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

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.

Keywords: back fat; carcass weight; genetic correlation; genome-wide association; marbling.

Figure 1

Manhattan plot for internal fat (KPH). Markers above −log10(p-value) of 5 × 10⁻⁸ (red line) are significant genome-wide association markers. Vertical clusters of markers are also of interest as they indicate potential quantitative trait loci (QTL) in those regions. Markers above −log10(p-value) of 5 × 10⁻⁵ (blue line) used to identify potential candidate genes for further research.