2008 Annual Report 1a.Objectives (from AD-416) Objective 1: Develop biological resources and computational tools to enhance characterization of the bovine genome sequence. Objective 2: Use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches. Objective 3: Characterize conserved genome elements and identify functional genetic variation. 1b.Approach (from AD-416) Completion of our objectives is expected, in the short term, to result in development and implementation of genome-wide selection. Ultimately the longer term objective of QTN discovery to better understand livestock biology will require a combination of quantitative genetics, LD-MAS, genome annotation, and gene expression analyses, all of which are components of this proposal and areas of expertise in our group. Efforts to characterize genome activity and structure conservation and variation are an extension of our current research program in QTL mapping and bioinformatics. This proposal completely leverages the resources derived from the Bovine Genome and HapMap projects, for which the authors of this proposal have played prominent roles. As more of the genetic variation for a specific trait is explained, a better understanding of pleiotropic and epistatic gene action will be needed. This knowledge will be developed through characterizing changes at a very fine level combined with studies of animals with known genotype associated with phenotypes resulting from selection programs. Tools used in this characterization are likely to include, but not be limited to, gene expression patterns, protein expression or structural changes, or regulatory changes. 3.Progress Report • Led a research consortium with the following partners: Animal Improvement Programs Laboratory (ARS-BARC), US Meat Animal Research Center (ARS-NPA), University of Missouri, Illumina, Inc., National Association of Animal Breeders (a trade group representing cattle artificial insemination organizations in N.A.), INRA (France), and Merial, Inc. The consortium developed, tested, and commercialized a genome-wide bovine single nucleotide polymorphism (SNP) beadchip that assays the allele content at approximately 58,000 genome locations. • Genotypes for over 10,000 cattle were generated on this SNP chip. Some of these genotypes were used to develop a whole genome selection (WGS) algorithm that produced genome enhanced predictions of genetic merit for three major dairy breeds. Over 3,000 genomic DNA samples were extracted from semen to support this work. The initial success of WGS to enhance selection in Holsteins led to release of unofficial genome enhanced genetic predictions in April. Genome enhanced evaluations are now provided quarterly to the NAAB and should become official by 2009. • Using the beadchip, two radiation hybrid panels were genotyped to aid physical mapping of 50,000 SNP, and genotypic data from our animals was combined with another 10,000 animals to construct a SNP-based genetic map. Physical maps have been completed, and genetic map development is still in progress. • Semen and tissue samples from the U.S. dairy industry continued to be collected and maintained in the Cooperative Dairy DNA Repository. Semen and extracted DNA was distributed to collaborators for mapping studies or to develop marker tools to determine parentage and traceback. Identified cooperators within NAAB to provide over 10,000 DNA samples for parentage testing using a yet to be developed low density SNP assay. • Completed a systematic study of the cattle copy number variation (CNV), a type of genetic variation where there is a difference in the number of copies of a particular region of the genome, was conducted using array comparative genomic hybridization (CGH). CGH arrays were designed and fabricated to cover all chromosomes with an average interval of 6 kb between oligonucleotide hybridization targets based on the genome assembly. Analyzing DNA from 100 popular dairy and beef breeds on these arrays identified approximately 100 CNV regions across the genome and confirming the phenomenon of CNV described less than 5 years ago in humans is also in cattle. To validate an initial CNV finding, a detailed breakpoint mapping and population frequency analysis was completed for a 214-kb microdeletion. This CNV removes multiple olfactory receptor genes, and the frequency of the deletion allele is over 51% in Holsteins. Developed a suite of perl scripts to translate pig and cow EST. This project addresses NP 101 - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources. This accomplishment directly addresses Component 1 of the NP 101 Action Plan. 4.Accomplishments 1. Developed a whole genome wide SNP assay containing 58,000 assays being sold commercially by Illumina Inc. (San Diego, CA). This accomplishment directly addresses Component 1 of the NP 101 Action Plan Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources, Problem Statement 1a: Develop Genome-Enabling Tools and Reagents. 2. Developed the first genome-wide analysis of cattle CNV. This accomplishment directly addresses Component 1 of the NP 101 Action Plan Understanding, Improving, and Effectively Using Animal Genetics and Genomics Resources. Problem Statement 1a: Develop Genome-Enabling Tools and Reagents. 3. Developed a suite of perl scripts to translate pig and cow EST. This accomplishment directly addresses Component 1 of the NP 101 Action Plan Understanding, Improving, and Effectively Using Animal Genetics and Genomics Resources. Problem Statement 1a: Develop Genome-Enabling Tools and Reagents. 4. Developed a spacing algorithm for developing well distributed whole genome wide SNP assays. This accomplishment directly addresses Component 1 fo the NP 101 Action Plan Understanding, Improving, and Effectively Using Animal Genetics and Genomics Resources. Problem 1a: Develop Genome-Enabling Tools and Reagents. 5.Significant Activities that Support Special Target Populations None 6.Technology Transfer Number of New CRADAS 1 Number of Active CRADAs 1 Review Publications Heaton, M.P., Keele, J.W., Harhay, G.P., Richt, J., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Casas, E., King, D.A., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chase, C.C., Kalbfleisch, T.S., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2008. Prevalence of the prion gene E211K variant in U.S. cattle. BioMed Central (BMC) Veterinary Research [journal online]. 4:25. Available: (http://www.biomedcentral.com/1746-6148/4/25). Miles, J.R., Blomberg, L.A., Krisher, R.L., Everts, R.E., Sonstegard, T.S., Van Tassell, C.P., Zuelke, K.A. 2008. Comparative transcriptome analysis of in vivo- and in vitro- produced porcine blastocysts by small amplified RNA-serial analysis of gene expression (SAR-SAGE). Molecular Reproduction and Development. 75:976-88. Van Tassell, C.P., Smith, T.P., Matukumalli, L.K., Taylor, J.F., Schnabel, R.D., Lawley, C.T., Haudenschild, C., Moore, S.S., Warren, W.C., Sonstegard, T.S. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods. 5:247-252. Gasparin, G., Miyata, L.L., Coutinho, L.L., Martinez, M.L., Teodoro, R.L., Furlong, J., Machado, M.A., Silva, M.V., Campos, A.L., Sonstegard, T.S., Regitano, L.C. 2007. Mapping of quantitative trait loci controlling parasite resistance in a F2 experimental bovine population. Animal Genetics. 38(5):453-459. Snelling, W.M., Chiu, R., Schein, J.E., Hobbs, M., Abbey, C.A., Adelson, D.L., Aerts, J., Bennett, G.L., Bosdet, I.E., Boussaha, M., Brauning, R., Caetano, A.R., Costa, M.M., Crawford, A.M., Dalrymple, B.P., Eggen, A., Everts-Van Der Wind, A., Floriot, S., Gautier, M., Gill, C.A., Green, R.D., Holt, R., Jann, O., Jones, S.J., Kappes, S.M., Keele, J.W., De Jong, P.J., Larkin, D.M., Lewin, H.A., Mcewan, J.C., Mckay, S., Marra, M.A., Mathewson, C.A., Matukumalli, L.K., Moore, S.S., Murdoch, B., Nicholas, F.W., Osoegawa, K., Roy, A., Salih, H., Schibler, L., Schnabel, R.D., Silveri, L., Skow, L.C., Smith, T.P., Sonstegard, T.S., Taylor, J.F., Tellam, R., Van Tassell, C.P., Williams, J.L., Womack, J.E., Wye, N.H., Yang, G., Zhao, S. 2007. A physical map of the bovine genome. Genome Biology. 8:R165 (17 pp).