2007 Annual Report 1a.Objectives (from AD-416) The first objective is to generate genotypic data on 10,000 SNP for 1200 Holstein bulls. This data will serve as a resource for the remaining components. The second objective is to infer haplotypes for genotyped bulls, create a Holstein-specific HapMap, and provide genotypic data to the bovine HapMap project. The final objective is to develop statistical methods and infrastructure to implement genomic selection and to combine the genetic merit prediction using genomic data with results from the national genetic evaluation system. 1b.Approach (from AD-416) The SNP genotyping will be conducted using the most-cost-effective platform available at the time. Data from the HapMap consortium will be used to identify the optimal set of SNP to genotype. For objective two, algorithms used to infer haplotypes can generally be divided into two groups, those that are based on pedigree information and those assuming unrelated individuals. We expect to evaluate algorithms or software packages representing each of these groups of algoithms. Further, we intend to identify haplotype blocks specific to the Holstein breed. By determining the haplotypes at any given region in the population, we can identify which SNP will be redundant and which can be used to represent the haplotype in further studies. The latter SNP are often referred to as haplotype tag SNP. The programs htSNPer and HapBlock will each be tested using these data. The final objective will be accomplished using the genomic selection procedure described by Meuwissen et al. (2001). Given haplotype data genetic merit is modeled as a function of haplotype effects. Several alternative strategies will be investigated to determine the best approach to model these data. 3.Progress Report This report documents research conducted under a reimburseable agreement between ARS and NRI from a funded grant proposal USDA NRI-CGP 43.1 Animal Genome. Award money was disbursed in February 2006 to the Beltsville Area. USDA, ARS, USMARC and LARRL research centers are also participating in this project. Additional details of the research can be found in the report for the parent in-house project 1265-3100-081-00D, “Identification, validation and fine-mapping of quantitative trait loci in dairy cattle.” The objectives of this grant proposal were to generate genotypic data on 10,000 SNP for 1,200 Holstein bulls, create a Holstein-specific HapMap, and then provide genotypic data to the bovine HapMap project. The final objective is to develop statistical methods and infrastructure to implement genomic selection and to combine the genetic merit prediction using genomic data with results from the national genetic evaluation system. Towards this end, we have developed more than 75,000 new bovine SNPs. Many of these new SNPs were used to develop a new 60,000 SNP-based assay. This assay is in manufacturing at Illumina and will be used for generating genotypes for the genome selection experiment. Monitoring activities associated with this project included annual updates presented to CSREES-NRI NPS in conjunction with Plant and Animal Genome Conferences and submission to CSREES-NRI of an annual progress report. This research continues to support two objectives of its related in-house project. The first is to 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 #2). The second is to characterize conserved genome elements and identify functional genetic variation (objective #3). This aligns to NP101 under the following component of Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources.