NC1004: Genetic and Functional Genomic Approaches to Improve Production and Quality of Pork

(Multistate Research Project)

Status: Inactive/Terminating

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SAES-422 Reports

Annual/Termination Reports:

[07/23/2002] [06/05/2003] [10/02/2004] [10/17/2005] [09/12/2006]

Date of Annual Report: 07/23/2002

Report Information

Annual Meeting Dates: 05/31/2002 - 06/01/2002
Period the Report Covers: 10/01/2001 - 09/01/2002

Participants

Dekkers, Jack-Iowa State; Bates, Ron-Michigan State; Robison, O.W.-NC State; Moeller, Steve-Ohio State; Johnson, Rodger-Nebraska; Freking, Brad-USDA-MARC; Baas, Tom-Iowa State; Lamont, Sue- Iowa State; Wang, Jing- Iowa State; Casey, David- Iowa State; Henderson, David- Iowa State; Woollard, John- Iowa State; Grapes, laura- Iowa State; Feuchter- Iowa State; McElroy- Iowa State; Schwab, Clint- Iowa State; Newcom, Doug- Iowa State; Mabry, John- Iowa State; Rothschild, Max- Iowa State; Cassady, Jow-NC State; Farenkrug, Scott-Minnesota; Staldeer, Ken-Tennessee; Frahm, Dick-USDA-CSREES; Stromberg, Bert-AA

Brief Summary of Minutes

Accomplishments

Publications

Impact Statements

Date of Annual Report: 06/05/2003

Report Information

Annual Meeting Dates: 05/30/2003 - 05/31/2003
Period the Report Covers: 10/01/2002 - 05/01/2003

Participants

Baas, Tom - Iowa State University,tjbaas@iastate.edu; Bates, Ron - Michigan State University, batesr@msu.edu; Beattie, Craig - University of Nevada-Reno, cbeattie@cabur.unr.edu; Beever, Jon - University of Illinois, j-beever@uiuc.edu; Brayton, Peter - USDA-CSREES, pbrayton@csrees.usda.gov; Cassady, Joe - North Carolina State University, jpcassady@ncsu.edu; Dekkers, Jack - Iowa State University, jdekkers@iastate.edu; DeSilva, Udaya - Oklahoma State University, udayad@okstate.edu; Ernst, Cathy - Michigan State University, ernstc@msu.edu; Fahrenkrug, Scott - University of Minnesota, fahre001@umn.edu; Firat, Mehmet Z. - Iowa State University, mzf@iastate.edu; Freking, Brad - USDA-ARS-MARC, freking@email.marc.usda.gov; Gere, Tiber - St. Stephen Univ. Hungary, j-zsuzsa@freemail.hu; Holl, Justin - University of Nebraska-Lincoln, jholl1@bigred.unl.edu; Hovey, Russ - University of Vermont, rhovey@zoo.uvm.edu; Johnson, Rodger - University of Nebraska-Lincoln, Rjohnson5@unl.edu; Kim, Jong Joo - Iowa State University, kimjj@iastate.edu; Lee, Go Hyun - Iowa State University, leegh.123@iastate.edu; Lunney, Joan - USDA-ARS-BARC, jlunney@anri.barc.usda.gov; Moeller, Steve - Ohio State University, moeller.29@osu.edu; Moody, Diane - Purdue University, moodyd@purdue.edu; Mote, Benny - Iowa State University, bmote@iastate.edu; Newcom, Doug - Iowa State University, dnewcom@iastate.edu; Petry, Derek - University of Nebraska-Lincoln, dpetry@unlserve.unl.edu; Pomp, Daniel - University of Nebraska-Lincoln, dpomp@unl.edu; Robison, O.W. - North Carolina State Univrsity, OW_Robison@nscu.edu, Rothschild, Max - Iowa State University, mfrothsc@iastate.edu; Schwab, Clint - Iowa State Universtiy, crschwab@iastate.edu; Stromberg, Bert - University of Minnesota, b-stro@umn.edu; Tuggle, Chris - Iowa State University, cktuggle@iastate.edu; Weber, Jack - University of Nebraska-Lincoln, jweber4@unl.edu; Zhang, Glenn - Oklahoma State University, zguolon@okstate.edu; Zhao, Shuhong - Iowa State University, shzhao@iastate.edu

Brief Summary of Minutes

Minutes Attachment:

Attachment

Accomplishments

The NC-1004 Regional Project (Genetic and functional genomic approaches to improve production and quality of pork) met on May 30-31 for their annual meeting. This represented the groups first meeting since approval of the project, and covered the period of October 1, 2002 to May 31, 2003. Given the brief period of time that the group was in existence prior to the meeting, a significant amount of effort was placed on learning more about individual efforts ongoing at participating stations, taking stock of resources and reagents that could be used for regional project activities, and strategic planning for future group endeavors and collaborations. A major accomplishment that the group has already realized is the deposit of well over 100,000 expressed sequenced tags (EST) into the public genetic database (GenBank). This includes ~85,000 contributed from ARS efforts, and ~30,000 from university stations. A second major accomplishment is the planning and development of a swine oligonucleotide microarray representing over 10,000 unique expressed genes. A limited number of arrays are available to participating members of NC-1004, while reagents to create larger numbers of arrays are publicly available for purchase. Key strategic planning accomplishments included development of two sub-committees for the project, including the NC-1004 Bioinformatics Working Committee and the NC-1004 Outreach Committee. The existence of extensive and well developed populations, genomics reagents and bioinformatics tools represents the raw materials with which the group plans to achieve significant accomplishments with important outcomes during the course of the 5-year project. A thorough inventory of existing resources was conducted to provide the base from which regional project collaborations can be developed. A summary of these (sorted by category and station) include: US Swine Genome Coordinator Resources (M.F. Rothschild) 1) DD-PCR (limited supply) and microsatellite primers 2) Oligonucleotide microarrays 3) Database resources (EST, QTL) 4) BAC libraries and filters cDNA Libraries 1) Illinois Three skeletal muscle libraries (various stages) 2) Iowa 21 libraries (embryos and reproductive tissues at various stages) 3) Michigan skeletal muscle, brain, mixed tissue 4) Nebraska ovarian follicle 5) MARC Four mixed tissue libraries Populations 1) Illinois Berkshire X Duroc F2; DNA and tissues available on collaborative basis 2) Iowa Berkshire X Yorkshire F2; Advanced intercrosses currently at F6; map candidate genes on collaborative basis 3) Michigan Duroc X Pietrain F2; DNA and tissues available on collaborative basis 4) Minnesota Developing Duroc X Yorkshire/Landrace reciprocal backcross population 5) Nebraska Litter size selection lines; DNA available 6) North Carolina Duroc testosterone selection lines, Litter size selection lines, PRRS induction model (B. Harrell); DNA and tissues available on collaborative basis 7) MARC White Composite selection lines; serially slaughtering 600 gilts at 5 stages of gestation and could collect tissues on a collaborative basis Mapping DNA Resources 1) IMpRH (available from M. Rutherford at U. of MN) 2) PiGMaP (available from M. Rothschild; supplies limited) 3) MARC Bioinformatics 1) Indiana database for microarrays 2) Iowa EST and QTL databases 3) Michigan EST database and microarray data analysis 4) Minnesota data analysis software tools In summary. significant progress has already been made towards achieving several of the outputs by which progress of the regional project will be measured. In additional, several of the milestones for Year 1 have been met although significantly less than a full year has elapsed since the project became active. Plans for the coming year include extensive use of resource populations and genomics reagents for integrated gene discovery, expansion of bioinformatic tools to aid in the discovery process, and an emphasis on outreach efforts to extend discoveries to the industry.

