NC1010: Interpreting Cattle Genomic Data: Biology, Applications and Outreach (NC-209)

(Multistate Research Project)

Status: Inactive/Terminating

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SAES-422 Reports

Annual/Termination Reports:

[12/03/2003] [03/11/2005]

Date of Annual Report: 12/03/2003

Report Information

Annual Meeting Dates: 10/04/2003 - 10/05/2003
Period the Report Covers: 10/01/2002 - 09/01/2003

Participants

Matthews, James (jmatthew@uky.edu) and Bullock, Darrh (dbullock@uky.edu) - University of Kentucky; Henderson, David (dnadave@ag.arizona.edu) - University of Arizona; Reecy, James (jreecy@iastate.edu) - Iowa State University; Davis, Mike davis.28@osu.edu) - Ohio State University; Burton, Jeanne (burton@jpilot.msu.edu) - Michigan State University; Da, Yang (yda@umn.edu) - University of Minnesota; Dentine, Gretel (mrdentine@cals.wisc.edu) - University of Wisconsin - Administrative Advisor; Hamernik, Deborah (dhamernik@csrees.usda.gov) USDA/CSREES

Members Absent:;
Hoeschele, Ina (inah@vt.edu) - Virginia Tech; Rodriguez-Zas, Sandra (rodgrzzs@uiuc.edu) - University of Illinios; Crooker, Brian, (crook001@umn.edu), Fahrenkrug, Scott (fahre001@umn.edu), Ponce de Leon, Abel (apl@umn.edu) and Hanson, Les (hanse009@umn.edu) - University of Minnesota; Marshall, Don - South Dakota State University; Gill, Clare (clare-gill@ancs.tamu.edu), Spencer, Thomas (tspencer@ansc.tamu.edu), and David Adelson (david.adelson@tamu.edu) - Texas A&M University; Kerr, David (dkerr@zoo.uvm.edu) and Zhao, Feng-Qi (fzhao@zoo.uvm.edu) - University of Vermont; Jerry, Joe (jjerry@vasci.umass.edu) - University of Massachussetts; Medrano, Juan (jfmedrano@ucdavis.edu) and Van Eenennaam, Alison (alvaneenennaam@ucdavis.edu) - University of California, Davis; Ashwell, Melissa (mashwell@anri.barc.usda.gov) USDA-ARS-Beltsville; Vallejo, Roger (rvallejo@psu.edu); Pennsylvania State University.

Guests in Attendance for Entire Meeting:;
Jerry Taylor - University of Missouri; Curt van Tassell (curtvt@aipl.arsusda.gov) - USDA Beltsville; John Pollack - Cornell University; Sally Madsen (MI graduate student); Brian Zanghi (UK graduate student); Kevin Veach (UK staff member).

Guests in Attendance for Invited Speaker Session:;
Bob Harmon (Chair, UK Department of Animal Science); James Strickland (Research Leader, USDA-ARS-FAPRU); Jim Boling (UK faculty member); David Harmon (UK faculty member); Geri Sipes (UK graduate student); Edwina Miles (UK graduate student); Beth Kitts (UK graduate student); Laurentia Van Rensburg (UK graduate student).

Brief Summary of Minutes

The meeting was held October 4, 2003 in the Weldon Suite of the Goode Barn facility, located on the campus of the University of Kentucky, Lexington. Dr. Jamie Matthews, 2003 Chairperson of NC-1010 organized and chaired the meeting.

The following agenda was followed:

8 AM: Welcome from Bob Harmon (Chairperson, Department of Animal Science)

8 9 AM: Invited Talk and Discussion: What Genetic Information Does the Beef Industry Need?; Speaker: Dr. Pollak, Cornell University and the National Beef Cattle Evaluation Consortium

9 - 10: Invited Talk 2 and Discussion: What Genetic Information Does The Dairy Industry Need?; Speaker: Dr. Curt Van Tassell, Gene Evaluation and Mapping Laboratory, USDA-ARS, BARC

10 11 AM: Invited Talk 3 and Discussion: Expected Outcomes from the Jointly-funded (NHGRI/State of Texas/Industry) Bovine Genome Sequencing Project: Information, Reagents, Methodologies. Speaker: Dr. Jeremy Taylor, Wurdack Chair in Animal Genomics, University of Missouri, Columbia.

11 AM - 11:15: Update on CSREES Funding Opportunities; Speaker: Dr. Deborah Hamernik; USDA-CSREES (National Program Director, Animal Physiology; Program Director, NRI Bovine Genome Sequencing Program; Program Director, Biotechnology Risk Assessment Research Grants)

11:30 AM 2:30 PM: Travel to and tour of the new University of Kentucky Agriculture Research Center

2:30 6 PM: Station Reports (approximately 30 min presentation and discussion) from IA, USDA-NADC, AZ, MI, OH, MN, KY.

6:30 PM 7:30 PM NC-1010 Business Meeting:

Dr. Margaret Dentine (Administrative Advisor) discussed several issues relating to NC-1010 function. (1) The NIMMS website was introduced to the group, as was the need to annually file reports using this system. It was noted that reports should reference project proposal milestones. It also was noted that the NIMSS website could be used for communication among Project members. (2) The poor current and past attendance by some NC-1010 participant stations was noted and identified as a weakness of this project. Dr. Dentine suggested sending a letter after missing one meeting to absent stations, followed by expulsion of stations that miss two meetings. (3) The excellence of the Invited Speaker Program for the present meeting was noted.

Dr. Alison Van Eenennaam (CA) was elected (in absentia with her permission) chairperson for 2004. Dr. David Henderson (AZ) was elected secretary for 2004.

The possibility of the NC-1010 Project hosting a one-half day workshop dealing with relevant issues associated with microarray and proteomic analyses at the 2005 PAG meetings was discussed. Dr. Deb Hamernik (USDA Administrator) suggested coupling the workshop with the bovine species group (NRSP-8). Dr. James Reecy agreed to investigate this possibility. Dr. Dentine suggested that the title of the workshop should be specific and related to NC-1010s project proposal and objectives, especially with regard to goal of hosting a hands-on workshop, as dictated by Objective III of the NC-1010 project proposal. Dr. Dentine also proposed an analysis competition similar to that for the MGED or GAW meetings. Dr. Yang Da agreed to organize the workshop.

The impending launch of the nascent NC-1010 website was discussed. (1) It was agreed that a one-page producer-targeted handout (Marker-Assisted Selection in Beef Cattle) prepared by Dr. Allison Van Eenennaam was appropriate and could act as a prototype for similar outreach information, with the provision that the flyer be modified to indicate an affiliation by the NC-1010 project. (2) The site for the NC-1010 website was discussed. Dr. Dentine noted that NIMMS would not be a good choice. An interim solution was devised whereby CA would house the site during its continuing development, with the intent that another station likely take over this responsibility once it was fully operational.

The issue of absentee members and potential recruitment of new NC-1010 members was addressed further. (1) It was noted that the anticipated attendance by IL and CA representatives to the present meeting did not occur due to illness. After discussion, it was agreed that Dr. Dentine would contact Experiment Station Directors of absent NC-1010 members to query interest in continued participation. It was suggested the a formal letter outlining this issue be sent to all members of the project by e-mail, in addition to a hard copy being sent to those members who had missed the last two meetings. (2) Specific suggestions were made to extend invitations to Jerry Taylor (University of Missouri), Artur Rosa (as SDSU representative), and Hasan Khatib (University of Wisconsin) to become NC-1010 members. Additionally, suggestions were made to send a general membership invitation to all Agricultural Experiment Station Directors, and to USDA-ARS-MARC scientists. To entice new membership, suggestions were made to invite perspective members to the 2005 meeting and to send them NC-1010s new webpage link.

It was agreed that our next full meeting would be in 2005, in conjunction with the 2005 Plant and Animal Genome Meeting.

The 2003 annual meeting of NC-1010 was adjourned about 7:30 PM

Following adjournment, a catered meal was served to participants in the Weldon Suite.

