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 in this project period focused on 1) continued genomic resequencing of animals for the purposes of single nucleotide polymorphism (SNP) discovery and diversity characterization, 2) analysis of Illumina BovineSNP50 data for the continued refinement of genetic prediction equations both within and across breeds, 3) collaborative development of the Illumina BovineLD beadchip as a replacement and improvement for the Illumina Bovine 3K assay, 4) development and genotyping of industry validation herds for the characterization of the accuracies of molecular estimates of breeding value in beef cattle, 5) identification of haplotypes affecting fertility in Holstein, Jersey, Brown Swiss, and Angus cattle, and 6) collaborative development of bovine exome capture assays with commercial vendors. Through industry partnerships, over 230,000 animals have now been genotyped on a variety of platforms, and these data are being used for the estimation of genomic breeding values in the dairy and beef industries. The rate of growth of genotype data collection continues to accelerate in both industries. The BovineLD assay was adopted rapidly in dairy cattle genetic evaluations. A total of five different haplotypes were identified that impact fertility through early embryonic loss in dairy cattle, and through the sequencing of 11 Angus bulls, loss-of-function alleles were found in 176 genes known to be embryonic or early development lethal in knockout mice. At least two commercial vendors are introducing products designed to capture bovine exonic regions for targeted re-sequencing using coordinates derived by ARS scientists. This research supports two objectives of its related in-house project: 1) 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 (obj. #2), and 2) to characterize conserved genome elements and identify functional genetic variation (obj. #3).