Publications

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 Berg, E. P., E. L. McFadin, K. R. Maddock, R. N. Goodwin, T. J. Baas, and D. H. Keisler. 2003. Serum concentrations of leptin in six genetic lines of swine and relationship with growth and carcass characteristics. J. Anim. Sci. 81:167-171. Chaiwong, N., J.C.M. Dekkers, R.L. Fernando and M.F. Rothschild. 2003. Introgressing Multiple QTL through Backcross Breeding Programs. Swine Research Reports. Iowa State University. Chen, P., T. J. Baas, J. W. Mabry, J. C. M. Dekkers, and K. J. Koehler. 2002. Genetic parameters and trends for lean growth rate and its components in U. S. Yorkshire, Duroc, Hampshire, and Landrace pigs. J. Anim. Sci. 80:2062-2070. Chen, P., T. J. Baas, J. W. Mabry, J. C. M. Dekkers, and K. J. Koehler. 2003. Genetic parameters and trends for litter traits in U. S. Yorkshire, Duroc, Hampshire, and Landrace pigs. J. Anim. Sci. 81:46-53. Ciobanu, D.C., S.M. Lonergan, M. Malek, J.R. Woollard, E.J. Lonergan and M.F. Rothschild. 2003. New Alleles in the Calpastatin Gene Associated with Improved Tenderness in Pigs. Swine Research Reports. Iowa State University Crock, A.M., D.S. Casey, and J.C.M. Dekkers. 2003. Feeding behavior of finishing boars and gilts on electronic feeders. J. Anim. Sci. 81 (Suppl. 2): Kim, K.S., N. T. Nguyen, J. M Reecy, L. L. Anderson, and M. F. Rothschild. 2003. Molecular genetic studies of porcine genes for obesity. Swine Research Reports. Iowa State University. Kulak, K., J. Wilton, G. Fox and J. Dekkers. 2003. Comparisons of economic values with and without risk for livestock trait improvement Livestock Production Science, 79: 183-191. Malek, M., D. C. Ciobanu, and M. F. Rothschild. 2003. Genetic and physical mapping of ACACB, PPP1CC and GPR49 genes on porcine chromosomes 5 and 14 help to define a break point on human chromosome 12. Proceedings Plant & Animal Genome XI meeting, January 11-15, San Diego, CA. Moeller, S. J., T. J. Baas, T. D. Leeds, R. S. Emnett, and K. M. Irvin. 2003. Rendement Napole gene effects and a comparison of glycolytic potential and DNA genotyping for classification of Rendement Napole status in Hampshire-sired pigs. J. Anim. Sci. 81:402-410. Newcom, D. W., T. J. Baas, and J. W. Lampe. 2002. Prediction of intramuscular fat percentage in live swine using real-time ultrasound. J. Anim. Sci. 80:3046-3052. Newcom, D. W., T. J. Baas, and R. N. Goodwin. 2003. Relationship between intramuscular fat percentage predicted from real-time ultrasound and meat quality traits in pigs. Midwest ASAS Abstracts, p. 5. Newcom, D. W., T. J. Baas, J. W. Mabry, and R. N. Goodwin. 2002. Genetic parameters for pork carcass components. J. Anim. Sci. 80:3099-3106. Nguyen, N-T, 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. Otieno, C.J., S. Vleck, C. Jelks, K.-S. Kim, N. T. Nguyen and M. F. Rothschild. 2003. Mapping of diabetes-related genes in the pig. Proceedings Plant & Animal Genome XI meeting, January 11-15, San Diego, CA. Rothschild, M.F. 2002. Approaches and limitations to measuring genetic diversity. EEC sponsored Conference on Swine Genetic Diversity, November 7, Cordoba, Spain. Rothschild, M.F. 2002. Transferring Biotechnology to Swine Genetic Programs: From Lab to Pork. Spanish Swine Breeders Conference. November 5, Barcelona, Spain Rothschild, M.F. and S. Newman. 2002. Intellectual property rights in animal breeding and genetics. CABI Press. 272 pages Schwab, C. R., T. J. Baas, S. J. Moeller, and D. W. Newcom. 2003. Accuracy of prediction in the National Swine Improvement Federation (NSIF) Ultrasound Certification Program. Midwest ASAS Abstracts, p. 14. Shi, X.W., Y.D. Zhang, and C.K. Tuggle. 2002. Linkage mapping of porcine STCH further refines the HSA3/21 breakpoint on pig chromosome 13. Anim. Genet. 33:395-396. Sun, H.S., C.K. Tuggle, A. Goureau, C.J. Fitzsimmons, P. Chardon, P. Pinton, and M. Yerle. 2002. Precise mapping of breakpoints in conserved synteny between human chromosome 1 and pig chromosomes 4, 6, and 9. Anim. Gen. 33:91-96. Sun, H.S., L. L. Anderson, T.-P. Yu, K.S. Kim, J. Klindt, and C. K. Tuggle. 2002. Neonatal Meishan pigs show POU1F1 genotype effects on plasma GH and PRL concentration. Anim. Reprod. Sci. 69:223-237. Thomsen, H., J. C. M. Dekkers, and M. F. Rothschild. 2003. Detection and characterization of QTL for growth and meat quality traits in the Berkshire-Yorkshire cross. Swine Research Reports. Iowa State University. Wang, J., J. Fulton, and J. Dekkers. 2003. Accuracy of detecting quantitative trait loci by selective DNA pooling. J. Anim. Sci. 81 (Suppl. 2): Wang, J., K. Koehler, M. Soller, and J.C.M. Dekkers. 2003. Least squares interval mapping to detect QTL with selective DNA pooling. Plant and Animal Genome XI: 69. MICHIGAN Farber, C.R., N.E. Raney, D.L. Kuhlers, K. Nadarajah and C.W. Ernst. 2003. Mapping of porcine genetic markers generated by representational difference analysis. Anim. Biotech. 14:87-102. Yao, J., P.M. Coussens, P. Saama, S. Suchyta and C.W. Ernst. 2002. Generation of expressed sequence tags from a normalized porcine skeletal muscle cDNA library. Anim. Biotech. 13:211-202. Zhao, S-H., D. Nettleton, W. Liu, C.W. Fitzsimmons, C.W. Ernst N.E. Raney, and C.K. Tuggle. 2003. cDNA macroarray analysis of differential gene expression in porcine fetal and postnatal muscle. J. Anim. Sci. (Accepted) Allison, C.P., R.O. Bates, A.M. Booren, R.C. Johnson and M.E. Doumit. 2003. Pork quality is not explained by activity of rate-limiting glycolytic enzymes. Meat Science 93:17-22. Bates, R.O., D.B. Edwards and R.L. Korthals. 2003. Sow performance when housed in groups with electronic sow feeders or stalls. Livestock Production Science 79:29-35. Bates, R.O., M.D. Hoge. B.E. Edwards and B. Straw. 2003. The influence of canine teeth clipping on nursing and nursery pig performance. Swine Health and Production 11(2):75-80. Edwards, D.B., R.O. Bates and W.N. Osburn. 2003. Evaluation of Duroc- vs Pietrain-sired pigs for carcass and meat quality measures. J. Anim. Sci. 81: (Accepted). Pagan, M. M.E. Davis, D.A. Stick, R.C.M. Simmen, N.E. Raney, R.J. Tempelman and C.W. Ernst. 2003. Evaluation of serum insulin-like growth factor binding proteins (IGFBP) in Angus cattle divergently selected for serum IGF-I concentration. Domest. Anim. Endocrinol. (Accepted). NORTH CAROLINA Holl, J. W. and O. W. Robison. 2003. Results from nine generations of selection for increased litter size in swine. J. Anim Sci. 81:624629, March 2003. Blowe, C. D., E. J. Eisen, O. W. Robison, and J. P. Cassady. Characterization of a line of pigs selected for increased litter size for genes known to affect reproduction. J. Anim. Sci. 81(Suppl 1): 56, March 2003. Walker, S., 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): 5, March 2003. Cassady, J. P., K. A. Leymaster, and L. D. Young. Heterosis and recombination effects on pig reproductive traits. J. Anim Sci. 80(9):2286-2302, Sept. 2002 Cassady, J. P., K. A. Leymaster, and L. D. Young. Heterosis and recombination effects on pig growth and carcass traits. J. Anim Sci. 80(9):2303-2315, Sept. 2002. OHIO Stoller G. M., H. N. Zerby, S. J. Moeller, T. J. Baas, C. Johnson, and L. E. Watkins. 2003. The effect of feeding Ractopamine (Payleand) on muscle quality and sensory characteristics in three diverse genetic lines of swine. J. Anim. Sci. 81:1508-1516. Moeller, S. J., T. J. Baas, T. D. Leeds, R. S. Emnett, and K. M. Irvin. 2003. Rendement Napole gene effects and a comparison of glycolytic potential and DNA genotyping for classification of Rendement Napole status in Hampshire-sired pigs. J. Anim. Sci. 81:402-410. Isler, B. J., K. M. Irvin, S. M. Neal, S. J. Moeller, and M. E. Davis. 2002. Examination of the relationship between the estrogen receptor gene and reproductive traits in swine. J. Anim. Sci. 80:2334-2339. NEBRASKA Bertani G, Johnson RK, Pomp D (2003) Mapping of porcine ESTs putatively differentially expressed in anterior pituitary Animal Genetics 34:132-134. Caetano A, RK Johnson, D Pomp (2003) Generation and Sequence Characterization of a Normalized cDNA Library from Swine Ovarian Follicles. Mammalian Genome 14:65-70. Childs KD, DW Goad, MF Allan, D Pomp, C Krehbiel, RD Geisert, JB Morgan, JR Malayer (2002) Expression of the NAT1 translational repressor in intramuscular adipocytes of Angus X Hereford steers. Physiological Genomics 10:49-56. Chiang, C. F., R. K. Johnson, and M. K. Nielsen. 2002. Maternal Behavior in Mice Selected for Large Litter Size. Appl. Anim. Behavior Sci. 79: 63-73. Chiang, C. F., R. K. Johnson, and M. K. Nielsen. 2002. Selection for Maternal Behavior in Mice Direct and Correlated Responses. Appl. Anim. Behaviour Sci. 79: 311-323. Gladney C, G Bertani, MK Nielsen, D Pomp (2003) Evaluation of gene expression in pigs selected for enhanced reproduction. I: Ovarian Follicles. J Anim Sci (In Revision). Leamy L, Pomp D, Eisen EJ, Cheverud J (2002) Pleiotropy of quantitative trait loci for organ weights and limb bone lengths in mice. Physiol. Genomics 10:21-29. Mesa, H. t. J. Safranski, R. K. Johnson, and W. R. Lamberson. 2003. Correlated response in placental efficiency in swine selected for an index of components of litter size. J. Anim. Sci. 81: 74-79. Risatti GR, D Pomp, RO Donis (2003) Patterns of cellular gene expression in cells infected with cytopathic or non-cytopathic bovine diarrhea virus. Animal Biotechnology (In Press). Tuggle C, Green JA, Fitzsimmons C, Woods R, Prather RS, Malchenko S, Soares MB, Tack D, Robinson N, O‘Leary B, Scheetz T, Casavant T, Pomp D, Edeal JB, Zhang Y, Rothschild MF, Garwood K, Beavis W (2003) EST-Based Gene Discovery in Pig: Virtual Expression Patterns and Comparative Mapping to Human. Mammalian Genome (In Press). Wesolowski S, Allan MF, Nielsen MK, Pomp D (2003) Evaluation of hypothalamic gene expression in mice selected for heat loss. Physiological Genomics 13:129-137. Williams RW, Broman KW, Cheverud JM, Churchill GA, Hitzemann RW, Hunter Kw, Muntz JD, Pomp P, Reeves RH, Schalkwyk LC, Threadgill DW (2002) A collaborative cross for high precision complex trait analysis. www.complextrait.org/Workshop1.pdf Ziemba EA, R. K. Johnson, and g. E. Duhamel. 2002. Identification of Brachyspira pilosicoli attachment phenotypes among purebred and crossbred pigs as determined by epithelial cell brush border adhesion. CRWAD, St. Louis, MO. Ziemba EA, E. M. Berberov, C. J. Stryker, R. Zhang, R. K. Johnson, and G. E. Duhamel. Attachment of Brachyspira pilosicoli to Pig Intestinal Brush Borders: Identification of Three Pig Phenotypes. CRWAD. Nov 12-13, St. Louis, MO. OKLAHOMA C. R. Krehbiel, S. R. Rust, G. Zhang, and S. E. Gilliland. 2003. Bacterial Direct-Fed Microbials in Ruminant Diets: Performance Response and Mode of Action. J. Anim. Sci. (In press). USDA, ARS, BARC Lunney, J.K. 2003. In Search of Disease-Resistant Pigs. National Hog Farmer, Apr 15, 2003, pp.30-34. 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. In Press. Lunney JK, Fossum C, Alm GV, Steinbach F, Wattrang E. 2002. Veterinary immunology: opportunities and challenges. Trends Immunol. 23: 4-6. Solano-Aguilar, G.I., Zarlenga, D., Beshah, E., Vengroski, K, Gasbarre, L., Junker, D., Cochran, M., Weston, C., Valencia, D., Chiang, C., Dawson H, Urban J, and Lunney, J.K. 2002. Limited effect of recombinant porcine Interleukin-12 on porcine lymphocytes due to a low expression of IL-122 receptor. Vet. Immunol. Immunopathol. 89: 133-148.