Accomplishments

OBJECTIVE 1 ACCOMPLISHMENTS: Year 2003 Milestone A: Develop Functional cDNA Microarrays for Distribution. Significant progress has been made in the effort to generate functional cDNA arrays with the development of two cDNA resources. (1) A cDNA microarray containing 18,263 unique expressed sequence tag transcripts that is derived from many different tissues types and various physiological states has been developed (MI). A web-accessible database (http://www.nbfgc.msu.edu) has been established to provide pertinent data relating to this microarray. (2) A different cDNA microarray has been completed (AZ) that contains about 4,600 cDNA sequences printed in triplicate, with the vast majority representing three primary tissues: mammary, pituitary and digestive tract. Year 2003 Milestone B: Initiate cDNA Microarray and Proteomics Experiments in Two Model Systems Each. This goal has been met with the use of developed cDNA chips for evaluation of gene expression profiles at 5 Experiment Stations under 7 model systems and the initiation of proteomic experiments (KY) in two model systems. (1) For gut epithelia, microarray evaluation of mRNA levels (two arrays per tissue) of the rumen, large intestine, and small intestine is ongoing (IL). Two response variables are being studied, the ratio of tissue to reference intensities and the intensities of each sample. For mammary tissue, (2) the effects of heat stress and media supplements such as prostaglandin E2 on growth of primary bovine mammary epithelial cells in collagen gels have been performed (AZ), whereas statistical analysis of this study is underway. (3) Development of a genomic analysis of mammary epithelial cell response to infection also is ongoing (VT), using primary cells infected with live Staphylococcus aureus, or exposed to lipopolysacharide (LPS) endotoxin from Escherichia coli. (4) The molecular genetic basis of Escherichia coli-induced mastitis also is ongoing (PA) using a commercially-available mouse microarray (GENE CHIP Mouse Expression Set 430, Affymetrix) to identify candidate genes for host genetic risk factors affiliated with E. coli induced inflammation. (5) The parturition-induced changes in neutrophil gene expression is being evaluated (MI) using a 1,056 cDNA microarray developed from bovine total leucocytes (BOTL-3). (6) This same BOTL-3 cDNA microarray is being used (MI) to evaluate alteration of ileal tissue gene expression patterns in Johnes infected and non-infected cattle, (7) whereas another cDNA microarray was used (MI) to compare gene expression profiles of peripheral blood mononuclear cells isolated from Johnes infected and non-infected cattle. (8) A proteomic approach (IEF, PAGE, mass spectrometry) to identifying regulatory proteins that control amino acid transport and metabolism capacity in cattle tissue has been initiated (KY). Protein expression profiles of gut epithelia, skeletal muscle, and/or adipose tissues collected from one physiological developmental (suckling, weanling, backgrounding, vs. fattening) and one nutrient partitioning (chlortetracyline, anabolic steroid, vs. no tissue composition-altering agent) model are being evaluated. Other Projects: (1) Transgenic modification of the composition of fatty acids in milk fat is being evaluated in transgenic mice generated by pronuclear microinjection of primary fatty acid synthesising genes and in stably-transfected mammary epithelial cells (CA). In a complementary study that seeks to modify the triacylglyceride structure of milk fat (CA), the echidna mammary lysophosphatidic acid acyltransferase gene is being cloned. (2) Associations between weights, gains, and carcass traits and polymorphisms in seven candidate genes of the insulin-like growth factor I and two genes involved with meat tenderness were and/or are being evaluated in Angus beef cattle from high and low IGF-I selection lines (OH). In addition, studies are being conducted to establish the relationships between selection lines and age of heifer puberty, and the relationship between IGF-I and male and female reproductive traits in cattle divergent in blood serum IGF-I levels. (3) A project (VT) to establish the distribution and regulation of glucose transporters to support whole-animal glucose homeostasis in mammary tissue is being well-advanced with the full-length cloning of bovine facilitative and concentrative glucose transporters, and characterization of their expression by liver, lung, kidney, spleen, intestine, skeletal muscle, and mammary tissues. (4) The influence of bovine viral diarrhea virus (BVDV) infection on the typical pattern of gene expression in bovine cells is being characterized using serial analysis of gene expression (SAGE) (USDA-ARS-NADC). To date, 7 SAGE libraries have been constructed and sequenced from BVDV-infected and -noninfected MDBK and BL3 cells, circulating gamma/delta T lymphocytes, and ileal Peyers patch follicular B lymphocytes. (5) In accordance with related cDNA microarray experiments, the putative mechanisms of Mycobacterium paratuberculosis-induced Johnes disease are being further investigated (MI) by evaluating the putative alteration in gene expression of immortalized bovine macrophage cells, peripheral blood mononuclear cells, intestinal legions, and/or mesenteric lymph nodes in three separate experiments. Year 2003 Milestone C: Continue Fine Mapping Using CDDR, DBDR, and Other Available Resource Populations. Five Experiment Stations continue work in this area. (1) Development of a cattle relational quantitative trait loci (QTL) database and browser compiling QTL and sequence information as a tool for comparative mapping and gene discovery continues (CA). The database will use a Generic Genome Browser (http://www.gmod.org), GBrowse, as a customizable software package for genome annotations browsing, and the backbone for the annotation will be human and mouse sequence data available from NCBI. (2) Work also continues (CA) towards development of an AA and BB kappa-casein and beta-lactoglobulin herd of lactating dairy cows to improve cheese yield in dairy cattle, using marker-assisted selection. (3) Using genotypic data from University of Illinois/ARO-Israel and USDA-ARS-BARC research groups, the same data used last year to identify QTL affecting milk production and pregnancy rate, 15 putative QTL have been identified for several conformational traits (USDA-ARS-BARC). (4) Using this same set of genotypic data, Holstein sire families are also being evaluated (IA, USDA-ARS-NADC) to identify putative QTL affecting perinatal survival of calves. (5) Generation of a bovine Y chromosome (BTAY) bacterial artificial chromosome (BAC) contig map and a high-resolution BAC-STS-RH map continues with the sequencing of 1400 BAC clones (MN) and construction of a high-resolution BAC-STS RH map. In addition, (6) characterization of BTAY microsatellite polymorphisms in DNA cattle, sheep, and goats is ongoing (MN) for the development of markers for use in genome analyses of Y-chromosome haplotypes in these species. OBJECTIVE 2 ACCOMPLISHMENTS: Interpret and Apply Genomics and Proteomics Information by Developing Statistical/bioinformatics Methods and Utilizing Molecular Tools in Cattle. Year 2003 Milestones A&B: Establish Microarray Designs (A) and Methods to Handle Microarray False Positives and Data Analysis (B). These milestones have been met by (1) the development of Bayesian and Factor Analysis statistical methods for microarray experiments (two) that assessed expression patterns of genes that encode proteins of various metabolic pathways (AZ); (2) by evaluation of normalization, replication, and significance tests used in cDNA microarray experiments (four) using robust local regression technique, ANOVA models and mixed model approaches (MI); (3) and by the design and evaluation of two-dye cNDA microarrays using alternative representations of the transcript level and associated models (IL). In addition, progress towards development of efficient algorithms to invert the gametic covariance matrix for the marked QTLs is well underway with development of an improved approximation of the gametic covariance matrix for marker assisted genetic evaluation by Best Linear Unbiased Prediction (BLUP) (IA). Year 2004 Milestone A: Establish Recommendations for Optimal Gene Mapping and Functional Genomics Study Designs. Progress towards this Year 2004 milestone already has been made with the analysis of disease simulation software to detect genes for clinical mastitis in cattle families (PA). Year 2004 Milestone B: Establish Statistical Methods for Mapping QTL with Non-additive Effects. Good progress has been made toward this goal in three studies. (1) A mixed model method combining marker and phenotypic information has been developed (MN) for genetic evaluation using BLUP. (2) A study (MN) to assess the effect of genetic sampling and chiasm interference on the accuracy of QTL mapping indicates that inclusion of chiasma interference in QTL analysis improves mapping accuracy. (3) A cost-effectiveness assessment (MN) of optimum marker spacing for QTL detection concludes that the optimum marker spacing for a genome scan ranges from 30 cM to 4 cM. OBJECTIVE 3 ACCOMPLISHMENTS: Develop and Deliver Educational Materials About Bovine Genomics Research to Consumers and Stakeholders. Year 2003 Milestone: Design and Location of Web Site Finalized. Year 2004 Milestone: Web Site Contents Fully Developed. Year 2005 Milestone A: Launch Web Site. The milestone for Year 2003 has been met with the development (CA, MI) of a preliminary website for NC1010 (http://animalscience.ucdavis.edu/LivestockBiotechnology/), while milestones for Years 2004 and 2005 already are nearing attainment. The current website has links to the NC1010 goals, participant contact links, bovine and other species genomic databases, cattle extension webpages, and breed associations. In addition, an outreach section currently contains a prototype producer-targeted handout and Powerpoint presentation (Marker-Assisted Selection in Beef Cattle) and provides links to relevant conferences and workshops. The web site will be launched (CA) in 2004 and hosted by Michigan State University (MI). Year 2005 Milestone B: Host an Outreach Workshop at the 2005 Plant and Animal Genome (PAG) Meeting. Attainment of this milestone also is well underway with the development (MN) of a tentative agenda and contacting of the PAG organizing committee with our intentions to conduct a Quantitative Genomics/Proteomics workshop. The current workgroup for this putative NC-1010 workshop includes NC-1010 members that possess statistical, genetic, and biological research expertise (AZ, IA, IL, KY, MI, MN, PA, TX, USDA-ARS-BARC) and is being co-organized by MN and AZ. Complementing the stated milestones for Objective 3, and acting as groundwork for Year 2005 Milestone B, an International Symposium on Animal Functional Genomics was hosted by MI (May 2003). One hundred-twenty academic, government, and/or industry administrators and researchers, representing 15 countries, assembled to learn the concepts and practical details of high-throughput gene expression profiling. An implicit goal of Objective 3 is the cross-education of industry representatives and academic and government researchers. Progress towards this goal has been made through the Invited Speaker Program for our 2004 Annual NC-1010 meeting. Three speakers presented current prospectuses for genomic-based research needs of the beef and dairy cattle industries and research communities. Importantly, two of the speakers participated in the whole meeting, contributing greatly to discussions of individual Experiment Station Reports.

