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United States Department of Agriculture

Agricultural Research Service

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2009 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 Wageningen University 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; and 4. Further Improve the Chicken Genome Assembly. For this agreement, only Objectives 1, 3, and 4 apply.

1b. Approach (from AD-416)
For Objective #1, to generate the SNPs that we will genotype, we will (1) Divide the latest chicken sequence assembly into ~60K bins of equal size based on chromosomal recombination rates, (2) Assign previously screened SNPs that were validated, have a MAF>0.1, and known to be segregating in one or more lines of interest to the appropriate bin, (3) For bins without a validated marker, identify 3 or more SNPs from either the public databases or our own sequencing efforts, giving preference to those SNPs identified two or more times in the discovery process, and (4) Submit all SNPs and their flanking sequences to the commercial vendor producing the SNP array to determine if a suitable assay can be designed. For Objective #3, DNA from Hendrix Genetics chickens will be extracted, quantified, and the concentration adjusted prior to shipment to our genotyping facility. For Objective #4, the East Lansing and Wageningen University reference families will be genotyped with the 60K SNP chip, and an improved consensus genetic map generated and aligned to the genome sequence to detect discrepancies in genetic marker order.

3. Progress Report
This project is directly linked to projects 3635-31320-008-19R, 25S, and 29S titled “Development and Field Evaluation of Genome-Wide Marker-Assisted Selection (GWMAS) Over Multiple Generations in Commercial Poultry.” The power of genome-wide marker-assisted selection (GWMAS) increases with the density of markers, thus, we needed to develop a tool that could assay many genetic markers quickly, accurately, and economically. Using targeted sequencing of commercial chickens, we developed a chip that can simultaneously score 56,702 genetic markers equally spaced through the entire chicken genome. This powerful tool is being applied in our GWMAS experiment as well as other studies including the identification of genes of agronomic importance, preservation of genetic diversity, and more. 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: 10/16/2017
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