Impact Statements

Publicly available genomic data bases have been greatly enhanced by provision of information from the Regional Project, allowing other researchers and industry to capitalize on developed information and methods.
Progress towards new methodologies and technologies for genetic improvement of pigs has been made, setting the stage for substantial advances in production efficiency and product quality, including increased litter size, improved growth rate and feed efficiency, and improved product quality.

Date of Annual Report: 10/02/2004

Report Information

Annual Meeting Dates: 01/10/2004 - 01/11/2004
Period the Report Covers: 06/01/2003 - 01/01/2004

Participants

Abrahamsen,Mitchell - abe@umn.edu,Univ. of MN;
Alexander,Lee - lee@carrl.ars.usda.gov,USDA-ARS;
Archibald,Alan - alan.archibald@bbsrc.ac.uk,Roslin Institute;
Ashwell,Melissa - melissa_ashwell@ncsu.edu,NCSU;
Baas,Tom - tjbaas@iastate.edu,Iowa State;
Bari,Alan - a-bari@uius.edu,UIUC;
Bates,Ron - batesr@msu.edu,MSU;
Beattie,Craig - cbeattie@cabnr.unr.edu,UN-Reno;
Beever,Jon - jbeever@uiuc.edu,Univ. of IL;
Bendixen,Christian - christian.bendixen@agrsci.dk,DIAS;
Berg,Frida - frida.berg@bmc.uu.se,Uppsala Univ.;
Bierman,Chad - chad@babcockgenetics.com,Babcock Genetics;
Binns,Matthew - matthew.binns@aht.org.uk,AHT;
Burfening,Pete - pburfening@csrees.usda.gov,USDA-CSREES;
Byatt,John - john.c.byatt@monsanto.com,Monsanto;
Cassady,Joe - joe_cassady@ncsu.edu,NCSU;
Clutter,Archie - archie.c.clutter@monsanto.com,Monsanto;
Cohen,Miri - cohenm@agri.huji.ac.il,Hebrew Univ.;
Coppieters,Wouter - wouter.coppieters@ulg.ac.be,VLG-Belgium;
Coutinho,Luiz - llcoutin@esalg.usp.br,Univ. San Paulo;
Da,Yang - yda@tc.umn.edu,Univ. MN;
Dekkers,Jack - jdekkers@iastate.edu,Iowa State;
Dentine,Margaret - mrdentine@cals.wisc.edu,Univ. Wisc;
DeSilva,Udaya - udaya@okstate.edu,OK State;
Ercman,Carolyn - caercman@ucdavis.edu,UCDAVIS;
Ernst,Cathy - ernstc@msu.edu,MSU;
Everts,Robin - everts@uiuc.edu,UIUC;
Everts-van der Wind - Annelie,vdwind@uiuc.edu,UIUC;
Fishback,Tony - tony.fishback@maxxamanalytics.com,Maxxam;
Fitzsimmons,Carolyn - carolyn.fitzsimmins@bmc.uu.se,Uppsala Univ.;
Glenn,Kim - kim@iastate.edu,Iowa State;
Golvan,Serguei - sgolovan@uoguelph.ca,U of Guelph;
Grapes,Laura - lgrapes@iastate.edu,Iowa State;
Green,Ronnie - rdg@ars.usda.gov,USDA-ARS;
Grosz,Michael - michael.d.grozz@monsanto.com,Monsanto;
Hamernik,Deb - dhamernik@csrees.usda.gov,USDA-CSREES;
Harlizius,Barbara - barbara_harlizius@ipg.nl,IPG;
Hayashi,Takeshi - hayatk@affrc.go.jp,NIAS;
Holm,Lars-Erik - larserik.holm@agrsci.dk,DIAS;
Hu,Zhiliang - zhu@iastate.edu,Iowa State;
Jacobsson,Lina - lina.jacobsson@bmc.uu.se,Uppsala Univ.;
Jiang,Zhihua - jiangz@wsu.edu,WSU;
Kappes,Steven - kappes@email.marc.usda.gov,USDA-MARC;
Kazlauskas,Audra - kazlasks@uiuc.edu,Univ. of IL;
Keil,Jeff - jkeil@uiuc.edu,Univ. of IL;
Kollers,Sonja - sk413@cam.ac.uk,Sygen International;
Kuorr,Christopher - ckuorr@gwdg.de,Univ. of Guttiugen;
Kuzmuk,Kristy - kuzmuk@uiuc.edu,Univ. of IL;
Larkin,Denis - dlarkin@uiuc.edu,UIUC;
Larsen,Knud - knud.larson@agrsci.dk,DIAS;
Leeb,Tosso - tosso.leeb@tiho-hannover.de,Vet School Hannover Germany;
Liu,Wansheng - wsliu@cabnr.unr.edu,UN-Reno;
Liu,Hsiao-Ching - hc_liu@ncsu.edu,NCSU;
Lohuis,Michael - michael.m.lohuis@monsanto.com,Monsanto;
Makarevich,Grigory - maka0022@umn.edu,UMN;
Malek,Massoud - massoud.malek@inwagrl.ethz.ch,ETH Zurich;
Marron,Brandy - bhaton@uiuc.edu,Univ. of IL;
Marshall,Kim - kim.marshall@mmigenomics.com,MMI-Davis;
Mazur,Meredith - mjmazur@uiuc.edu,Univ. of IL;
McDaneld,Tara - ksufaninindiana@hotmail.com,Purdue;
Mcewan,John - john.mcewan@agresearch.co,nz,Ag Research;
Meyers,Stacey - smeyers@uiuc.edu,Univ. of IL;
Mican,Davis - milan@toulouse.inra.fr,INRA;
Mikawa,Satoshi - mikawa@affrc.go.jp,NIAS-Tsukuba;
Moeller,Steve - moeller.29@osu.edu,Ohio State;
Mote,Benny - bmote@iastate.edu,Iowa State;
Najar,Fares - fznajar@ou.edu,Univ. of OK;
Nonneman,Dan - nonneman@email.marc.usda.gov,US MARC-ARS;
Pahriah,Chardon - chardon@joey.inva.fr,INRA;
Pauitz,Frank - frank.pauitx@agrsci.dk,DIAS;
Prather,Randy - prather@missouri.edu,Univ. of MO;
Pruitt,Kim - pruitt@ncbi.nlm.nih.gov,NIH/NCBI;
Rathje,Tom - tomrathje@danbredna.com,Danbred NA;
Reecy,James - jreecy@iastate.edu,Iowa State;
Rothschild,Max - mfrothsc@iastate.edu,Iowa State;
Rund,Laurie - larund@uiuc.edu,Univ. of IL;
Rutherford,Mark - ruthe003@umn.edu,Univ. of IL;
Schook,Larry - schook@uiuc.edu,Iowa State;
Schreiwers,Melissa - missa@ourdue.edu,Purdue;
Spencer,Tom - tsspencer@tamu.edu,TAMU;
Squires,Jim - jsquires@uoguelph.ca,U of Guelph;
Stromberg,Bert - b-stro@umn.edu,U of Mn;
Swanson,Kelly - ksswanso@uiuc.edu,Univ. of IL;
Takasuga,Akiko - takasuga@siag.or.jp,Shirakawa Institute;
Talbot,Richard - richard.talbot@bbsrc.ac.uk,Roslin Institute;
Tanaka,Maiko - maiko@gene.staff.or.jp,Staff-Institute;
Tuggle,Christopher - cktuggle@iastate.edu,Iowa State;
van Dorp,Renate - vandorp@msu.edu,MSU;
Van Haeringen,Wim - info@vhlgenetics.com,VHL Genetics;
Venishi,Hirohide - huenishi@affrc.go.jp,NIAS;
Warkup,Chris - chris.warkup@genesis-faraday.org,Genesis Faraday;
Watanabe,Toshio - toshiow@siag.or.jp,Shirakawa Inst.;
Weber,Jack - jweber4@unl.edu,Univ. of Ne;
Wiebe,Robert - robert.wiebe@maxxamanalytics.com,Maxxam;
Wu,Xiao-Lin - nickwu@juno.ansci.wsu.edu,WA State;
Yamada,Takahisa - tyamada@kais.kyoto-u-ac.jp,Kyoto Univ.;
Zhang,Glenn - gulong_zhang@hotmail.com,OSU;

Brief Summary of Minutes

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

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

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.