Publications

ARIZONA Henderson, D.A. 2003. A Bayesian Statistical Method for the Detection of Differential Gene Expression and Control of Multiple Hypothesis Testing With Gene Expression Microarray Data. International Symposium on Animal Functional Genomics, Michigan State University, East Lansing, MI. Henderson, D.A., A. de la Fuente, P. Mendes, and I. Hoeschele. 2003. Factor analysis for the identification of metabolic pathways from microarray expression data. J. Comp. Biol., submitted. Henderson, D.A., and I. Hoeschele. 2003. Bayesian Exploratory Factor Analysis with an Application to the Identification of Metabolic Pathways from Microarray Expression Data. Biostatistics, submitted. Henderson, D.A. 2003. A Bayesian Statistical Method for the Detection of Differential Gene Expression and Control of Multiple Hypothesis Testing With Gene Expression Microarray Data. Bioinformatics, submitted. Stiening, C.M., A.M. Hoying, D.A. Henderson, J.B. Hoying, P.C. Gentry, Y. Kobayashi, and R.J. Collier. 2003. Characterization of a 4,600-cDNA Bovine Microarray. J. Anim. Sci. 86:W22 Suppl. 1. CALIFORNIA Rincon, G. and J.F. Medrano. 2003. Single nucleotide polymorphism (SNP) genotyping of bovine milk protein genes using the tetra primer ARMS-PCR. Animal Breeding and Genetics 120:1-9. Ward, W. 2003. Mammary Growth and Development in the High Growth (hg/hg) Mouse. M.S. Thesis. Website for NC1010: http://animalscience.ucdavis.edu/LivestockBiotechnology/ ILLINOIS Band, M. R., R. E. Everts, Z. L. Liu, D. E. Morin, J. U. Peled, S. L Rodriguez-Zas, and H. L. Lewin. 2003. Gene expression profiling of 17 cattle tissues reveals unique patterns related to tissue function. Plant, Animal and Microbe Genomes XI Conference. Jan. 11-15, 2003. Microarrays section. http://www.intl-pag.org/11/abstracts/P7a_P745_XI.html Unpublished presentation. Loor, J. J., J. K. Drackley, H. M. Dann, R. E. Everts, S. L. Rodriguez-Zas, and H. A. Lewin. 2003. Mammary gene expression analysis in peripartal dairy cows using a bovine cDNA microarray. Journal Animal Science, 81(Suppl. 1): W8. Loor, J. J., J. K. Drackley, H. M. Dann, R. E. Everts, S. L. Rodriguez-Zas, and H. A. Lewin. 2003. Hepatic gene expression analysis in peripartal dairy cows using a bovine cDNA microarray. Journal Animal Science, 81(Suppl. 1): W9. Rodriguez-Zas, S. L., M. R. Band, R. E. Everts, B. R. Southey, Z. L. Liu, and H. A. Lewin. 2003. Analysis of gene expression patterns in the cattle digestive system. Journal Animal Science, 81(Suppl. 1): 628. IOWA Reecy, J.M., and Nettleton, D. (2002) Statistical Analysis of Gene Expression Data from Hypertrophying and Normal Muscle Tissue. International Society of Animal Genetics. Goettigen, Germany. Reecy, J.M., Potts, J., and Smith, T.P.L. (2002) Beyond myostatin; the search for interacting alleles. PAG X proceedings W61. Carson, J.A., D. Nettleton, and J.M. Reecy. 2001. Differential gene expression in the rat soleus muscle during early work overload-induced hypertrophy. The FASEB Journal Express Article 10.1096/fj.01-0544fje Published online December 14, 2001. Stricker, C., M. Schelling, F. Du, I. Hoeschelle, S. A. Fernandez and R. L. Fernando. 2002. A comparison of efficient genotype samplers for complex pedigrees and multiple linked loci. 7th World Congress Genet. Appl. Livest. Prod. CD-ROM Communication N o 21-12. Fernando, R. L., J. C. M. Dekkers and M. Soller. 2002. Controlling the proportion of false positives (PFP) in a multiple test genome scan for marker QTL linkage. 7th World Congress Genet. Appl. Livest. Prod. CD-ROM Communication N o 20-01. KENTUCKY Fan, M. Z., J. C. Matthews, D. G. Burrin, and D. Lackeyram. 2003. EAAC1 is the Major High-Affinity L-Glutamate Transporter and Expression is Upregulated During Differentiation of Neonatal Porcine Enterocytes. FASEB Journal 17(5):A305. Gissendanner, S. J., N. M. P. Etienne, and J. C. Matthews. 2003. Differential Expression of EAAC1 and GLT-1 Glutamate Transporters by Bovine Epithelial Tissues is not Altered by Physiological Development. FASEB Journal 17(5):A305. Gissendanner, S. J., N. M. P. Etienne, K. R. McLeod, and J. C. Matthews. 2003. The Pattern of EAAC1 and GLT-1 Glutamate Transporter Expression by Skeletal Muscle and Adipose Tissues of Fattening Cattle Differs from that of Glutamine Synthetase. FASEB Journal 17(5):A738. Gissendanner, S. J., N. M. P. Etienne, K. R. McLeod, and J. C. Matthews. 2003. The Patterns of EAAC1 and GLT-1 Glutamate Transporters and Glutamine Synthetase Expression by Skeletal Muscle and Adipose Tissues Change as Cattle Grow and Fatten. Oral presentation, March 2003, MANRRS 18th Annual National Career Fair and Training Conference, Atlanta, GA. Howell, J. A., A. D. Matthews, T. C. Welbourne, and J. C. Matthews. 2003. Content of Ileal EAAC1 and Hepatic GLT-1 High-Affinity Glutamate Transporters is Increased in Growing Versus Non-Growing Lambs, Paralleling Increased Tissue Concentrations of D- and L-Glutamate and Plasma Glutamine and Alanine. Journal of Animal Science 81:1030-1039. Krehbeil, C. R. and J. C. Matthews. Absorption of Amino Acids and Peptides. 2003. In: J. P. F. DMello (Ed.) Amino Acids in Animal Nutrition, 2nd edition. Chapter 3, pp. 41-70. CAB International, Wallingford. Novak, D. A. and J. C. Matthews. 2003. Glutamate transport by Rcho-1 cells derived from rat placenta. Pediatric Research 53(5):1-5. MICHIGAN Aho, A.D., A.M. McNulty, and P. M. Coussens. 2003. Enhanced expression of IL-1a and TRAF1 in ileal tissues of cattle infected with Mycobacterium paratuberculosis. Infection and Immunity, 71(11), 6479-6486. Burton, J., P. Coussens, M. VandeHaar, M. Allen, G. Smith, and J. Ireland. 2004. Functional Genomics and the Dairy Cow: From Genes to the Farm. Michigan Dairy Review. (paper copy in press for Jan 2004 issue; also see http://www.msu.edu/user/mdr/). Burton, J.L., and R.J. Erskine. 2003. Mastitis and immunity: some new ideas for an old disease. Veterinary Clinics of North America: Food Animal Practice 19:1-45. Rosa, G.J.M., R.J. Tempelman, S. Suchyta, S.A. Madsen, J.L. Burton, and P.M. Coussens, 2003. Normalization, replication, and significance tests in cDNA microarray experimentation. J. Dairy Sci. 86 (Suppl. 1):159 (abstr. 630). Burton, J.L. 2003. Functional Genomics of the Stress-Immune Axis. International Agriculture Biotechnology Short Course. Michigan State University. May, July, and August, 2003. Burton, J.L. 2003. Animal model: Neutrophil adhesion molecules and apoptosis in inflammation and parturition. Biomarkers of Pre-term Delivery Workshop, Michigan State University. March 21, 2003. Chang, L-C., S.A. Madsen, P.S.D. Weber, T. Toelboell, and J.L. Burton. 2003. Glucocorticoid-Induced Down Regulation of Fas mRNA Abundance in Bovine Neutrophils. International Symposium on Animal Functional Genomics. May 9-11, 2003. Kellogg Center, Michigan State University. (poster presentation). Coussens, P.M. 2003. A model for immune responses to M. avium subspecies paratuberculosis in cattle. Infection and Immunity (Submitted for Publication) Coussens, P.M., A. Jeffers, and C. Colvin, 2003. Rapid and transient activation of gene expression in peripheral blood mononuclear cells from Johnes Disease positive cows exposed to Mycobacterium paratuberculosis in vitro. Microbial Pathogenesis (In press). Coussens, P.M. C.J. Colvin, G.J.M. Rosa, J.Perez Laspiur, and M.D. Elftman. 2003. Evidence for a novel gene expression program in peripheral blood mononuclear cells from M. paratuberculosis infected cattle. Infection and Immunity 71(11), 6487-6498. Coussens, P.M., N. Verman, M.A. Coussens, and A.M. McNulty. 2003. Cytokine gene expression in peripheral blood mononuclear cells and tissues of cattle infected with Mycobacterium avium subspecies paratuberculosis: Evidence for an inherent pro-inflammatory gene expression pattern. Infection and Immunity (Submitted for Publication). Elftman M., P.M. Coussens, and J.J. Ireland. 2003. Effects of estrogen on bovine macrophage gene expression and function. International Symposium on Animal Functional Genomics, Michigan State University, May 9-11, 2003. Ireland, J.J., and D.S. Burns. 2003. Numbers of antral follicles that grow during different follicular waves in individual cattle are highly repeatable. Abstract presented to 36th Annual Meeting of the Society for Study of Reproduction, July 19-22, Cincinnati, OH. Jimenez-Krassel, F., and J.J. Ireland. 2003. The negative action of inhibin on estradiol production by bovine granulosa cells is calcium dependent. Abstract presented to 36th Annual Meeting of the Society for Study of Reproduction, July 19-22, Cincinnati, OH. Jimenez-Krassel, F., Winn, M.E., Burns, D., Ireland, J.L.H., and Ireland, J.J. 2003. Evidence for a negative intrafollicular role for inhibin in regulation of estradiol production by granulosa cells. Endocrinology 144:1876-1886. Kizilkaya, K., P. Carnier, A. Albera, G. Bittante, and R.J. Tempelman. 2003. Cumulative t-link threshold models for the genetic analysis of calving ease scores. Genetics, Selection, Evolution 35:489-512. Kobayashi, Y., Huang, R., Yao, J., Jimenez-Krassel, F., Ireland, J.J., Coussens, P.M., and Smith, G.W. 2003. Differential expression of cocaine and amphetamine regulated transcript (CART) mRNA within the bovine ovary. Abstract presented to 36th Annual Meeting of the Society for Study of Reproduction, July 19-22, Cincinnati, OH. Madsen, S.A., L-C. Chang, M-C. Hickey, G.J. M. Rosa, P.M. Coussens, and J.L. Burton. 2003. Microarray analysis of gene expression in blood neutrophils of parturient cows. Physiological Genomics (in press; also see http://physiolgenomics.physiology.org/papbyrecent.shtml). Madsen, S.A., L-C. Chang, M-C. Hickey, P.M. Coussens, G.J.M. Rosa, and J.L. Burton. 2003. Gene expression profiling and apoptosis phenotyping indicate that parturient steroids promote survival in bovine blood neutrophils. International Symposium on Animal Functional Genomics. May 9-11, 2003. Kellogg Center, Michigan State University. (poster presentation). Pagan, M., Davis, M.E., Stick, D.A., Simmen, R.C.M., Raney, N.E., Tempelman, R.J., 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. Domestic Animal Endocrinology (in press). Suchyta, S.P., S. Sipkovsky, M. Coussens, R. Kruska, A. Jeffers, A. McNulty, R.J. Tempelman, R.G. Halgren, P.M. Saama, D.E. Bauman, Y.R. Boisclair, J.L. Burton, R.J. Collier, E.J. DePeters, T.A. Ferris, M.C. Lucy, M.A. McGuire, J.F. Medrano, T.R. Overton, T.P. Smith, G.W. Smith, T.S. Sonstegard, J.N. Spain, D.E. Spiers, J. Yao, and P.M. Coussens. 2003. Development and testing of a high-density cDNA microarray resource for cattle. Physiological Genomics (in press; also see http://physiolgenomics.physiology.org/cgi/reprint/00094.2003v1). Toelboell, T., P.S.D. Weber, L-C. Chang, K. Buckham, and J.L. Burton. 2003. Dexamethasone-Induced Down Regulation of CD62L Gene Expression in Neutrophils is Mediated by the Glucocorticoid Receptor (GR). International Symposium on Animal Functional Genomics. May 9-11, 2003. Kellogg Center, Michigan State University. (poster presentation). Tooker, B.C., and P.M. Coussens. 2003. Phagocytosis of M. paratuberculosis fails to activate expression of NADH Dehydrogenase and Nucleolin-Related Protein in bovine macrophagesImmunology Letters (Accepted for Publication). Weber, P.S.D., T. Toelboell, J. Durrett-Tirrill, P.M. Saama, and J.L. Burton. 2003. Bone marrow neutrophils contribute minimally to the CD62L mRNA and protein expression profiles of blood neutrophils in glucocorticoid-challenged cattle. International Symposium on Animal Functional Genomics. May 9-11, 2003. Kellogg Center, Michigan State University. (poster presentation). Yao, J., R. Huang, Y. Kobayashi, A. Bettegowda, P.M. Coussens, J.J. Ireland, and G.W. Smith. 2004. Identification and characterization of expression of JY-1: A novel oocyte-specific gene in cattle. Abstract presented to 36th Annual Meeting of the Society for Study of Reproduction, July 19-22, Cincinnati, OH. Yao J, Ren X, Ireland JJ, Coussens PM, GW Smith. 2004. Generation of a bovine oocyte cDNA library: A valuable resource for identification of key oocyte-specific genes. Plant & Animal Genomes XII Conference, Town & Country Convention Center, San Diego, CA, January 10-14, 2004. MINNESOTA Chrystal, M.A. (2003) Marker assisted selection in dairy cattle using a mixed model approach. Ph.D. Thesis (Thesis advisor: Y. Da), Department of Animal Science, University of Minnesota, September 20, 2003. Garbe, J. R. and Y. Da. (2003) Genealogy graphing for large complex populations: the example of European royal genealogy data. Journal of American Human Genetics, Supplement to Vol. 73, p.605, The 53rd Annual Meeting of The American Society of Human Genetics. London, N. R. and Y. Da. (2003) Optimum marker spacing for QTL detection. Journal of American Human Genetics, Supplement to Vol. 73, p.615, The 53rd Annual Meeting of The American Society of Human Genetics. London, N.R, J.R. Garbe, S.M. Schmutz, M.S. Abrahamsen, and Y. Da. (2003) Linkage analysis for mapping genes of sex-influenced traits. Mammalian Genome 14:261-267. Patterson, E.E., J.R. Mickelson, Y. Da, M.C. Roberts, A. McVey, D. OBrien, G. Johnson, and P.J. Armstrong.(2003) Clinical characteristics and inheritance of idiopathic epilepsy in Vizslas. Journal of Veterinary Internal medicine. 17: 319-325. Reed, K. M., L. D. Chaves, J. R. Garbe, Y. Da, and D. E. Harry. (2003) Allelic variation and genetic linkage of avian microsatellites in a new turkey population for genetic mapping. Cytogenetics and Genome Research (In press) Wansheng Liu, Craig W. Beattie, F. Abel Ponce de Lesn. 2003. Bovine Y chromosome microsatellite polymorphisms. Cytogenet. Genome Res. (in press) Wansheng Liu & F. Abel Ponce de Lesn. 2003. Development of a BAC-based physical map of the euchromatic region of the bovine Y-chromosome. Conference Abstract, PAG-XI. P586. Wan-Sheng Liu, Craig W. Beattie, Noelle E. Cockett, F. Abel Ponce de Lesn. 2004. Comparative Analysis of 38 Bovine Y-Chromosome Microsatellites in Cattle, Sheep and Goat. Conference Abstract, PAG-XII. Submitted. Xu, J. and Y. Da. (2003) Genetic sampling and chiasm interference affect QTL mapping accuracy. Journal of American Human Genetics, Supplement to Vol. 73, p.617, The 53rd Annual Meeting of The American Society of Human Genetics. OHIO Chung, H., S. Chen, D. Yoon, I. Cheong, S. Lee, M. Davis, and C. Hines. 2003. Detection of SNPs on the ovine skeletal muscle specific calpain gene using PCR-SSCP analysis. J. Anim. Sci. 81 (Suppl. 1):252. Davis, M.E., S.L. Boyles, S.J. Moeller, and R.C.M. Simmen. 2003. Genetic parameter estimates for serum insulin-like growth factor I concentration and ultrasound measurements of backfat thickness and longissimus muscle area in Angus beef cattle. J. Anim. Sci. 81:2164-2170. Ge, W., M.E. Davis, H.C. Hines, K.M. Irvin, and R.C.M. Simmen. 2003. Association of single nucleotide polymorphisms in the growth hormone and growth hormone receptor genes with blood serum insulin-like growth factor I concentration and growth traits in Angus cattle. J. Anim. Sci. 81:641-648. Yilmaz, A., M.E. Davis, and R.C.M. Simmen. 2003. Estimation of (co)variance components for reproductive traits in Angus beef cattle divergently selected for blood serum IGF-I concentration. J. Anim. Sci. (submitted). Yilmaz, A., M.E. Davis, H.C. Hines, and R.C.M. Simmen. 2003. Age at puberty in heifers divergently selected for blood serum IGF-I concentration. J. Anim. Sci. (submitted). Yilmaz, A., M.E. Davis, and R.C.M. Simmen. 2003. Divergent selection for blood serum insulin-like growth factor I concentration does not change age of Angus heifers at puberty. J. Anim. Sci. 81 (Suppl. 1):255. Yilmaz, A., M.E. Davis, R.C.M. Simmen, and M. Yamaguchi. 2003. Densitometric analysis of myofibrillar proteins in muscle samples from Angus bulls with high or low blood serum IGF-I concentration. J. Anim. Sci. 81 (Suppl. 1):314. Zhao, Q., M.E. Davis, and H.C. Hines. 2003. Associations of polymorphisms in the Pit-1 gene with growth and carcass traits in Angus beef cattle. J. Anim. Sci. (submitted). Yilmaz, A., M.E. Davis, R.C.M. Simmen, and H.C. Hines. 2003. Estimation of correlations of reproductive traits with blood serum IGF-I concentration in Angus beef cattle. J. Anim. Sci. 81 (Suppl. 1):315. Zhao, Q., M.E. Davis, and H.C. Hines. 2002. Polymorphisms in the bovine Pit-1 gene and their associations with growth and carcass traits in beef cattle. Bos taurus Pit-1 gene, exon 3. GenBank Accession No. AY183915. Zhao, Q., M.E. Davis, and H.C. Hines. 2002. Polymorphisms in the bovine Pit-1 gene and their associations with growth and carcass traits in beef cattle. Bos taurus Pit-1 gene, exon 4 and partial cds, bases 1 to 1353. GenBank Accession No. AY183916. Zhao, Q., M.E. Davis, and H.C. Hines. 2002. Polymorphisms in the bovine Pit-1 gene and their associations with growth and carcass traits in beef cattle. Bos taurus Pit-1 gene, exon 4 and partial cds, bases 1 to 885. GenBank Accession No. AY183917. PENNSYLVANIA Vallejo, R.L., Y.L. Li, G.W. Rogers, and M.S. Ashwell. 2003. Genetic diversity and background linkage disequilibrium in the North American Holstein cattle population. J. Dairy Sci., Accepted. Vallejo, R.L. 2003. Power to detect loci linked to common diseases of dairy cattle using identical-by-descent based methods of half-sib pair linkage analysis. J. Anim. Sci. 81:160 (Suppl. 1). USDA-ARS-BARC Koltes, J., Berger, P.J., Dekkers, J.C., Healey, M.H., Ashwell, M.S., Shanks, R.S., Schlesser, H., Lewin, H.A. Evidence for major quantitative trait loci affecting perinatal survival in two elite Holstein sire families. Proceedings of the John M. Airy Beef Cattle Genetics Symposium. 2003. p. 131. Berger, P.J., Koltes, J., Healey, M.H., Ashwell, M.S., Shanks, R.S., Schlesser, H., Lewin, H.A. Putative quantitative trait loci affecting perinatal survial in eleven Holstein families. Journal of Dairy Science. 2003. v. 86. p. 161. USDA-ARS-NADC Neill, J.D., and J.F. Ridpath. 2003. Gene expression changes in BVDV2-infected MDBK cells. Biologicals 31:97-102. Neill, J.D., and J.F. Ridpath. 2003. Gene expression changes in MDBK cells infected with genotype 2 bovine viral diarrhea virus. Vet. Microbiol. 96:301-312. Neill, J.D., and J.F. Ridpath. 2003. Remodeling of cellular functions following infection with bovine viral diarrhea virus type 2 as determined using serial analysis of gene expression. International Symposium on Animal Functional Genomics, Michigan State University, East Lansing, MI. Neill, J.D., and J.F. Ricpath. 2003. Serial analysis of gene expression in bovine viral diarrhea virus 2 infected cells provides evidence for inhibition of cap-dependent translation initiation. American Society for Virology , Davis CA. VERMONT Wellnitz, O. and D.E. Kerr. 2003. Establishment of a bovine cell-culture system to study the genomic response of mammary epithelial cells to infection with Staphylococcus aureus. Journal of Dairy Science 86 (Suppl. 1):92.

