1a. Objectives (from AD-416):
Use the BovineSNP50 assay to provide high-accuracy predictions of genetic merit to U.S. beef breeds; 2) Enable the adoption of whole genome enabled animal selection (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 methodologies to: a) fully integrate SNP genotype or haplotype effects into existing genetic evaluation technologies, and b) supplement or replace pedigree data; and 4) Collaborate and coordinate U.S. and European Union WGEAS activities.
1b. Approach (from AD-416):
Genetic prediction using high-density SNP data will be implemented using MTDFREML. Implementation of more sophisticated strategies will follow using the MTGSAM programs that will be modified to accommodate extensions to the prediction model. Collaboration with a biotechnology company to develop a 384-SNP assay that is expected to dramatically decrease genotyping costs and increase sample throughput. A machine learning approach using a two-step feature subset selection algorithm will be evaluated for SNP selection for this assay. Develop BLUP approaches for the prediction of genetic merit in non-pedigreed populations using molecular relationship matrices. We shall manage this coordination and collaboration via e-mail and teleconference calls, however, we shall also meet at least annually in conjunction with the PAG or ISAG meetings alternating between the US and Europe to coordinate activities.
3. Progress Report:
Activities in this project period focused on: 1) continued genomic re-sequencing of animals for the purposes of 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) development and genotyping of industry validation herds for the characterization of the accuracies of molecular estimates of breeding value in beef cattle, and 4) identification of haplotypes affecting fertility in Angus cattle. Through industry partnerships, over 30,000 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 beef industry. The rate of growth of genotype data collection continues to accelerate. 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. 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).