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United States Department of Agriculture

Agricultural Research Service

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Research Project: IMPLEMENTATION OF WHOLE GENOME SELECTION IN THE U.S. BEEF CATTLE INDUSTRIES

Location: Animal Genomics and Improvement Laboratory

Project Number: 1245-31000-104-09
Project Type: General Cooperative Agreement

Start Date: Jun 02, 2009
End Date: Aug 31, 2013

Objective:
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.

Approach:
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.

Last Modified: 9/10/2014
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