Impact Statements

Microarray and proteomic analyses identify specific biochemical pathways that support production traits and diseases, thus well-complementing DNA-characterization research to identify superior cattle.
Establishment of statistical models and methods to provide adequate levels of confidence for interpretation of microarray, QTL, and marker-assisted selection data allows application of this basic research.
Our current outreach activities of workshops, websites, and interactions with vested interest groups provide critical resources to the cattle industry.

Date of Annual Report: 03/11/2005

Report Information

Annual Meeting Dates: 01/15/2005 - 01/15/2005
Period the Report Covers: 11/01/2003 - 01/01/2005

Participants

Members in attendance:

;Melissa Ashwell - North Carolina State University;
Erin Connor BARC;
Alison Van Eenennaam and Juan Medrano University of California Davis;
Khatib Hasan University of Wisconsin;
Dave Henderson University of Arizona;
Clare Gill Texas A&M University;
James Reecy Iowa State University;
Mike Davis Ohio State University;
Sandra Rodriguez-Zas University of Illinois Urbana;
Jeanne Burton Michigan State University;
Yang Da University of Minnesota;
Feng-Qi Zhao University of Vermont;
F. Abel Ponce de Leon - University of Minnesota;
Gretel Dentine - University of Wisconsin;
Deborah Hamernik USDA

Members absent:

;Jamie Matthews and K. Darrh Bullock University of Kentucky;
John Neill VPDLRU-National Disease Center;
Brian Crooker, Leslie Hansen, and Scott Fahrenkrug University of Minnesota;
Rohan Fernando - Iowa State University;
Harris Lewin University of Illinois;
Thomas Spencer Texas A&M University;
David Kerr University of Vermont;
Joe Jerry University of Massachusetts;
Erdogan Memili - Mississippi State University;
John D. Neill USDA/ARS;
Curt Van Tassell, BARC

Guests in attendance:

;Dr. Michael Cowan, Genetic Visions, Inc;
Dr. Marjorie Faust, ABS Global, Inc.;
Dr. Michael Heaton from USDA ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska

Brief Summary of Minutes

The NC-1010 annual meeting was held in the Pacific Salon at the Town and Country Hotel, San Diego, CA, on January 15, 2005, in conjunction with the PAG-XI meetings. Dr. Alison Van Eenennaam, 2004 Chairperson of NC-1010, organized the meeting.

The following Agenda was followed:

Multistate Research Project NC-1010 Annual Meeting
Interpreting Cattle Genomic Data: Biology, Applications and Outreach

Saturday January 15th 2005
1:40 pm - 6:20 pm
Plant and Animal Genome XIII Conference
Town and Country Hotel, San Diego, CA
Pacific Salon 6 & 7

1:40 pm Welcome and Introduction - Alison Van Eenennaam

1:50 2:20 "Accelerated Genetics' Application of DNA Technologies."
Dr. C. Michael Cowan, General Manager, Genetic Visions, Inc.

2:20 2:50 How do we move from the laboratory to the bull barn?
Dr. Marjorie A. Faust, Director of External Research, ABS Global, Inc.

2:50 3:20 "Bovine single nucleotide polymorphisms: implications for animal/food identification, traceback and pedigree verification"
Dr. Michael P. Heaton, Animal Health Research Unit, USDA ARS,
U.S. Meat Animal Research Center, Clay Center, Nebraska

3:20 3:30 Wrap-up of Speaker Session

3:30- 4:00 Coffee Break

4:00- 6:00 Station Reports

6:00 6:20 Election of new officers, discussion of future plans and wrap-up

6:20 pm Adjourn

A. The meeting began at 1:40pm with a series of invited speakers. Dr. Van Eenennaam started the session with an introduction The first speaker was Dr. Michael Cowan of Genetic Visions, Inc. who spoke on Accelerated Genetics' Application of DNA Technologies. Next was Dr. Marjorie Faust from ABS Global, Inc. who gave a talk on How do we move from the laboratory to the bull barn? The final speaker was Dr. Michael Heaton from USDA ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska who presented work on Bovine single nucleotide polymorphisms: implications for animal/food identification, traceback and pedigree verification. Following discussion of the three talks, we broke for coffee and resumed the meeting at 4:00 PM.

Dr. Van Eenennaam called the meeting to order at 4:00 PM on Saturday, January 15 and invited participants to introduce themselves. Several Experiment Station reports were given this evening, followed by the Business meeting.

Experiment Station Reports, and/or descriptions of intended areas of research by new members, were presented by: James Reecy Iowa State University, Melissa Ashwell - North Carolina State University , Jeanne Burton Michigan State University, Erin Connor BARC, Yang Da University of Minnesota, Mike Davis Ohio State University, Clare Gill Texas A&M University, Khatib Hasan University of Wisconsin, David Henderson University of Arizona, Feng-Qi Zhao University of Vermont, Sandra Rodriguez-Zas University of Illinois, and Alison Van Eenennaam University of California Davis.

B. Dr. Deb Hamernik (acting CSREES Administrator) of USDA-CSREES provided an update of developments at the USDA. Specifically:
1. New Secretary of Agriculture has been nominated, Gov. Mike Johanns of Nebraska.
2. CSREES plans to sunset the Animal Genome Reagent and Tools program. Discussion to occur at NRSP-8 business meeting this PAG.
3. Materials describing current research funding at USDA-CSREES for various programs, and current future proposed research budgets were distributed.

C. Future Meetings
A discussion of future meeting sites was held. A motion was made and accepted that the 2006 NC-1010 annual meeting would be held in the fall (in November) of 2005 at Tucson, AZ, with the 2005 NC-1010 chairperson (Dr. David Henderson, see below) and the University of Arizona acting as hosts. A poster session for the presentation of graduate student projects would be held at the meeting, as well.

D. Election of Officers

Dr. David Henderson (2005 secretary) was elected chairperson for 2006. Dr. Clare Gill was elected secretary for 2006.

