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United States Department of Agriculture

Agricultural Research Service

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2010 Annual Report

1a. Objectives (from AD-416)
As described in grant entitled “Development and field evaluation of genome-wide marker-assisted selection (GWMAS) over multiple generations in commercial poultry,” the consortium that includes members from Cobb Vantress, Hendrix Genetics, and many universities will: 1. Develop a Higher Density and More Informative Chicken SNP Panel 2. Refine the Theoretical and Molecular Aspects of GWMAS 3. Field Assessment of GWMAS 4. Further Improve the Chicken Genome Assembly For this agreement, only Objectives 2 and 3 apply.

1b. Approach (from AD-416)
For Objective #2, alternative methods of utilizing GWMAS will be explored. The first method will be a multistep procedure as is used currently commercially. It starts with a regular evaluation using only phenotypic records, followed by a separate evaluation for animals using only genomic information (using Ridge regression, BayesA, BayesB, or BLUP with genomic relationships), and the resulting genetic values from each evaluation are combined using a weighting process. The second method will be a one step evaluation where a pedigree based relationship matrix in a regular BLUP procedure is replaced by a relationship matrix that blends the pedigree and genomic relationships. A simulation study as well as experiments using the field data will determine which of the methods is more suitable for commercial poultry breeding. For Objective #3, the expected breeding values (EBV) will be computed for each normalized trait of each animal based on genotypic information and phenotypes (if present). These EBV would in turn be used to determine total merit by use of the appropriate weights given by the companies. The companies will do their own BLUP evaluations based on phenotype as per their usual breeding programs. The goal is to make selection decisions based on the EBVs for each trait and/or total merit the same for each method of selection [BLUP, GWMAS], the only difference being the way in which the EBVs will be estimated.

3. Progress Report
This project is directly linked to projects 3635-31320-008-19R, 3635-31320-008-37R, Specific Cooperative Agreements 3635-31320-008-20S, 25S, and 29S,titled “Development and Field Evaluation of Genome-Wide Marker-Assisted Selection (GWMAS) Over Multiple Generations in Commercial Poultry.” To meet the growing demands of consumers, the poultry industry will need to continue to improve methods of selection in breeding programs for production and associated traits. One possible solution is genome-wide marker-assisted selection (GWMAS). First proposed by one of us, evenly-spaced genetic markers spanning the entire genome are genotyped (scored) on individuals to estimate their breeding value, which in theory could substantially increase the rate of genetic gain compared to traditional selection methods. To test the power of GWMAS, meat-type and egg-type chicken lines are being selected in parallel using either traditional or GWMAS. This year, after completing two rounds of selection, we conclude that compared to birds selected in parallel using current state-of-the-art breeding methods, genomic selection is superior for the vast majority of the traits selected including body weight and breast yield. This research strongly suggests that genomic selection is an improved breeding method. If costs for genetic testing continue to go down, then poultry breeders should be able to economically breed chickens faster using genomic selection and adapt more readily to changing consumer demands. The economic impact could be great with 1 million meat-type birds being processed per hour in the U.S. alone, the net effect of even small improvements are large and worth millions of dollars. This project is monitored by weekly e-mail and telephone calls between the two parties, a monthly teleconference and, when possible, direct interactions at scientific meetings.

4. Accomplishments

Last Modified: 2/23/2016
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