray analyses of differential gene expression in porcine fetal and postnatal muscle. J. Anim. Sci. 81:2179-2188. MICHIGAN *Ernst, C.W., N.E. Raney, V.D. Rilington, G.A. Rohrer, J.A. Brouillette and P.J. Venta. 2004. Mapping of the FES and FURIN genes to porcine chromosome 7. Anim. Genet. In Press. Farber, C.R., N.E. Raney, V.D. Rilington, P.J. Venta and C.W. Ernst. 2004. Comparative mapping of genes flanking the human chromosome 12 evolutionary breakpoint in the pig. Cytogenet. Genome Res. In Press. Wesolowski, S.R., N.E. Raney and C.W. Ernst. 2004. Developmental changes in the fetal pig transcriptome. Physiol. Genomics. In Press. *Zhao, S-H., D. Nettleton, W. Liu, C.W. Fitzsimmons, C.W. Ernst, N.E. Raney and C.K. Tuggle. 2003. Complementary DNA macroarray analysis of differential gene expression in porcine fetal and postnatal muscle. J. Anim. Sci. 81:2179-2188. NEBRASKA 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 (In Press). Gladney C, G Bertani, MK Nielsen, D Pomp (2004) Evaluation of gene expression in pigs selected for enhanced reproduction. I: Ovarian Follicles. J Anim Sci (In Press). *Rocha J, Eisen EJ, Van Vleck DL, Pomp D (2004) A large sample QTL study in mice. I: Growth. Mammalian Genome (In Press) *Rocha J, Eisen EJ, Van Vleck DL, Pomp D (2004) A large sample QTL study in mice. II: Body Composition. Mammalian Genome (In Press) Pomp D, Allan MF, Wesolowski S. Quantitative Genomics: Exploring the genetic architecture of complex trait predisposition. J Anim Sci (In Press). NORTH CAROLINA Walker, S. E., O.W. Robison, C.S. Whisnant, and J.P. Cassady. Effect of selection for testosterone production on testicular morphology and daily sperm production in pigs. J. Anim Sci.. 81(Suppl. 1), 23 Jun 2003 Walker, S. E., O.W. Robison, C.S. Whisnant, and J.P. Cassady. Effect of selection for testosterone production on testicular morphology. (Submitted) OKLAHOMA Patil, A., Y. Sang, K. Rune, F. Blecha, J.E. Minton, and G. Zhang. 2003. Porcine Innate Immunity: Distinct Tissue Expression and Transcriptional Regulation Patterns of Porcine Beta-Defensin-1 and 2. Proceedings of the 84th Annual Meeting of the Conference of Research Workers in Animal Diseases (CRWAD), Chicago, IL. Xiao, Y., S. Eicher, H.-W. Cheng, J.-F. Cheng, D. Skinner-Noble, and G. Zhang. 2003. Identification and Characterization of a Beta-Defensin Gene Cluster in the Chicken. Proceedings of the 84th Annual Meeting of the Conference of Research Workers in Animal Diseases (CRWAD), Chicago, IL. Zhang, G. 2003. Genome-wide analysis of rat _- and _-defensin gene loci: evidence for the existence of four syntenic defensin gene clusters. 2004 Experimental Biology Meeting abstracts. FASEB J. (in press) USDA, ARS, BARC Martens G W, Lunney J K, Baker J E, Smith D M. 2003. Rapid Assignment of Swine Leukocyte Antigen (SLA) Haplotypes in Pedigreed Herds using a Polymerase Chain Reaction Based Assay. Immunogenetics. 55: 395-401. Dawson HD, Beshah E, Nishii S, Solano-Aguilar G, Morimoto M, Zhao A, Madden KB, Ledbetter TK, Dubey JP, Shea-Donohue T, Lunney JK, Urban, JF Jr. Localized multi-gene expression patterns support an evolving Th1/Th2-like paradigm in response to infections with Toxoplasma gondii and Ascaris suum in pigs. Submitted. Lunney, J.K. 2003. Are there immune gene alleles that determine whether a pig will be healthy? Genetics of Pig Health Symposium, Des Moines, IA. Bannerman, D., Paape, M.J., Lunney, J.K. 2004.Immunity: Innate. In Encyclopedia of Animal Science; Pond, W.G., Bell, A.W. Eds.; Marcel Dekker, Inc., New York. Lunney, J.K., Paape, M.J., Bannerman, D. 2004. Immunity: Acquired. In Encyclopedia of Animal Science; Pond, W.G., Bell, A.W. Eds.; Marcel Dekker, Inc., New York. Royaee AR. Zuckermann FA, Husmann R, Calzada-Nova G, Schnitzlein W, Lunney JK, T cell cytokine response and gene expression profile of porcine lymphoid cells in response to vaccination with PRRS virus. Proceedings Conf. of Research Workers in Animal Disease 2003. *Smith DM, Martens GW, Lunney JK, Ando A, Lee J-H, Ho C-S, Schook L, Renard C, Chardon P. 2004. Nomenclature for Factors of the SLA Class I System, 2004. Tissue Antigens. Submitted. Dawson HD, Royaee AR, Nishii S, Kuhar D, Schnitzlein WM, Zuckermann F, Urban JF, Lunney JK. 2004. Identification of Key Immune Mediators Regulating T helper 1 Responses in Swine. Vet. Immunol. Immunopathol. Submitted. Harry Dawson, Sandra Nishi, Ethiopia Beshah, Gloria Solano-Aguilar, Dante Zarlenga, Joseph F. Urban, Joan Lunney. 2003. Use of real-time assays of immune gene expression to assess the genetic basis of disease resistance. http://www.intl-pag.org/11/abstracts/W52_W330_XI.html Nishi, S., Dawson, H., Dubey, J.P., Urban, J.F., Lunney, J. 2003. Immune responses controlling Toxoplasma gondii infection in pigs. Proceedings of the American Association of Veterinary Parasitologists, 2003. v.48. Abstract. p.52.