Impact Statements

Expansion of publicly available information developed from the NC1004 Regional Project members has resulted in new shared resources and tools to allow researchers and industry to capitalize on the developed information and methods.
Direct application of developed technology to genetic improvement of pigs has progressed significantly with extended effort to facilitate industry adaptation.

Date of Annual Report: 10/17/2005

Report Information

Annual Meeting Dates: 12/10/2004 - 12/11/2004
Period the Report Covers: 01/01/2004 - 12/01/2004

Participants

Bates, Ron Michigan State University, batesr@msu.edu;
Cassady, Joe North Carolina State University, Joe-cassady@ncsu.edu;
Dekkers, Jack Iowa State University, jdekkers@iastate.edu;
Grapes, Laura Iowa State University, lgrapes@iastate.edu;
Hamernik, Deb USDA-CSREES, dhamernik@csrees.usda.gov;
Irvin, Keith Ohio State University, Irvin.3@osu.edu;
Johnson, Rodger University of Nebraska, Rjohnson@unl.edu;
Kim, Jae Woo Iowa State University, jaewoo@iastate.edu;
Leeds, Tim Ohio State University, Leeds.10@osu.edu;
Mabry, John Iowa State University, jmabry@iastate.edu;
McElroy, Joe Iowa State University, jmclry@iastate.edu;
Moeller, Steve Ohio State University, Moeller.29@osu.edu;
Mote, Benny Iowa State University, bmote@iastate.edu;
Piyasatian, Napapan Iowa State University, napapan@iastate.edu;
Ramos, Marcos Iowa State University, mramos@iastate.edu;
Stromberg, Bert University of Minnesota, b-stro@umn.edu;
Tuggle, Chris Iowa State University, cktuggle@iastate.edu;
Yu, Mei Iowa State University, meiyu@iastate.edu;
Zhao, Shuhong Iowa State University, shzhao@iastate.edu;
Zhao, Honghua Iowa State University, hhzh@iastate.edu

Brief Summary of Minutes

Minutes Attachment:

Attachment

Accomplishments

Members of the NC1004 Multistate Project (Genetic and Functional Genomic Approaches to Improve Production and Quality of Pork) met on December 10-11, 2004 in conjunction with the National Swine Improvement Federation Annual Meeting in Ames, IA. This was the third meeting of the committee and covered the period January 11 through December 10, 2004. Transcriptional profiling of specific tissues has been a major emphasis of member stations and several stations have utilized the 13,000 70-mer oligonucleotide microarray developed with support from NRSP8 swine genome coordination funds. The Iowa station has used this microarray to identify tissue-specific expression patterns in adult pig lung, liver, small intestine and skeletal muscle tissues. The Michigan station has used this array to evaluate expression patterns in skeletal muscle tissue during secondary fiber formation in mid-gestation and in early postnatal growth. The Iowa station has also used this array along with the technique of subtractive suppression hybridization to identify genes responding to Salmonella infection in mesenteric lymph nodes and lung tissue. The USDA-BARC station has used gene expression assays to assess responses to vaccination for porcine reproductive and respiratory syndrome virus (PRRSV) and also to characterize the immune factors which regulate interferon-gamma dominated immune responses in order to help identify populations of pigs that are susceptible or resistant to respiratory infections. In addition, the Iowa and Oklahoma stations have initiated a project to evaluate gene expression patterns in endometrium and embryo/conceptus during the elongation and implantation phase of reproduction in the Yorkshire and Meishan breeds of pigs. Efforts have continued at several stations to pursue detection of quantitative trait loci (QTL), with efforts at Michigan and Iowa focused primarily on meat quality traits. The Michigan station completed data collection on an F2 Duroc/Pietrain resource population with a total of 958 F2 progeny having complete phenotypic records, and microsatellite genotyping of this population is currently underway. The Iowa station has begun to implement discriminant analysis methods for multitrait QTL detection. The Iowa station also completed a joint QTL analysis of the Iowa State University Berkshire/Yorkshire resource population and the University of Illinois Berkshire/Duroc resource population. The Nebraska station is pursuing fine mapping of QTL for reproductive traits in the NE selection lines. They have used pigs with phenotypic records from several generations of the selection project, and have genotyped these animals using a panel of single nucleotide polymorphism (SNP) markers for four putative QTL regions. The Iowa station has also continued to develop marker-assisted selection strategies, with recent emphasis on efficiency of selection for multiple QTL for a trait in a crossbred population. Evaluation of candidate genes for various traits remains a major emphasis of several stations. The Iowa station has studied several genes affecting meat quality and has also begun to target genes associated with sow longevity. The North Carolina station has begun to characterize follistatin as a candidate gene for litter size. The Vermont station is studying the biological functions of the porcine prolactin receptor in reproduction and lactation. The Oklahoma station has mapped the porcine Kallikreine gene family and has evaluated the expression patterns for several of these genes during early embryonic development in both endometrial and conceptus tissues. Development of selection lines and evaluation of unique genetic resources continued at several member stations. The Nebraska station continued a project begun in 1981 to select for litter size and its component traits, which involved development of five lines. These lines have now been crossed in order to maintain the high reproductive rate, preserve the integrity of the index selection line and reduce inbreeding levels. The North Carolina station has two Duroc selection lines differing in endogenous testosterone production, and purebred and crossbred progeny from these lines have been evaluated for growth and carcass composition traits. The Ohio station has initiated a selection experiment for improved pork quality using the Landrace breed. The Iowa station has continued selection projects for residual feed intake and intramuscular fat deposition. The Iowa station has used frozen semen to produce offspring from Duroc sires used in the 1980s and current Duroc sires in order to evaluate the impact of selection for leanness on carcass and meat quality traits. The Iowa station has studied factors influencing sow longevity and determined that selection for leg confirmation is beneficial for improving longevity. The Iowa station has also studied the relationship between myoglobin content and longissimus muscle color. Finally, the North Carolina station in collaboration with the USDA-MARC station has estimated variance components due to genetic competition effects in pigs. In summary, significant progress has been made toward accomplishing the outcomes and outputs defined for the NC1004 multistate project. Numerous collaborative linkages have developed between the NC1004 member stations (examples include IA/IL, IA/BARC/OK, MI/OK, NE/BARC, NC/MARC, VT/MARC) and many of these partnerships are resulting in successful grant funding, which is allowing research efforts for the project to move forward. Shared resources and public availability of data have been a cornerstone of the project and these continue to be developed and distributed. Integration of quantitative and molecular information facilitates rapid discovery of genetic variation influencing pig health, production efficiency and pork quality. In addition, outreach activities and interaction with industry scientists and producers allow transfer of knowledge to the industry.