E. Web Site
An informal discussion was held regarding the NC-1010 web site:
1. It was agreed that the web site would continue to be hosted by UC Davis and maintained by Dr. Alison Van Eenennaam.
2. Any additional links or new pages should be sent to Dr. Van Eenennaam.
3. Links to pages developed for other projects would be accepted, as well.

The annual meeting of NC-1010 was adjourned around 9:30 PM.

The Joint NRSP-8 / NC-1010 Quantitative Genomics/Proteomics Workshop was also held at PAG on Sunday, 16 January 2005 from 8:00 am-6:20 pm. The workshop was organized by Milt Thomas/Yang Da, and followed the following program

Minutes Attachment:

Attachment

Accomplishments

Year 2004 Milestone A: Establish gene & protein expression profiles in the 2003 model systems & initiate new experiments in at least two additional model systems each. Extensive work is ongoing to establish and refine the gene and protein expression profiles in the model systems that were being worked on in 2003. This includes microarray work using tissues from the bovine rumen, large intestine, and small intestine (IL), primary bovine mammary epithelial cells in collagen gels (AZ), mammary epithelial cells responding to an infection using live Staphylococcus aureus, or exposure to lipopolysacharide (LPS) endotoxin from Escherichia coli (VT), and ileal tissue and peripheral blood mononuclear cells from Johnes infected and non-infected cattle (MI). Additionally, a proteomic approach is being used to identifying regulatory proteins that control amino acid transport and metabolism capacity in cattle tissue has been initiated (KY). Experiments have been initiated in four new model systems. (1) An intramammary infusion technique in lactating mice has been established to examine the acute response to LPS (VT), (2) the treatment of bovine neutrophils with endogenous and exogenous glucocorticoids is being used to examine the effect on Fas gene expression (MI), (3) peripheral blood mononuclear cells from cattle experimentally infected with Trypanosoma congolense is being used to help understand bovine trypanosomiasis and trypanotolerance (MI), and (4) serial analysis of bovine viral diarrhea virus (BVDV)-infected cells is being used to investigate the mechanism of immunosuppression in BVDV2-infected cattle (USDA/ARS/NADC). Year 2004 Milestone B: SNP analysis and mapping of ~ 50 candidate genes from model systems in 2003 Expression profiles of 302 genes on a bovine total leukocyte array were found to be influenced by parturition. Predominant clusters of genes with changed expression at parturition were involved in neutrophil, transendothelial migration, and extracellular matrix degradation, but not phagocytosis or killing. Genome sequence trace files encompassing the differentially expressed genes are being analyzed for SNP discovery (MI). Representational Difference Analysis (RDA), was performed using genomic DNA from bulls with high and low EPDs for marbling. Sequence homology analysis indicated that some of the difference products had homology with known genes from bovine, human or mouse, while most had no significant match. Genotype tests were generated for SNPs identified by RDA. Of these, six SNPs are associated with marbling, retail product yield, or back fat in purebred American Angus cattle (IA). In addition to SNP analysis, other type of follow up work is being done on numerous leads/candidate genes obtained from the genomic studies on the model systems outlined above, in addition to other livestock resource populations. Three bovine glucose transporters were cloned and studied for their tissue distributions and developmental regulation in the mammary gland (VT), four genes in mammary epithelial cells were shown to be rapidly and robustly induced by LPS (VT), somatostatin and somatostatin receptor genes are currently being examined for polymorphisms (OH), two cytoskeleton-associated proteins were down-regulated in liver tissue of chlortetracycline-fed but not Synovex-S-treated finishing steers, whereas two amino acid transporters, two anti-oxidant enzymes, and one transcriptional factor were found to be up-regulated (KY). Over 400 genes were identified as differentially expressed in bovine mammary epithelial cells in response to heat stress. Genes involved in trafficking and remodeling, as well as temperature-responsive genes, were among the most significant up-regulated genes. Downregulated genes included those involved in glycolysis, peptide metabolism, and cell morphology. Also of interest were a large number of differentially expressed genes related to G-protein signaling (AZ). Expression profiles of at least 42 genes were found to have inherently different expression profiles in freshly isolated peripheral blood mononuclear cells from M. paratuberculosis infected cattle when compared to similar cells from uninfected controls (MI). Polymorphisms in the protease inhibitor gene associated with milk and fat yields, productive life, and somatic cell score (WI). Year 2004 Milestone C: Intron/exon boundary and promoter analyses of ~10 candidate genes from model systems studied in 2003. Promoter analysis on the bovine somatostatin gene is ongoing in the Angus cattle from the IGF-I selection lines revealed an A to C transversion. Two alleles, E and F, and three genotypes, EE, EF, and FF were observed (OH). A number of other studies meet the objectives and/or achieve the goals of Objective 1. (1) Putative quantitative trait loci affecting conformation traits and calving ease were identified using the merged DBDR genotypic data generated at the University of Illinois and USDA-Beltsville. Regression interval mapping was used to detect QTL affecting 22 conformation traits, including body, udder, feet and legs, and dairy conformation as well as calving ease. Two genome-wise significant QTL influencing calving ease were detected on two chromosomes. Comparison of these results with other published reports identifies many common QTL affecting conformation traits (NC). (2) Putative marker-trait associations between two regions of bovine chromosome 27 and the conformation trait, dairy form were evaluated. There was some evidence of associations with milk fat percentage in the same region (BARC). (3) A cattle genome database and browser compiling QTL and sequence information as a tool for comparative mapping and gene discovery was developed. The database contains 580 QTL entries for 109 traits and 295 molecular markers compiled from 131 literature references (CA). (4) Transgenic modification of the composition of fatty acids in milk fat is being evaluated in transgenic mice. In a complementary study that seeks to modify the triacylglyceride structure of milk fat, the echidna mammary lysophosphatidic acid acyltransferase gene is being cloned (CA). (5) Research is ongoing to evaluate the effect of individual kappa-casein (k-CN) and beta-lactoglobulin (b-LG) genotypes on milk production, milk composition, reproductive performance, disease susceptibility, overall cow performance, and cost/benefits to the producer and industry (CA). IMPACTS OF OBJECTIVE 1: Members of NC1010 are using genomic approaches to identify the candidate genes associated with a variety of traits of importance to cattle production such as skeletal muscle growth, carcass and meat quality, milk production, conformation traits, milking rate, milk quality, digestion/nutrient utilization, female reproduction, stress susceptibility/adaptation, and susceptibility to infectious diseases (mastitis, Bovine viral diarrhea virus, trypanosomiasis, and Johnes disease). Genomic tools have yielded many candidate genes or leads, and researchers are now working to identify functionality and polymorphisms associated with these genes. If markers are derived from this work and found to be associated with the trait of interest in commercial cattle populations, then they may be incorporated into marker-assisted selection programs to accelerate the rate of genetic improvement. Representative examples include the polymorphisms found in the IGF-I, growth hormone, growth hormone receptor, calpain, calpastatin, Pit-1, GHRH-R, IGF-II, somatostatin, and somatostatin receptor 2 loci may be useful in marker assisted selection programs designed to improve growth rates and carcass characteristics of beef cattle (OH), and the QTL and/or candidate genes identified for pregnancy rate and conformation traits (NC, BARC) may be useful for marker-assisted selection for these sustainability traits in dairy cattle. OBJECTIVE 2. Interpret and apply genomics and proteomics information by developing statistical/bioinformatics methods and utilizing molecular tools in cattle. ACCOMPLISHMENTS Year 2004 Milestone A: Recommendations for optimal gene mapping and functional genomics study designs. Several groups are working in this area including studies on (1) the influence of different normalization and parametric models in the detection of genes differentially expressed across conditions using cDNA microarrays was evaluated (IL), (2) the repeatability of the Affymetrix bovine GeneChip (IA), (3) power and sample size calculations for two color microarray experiments with biological and technical replication (MI), and (4) assessing statistical precision, power, and robustness of alternative experimental designs for two color microarray platforms based on mixed effects models (MI). Year 2004 Milestone B: Establish statistical methods for mapping QTL with non-additive effects Statistical methods are being developed to detect imprinted QTL with gender specific recombination frequencies (MN), and to determine the statistical power for detecting epistasis QTL effects under the F-2 Design (MN). This statistical methods research will provide new tools for mapping genes with complex inheritance, for planning experiment to map QTLs with imprinted effects, gender-specific marker-QTL recombination frequencies, and epistasis effects. Other work that meets the goal of utilizing molecular tools in cattle includes research to identify an approach to increase the efficiency of the creation of transgenic animals. This project seeks to find a more rapid way to determine the rate of homologous recombination. Strategies to quantify rates and type of DNA repair among individual cells so as to enable the selection of individuals that support the highest rates of gene targeting are being investigated (MA). Project members have also developed statistical software including a program which was written in R and that performs a global normalization analysis with a linear model simultaneously with assessing significance of gene specific treatment contrasts through bootstrapping of residuals. The software also scales the bootstrap p-value to control the dependent false discovery rate at a user defined level. A developmental version of Stochastic Search Variable Selection has also been performed with the statistical package R (AZ). Two computer packages, Pedigraph 2.0 and MiniInbred, have been developed with the support from Cargill. These programs allow graphical visualization gene flow in a large and complex pedigrees and minimization of inbreeding in animal breeding plans. Trial versions of these programs are available from http://animalgene.umn.edu. (MN). IMPACTS OF OBJECTIVE 2: The successful use of cDNA microarrays to elucidate biological phenomena depends on adequate control of experimental-induced error and characterization of animal-to-animal variation. Therefore, the development and validation of appropriate spotting patterns and hybridization schemes for microarray construction, and establishment of statistical models to provide adequate levels of confidence to identify false positive and negative results, represent major accomplishments. Similarly, the continued development of appropriate statistical methods and software to support QTL analyses and marker-assisted selection are of tremendous importance to the cattle industry. The impact of this objective will be an accelerated rate of productive leads from microarray experiments, and more expeditious analysis of the data. OBJECTIVE 3. Develop and deliver educational materials about bovine genomics research to consumers and stakeholders ACCOMPLISHMENTS Year 2004 Milestone A: Web site contents fully developed Progress on objective three during the past year includes maintenance of the NC1010 website (http://animalscience.ucdavis.edu/LivestockBiotechnology). This website has links to the North Central Regional Association of Agricultural Experiment Station Directors website, NC1010 goals, participant contact links, bovine and other species genomic databases, cattle extension webpages, breed associations, and outreach. Producer-targeted publications on the use of DNA-based markers in dairy and beef cattle selection programs were made available on the outreach section of the website as .pdf downloadable documents. Year 2004 Milestone B: Quantitative Genomics/Proteomics Workshop The Joint NRSP-8 / NC-1010 Quantitative Genomics/Proteomics Workshop was held at the 2005 Plant and Animal Genome Conference on Sunday, 16 January 2005. The workshop was organized by Milt Thomas/Yang Da and had excellent attendance and lively discussions. A number of other outreach events meet the objectives and/or achieve the goals of Objective 3. Two workshops on microarrays were offered at The University of Arizona in 2004. These workshops cover array laboratory techniques and statistical methodology for the analysis of array data. Statistical Analysis course developed at The University of Arizona that covers the analysis of molecular laboratory data (AZ). An article was written for the Michigan Dairy Review (MI) Multiple presentations were made to cattle producers and allied industry throughout California on the use of markers in cattle breeding programs (CA). IMPACTS OF OBJECTIVE 3: The NC1010 website (http://animalscience.ucdavis.edu/LivestockBiotechnology) has been established. Producer-targeted publications on the use of DNA-markers in dairy and beef cattle selection programs have been made available on the outreach section of the website. Members have been involved in various outreach activities including events aimed at both scientific (workshops on microarray analysis, animal functional genomics, quantitative genomics/proteomics) and producer audiences (e.g. use of markers in cattle breeding programs).

