Single-step genome-wide association study for carcass quality traits in Angus beef cattle

Abstract

The identification of genomic regions and genes that influence carcass quality traits is important for improving beef cattle selection. We aimed to identify genomic regions and candidate genes associated with the ribeye area (REA), marbling (MARB), backfat thickness (BFT) and rump fat thickness (RFT). All phenotypes were recorded using real-time ultrasound. The pedigree file contained data for 2,446 animals and a total of 1,391 animals were genotyped with the GGP Bovine 150 K (Illumina). The single-step approach for genome-wide association study (ssGWAS) was performed to estimate the single nucleotide polymorphism (SNP) effects and variances accounted by 10-SNP sliding windows. Were identified for REA, MARB, BFT and RFT, respectively, 23, 23, 22, and 31 genomic windows that explained more than 0.5% of the additive genetic variance. Several protein‐coding genes were identified within those genomic regions: MAMSTR, CTNNA3, AGAP1 and CDH6, located on 18:55.35–55.36, 28:22.29–24.12, 3:11.50-11.56 and 20:42.35–42.35 Mb, respectively. Functional enrichment analysis was performed by DAVID tool and also revealed several significant (p < 0.05) KEGG pathways and Gene Ontology terms. These included RNA polymerase II transcription regulatory region sequence-specific binding; glycosphingolipid biosynthesis - globo and isoglobo series; glycosphingolipid biosynthesis - lacto and neolacto series; glycerophospholipid catabolic process; phospholipid catabolic process and lipid catabolic process. These results contribute to improving the knowledge of the genetic architecture of carcass quality traits in Angus beef cattle and may contribute to improving the genetic evaluations.