Publications

* Indicates joint publications of stations within NC1004 project IOWA *Baas, T. J., K. J. Stalder, J. W. Mabry, and M. T. See. 2004. Effect of off test backfat, loin muscle area, and days to 114 kg on the genetic merit of Yorkshire females for reproductive traits. 15th International Congress on Animal Reproduction, Porto Seguro, Brazil. *Cassady, J. P., O. W. Robison, R. K. Johnson, J. W. Mabry, L. L. Christian, M. D. Tokach, R. K. Miller, and R. N. Goodwin. 2004. National Pork Producers Council Maternal Line Genetic Evaluation: A comparison of growth and carcass traits in terminal progeny. J. Anim. Sci. 82:3482-3485. Ciobanu, D.C., J.W.M. Bastiaansen, S.M. Lonergan, H. Thomsen, J.C.M. Dekkers, G.S. Plastow, and M.F. Rothschild. 2004. New alleles in calpastatin gene are associated with meat quality traits in pigs. J. Animal Sci. 82:2829-2839. Ciobanu, D.C., Lonergan, S.M., Bastiaansen, J.W.M.,Mileham, Miculinich,, Schultz-Kaster, C., Sosnicki, A.A., Plastow , G.S. and M.F. Rothschild. 2004. Association of new Calpastatin alleles with meat quality traits in commercial pigs. 50th Int. Congress of Meat Science and Technology, Helsinki, Finland. Dekkers, J.C.M. 2004. Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci. 82: E313-328E Dekkers, J.C.M., and R. Chakraborty. 2004. Optimizing purebred selection for crossbred performance using QTL. Genet. Sel. Evol. 36: 297-324. Fernando, R.L., B. R. Southey, J.C.M. Dekkers, M.F. Rothschild, and M. Soller. 2004. Controlling the proportion of false positives (PFP) in a multiple test situation. Genetics 166: 611-619. Gaboreanu, A.M., L. Grapes, A. M. Ramos, J.-J. Kim and M. F. Rothschild. 2004. Characterization of an X-chromosome PCR-RFLP marker associated with fat deposition and growth in the pig. Animal Genetics 35: 401-403. Grapes, L., J.C.M. Dekkers, M.F. Rothschild, and R.L. Fernando. 2004. Comparing linkage disequilibrium-based methods for fine mapping quantitative trait loci. Genetics 166: 1561-1570. Grapes, L., M. Z. Firat, J. C. M. Dekkers, M. F. Rothschild, and R. L. Fernando. 2004. Optimal haplotype structure for linkage disequilibrium-based fine mapping of quantitative trait loci. American Association of Animal Science Midwest Region, Mar 15-17, Des Moines, IA Grapes, L., S. Rudd, R. L. Fernando, and M. F. Rothschild. 2004. In silico SNP identification from porcine EST sequences and comparative analysis with human SNP density. Plant and Animal Genome XII, Jan 10-14, San Diego, CA Grindflek, E, N Hoen, H Sundvold, MF Rothschild, G Plastow, and S Lien. 2004. Investigation of a Peroxisome Proliferator Activated Receptor gamma (PPARG) haplotype effect on meat quality and carcass traits in pigs. Anim. Genet 35:238-241. Houser, T. A., J. G. Sebranek, B. J. Thacker, T. J. Baas, D. Nilubol, E. L. Thacker, and F. Kruse. 2004. Effectiveness of transdermal, needle-free injections for reducing pork carcass defects. Meat Science 68:329-332. Hu, Z-L, K. Glenn, A. M. Ramos, C. J. Otieno, and M. F. Rothschild. 2004. Expeditor: A Pipeline for Designing Pig Primers Using Human Gene Structure and Pig EST Information. Plant and Animal Genome XII, Jan 10-14, San Diego, CA *Johnson, R. K., E. P. Berg, R. Goodwin, J. W. Mabry, R. K. Miller, O. W. Robison, H. Sellers and M. D. Tokach. 2004. Evaluation of procedures to predict fat-free lean in swine carcasses. J. Anim. Sci. 82:2428-2441. Kim, J.-J. and J. C. M. Dekkers. 2004. A combined line-cross and halfsib model to detect and characterize QTL in an F2 outbred cross population. American Society of Animal Science Annual meeting (Abstract). http://www.fass.org/2004/abstracts/414.PDF Kim, K.S., J. J. Kim, J. C. M. Dekkers, and M. F. Rothschild. 2004. Polar overdominant inheritance of a DLK1 polymorphism is associated with growth and fatness in pigs. Mammalian Genome 15:552-559. Kim, K.S., J.J. Kim, J.C.M. Dekkers, and M.F. Rothschild. 2004. Polar overdominance imprinting is associated with growth and fat deposition in pigs. PAG XII p240 Kim, K.S., J.M. Reecy, W.H. Hsu, and L.L. Anderson. 2004. Functional and phylogenetic analyses of a melanocortin-4 receptor mutation in domestic pigs. Domestic Animal Endocrinology 26: 75-86. Martin, B. D., T. J. Baas, C. Schwab, D. W. Newcom, J. F. Lampe, and K. J. Stalder. 2004. Comparison of deposition rates for loin muscle area, backfat, and intramuscular fat percentage among breeds in the 2003 National Barrow Show Sire Progeny Test. J. Anim. Sci. 82 (Suppl. 1):455. *Moeller, S. J., R. N. Goodwin, R. K. Johnson, J. W. Mabry, T. J. Baas, and O. W. Robison. 2004. The National Pork Producers Council Maternal Line National Genetic Evaluation Program: A comparison of six maternal genetic lines for female productivity measures over four parities. J. Anim Sci. 82:41-53. *Moller, M., F. Berg, J. Riquet, D. Pomp, A. Archibald, S. Anderson, K. Feve, Y. Zhang, M.F. Rothschild, D. Milan, L. Andersson and C.K. Tuggle. 2004. High-resolution comparative mapping across pig chromosome 4 (SSC4), emphasizing the FAT1 region. Mammalian Genome 15: 717-31. Mote, B. E., J. D. Loy, and M. F. Rothschild. 2004. Identification of SNPs in the insulin-like growth factor gene family and subsequent mapping of IGF2R and IGFBP1 in pigs. Plant and Animal Genome XII, Jan 10-14, San Diego, CA Newcom, D. W., J. L. Burkett, T. J. Baas, C. R. Schwab, S. J. Moeller, and K. J. Stalder. 2004. Effect of technician, machine, and animal body composition on accuracy of ultrasonic measures of backfat and loin muscle area in swine. J. Anim. Sci. 82 (Suppl. 2):46. Newcom, D. W., K. J. Stalder, T. J. Baas, R. N. Goodwin, F. C. Parrish, and B. R. Wiegand. 2004. Breed differences and genetic parameters of myoglobin concentration in porcine longissimus muscle. J. Anim Sci. 82:2264-2268. Newcom, D. W., T. J. Baas, and K. J. Stalder. 2004. Relationship between backfat depth and its individual layers and intramuscular fat percentage in swine. J. Anim. Sci. 82 (Suppl. 2):39. Rothschild, M.F. 2004. Porcine genomics delivers new tools and results: This little piggy did more than just go to market. Genetical Research 83:1-6. Rothschild, M.F. 2004. DNA advances offer big payoffs. Pig Progress Magazine. 20:1-3. Rothschild, M.F. J. P. Bidanel and D.C. Ciobanu. 2004. Genome Analysis of QTL for Muscle Tissue Development and Meat Quality. In: Muscle Development of Livestock Animals. Physiology, Genetics and Muscle Quality. Eds: M.F. W. te Pas, H.P. Haagsman and M.E. Everts. CABI Publishing pgs 247-266. Rothschild, M.F., G.S. Plastow and S. Newman. 2004. Patenting in animal breeding and genetics. In: WAAP Book of the Year 2003, Eds: A. Rosati, A. Tewolde and C. Mosconi. Pgs 269-280. Schwab, C. R., T. J. Baas, D. W. Newcom, and K. J. Stalder. 2004. An evaluation of performance and carcass characteristics between pigs sired by boars from two different time periods. J. Anim. Sci. 82 (Suppl. 1): 453. Schwab, C. R., T. J. Baas, D. W. Newcom, and K. J. Stalder. 2004. An evaluation of meat and eating quality traits between pigs sired by boars from two different time periods. J. Anim. Sci. 82 (Suppl. 1): 454. Schwab, C. R., T. J. Baas, D. W. Newcom, and K. J. Stalder. 2004. Comparison of growth patterns for loin muscle area, backfat, and intramuscular fat percentage between pigs sired by boars from two different time periods. J. Anim. Sci. 82 (Suppl. 2): 9. Serenius, T., and K. J. Stalder. 2004. Genetics of length of productive life and lifetime prolificacy in the Finnish Landrace and Large White pig populations. J. Anim. Sci. 82:3111-3117. Stalder, K. J., M. Knauer, T. J. Baas, M. F. Rothschild, and J. W. Mabry. 2004. Sow Longevity. Pig News and Information. 25:53N-74N. Thomsen, H., J. C. M. Dekkers, H. K. Lee, and M. F. Rothschild. 2004. Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine J. Anim. Sci. 82:2213-2228. Totir, L.R., R.L. Fernando, J.C.M. Dekkers, and S.A. Fernandez. 2004. A study of the minimum number of loci required for genetic evaluation using a finite locus model. Genet. Sel. Evol. 36: 395-414 Totir, L.R., R.L. Fernando, J.C.M. Dekkers, S.A. Fernandez, and B. Guldbrandtsen. 2004. Effect of using approximate gametic variance covariance matrices on marker assisted selection by BLUP. Genet. Sel. Evol. 36:29-48. Tuggle, C.K., and Midwest Consortium. 2004. Finding the genes expressed in female reproductive tissues in pigs. Bulletin AS 650, January, 2004, Animal Industry Report 2004, Iowa State University, Ames, IA ASL-R1950. Tuggle, C.K., X.W. Shi, L. Marklund, A. Stumbaugh, T.J. Stabel, M.A Mellencamp, L. Galina-Pantoja, and J. Bastiaansen 2004. Association of bacterial infection traits with genetic variation at candidate genes for porcine disease resistance. Bulletin AS 650, Animal Industry Report 2004, Iowa State University, Ames, IA ASL-R1952. *Tuggle, C.K., Y. Zhang, M.F. Rothschild, M.Moller, F. Berg, L. Anderson, J. Riquet, D. Milan, D. Pomp, A. Archibald, and S. Anderson. 2004. A detailed gene map of pig chromosome 4, where the first quantitative trait locus in livestock was mapped. Bulletin AS 650, Animal Industry Report 2004, Iowa State University, Ames, IA ASL-R1951. Villanueva, B., J.C.M. Dekkers, J. A. Woolliams, and P. Settar. 