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United States Department of Agriculture

Agricultural Research Service

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2011 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 3635-31320-008-37R, Specific Cooperative Agreements 3635-31320-008-25S, 29S and 31S 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 our team members, GWMAS utilizes markers spanning the entire genome to increase accuracy and efficiency of estimating breeding values (EBV). This new method promises significant benefits, but there are many unanswered questions calling for proof that GWMAS actually works. Retrospective analysis has shown that genome-wide marker-based EBV correlates highly with phenotypic Best Linear Unbiased Prediction (BLUP) EBV. However, there are concerns that these analyses will not reflect reality once implemented because selection may rapidly change variances, allele frequencies, and generate unfavorable linkage disequilibrium (LD) which only becomes apparent after the second round of selection. As planned, two meat-type and three egg-type chicken pure 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 since with 1 million meat-type birds processed per hour in the US 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 collaborating parties, a monthly teleconference and, when possible, direct interactions at scientific meetings.

4. Accomplishments

Last Modified: 10/17/2017
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