2012 Annual Report
1a.Objectives (from AD-416):
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.
1b.Approach (from AD-416):
(1) Identify knowledge gaps in genomic selection, research through computer simulations to close these gaps, and implement bioinformatic-based tools for data management, selection, and breeding decisions, and (2) conduct genomic selection in at least two commercial poultry lines. Phenotype and genotype two generations from training, then compare traditional selection with two genomic selected lines over two additional generations.
This project is directly linked to Specific Cooperative Agreements 3635-31320-008-20S, 3635-31320-008-29S, and 3635-31320-008-31S 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 three rounds of selection, we conclude that in comparison 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 with accuracies improving by more than 100% depending on the trait and generation. 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.