2004. Maximizing genetic gain over multiple generations with quantitative trait locus selection and control of inbreeding. J. Anim Sci. 82: 1305-1314. Wilke, V. L., B. P. Kinghorn, M. G. Conzemius, and M. F. Rothschild. 2004. Prediction of inheritance for cranial cruciate ligament disease in the Newfoundland dog. Abstract to be presented at the 31st Annual Conference of the Veterinary Orthopedic Society. Wilke, V. L., B. P. Kinghorn, M. G. Conzemius, and M. F. Rothschild. 2004. Prediction of inheritance for cranial cruciate ligament disease in the Newfoundland dog. Presented at the 2004 ASAS/ADSA Midwestern Meeting, Des Moines, IA. Zhao, H., D. Nettleton, M. Soller, and J. C. M. Dekkers. 2004. Linkage disequilibrium measures between markers as predictors of linkage disequilibrium between markers and QTL. J. Anim Sci. 82 (Suppl. 2) p.9. Zhao, H., J.-J. Kim , M. Perez-Enciso, and J. C. M. Dekkers. 2004. Detection of quantitative trait loci segregation within pure breeds in a Berkshire x Yorkshire F2 population.American Society of Animal Science Annual meeting (Abstract). http://www.fass.org/2004/abstracts/452.PDF Zhao, S.-H. A. Erickson, and C.K. Tuggle. 2004. Physical and Linkage mapping of lymphocyte antigen 86 (Ly86) gene to porcine chromosome 7. Anim. Genet. 35:164. Zhao, S.-H. and C.K. Tuggle. 2004. Linkage mapping and expression analyses during early gestation in the pig of a novel gene, PLacentally Expressed Transcript 1 (PLET1). Anim. Genet. 35:72-74. Zhao, S.-H., D. G. Simmons, J.C. Cross, T.E. Scheetz, T.L. Casavant, M. B. Soares, and C.K. Tuggle. 2004. PLET1, a highly expressed and processed novel gene in pig and mouse placenta is transcribed but poorly spliced in human. Genomics 84:114-125. 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. 35:142-143. Farber, C.R., N.E. Raney, V.D. Rilington, P.J. Venta and C.W. Ernst. 2003. Comparative mapping of genes flanking the human chromosome 12 evolutionary breakpoint in the pig. Cytogenet. Genome Res. 102:139-144. Wesolowski, S.R., N.E. Raney and C.W. Ernst. 2004. Developmental changes in the fetal pig transcriptome. Physiol. Genomics. 16:268-274. NEBRASKA *T. J. Baas, 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. 2003. 81:2409-2418. *J. P. Cassady, O. W. Robison, R. K. Johnson, J. W. Mabry, L. L. Christian, M. D. Tokach, R. K. Miller and R. N. Goodwin. 2004. National Pork Producers Council Maternal Line Genetic Evaluation: A comparison of growth and carcass traits in terminal progeny. J. Anim. Sci. 2004. 82:3482-3485. *J. W. Holl, J. P. Cassady, D. Pomp and R. K. Johnson. 2004. A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs. J. Anim. Sci. 2004. 82:3421-3429. *R. K. Johnson, E. P. Berg, R. Goodwin, J. W. Mabry, R. K. Miller, O. W. Robison, H. Sellers and M. D. Tokach. 2004. Evaluation of procedures to predict fat-free lean in swine carcasses. J. Anim. Sci. 2004. 82:2428-2441. D. B. Petry and R. K. Johnson. 2004. Responses to 19 generations of litter size selection in the Nebraska Index line. I. Reproductive responses estimated in pure line and crossbred litters. J. Anim. Sci. 2004. 82:1000-1006. D. B. Petry, J. W. Holl and R. K. Johnson. 2004. Responses to 19 generations of litter size selection in the NE Index line. II. Growth and carcass responses estimated in pure line and crossbred litters. J. Anim. Sci. 2004. 82:1895-1902. *S. J. Moeller, R. N. Goodwin, R. K. Johnson, J. W. Mabry, T. J. Baas and O. W. Robison. 2004. The National Pork Producers Council Maternal Line National Genetic Evaluation Program: A comparison of six maternal genetic lines for female productivity measures over four parities. J. Anim. Sci. 2004. 82:41-53. G. R. Bertani, C. D. Gladney, R. K. Johnson and D. Pomp. 2004. Evaluation of gene expression in pigs selected for enhanced reproduction using differential display PCR: II. Anterior pituitary. J. Anim. Sci. 2004. 82:32-40. C. D. Gladney, G. R. Bertani, R. K. Johnson and D. Pomp. 2004. Evaluation of gene expression in pigs selected for enhanced reproduction using differential display PCR and human microarrays: I. Ovarian follicles. J. Anim. Sci. 2004. 82:17-31. Petry, D. B., J. Holl, J. Weber, A. Doster, F. Osorio, and R. Johnson. 2004. Different biological responses of pigs of two genetic populations to PRRSV challenge suggests underlying genetic variation in susceptibility/resistance to PRRSV. NE Swine Report, EC 04-219 A: 24-28. Holl, J. and R. Johnson. 2004. Major genes affect reproduction and early growth. 2004. NE Swine Report, EC 04-219 A: 28-31. *J. Holl, J. P. Cassady, D. Pomp , and R. K. Johnson. 2004. Identification of quantitative trait loci affecting reproduction and early growth in pigs. J Anim. Sci. Vol. 82, Suppl. 1: 452. D. B. Petry, J. W. Holl, F. A. Osario, A. R. Doster, J. S. Weber, and R. K. Johnson. 2004. Biological responses of pigs from two populations to PRRSV challenge. Journal of Animal Science Vol. 82, Suppl. 2: 39. *J. W. Holl, J. P., Cassady, and R. K. Johnson. 2004. Identification of quantitative trait loci affecting birth and weaning weights in pigs. J. Anim. Sci. Vol. 81, Suppl. 1: 195. NORTH CAROLINA *Cassady, J. P., O. W. Robison, R. K. Johnson, J. W. Mabry, L. L. Christian, M. D. Tokach, R. K. Miller, R. N. Goodwin. National Pork Producers Council Maternal Line Genetic Evaluation: A comparison of growth and carcass traits in terminal progeny. Journal of Animal Science. 82(12): 3482-5, 01 Dec 2004. *Holl, J. W., J. P. Cassady, D. Pomp, R. K. Johnson. A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs. Journal of Animal Science. 82(12): 3421-9, 01 Dec 2004. House, R.L., J.P. Cassady, E.J. Eisen, T.E. Eling, and J. Odle. Functional genomic characterization of polygenic obese mice fed t10, c12 conjugated linoleic acid (CLA). FASEB J. 18(4&5), 2004. *Van Vleck, L. D., J. P. Cassady. Unexpected estimates of variance components with a true model containing genetic competition effects. Journal of Animal Science. 2005 Accepted. Walker, S. E., O.W. Robison, C.S. Whisnant, and J.P. Cassady. Effect of divergent selection for testosterone production on testicular morphology and daily sperm production in boars. Journal of Animal Science. 82(8): 2259-63, 01 Aug 2004. Bender, J.M., J.P. Cassady. 2004. Growth and carcass composition in lines divergently selected for testosterone production and their crossbred progeny. Journal of Animal Science Supplement 1 *Van Vleck, L.D., J.P. Cassady. 2004. Random models with direct and competition genetic effects. Proceedings, 2004 Conference on Statistics in Agriculture, Manhattan, KS *Van Vleck, L.D., J.P. Cassady. 2004. Unexpected estimates of variance components with a true model containing genetic competition effects. Journal of Animal Science Supplement 1 *Cassady, J.P., L.D. Van Vleck. 2004. Estimation of (co) variance components due to genetic competition effects in pigs. Journal of Animal Science Supplement 1 *Holl, J.W., J.P. Cassady, R.K. Johnson. 2004. Identification of quantitative trait loci affecting birth and weaning weights in pigs. Journal of Animal Science Supplement 1 *Holl, J.W., J.P. Cassady, D. Pomp, R.K. Johnson. 2004. Identification of quantitative trait loci affecting reproduction and early growth in pigs. Journal of Animal Science Supplement 1 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 C. D. Blowe, E. J. Eisen, O. W. Robison, and J. P. Cassady. Journal of Animal Science Supplement 1 OHIO *Moeller, S. J., R. N. Goodwin, R. K. Johnson, J. W. Mabry, T. J. Baas, O. W. Robison. 2004. The National Pork Producers Council Maternal Line National Genetic Evaluation Program: A comparison of six maternal genetic lines for female productivity measures over four parities. J. Anim. Sci. 82: 41-53 OKLAHOMA Vonnahme,K.A., Fernando,S.C., Ross,J.W., Ashworth,M.D., DeSilva,U., Malayer,J.R., and Geisert,R.D. (2004). Porcine endometrial expression of kininogen, factor XII, and plasma kallikrein in cyclic and pregnant gilts. Biology of Reproduction 70, 132-138 USDA-BARC Martens GW, Lunney JK, Baker JE, Smith DM. 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, Nishi 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. Infection and Immunity. In Press. *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. In Press. Dawson HD, Royaee AR, Nishi 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. 100: 105-111. Royaee AR, Husmann R, Dawson HD, Calzada-Nova G, Schnitzlein WM, Zuckermann F, Lunney JK. 2004. Deciphering the involvement of innate immune factors in the development of the host responses to PRRSV vaccination. Vet. Immunol. Immunopathol. 102: 199-216. Meier WA, Husmann RJ, Calzada-Nova G, Schnitzlein WM, Lunney JK, Zuckermann FA. 2004. In vivo modulation of the PRRS virus vaccine-induced immune responses of swine toward a Th1 phenotype. Vet. Immunol. Immunopathol. 102: 299-314. Galina-Pantoja L, Solano-Aguilar GI, Mellencamp MA, Bastiaansen J, Lunney JK. 2004. Relationship between immune cells and pig growth on a commercial farm. Proc. 18th IPVS Congress, Hamburg, Germany, 2004, Vol. I. p.381. Bannerman D, Paape MJ, Lunney JK. 2004. Immunity: Innate. In Encyclopedia of Animal Science; Pond, W.G., Bell, A.W. Eds.; Marcel Dekker, Inc., New York. p.552-554. Lunney JK, Paape MJ, Bannerman D. 2004. Immunity: Acquired. In Encyclopedia of Animal Science; Pond, W.G., Bell, A.W. Eds.; Marcel Dekker, Inc., New York. p.548-551.

