1a. Objectives (from AD-416):
1) Use the BovineSNP50 assay to provide high-accuracy predictions of genetic merit to U.S. dairy and beef breeds. 2) Enable the adoption of WGEAS by developing low-density and low-cost SNP assays for: a) intermediate-accuracy genetic prediction, b) mate selection, and c) parentage verification and traceability. 3) Develop, adapt and optimize statistical metodologies to: a) fully integrate SNP genotype or haplotype effects into existing genetic evaluation technologies, and b) supplement or replace pedigree data. 4)Collaborate and coordinate U.S. and European Union WGEAS activities.
1b. Approach (from AD-416):
1) Collect genotypic data using the bovineSNP50 in both dairy and beef cattle breeding programs. 2) Develop statistical algorithms needed to implement whole genome enabled animal selection specific to dairy and beef cattle populations as needed. 3) Determine subset of markers needed for low density SNP assay for application to parentage verification and reduced accuracy genetic prediction. 4) Collaborate with many organizations to utilize data generated by this project as well as other projects to obtain maximum utilization of resources generated.
3. Progress Report:
Activities during this project period included: 1) continued genomic re-sequencing of animals for the purposes of single nucleotide polymorphism (SNP) discovery, diversity characterization, and fine mapping of causative mutations, 2) analysis of beadchip genotypic data for the continued refinement of genetic prediction equations within breed, 3) collaborative development of the beadchips as enhanced-value genotyping platforms optimized for value and imputation, and 4) identification of haplotypes affecting fertility in Holstein, Jersey, and Brown Swiss breeds of cattle. Through industry partnerships, over 500,000 animals to date were genotyped using a variety of platforms. These data are being used for the estimation of genomic breeding values in the dairy and beef industries. The rate of growth of data collection for genotypes continues to accelerate in both industries. The BovineLD assay and products derived from this platform were rapidly adopted in dairy cattle genetic evaluations. The vast majority of animals recently genotyped were done using a BovineLD or derived assay. This research supports two objectives of its related in-house project: 1) to use genotypic data and the 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), and 2) to characterize conserved genome elements and identify functional genetic variation (Objective 3).