Publications

ARIZONA Henderson, D.A. 2005. A Bayesian Statistical Method for the Detection of Differential Gene Expression and Control of Multiple Hypothesis Testing With Gene Expression Microarray Data. 2005 ENAR Meeting, Austin, TX Henderson, D.A. 2005. Stochastic Search Variable Selection For The Detection Of Differential Gene Expression. Intl. PAG XIII, San Diego, CA Henderson, D.A. 2004. Microarray Data Analysis. In Bioinformatics. David Mount, Ed. Cold Spring Harbor Press. Stiening CM, Hoying JB, Abdallah MB, Coussens PM, Collier RJ. 2005. Effects of heat stress on morphology and gene expression of bovine mammary epithelial cells (BMEC) in collagen gel culture. J. Dairy Sci. submitted abstract. CALIFORNIA Kao, B. T., E. J. DePeters, and A. L. Van Eenennaam. 2005. Endogenous Production of Omega-3 Fatty Acids in the Mammary Gland of Transgenic Mice. Abstract # P763. Final program and abstract guide. XIII International Plant & Animal Genome Meeting, San Diego, CA, Jan.15-19, 2005. http://www.intl-pag.org/pag/13/abstracts/PAG13_P763.html Morimoto, K.C. 2004. transgenic expression of C. elegans omega-3 and delta-12 desaturases in mammalian cells. M.S. thesis in Animal Science, UC Davis. Morimoto, K.C., A. L. Van Eenennaam, E. J. DePeters and J. F. Medrano 2005. Endogenous Production of Omega-3 and Omega-6 Fatty Acids in Mammalian Cells. J. Dairy Science 88(3) 1142-1146. Van Eenennaam, A. L. 2004. Genetic Engineering in California Agriculture. 30 minute UC peer-reviewed video. ANRUCTV 04-06, University of California, Division of Agriculture and Natural Resources. 6502V (VHS) or 6502D (DVD) http://groups.ucanr.org/anronuctv/Video_Program_Sales_Information/ Van Eenennaam, A. L. 2004. DNA-based Marker-Assisted Selection in Beef Cattle. Chapter in Cow-Calf Management Guide & Cattle Producers Library. University of Idaho Moscow, ID. (In press.) Van Eenennaam, A. L. 2005. DNA-based Biotechnologies. Chapter in Beef Sire Selection Manual, National Beef Cattle Evaluation Consortium Educational Committee. Submitted. Van Eenennaam, A. L. 2005. What is the future of animal biotechnology ? California Agriculture. Submitted. Van Eenennaam, A. L. NC1010 website (http://animalscience.ucdavis.edu/LivestockBiotechnology) Van Eenennaam, A. L. UC Davis Animal Genomics and Biotechnology Cooperative Extension Program website (http://animalscience.ucdavis.edu/animalbiotech) Wong, M.I. and J.F. Medrano 2005. A Primer on Real Time PCR for mRNA Quantitation. (Review) BioTechniques (in press). ILLINOIS Loor, J. J., J. K. Drackley, H. M. Dann, R. E. Everts, S. L. Rodriguez-Zas, H. A. Lewin. 2004. Gene expression patterns in liver of dairy cows from dry-off through early lactation using a bovine cDNA microarray. Federation of American Societies for Experimental Biology Experimental Biology April 2004, Abstract # 822.4 (http://select.biosis.org/faseb/eb2004_data/FASEB004847.html) Loor, J. J., H. M. Dann, R. E. Everts, S. L. Rodriguez-Zas, H. A. Lewin, and J. K. Drackley. 2004. Mammary and hepatic gene expression analysis in peripartal dairy cows using a bovine cDNA microarray. Annual Meeting of the American Society of Animal Sciences. J. Anim. Sci. 82(Suppl. 1):103, T134. Loor, J. J., D. B. Carlson, R. E. Everts, S. L. Rodriguez-Zas, H. A. Lewin, and J. K. Drackley. 2004. Gene expression profiles in liver of dairy cows in response to feed restriction using a bovine cDNA microarray. Annual Meeting of the American Society of Dairyl Sciences. J. Dairy Sci. 87(Suppl. 1):103, T136. Loor, J. J., N. A. Janovick, R. E. Everts, S. L. Rodriguez-Zas, H. A. Lewin, and J. K. Drackley. 2004. Adipose, mammary, and hepatic gene expression profiling in lactating dairy cows using a bovine cDNA microarray. Annual Meeting of the American Society of Dairy Sciences. J. Dairy Sci. 87(Suppl. 1):103, T135. Rodriguez-Zas, S. L., M. R. Band, R. E. Everts, B. R. Southey, Z. L. Liu, H. A. Lewin. 2004. Comparison of normalization and models for the analysis of gene expression data. Annual Meeting of the American Society of Animal Sciences. J. Anim. Sci. 82(Suppl. 1):377, W256. Rodriguez-Zas, S. L., J. J. Loor, J. K. Drackley, and H. A. Lewin. 2004. Application of a random regression model to gene expression profiling. Annual Meeting of the American Society of Animal Sciences. J. Anim. Sci. 82(Suppl. 1): 242, abs. 365. IOWA Hu, Z.-L., K. Glenn, A.M. Ramos, C.J. Otieno, J.M. Reecy, and M.F. Rothschild. 2005. Expeditor: A pipeline for designing primers Using Human Gene Structure and Livestock Animal EST Information. Journal of Heredity 96:1-3. Soller, M. and J.M. Reecy. 2004. QTL mapping and cloning in beef cattle. AgBioTechNet Proceedings 004 paper 3:1-8. Max F. Rothschild, Susan J. Lamont, James M. Reecy. Current Status of Animal Genomics. Proceedings Annual AAAS meeting, Washintgon DC Feb 17-19, 2005 KENTUCKY M. Z. Fan, J. C. Matthews, N. M. P. Etienne, D. G. Burrin, and B. Stoll. 2004. Expression of Apical Membrane L-glutamate Transporters in Neonatal Porcine Epithelial Cells Along the Small Intestinal Crypt-villus Axis. American Journal of Physiology- Gastrointestinal and Liver Physiology 287:G385-G398. Novak, D., F. Quiggle, and J. C. Matthews. 2004. Androgen Secretion by Rcho-1 Cells is Independent of Extracellular Glutamate Concentration. Placenta 25:548-552. J. C. Matthews. Expression and Function of Non-Organelle Glutamate Transporters To Support Peripheral Tissue Function. 2004. In: S. Gill and O. Pulido (Eds.) Glutamate Receptors in Peripheral Tissues: Excitatory Transmission Outside the Central Nervous System. Chapter 1, pp. 1-30. Kluwer Academc/Plenum Press, New York. G. L. Sipe, S. E. Kitts, K. R. McLeod, and J. C. Matthews. 2004. Chlortetracycline, but not Synovex-S, Differentially Affects Tissue Expression of High-Affinity Glutamate Transporters in Fattening Steers. Journal of Animal Science 82 (suppl. 1):42. S. E. Kitts, J. C. Matthews, G. L. Sipes, T. S. Rumsey, T. H. Elasser, R. L. Baldwin, and K. R. McLeod. 2004. Effects of Chlortetracycline (CTC) and Steroidal Implant on Growth and Plasma Growth Hormone (GH) and Thyroid-Stimulating Hormone (TSH) After Challenge with Thyroid-Releasing Hormone (TRH) and GH-Releasing Hormone (GHR) on Finishing Beef Steers. Journal of Animal Science 82 (suppl. 1):41. MASSACHUSETTS Blackburn, A.C., McLary, S.C., Naeem, R., Luszcz, J., Stockton, D.W., Donehower, L.A., Mohammed, M., Mailhes, J.B., Soferr, T., Naber, S.P., Otis, C.N., and Jerry, D.J. 2003. Loss of heterozygosity occurs via mitotic recombination in Trp53+/- mice and associates with mammary tumor susceptibility of the BALB/c strain. Cancer Res. 64:5140-5147. MICHIGAN Abdel-Azim, G.A., A.E. Freeman, M.E. Kehrli, Jr., S.C. Kelm, J.L. Burton, A.L. Kuck, and S. Schnell. 2005. Genetic basis and risk factors for infectious and noninfectious diseases in US Holsteins. I. Estimation of genetic parameters for single diseases and general health. J. Dairy Sci. 88 (in press, to appear in the March 2005 issue). Burton, J.L. 2003. Functional Genomics of the Stress-Immune Axis. International Agriculture Biotechnology Short Course. Michigan State University. May, July, and August, 2003. (three invited lectures). Burton, J.L. 2003. Animal Functional Genomics Research at Michigan State University: Connecting Animal Agriculture With Mainstream Biology. Department of Biology seminar series, Hope College, Michigan. Nov 21, 2003. Burton, J.L. 2004. Stress-Immune Interactions in Dairy Cattle: New Understanding From a Functional Genomics Perspective. In: Proceedings of the Prince Agri Products, Inc. 24th Annual Feed Ingredients Conference. Held at the West Des MoinesMarriot Hotel, Des Moines, IA, August 17-18, 2004 (CD available from Prince Agri, Inc.). Burton, J.L, P. Coussens, M. VandeHaar, M. Allen, G. Smith, and J. Ireland. 2004. From Genes to Dairy Farms. Michigan Dairy Review 9(1): 12-15 (see Jan 2004 issue of the MDR at http://www.msu.edu/user/mdr/). Burton, J.L., S.A. Madsen, L-C. Chang, P.S.D. Weber, G.J.M. Rosa, L.K. Matukumalli, and T.S. Sonstegard. 2005. Expression Profiles and SNP Analysis of Genes That Regulate Neutrophil Apoptosis, Endothelial Adhesion, and Extracellular Matrix Remodeling at Parturition in Dairy Cows. Proceedings of the Plant and Animal Genome conference, Jan 2005. San Diego, Ca. Confirmation String: jeanneburton_100404_1839 (poster P694). Burton, J.L., S.A. Madsen, L-C. Chang, P.S.D. Weber, K.R. Buckham, and L. Neuder. 2004. Gene Expression Changes During Glucocorticoid Challenge of Bovine Neutrophils and Implications for Immune Cell Function. Session on Genetic and Genomic Techniques in the Study and Management of Production Diseases. 12th International Conference on Production Diseases. Michigan State University. July, 2004 [invited abstract and oral presentation]. Burton, J.L., S.A. Madsen, L-C. Chang, P.S.D. Weber, K.R. Buckham, and P.M. Coussens. 2004. Parturition-Induced Changes in Neutrophil Gene Expression: Implications for Cell Function. FASS annual joint ADSA/ASAS/PSA Animal Health Program Symposium: Integrative aspects of immunity, nutrient metabolism, and production in livestock. St. Louis, MO. July, 2004 [abstract and invited oral presentation]. Burton, J.L, S.A. Madsen, L-C. Chang, P. S.D. Weber, K.R. Buckham, R. van Dorp, M-C. Hickey, and B. Earley. 2005. Gene Expression Signatures in Neutrophils Exposed to Glucocorticoids: a New Paradigm to Explain Neutrophil Dysfunction in Parturient Dairy Cows. Invited Review, Vet. Immunol. Immunopathol. (in press). Burton, J.L., S.A. Madsen, L.-C. Chang, K.R. Buckham, L.E. Neuder, and P.S.D. Weber. 2005. Microarray analysis of bovine neutrophils around parturition: implications for mammary gland and reproductive tract health. Invited paper in the Proceedings of the 12th International Conference on Production Diseases (ICPD) in Farm Animals. Held at the Kellogg Center, Michigan State University, East Lansing. MI, July 19-22, 2004 (in press). Chang, L-C, P.S.D. Weber, S.A. Madsen, T. Toeboell, and J.L. Burton. 