2011 Annual Report
1)Genome resequencing of animals from important cattle breeds for the purpose of SNP discovery to allow development of high-density genotyping assays,.
2)analysis of Illumina BovineSNP50 data sets for the development and refinement of genetic value prediction models, and.
3)continued genotyping of animals from different beef breeds of registered cattle for the development of across breed molecular breeding value prediction equations. In total, about 600 billion base pairs of cattle DNA sequence information was produced by BFGL, University of Missouri, and collaborators. Sequences were aligned to the bovine UMD3.1 reference sequence to identify nearly 50 million SNP across more than 15 breeds. From these SNP, BFGL designed a second-generation 860K genotyping assay collaboratively with Illumina. Illumina has launched their 777K SNP genotyping product known as the BovineHD assay. Subsequently, Affymetrix released their 650K SNP genotyping product (BOS1) in January, 2011. We have also shown that molecular breeding value prediction equations developed for one breed perform poorly when applied to other distinct breeds. Thus, we generated BovineSNP50 genotypes for 3600 Angus, 2200 Limousin and 900 Hereford registered cattle and have production information available through the respective breed associations to aid across breed prediction equations. Fewer registered animals within each breed also results in slightly lower overall molecular breeding value accuracies relative to the dairy industry. Therefore, the cost of the BovineSNP50 assay prohibits wide application within the beef industry. To ameliorate this limitation we previously developed a reduced 384 SNP assay which predicts molecular breeding values in Angus cattle for marbling, ribeye muscle area, backfat thickness and yearling weight with accuracies up to 42%. This assay has been adopted by the American Angus Association, which now computes composite estimates of breeding value using all sources of information (phenotype, pedigree and molecular) and runs their national genetic evaluation software biweekly (rather than biannually) to deliver molecular test results to breeders. The first objective to provide high-accuracy predictions of genetic merit enhanced by DNA marker data (BovineSNP50) in U.S. cattle has been met in dairy cattle and progress has been achieved in beef cattle. Monitoring activities associated with this project included regular email correspondence and conference calls. 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).