Project Number: 1265-31000-098-11
Project Type: Reimbursable

Start Date: Sep 01, 2008
End Date: May 31, 2012

Objective:
1)Use the BovineSNP50 assay to provide high-accuracy perdictions 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 US and European Union WGEAS activities.

Approach:
1)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. 2)Collaboration will Illumina will 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. 3)Develop BLUP approaches for the prediction of genetic merit in non-pedigreed populations using molecular relationship matrices. 4)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 U.S. and Europe to coordinate activities.