2004. Fas gene expression is transcriptionally regulated by glucocorticoids in bovine blood neutrophils. Proceedings of the 85th Annual Meeting of the Conference of Research Workers in Animal Diseases. Chicago, IL. Nov. 14-16, 2004. (abstract 127 and oral presentation). Chang, L-C., R. van Dorp, P.S.D. Weber, K.R. Buckham, and J.L. Burton. 2004. Parturition-induced gene expression signatures in bovine peripheral blood mononuclear cells. Session on Genetic and Genomic Techniques in the Study and Management of Production Diseases. 12th International Conference on Production Diseases. Michigan State University. July, 2004 [abstract and oral presentation]. Chang, L.-C., S.A. Madsen, T. Toelboell, P.S.D. Weber, and J.L. Burton. 2004. Effects of glucocorticoids on Fas gene expression in bovine blood neutrophils. J. Endocrinol. 183:569-583. Coussens, P.M. 2004. A Model for Immune Responses to Mycobacterium paratuberculosis. Infect. Immunity (Minireviews), 72:3089-3096. Coussens, P.M. 2004. Development of gene expression signatures for chronic infectious diseases, a bovine model. International Conference on Immunogenomics, Budaphest Hungary October 11-14, 2004. Coussens, P.M. 2004. Use of Host Genomics to Elucidate Immune Effector Mechanisms. International Veterinary Immunology Symposium, Quebec City, Quebec. July 25-30, 2004. Coussens, P.M., C. B. Pudrith, X. Ren, S. P. Suchyta, J. R. Stabel, K. Skovgaard, and P.M.H. Heegaard. 2005. Johnes disease in cattle is associated with enhanced expression of genes encoding IL-5, GATA-3, tissue inhibitors of matrix metalloproteinases 1 and 2, and factors promoting apoptosis in peripheral blood mononuclear cells. Vet. Immunol. Immunopathol. (in press). Coussens, P.M., M.J. Coussens, B.R. Tooker, and W. Nobis. 2004. Structure of the bovine NRAMP1 gene and identification of novel polymorphisms. DNA Sequence. 15:15-25. Coussens, P.M., N. Verman, M.A. Coussens, M.D. Elftman, and A.M. McNulty. 2004. Cytokine Gene Expression in Peripheral Blood Mononuclear Cells and Tissues of Cattle Infected with Mycobacterium avium subspecies paratuberculosis: Evidence for an Inherent Pro-inflammatory Gene Expression Pattern. Infect. Immunity 72:1409-1422. Eicher, S., and J.L. Burton. 2005. Immune System: Stress Effects. Encyclopedia of Animal Science. Ed. W.C. Pond and A.W. Bell. Marcel Dekker Publisher, New York, NY (in press; see www.dekker.com). Evans, A.C.O., J.L.H. Ireland, M.E. Winn, P. Lonergan, G.W. Smith, P.M. Coussens, and J.J. Ireland. 2004. Identification of candidate estradiol target genes involved in apoptosis and selection of dominant follicles during follicular waves. Biol. Reprod. 70:1475-1484. Glass, E., and P.M. Coussens. 2005. Functional genomics of host pathogen interactions in species of veterinary importance. Vet. Immunol. Immunopathol. (in press). Hill, E.W., G. M. OGorman, M. Agaba, J.P. Gibson, O. Hanotte, S.J. Kemp, J. Naessens, P.M. Coussens, and D.E. MacHugh. 2005. Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics. Vet. Immunol. Immunopathol. (in press). Kobayashi, Y., F. Jimenez-Krassel, Q Li, J.Yao, R. Huang, J.J. Ireland, P.M. Coussens, and G.W. Smith. 2004. Evidence that Cocaine- and Amphetamine- Regulated Transcript is a Novel Intraovarian Regulator of Follicular Atresia. Endocrinol. 145:5373-5383. Madsen, S.A., L-C. Chang, and , J.L. Burton. 2004. Glucocorticoid modulation of Bcl-2 family members A1 and Bak in bovine blood neutrophils. Proceedings of the 85th Annual Meeting of the Conference of Research Workers in Animal Diseases. Chicago, IL. Nov. 14-16, 2004. (abstract 136 and oral presentation). Placed 1st in the American Association of Veterinary Immunologists graduate student oral competition. Madsen, S.A., L-C. Chang, M-C. Hickey, G.J. M. Rosa, P.M. Coussens, and J.L. Burton. 2004. Microarray analysis of gene expression in blood neutrophils of parturient cows. Physiol. Genomics 16:212-221. Madsen, S.A. M-C. Hickey, and J.L. Burton. 2003. Glucocorticoids in parturient serum activate steroid receptors to modulate apoptosis in bovine blood neutrophils. Proc. 84th Annual Meeting of the Conference of Research Workers in Animal Diseases. Nov. 12-14, 2003. Chicago, IL (abstract 100 and oral presentation; 2nd place award in the American Association of Veterinary Immunologists graduate student oral competition; also see the AAVI On-line Newsletter at: http://www.cvm.missouri.edu/aavi/newsletter_3_04/newsletter_3_04.htm#StudentAwards. Ortiz-Colón, G., A.C. Grant, J.L. Burton, M.E. Doumit and D.D. Buskirk. 2004. Dexamethasone Downregulates Glucocorticoid Receptor Expression in Cultured Bovine Preadipocytes. FASS annual joint ADSA/ASAS/PSA meeting. St. Louis, MO. July, 2004 (abstract and oral presentation). Patel, O.V., S.P. Suchyta, S.S. Sipkovsky, J. Yao, J.J. Ireland, P.M. Coussens, and G.W. Smith. 2005. Validation and application of a high fidelity mRNA linear amplification procedure for profiling gene expression. Vet. Immunol. Immunopathol. (in press). Rhoads, R.P., J.D. Sampson, R.J. Tempelman, S.S. Sipkovsky, P.M. Coussens, M.C. Lucy, J.N. Spain, and D.E. Speiers. 2004. Hepatic gene expression profiling in lactating dairy cows during an initial period of hyperthermia. Presented at the Joint ADSA-ASAS Meetings, St. Louis, MO, July 24-28,2004. Saama, P.M., J. B. Jacob, M.E. Kehrli, Jr., A. E. Freeman, S.C. Kelm, A.L. Kuck, R. J. Tempelman, and J.L. Burton. 2004. Genetic Variation in Bovine Mononuclear Leukocyte Responses to Dexamethasone. J. Dairy Sci. 87:3928-3937. Steibel, J. P., Tempelman, R. J., Rosa, G. J. M. Power and sample size calculations for two color microarray experiments with biological and technical replication. J. Anim. Sci. 82 (Suppl. 1): 415, 2004. Steibel, J. P., Rosa, G. J. M., Tempelman, R. J. Thick-tailed and heteroskedastic linear models for the analysis of cDNA microarray data. Presented at the Joint Statistical Meetings 2004 Abstracts, Toronto - Canada, 2004. Suchyta, S.P., Sipkovsky S., Halgren, R.G., Kruska, R.,Elftman, M., Weber-Nielsen, M., Vandehaar, M.J., Xiao, L., Tempelman, R.J., and Coussens, P.M. 2003. Bovine Mammary Gene Expression Profiling Using A cDNA Microarray Enhanced For Mammary Specific Transcripts Physiological Genomics 16: 8-18. Tempelman, R.J. 2005. Assessing statistical precision, power, and robustness of alternative experimental designs for two color microarray platforms based on mixed effects models. Veterinary Immunology and Immunopathology (in press). Tempelman, R.J. 2004. Experimental Design for Gene Expression Microarrays. 2004. Presented at the Second Long OligoNucleotide Microarray Workshop, University of Arizona, Tuscon, May 14, 2004. http://ag.arizona.edu/microarray/workshopMay2004.html . Tempelman, R.J. 2004. Experimental Design for Gene Expression Microarrays. 2004. Presented at the Third Long OligoNucleotide Microarray Workshop, University of Arizona, Tuscon, December 16, 2004. http://ag.arizona.edu/microarray/workshopDec2004.html . Tempelman, R.J., L. D. Douglass, and B.A. Craig. 2004. Mixed Model Workshop. A 2-day workshop presented at the ASAS-ADSA Joint Meetings, St. Louis, MO July 27-28, 2004. Tempelman, R.J. and G.J.M. Rosa. 2004. Design and Analysis of Gene Expression Studies Using Microarrays (1-Day Continuing Education Course), Presented at the Joint Statistical Meetings, Toronto - Canada, 2004. Tooker, B.C., and P.M. Coussens. 2004. Phagocytosis of M. paratuberculosis fails to Activate Expression of NADH Dehydrogenase and Nucleolin-Related Protein in Bovine Macrophages. FEMS Immunol. Lett. 93:137-142. Weber, P.S.D., L.-C. Chang, T. Toelboell, and J.L. Burton. 2004. Mechanisms of glucocorticoid-induced L-selectin (CD62L) down-regulation in bovine blood neutrophils. Session on Genetic and Genomic Techniques in the Study and Management of Production Diseases. 12th International Conference on Production Diseases. Michigan State University. July, 2004 [abstract and oral presentation]. Weber, P.S.D., T. Toelboell, L-C. Chang, J. Durrett Tirrell, P.M. Saama, G.W. Smith, and J.L. Burton. 2004. Mechanisms of glucocorticoid-induced down regulation of neutrophil L-selectin: Evidence for effects at the gene expression level and primarily on blood neutrophils. J. Leuk. Biol. 75:815-827. Weber, P.S.D., T. Toeboell, L-C Chang, and J.L. Burton. 2003. Glucocorticoid-induced down-regulation of L-selectin (CD62L) gene expression in bovine blood neutrophils is mediated by the glucocorticoid receptor (GR). Proc. 84th Annual Meeting of the Conference of Research Workers in Animal Diseases. Nov. 12-14, 2000. Chicago, IL (abstract 99 and oral presentation). Yao, J., X. Ren, J.J. Ireland, P.M. Coussens, and G.W. Smith. 2004. Generation of a Bovine Oocyte cDNA Library and Microarray: Resources for Identification of Genes Important for Follicular Development and Early Embryogenesis. Physiol. Genomics 19:84-92. Yao,J., X. Ren, J.J. Ireland, P.M. Coussens, and G.W. Smith. 