THE POULTRY INDUSTRY HAS A WORRYING CONCERN OF HOW BREEDING SCHEMA CAN CONTINUE PROGRESS ON PHENOTYPIC VARIATION WITH ECONOMIC VALUE, GROWTH (BROILERS) AND REPRODUCTION (EGG LAYERS) WHILE BALANCING SELECTIVE PROCESSES OF OTHER TRAITS. AN EFFICIENT AND ROBUST ACCOUNTING OF SEGREGATING VARIANTS IS KEY TO UNDERSTANDING THE COMPLEXITIES OF GENOTYPE-PHENOTYPE INTERACTIONS. MOST STUDIES CURRENTLY CONSIDER ONLY SINGLE NUCLEOTIDE VARIANTS IN GENOME-WIDE ASSOCIATION STUDIES (GWAS), WITH STRUCTURAL VARIATION IS ALMOST COMPLETELY OVERLOOKED. MAJOR QUESTIONS REMAIN AFTER DECADES OF CHICKEN GWAS STUDIES THAT HAVE IDENTIFIED THOUSANDS OF TRAIT LOCI. THESE QUESTIONS INCLUDE BUT ARE NOT LIMITED TO: HOW MUCH STRUCTURAL VARIATION (SV) IS ASSOCIATED WITH TRAITS OF INTEREST AND HOW MANY SVS THAT RESIDE WITHIN ARE UNDETECTABLE WITH CURRENT TECHNOLOGY. EVEN INCOMPLETE ANSWERS TO THESE QUESTIONS COULD GUIDE NEW EFFORTS TOWARD DESIGNING MARKER SELECTION STRATEGIES THAT ARE OPTIMAL FOR GROWTH, REPRODUCTION, AND DISEASE RESPONSE TRAIT OUTCOMES. STRUCTURAL SEQUENCE COMPLEXITY IS OFTEN EMBEDDED IN TRAIT LOCI, WITH RESEARCHERS NOT KNOWING HOW THEIR VARIABLE PRESENCE IS IMPORTANT TO BIRD HEALTH AND PRODUCTIVITY. THE CURRENT LINEAR CHICKEN REFERENCE GRCG6A ALONE IS INSUFFICIENT FOR THIS PURPOSE. TO WHOLLY PROMOTE A POULTRY INDUSTRY-SUPPORTED CONCEPT OF GENETIC RESILIENCE IN CHICKEN BROODSTOCK, WE PLAN TO DEVELOP AN IMPROVED UNDERSTANDING OF THE OVERLOOKED SV CONTENT. SHOULD WE WIDELY SHARE THIS RESULTING GENOME-WIDE SV KNOWLEDGE THE DEVELOPMENT OF NEW SV QUANTITATIVE TRAIT MODELS IN AVIAN GENETIC STUDIES WILL EMERGE.
$465,034FY2022National Institute of Food and AgricultureUSDA
University Of Missouri System, Columbia MO