Impact Statements

NC1004 member stations have made significant contributions to publicly available pig genomic resources, allowing other researchers and industry to capitalize on the developed information and methods.
Application of discoveries to genetic improvement of pigs has progressed rapidly facilitating technology transfer and adaptation of new technologies by the US swine industry.

Date of Annual Report: 09/12/2006

Report Information

Annual Meeting Dates: 01/14/2006 - 01/15/2006
Period the Report Covers: 01/01/2005 - 12/01/2005

Participants

Participants Attachment:

Attachment

Brief Summary of Minutes

Minutes Attachment:

Attachment

Accomplishments

Members of the NC1004 Multistate Project (Genetic and Functional Genomic Approaches to Improve Production and Quality of Pork) met on January 14, 2006 in conjunction with the NRSP-8 swine sub-committee and the Plant and Animal Genome Meetings in San Diego, CA. This was the fourth meeting of the committee and covered the period January 1 through December 31, 2005 Efforts have continued at several stations to pursue detection of quantitative trait loci (QTL), with efforts at Michigan and Iowa focused primarily on meat quality traits. Iowa has continued their analyses of the Berkshire x Yorkshire population and joint analyses of the ISU Berkshire x Yorkshire and the Univ. of Illinois Berkshire x Duroc populations. Joint data from two F2 crosses between commercial breeds (Berkshire-Yorkshire at Iowa State University (ISU), and Berkshire-Duroc at the University of Illinois (UOI)) were used to detect QTL with a unique mode of genomic imprinting, polar overdominance (POD), in which all genotypes have equal effect, except one of the heterozygotes (Qq or qQ). All animals were genotyped for 39 (ISU) and 32 (UOI) markers on chromosomes (SSC) 2, 6, 13, and 18. Twenty-six growth, carcass composition, and meat quality traits were analyzed, and tests to differentiate POD QTL from Mendelian, paternal or maternal expression QTL were applied. Two POD QTL, for 24-hr Loin pH (49 cM) and lipid % (151 cM) were detected on SSC2 at a 5% genome-wise (GW) level in the ISU population. An additional two QTL for firmness and juiciness were detected at a 5% chromosome-wise (CW) level on SSC2 and SSC13, respectively. Three POD QTL were detected at the GW level in UOI population, for 24-hr Loin Hunter (89 cM in SSC2), last-rib and average back fat (72 cM, 115 cM in SSC6), and four POD QTL at the CW level, for last-rib and tenth-rib back fat in SSC6, and color score and 24-hr Loin Hunter in SSC18. Joint analyses revealed 3 POD QTL at the GW level for last-rib back fat, lipid %, and 24-hr Loin pH in SSC6, which were detected at the GW level in ISU or UOI. An additional 9 POD QTL were detected at the CW level, of which 5 were not detected in either ISU or UOI. Although false positive results cannot be excluded, their study suggests evidence of POD QTL in pigs and advantages of combining data to increase power for QTL detection. Mode of expression of detected QTL requires verification in other studies. Iowa is also using QTL regions identified to investigate biological and positional candidate genes that are associated with growth, backfat, appetite, and meat quality in commercial pigs. Genes are identified, polymorphisms detected and mapped, and association analyses are conducted. In addition, reproduction and reproductive longevity candidate genes are being identified, mapped and association studies conducted. While Michigan report results from their Duroc x Pietrain reference population. A total of 55 QTL for 22 of the 29 measured growth traits were found to be significant at the 5% chromosome-wise level. Of these 55 QTL, 16 were significant at the 1% chromosome-wise, 11 at the 5% genome-wise, and 10 at the 1% genome-wise significance thresholds. A total of 33 QTL for 15 of the 16 animal random regression terms were found to be significant at the 5% chromosome-wise level. Of these 33 QTL, 11 were significant at the 1% chromosome-wise, 2 at the 5% genome-wise, and 2 at the 1% genome-wise significance thresholds. Putative QTL were discovered for 10th rib and last rib backfat on SSC 6, body composition traits on SSC 9, backfat and lipid composition traits on SSC 11, 10th rib backfat and total body fat tissue on SSC 12, and linear regression of body weight, longissimus muscle area, and 10th rib backfat on SSC 18. A total of 94 QTL for 35 of the 38 carcass and meat quality traits analyzed were found to be significant at the 5% chromosome-wise level. Of these 94 QTL, 43 were significant at the 1% chromosome-wise, 27 at the 5% genome-wise, and 14 at the 1% genome-wise significance thresholds. Putative QTL were discovered for 45 min pH and pH decline on SSC 3, marbling score and carcass backfat on SSC 6, carcass length and number of ribs on SSC 7, marbling score on SSC 12, and color measurements and tenderness score on SSC 15. These results will facilitate fine mapping efforts to identify genes controlling growth, composition and meat quality traits that can be incorporated into marker-assisted selection programs to accelerate genetic improvement in pig populations. The Nebraska station furthered their search for QTL affecting reproduction and applied new statistical models to existing data. Data from the F2 resource population were reanalyzed with models that allowed composite interval mapping and search for chromosomal regions with imprinted effects. Based on these findings, a simulation program was developed to simulate the pedigree structure and selection background from Generation 0 to 23 in the Nebraska lines. A QTL for litter size, the one with the largest effect identified in the genome scan, with frequency of .5 for each of two alleles was incorporated at a known position on one chromosome and SNP were inserted at 1 cM intervals along this chromosome. The objective was to determine the number of SNP to include in haplotypes to maximize the efficiency of fine mapping QTL of the magnitude found in the NE selection lines and with a similar population structure. Simulated data were compared with actual selection responses and parameter estimates to validate the simulation model. Fine mapping of QTL identified in previous scans was accomplished by using phenotypic and genotypic data from pigs of several generations from the lines described above. Phenotypic data were collected for birth weight (BWT, n = 1422), weaning weight (WWT, n = 1311), age at puberty (AP, n = 669), ovulation rate (OR, n = 797), number of fully formed pigs (FF, n = 841), number of pigs born alive (BA, n = 841), number of mummified pigs (MUM, n = 841), number of nipples (NN, n = 1434), splayleg incidence (n = 458), and number of stillborn pigs (SB, n = 841). Age at puberty was recorded in gilts of Lines I and C1 from Generation 2 through Generation 15 and in gilts of Lines IOL, COL, and C2 through Generation 16. Ovulation rate was recorded in gilts of Lines I and C1 through Generation 11, and in gilts of Lines IOL, COL, and C2 through Generation 16. Number of fully formed pigs, MUM, SB, and BA were recorded in gilts within 24 h of parturition each generation. Four regions on chromosomes 6, 11, 12, and 13 were chosen to fine map and validate QTL because these regions had previously shown to harbor QTL in the F2 resource population (Cassady et al., 2001; Holl et al., 2004). Monsanto Choice Genetics developed SNP panels to genotype samples. A total of 1167 animals were genotyped for 118 single nucleotide polymorphism (SNP) markers. The Iowa, Nebraska, North Carolina, and Ohio stations continue to create and maintain selection lines of pigs. At Iowa after four generations of selection for intramuscular fat (IMF), the average EBV for select line pigs is 1.03% greater than for control line pigs. Of the pigs harvested in generation four, line LS means for tenth rib backfat and loin muscle area were 18.58 mm and 42.94 cm2 in the control line, and 21.62 mm and 39.22 cm2 in the select line (P < 0.05), respectively. Analysis of STAGES data evaluated on all 810 pigs in generation four revealed no significant difference between lines for days to 114 kg, however, compositional differences similar to those found in the pigs harvested were noted. Results through generation four indicate that selection for IMF has resulted in slightly more tenth-rib backfat and less LMA, while having no significant effect on growth performance. Chemical analysis of a loin sample from pigs harvested revealed a significant phenotypic response in IMF (3.04% in the control line vs. 3.97% in the select line) similar to the difference between lines for IMF EBV. Line LS means for pigs harvested in generation four for 24 h Hunter L and Minolta were 45.77 and 21.99 in the control line, and 49.79 and 24.67 in the select line (P < 0.05), respectively. Subjective measures of marbling were significantly different between lines (2.25 in the control line vs. 3.00 in the select line); however, subjective measures of color and firmness revealed no significant difference. Other meat quality characteristics such as Instron tenderness, pH, and percent cooking loss, as well as sensory panel evaluations of juiciness, tenderness, chewiness, flavor, and off-flavor were not significantly different after four generations of selection for IMF. Selection on IMF EBV has yielded correlated responses in terms of slightly lighter and less desirable objective measures of color; however, it has had no effect on other objective measures of meat quality. At Nebraska selection for litter size and its component traits ovulation rate, embryonic survival, and uterine capacity was initiated 1981. Five lines were developed including 1) Line I: Index selection line, selected 11 generations for ovulation rate and embryonic survival, and an additional 13 generations for increased litter size; 2) C1, randomly selected control line contemporary to I, 3) Line IOL; derived from Line I at Generation 8 and subsequently selected 8 generations for ovulation rate and uterine capacity followed by 7 generations of litter size selection; 4) Line COL: derived from Line C1 at Generation 8 and subsequently selected 8 generations for ovulation rate and uterine capacity followed by 7 generations of litter size selection; and 5) Line C2: a line contemporary with Lines IOL and COL, derived from Line C1 at Generation 8 and subsequently selected randomly. At Ohio data were collected from the initial random mated population of Landrace and Berkshire purebred