2004. Generation of a bovine oocyte cDNA library: a valuable resource for identification of key oocyte-specific genes. Plant and Animal Genome Meeting San Diego, CA January 11-14, 2004. MINNESOTA Garbe, J. R. and Y. Da. (2004) Pedigraph 2.0, a software tool for the graphing and analysis of large complex pedigrees. Abstract book, p. 242, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. Garbe, J. R. and Y. Da. (2004) A computerized approach to minimize inbreeding of breeding plans. Abstract book, p. 376, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. Garbe, J. R. and Y. Da. (2004) Graphical visualization of two large complex populations using Pedigraph 2.0. Abstract book, p. 377, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. Liu, W., C.W. and F. A. Ponce de León. 2004. Assignement of SRY, ANT3 and CSF2RA to the Bovine Y Chromosome by FISH and RH mapping. Animal Biotechnology, 15: 103-109. London, N.R. (2004) Statistical theory and methods for mapping gender-affected genes and quantitative trait loci. Ph.D. Thesis. Department of Animal Science and Program in Molecular Veterinary Bioscience, University of Minnesota. London, N. R. and Y. Da (2004) Statistical methods to detect imprinted QTL with gender specific recombination frequencies. Abstract book, p. 416, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. London, N. R. and Y. Da (2004) Linkage analysis and experimental design for mapping imprinted genes. Final Abstracts Guide, page 254. Plant and Animal Genome XI, San Diego, USA, January 11 15, 2003. Mao, Y. a and Y. Da. (2004) Statistical power for detecting epistasis QTL effects under the F-2 Design. Abstract book, p. 414, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. Mizoshita, K., N. Ihara, C.M. Carpio, G.L. Bennett, F.A. Ponce de León, C.W. Beattie and Y. Sugimoto. Chromosomal mapping of 65 microsatellites developed from microdissected BTA14 and BTA20 chromosome-specific genomic libraries. Animal Genetics 35:408-410. Xu, J. (2004) Statistical analysis for mapping linked quantitative trait loci. Ph.D. Thesis. Department of Animal Science, University of Minnesota. Xu, J., J.R. Garbe, N.R. London, Y. Mao and Y. Da. (2004) Evaluation of three statistical methods for QTL analysis. Abstract book, p. 243, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. MISSISIPPI None reported NORTH CAROLINA Ashwell, M.S., Heyen, D.W., Sonstegard, T.S., Van Tassell, C.P. and Lewin, H.A. (2004) Detection of quantitative trait loci affecting conformation traits in Holstein cattle. Journal of Dairy Science. 87 (Suppl. 1): 414. Ashwell, M.S., Heyen, D.W., Sonstegard, T.S., Van Tassell, C.P., Da, Y. VanRaden, P.M., Ron, M. Weller, J.I. and Lewin, H.A. (2004) Detection of quantitative trait loci affecting female fertility and milk production in ten Dairy Bull DNA Repository families. Journal of Dairy Science. 87: 468-475. Connor, E.E., Sonstegard, T.S., Ashwell, M.S., Bennett, G.L. and Williams, J.L. (2004) Chromosomal mapping of 12 gene-associated markers in cattle identified novel regions of conserved synteny between the human and bovine genomes. Plant and Animal Genome XII: P630. Connor, E.E., Sonstegard, T.S., Ashwell, M.S., Bennett, G.L. and Williams, J.L. (2004) An expanded comparative map of bovine chromosome 27 targeting dairy form QTL regions. Animal Genetics. 35: 265-269. Connor, E.E., Sonstegard, T.S., Keele, J.W., Bennett, G.L., Williams, J.L., Papworth, R., Van Tassell, C.P. and Ashwell, M.S. (2004) Physical and linkage mapping of mammary-derived expressed sequence tags in cattle. Genomics. 83: 148-152. Van Tassell, C.P., Sonstegard, T.S. and Ashwell, M.S. (2004) Mapping quantitative trait loci for dairy form in regions of chromosome 27 in two families of Holstein. Journal of Dairy Science. 87: 450-457. OHIO 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. Domestic Anim. Endocrin. 25:345-358. Yilmaz, A., M.E. Davis, and R.C.M. Simmen. 2004. Estimation of (co)variance components for reproductive traits in Angus beef cattle divergently selected for blood serum IGF-I concentration. J. Anim. Sci. 82:2285-2292. Zhao, Q., M.E. Davis, and H.C. Hines. 2004. Associations of polymorphisms in the Pit-1 gene with growth and carcass traits in Angus beef cattle. J. Anim. Sci. 82:2229-2233. TEXAS Bryan, T.M., Abbey, C.A., Raudsepp, T., Chowdhary, B.P., Gill, C.A., Ing, N.H., Blanchard, T. and Welsh, T.H., Jr (2004) Chromosome assignment of an equine glucorticoid receptor gene (GR) using fluorescence in situ hybridization (FISH) and radiation hybrid (RH) mapping. Anim. Genet. (accepted). Dikeman, M.E., Pollak, E.J., Zhang, Z., Moser, D.W., Gill, C.A. and Dressler, E.A. (2004) Phenotypic ranges and relationships among carcass and meat palatability traits for fourteen cattle breeds, and heritabilities and expected progeny differences for Warner-Bratzler shear force in three beef cattle breeds. J. Anim. Sci. (submitted). Fluharty, F.L., Gill, C.A., Raudsepp, T., Chowdhary, B.P. and Jackwood, D.L. (2004) Identification of a sequence characterized, amplified DNA marker associated with the potential for marbling in steers. Anim. Genet. (submitted). Gill, C.A., Herring, A.D., Lunt, D.K., and Sanders, J.O. (2004) An overview of the McGregor Genomics Project: Mapping genes for production efficiency. Proceedings of the 50th annual Beef Cattle Short Course, August 2-4, College Station, TX. pp. H1-H8. Herring, A. D. and Gill, C.A. (2004) Genetic Markers and Marker Assisted Selection in Beef Cattle. Proceedings of Ovagenix Customer Information Field Day, July 31, College Station, TX. Amen, T.S., Herring, A.D., Gill, C.A. and Sanders, J.O. (2004) Investigation of birth weight and gestation length in Bos indicus-Bos taurus reciprocal cross calves produced through embryo transfer. 2004 Beef Cattle Research in Texas, pp. 1-3. Moser, D.W., Thallman, R.M., Pollak, E.J., Dikeman, M.E., Gill, C.A., Koontz, S.R., Holm, T.R. and Dressler, E.W. (2004) Meeting consumer demands through genetic selection: the NCBA Carcass Merit Project. Proceedings of the 36th annual meeting of the Beef Improvement Federation, Sioux Falls, SD. pp. 42-44. Rakowitz, K.R., Abbey, C.A., Schein, J., Adelson, D.L. and Gill, C.A. (2004) A 3Mb BAC contig and STS content map of the POLL critical interval on bovine chromosome one. (Abstract) Proceedings of the 29th International Conference on Animal Genetics, Tokyo, Japan, Sept. 11-16. Amen, T.S., Herring, A.D., Gill, C.A. and Sanders, J.O. (2004) Investigation of gestation length in Bos indicus-Bos taurus reciprocal backcross calves produced through embryo transfer. J. Anim. Sci. 82 (Suppl. 1): 449 (Abstract #882). Amen, T.S., Herring, A.D., Gill, C.A. and Sanders, J.O. (2004) Investigation of birth weight in Bos indicus-Bos taurus reciprocal backcross calves produced through embryo transfer. J. Anim. Sci. 82 (Suppl. 1): 449 (Abstract #882). Chiu, R., Bosdet, I., Mathewson, C., Wye, N., Lee, D., Barber, S., Yang, G., Stott, J., Abbey, C., Motta de Carmo Costa, M., Gill, C., Hansen, C., Keele, J., Larkin, D., Meng, Y., Osoegawa, K., Schibler, L., Siddiqui, A., Snelling, W., Williams, J.L., Adelson, D., Archibald, A., Benkel, B., Caetano, A.R., Eggen, A., Holt, R., Jones, S., de Jong, P.J., Lewin, H., McEwan, J.C., Moore, S., Tellam, R., Zhao, S., Kappes, S., Marra, M. and Schein, J. (2004) A BAC physical map of the bovine genome. (Abstract) Proceedings of Plant and Animal Genome XII, San Diego, California, USA. USDA-ARS-BARC Ashwell, M.S., Heyen, D.W., Sonstegard, T.S., Van Tassell, C.P., Da, Y., VanRaden, P.M., Ron, M., Weller, J.I., Lewin, H.A. Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle. J. Dairy Sci. 2004. v. 87. pp. 468-475. Connor, E.E., Sonstegard, T.S. Ashwell, M.S., Bennett, G.L., Williams, J.L. An expanded comparative map of bovine chromosome 27 targeting dairy form QTL regions. Anim. Genet. 2004. v. 35. pp. 265-269. Van Tassell, C.P., Sonstegard, T.S., Ashwell, M.S. Mapping quantitative trait loci affecting dairy conformation to chromosome 27 in two Holstein grandsire families. J. Dairy Sci. 2004. v. 87. pp. 450-457. USDA-ARS-NADC Neill, J.D. and J.F. Ridpath. 2004. Remodeling of cellular functions following infection with bovine viral diarrhea virus type 2 as indicated using Serial Analysis of Gene Expression. American Society for Virology. Montreal , Quebec, Canada Neill, J.D. 2004. Functional genomics analysis of bovine viral diarrhea virus-infected cells: unraveling an enigma. International Conference on Production Diseases in Farm Animals, East Lansing, Michigan. Neill, J.D., 2004. Functional genomics analysis of infection by bovine viral diarrhea virus type 2 in a bovine B-cell lymphosarcoma cell line. Conference of Research Workers in Animal Disease, Chicago, Illinois. VERMONT Wellnitz, O. and D.E. Kerr. 2004. Cryopreserved bovine mammary cells to model epithelial response to infection. Veterinary Immunology and Immunopathology 101:191-202. Zhao, F.-Q., Zheng, Y.-C., Wall, E.H., and McFadden, T.B. 2005. Cloning and expression of bovine sodium/glucose cotransporters. J. Dairy Sci. 88, 182-194. Zhao , F.-Q., Miller, P. J., Wall, E. H., Zheng, Y.-C., Dong, B. Neville, M. C., and McFadden, T. B. 2004. Bovine glucose transporter GLUT8: cloning, expression, and developmental regulation in mammary gland. Biochim. Biophys. Acta, 1680, 103-113. Kerr, D.E. and O. Wellnitz. 2004. Cryopreserved bovine mammary cells to model epithelial response to infection. 7th International Veterinary Immunology Symposium. Quebec City, Canada. Wellnitz, O. and D.E. Kerr. 2004. 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Impact Statements

A cattle genome database compiling QTL and sequence information as a tool for comparative mapping was developed. The database contains 580 QTL entries for 109 traits and 295 molecular markers (CA).
Project members have also developed statistical software including a program which was written in R and that performs a global normalization analysis with a linear model simultaneously with assessing significance of gene specific treatment contrasts through bootstrapping of residuals (AZ).
Two computer packages, Pedigraph 2.0 and MiniInbred, have been developed with the support from Cargill. Trial versions of these programs are available from http://animalgene.umn.edu. (MN).
Progress on objective three during the past year includes maintenance of the NC1010 website (http://animalscience.ucdavis.edu/LivestockBiotechnology).
The Joint NRSP-8 / NC-1010 Quantitative Genomics/Proteomics Workshop was held at the 2005 Plant and Animal Genome Conference.
Two workshops on microarrays were offered at The University of Arizona in 2004.
An article was written for the Michigan Dairy Review (MI). Multiple presentations were made to cattle producers and allied industry throughout California on the use of markers in cattle breeding programs (CA).