Project Number: 3635-31320-009-08
Project Type: Specific Cooperative Agreement

Start Date: Aug 21, 2009
End Date: Aug 31, 2013

Objective:
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.

Approach:
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.