Identification of Genomic Regions for Carcass Quality Traits within the American Simmental Association Carcass Merit Program

SIMPLE SUMMARY: The American Simmental Association has an ongoing project assessing carcass composition and quality. Typically, when animals for mating are selected on maternal traits, there is a concomitant reduction in carcass value as many maternal traits are antagonistic to carcass traits. Analysis of the current data showed the correlation between hot carcass weight and calving ease direct to be lower than previously reported. This shows that multi-trait selection reduced the problem that arose when selecting for carcass traits or maternal traits individually. ABSTRACT: USDA quality and yield grade are primary driving forces for carcass value in the United States. Carcass improvements can be achieved by making selection decisions based on the results of genetic evaluations in the form of expected progeny differences (EPD), real-time ultrasound imaging, and physical evaluation of candidate breeding animals. In an effort to advance their ability to accurately predict the breeding value of potential sires for carcass traits, the American Simmental Association launched the Carcass Merit Program as a means to collect progeny sire group carcass information. All records were extracted from the American Simmental Association database. Progeny data were organized by sire family and progeny performance phenotypes were constructed. Sire genotypes were filtered, and a multi-locus mixed linear model was used to perform an association analysis on the genotype data, while correcting for cryptic relatedness and pedigree structure. Three chromosomes were found to have genome-wide significance and this conservative approach identified putative QTL in those regions. Three hundred ninety-three novel regions were identified across all traits, as well as 290 novel positional candidate genes. Correlations between carcass characteristics and maternal traits were less unfavorable than those previously reported.