swine were used to estimate genetic (co)variance parameters for use in establishing within and across breed heritability and genetic correlation estimates for use in subsequent long-term genetic selection programs for improved pork quality in the swine species. Data from 1,065 purebred Landrace and 203 purebred Berkshire barrow and gilt progeny were included in the estimation process. Heritability estimates were as follows: Days to 113.4 kg (0.22), Backfat (0.62), Loin Muscle Area (0.57), Minolta Color (0.36), Visual Marbling Score (0.26), Intramuscular Fat Percentage (0.35), Warner-Bratzler Shear Force (0.35), and 24 Hour pH (0.25). Notable genetic correlations were Backfat and pH (r = 0.17), Minolta Color and pH (r = -0.50), Marbling Score and Warner-Bratzler Shear (r = -0.40), Intramuscular Fat Percentage and Warner-Bratzler Shear (r = -0.45). Analyses also showed significant breed effects for most production, carcass, and pork quality traits. In general, Berkshire pigs grew slower, having more tenth rib backfat and smaller tenth rib loin muscle area. In addition, loins from Berkshire pigs were darker in visual and instrumental color, with more visual and chemical marbling content, less purge loss and much more tender measures of instrumental tenderness. The data provided to date are being used to initiate a long-term selection project to improve pork quality in the Landrace breed. North Carolina evaluated the relationships between indirect measures of behavior and performance. The objective of this research was to test the phenotypic relationships among the backtest, resident-intruder test scores (RIS), growth, LM area, and backfat in pigs. Little is known about relationships among measures of pig behavior and economically important traits. However, it may be expected that a pigs behavior affects its performance and the performance of its pen mates. The backtest and resident-intruder test were each done twice on pigs (n = 145) from 20 litters. During the backtest a pig was gently restrained in a supine position for 60 s. Number of bouts of struggling by the pig and total time spent struggling were recorded. Cumulative number of escape attempts (BTS) and cumulative time spent struggling (TTS) during both backtests were analyzed. The resident intruder tests, done with 30 to 50 d old pigs, measures the tendency for aggressive behavior toward other pigs. A solid divider was placed down the center of the pen to separate the resident pig from its penmates. An intruder pig of the same sex and smaller size was placed into the pen with the resident pig. When an attack initiated by the resident pig occurred pigs were immediately separated and the test was terminated (RIS = 1). If after 5 minutes no attack occurred, the test was terminated (RIS = 0). The BTS and TTS were correlated (r = 0.77; P < 0.05) and RIS and BTS were uncorrelated (r = 0.1; P = 0.29). Dam effects influenced BTS, TTS, and RIS (P < 0.03). The BTS and TTS affected ADG in the nursery (P < 0.04) and BTS also affected backfat (P < 0.07) and LM area (P < 0.06). The RIS affected ADG in the nursery, Kg of acceptable standardized fat-free lean per day, total Kg of acceptable standardized fat-free lean and backfat (P < 0.05) and tended to affect days to 110 Kg and LM area (P < 0.1). Piglets with RIS = 2, showing more aggression, had fewer days to 110 Kg, greater lean gain, and more Kg of fat-free lean than pigs with RIS = 1 or 0 (P < 0.05). Increased BTS and RIS were associated with increased kilograms of lean. In conclusion, phenotypic associations do exist among measures of behavior and performance traits, and increased lean gain was associated with increased aggression. Groups at Iowa, Nebraska, and Minnesota have also developed bioinformatic tools. Minnesota continues their work on a relational database for conducting comparative and functional genomics research. MANGOdb contains an exhaustive laboratory information management system (LIMS) for storing data about such diverse topics as animal pedigrees and treatment, tissue and nucleic acid isolation, library production and sequencing, contig building and annotation, genetic and physical mapping, and macro and microarray annotation and hybridization. Current work on the database is focused on the storage and analysis of microarray-based gene expression data and is incorporating the front end and tables from the Stanford Microarray Database, with annotation from a customized version of SOURCEdb. While Iowa and Nebraska have developed computer modeling and simulation programs to develop, optimize, and evaluate strategies for marker-assisted selection. Groups at Nebraska and BARC continue to collaborate on project related to pig disease. At Nebraska two replications of a PRRSV challenge experiment with a total of 400 pigs were conducted. Replication 1 occurred during summer 2002, and Replication 2 in winter of 2003. In each replicate a total of 100 PRRSV-negative, SEW pigs of the NE Index line (Line I) and 100 pigs of a commercial Duroc-Hampshire (DH) line were used. Line I is an inbred Large White-Landrace population that has been closed for 24 generations and selected for increased litter size. It was expected to have low resistance to disease because of its relatively high inbreeding (~25%). Line DH is a non-inbred, terminal sire line that excels in growth and leanness and was expected to have greater disease resistance than Line I. Genetically diverse lines were used to maximize the opportunity to detect genetic resistance to PRRSV. Two pigs from each of 200 litters by 163 dams and 83 sires were sampled to ensure genetic diversity within lines to maximize the chance that genes for both resistance and susceptibility to PRRSV existed in the sample. Pigs were transferred from their farm of origin at approximately 25 d of age to the University of Nebraska Veterinary Biomedical Sciences animal research facility and randomly assigned within line and litter to isolated rooms for PRRSV challenge. Each replicate included four rooms with 25 pigs per room (12 or 13 from each population). Littermates were assigned to different rooms. Rooms were randomly assigned to treatments with two being control (no PRRSV challenge) and two rooms containing littermates to the pigs in the control rooms assigned to PRRSV challenge. Each uninfected littermate served as a control for its infected littermate. After a 5-d adaptation period, body temperature was recorded and blood was withdrawn from all pigs. Challenged pigs were infected with PRRSV RFLP-Iowa Strain, the standard virulent strain used by the VBMS virology lab of F. Osorio. Blood was withdrawn and body temperature recorded at 4, 7, and 14 d post-challenge. All pigs were sacrificed at d-14, and lung and lymph tissue collected and frozen. Blood, lymph tissue, and lung tissue were analyzed for presence of virus with a procedure that measures the ability of the pig to replicate the PRRSV virus. The presence of lesions in lungs and lymph nodes was characterized. Principal component analyses were used to identify pigs from each population with high and low phenotypic response to PRRSV. Traits included in analyses were weight gain, change in body temperature, viremia, lymph and spleen PRRSV titer, ELISA antibody ratio, and lung lesion score. Variation in the first principal component described overall phenotypic response to PRRSV. The left tail of the distribution contained pigs that had been infected with PRRSV, but showed very few symptoms of disease, whereas those in the right tail were infected and had severe cases of PRRS. Pigs in these tails were arbitrarily categorized as resistant or susceptible. Seven to eight pigs within each category within each population were identified. RNA was extracted from lung tissue from these pigs and their littermates and cDNA was created. Differences in expression of genes was evaluated with microarray analyses. In addition, a sample of lung of each pig was sent to Dr. Joan Lunney, USDA BARC, who evaluated differences in expression of 12 specific immune function genes. During 2005, RNA was extracted from lymph tissue of these same pigs and differences in gene expression between resistant and susceptible pigs was determined. BARC has focused on PRRS. They utilized real-time expression assays for panels of immune markers known to control vaccine and disease immunity (see database www.ba.ars.usda.gov/nrfl/nutri-immun-db/nrfl_query1new.html). Their infectious disease work has been aimed at determining effect or mechanisms which lead to innate resistance to infection or promote protective responses against infection. They have used real time gene expression assays to monitor immune gene activation during innate and adaptive [T helper 1 (Th1) and Th2] immune responses. They tested samples, collected as part of the national PRRS CAP grant, from swine infected with, or vaccinated for PRRS virus. Their data indicated that the slow and weak development of innate immunity as evidenced by interferon-alpha (IFNA), intereukin-1 (IL1), IL6, IL8 responses result in a weak interferon-gamma (IFNG) response, thus preventing protective responses and enabling PRRSV to persist in infected pigs. In summary, significant progress has been made toward accomplishing the outcomes and outputs defined for the NC1004 multi-state project. Numerous collaborative linkages have developed between the NC1004 member stations (examples include IA/IL, IA/BARC/OK, MI/OK, NE/BARC, NC/MARC, VT/MARC) and many of these partnerships are resulting in successful grant funding, which is allowing research efforts for the project to move forward. Shared resources and public availability of data has been a cornerstone of the project and these continue to be developed and distributed. Integration of quantitative and molecular information facilitates rapid discovery of genetic variation influencing pig health, production efficiency and pork quality. In addition, outreach activities and interaction with industry scientists and producers allow transfer of knowledge to the industry.

Publications

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Impact Statements

1. NC1004 member stations have made significant contributions to publicly available pig genomic resources, allowing other researchers and industry to capitalize on the developed information and methods.
2. Application of discoveries to genetic improvement of pigs has progressed rapidly facilitating technology transfer and adaptation of new technologies by the US swine industry.