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. Within this context, the objective of this study was to identify genomic regions and putative candidate genes associated with the ribeye area (REA), marbling (MARB), backfat thickness (BFT) and rump fat thickness (RFT) in Angus beef cattle. The pedigree file contained data for 2,446 animals and a total of 1,391 animals were genotyped with the GGP Bovine 150K (Illumina). The single-step approach for genome-wide association study (ssGWAS) was performed to estimate the SNP effects and variances accounted by 10‐ SNP sliding windows. Confirming the polygenic nature of the studied traits, 23, 23, 22, and 31 genomic windows that explained more than 0.5% of the additive genetic variance were identified for REA, MARB, BFT and RFT, respectively. A total of 66, 56, 36, and 105 protein- coding genes were found in windows associated with REA, MARB, BFT and RFT, respectively. Several protein‐coding genes were identified within those genomic regions, such as SIRT6, CREB3L3, HNRNPH1, RUFY, EEF2, NMRK2, FDS1, CTNNA2, MAMSTR, PCCB, GALNT13, CTNNA3, EPHB2, PLA2G4E, APOD, RPL9, AGAP1, MFSD2A, FAM13A, DDHD1, CAST, CISD1, PLA2G1B, DROSHA, CDH6, FAM83A, SPHK2, and NEIL3 gene, according to its function. Functional enrichment analysis by DAVID tool also revealed several significant (p< 0.05) KEGG pathways and Gene Ontology terms such as glycerophospholipid catabolic process (GO:0046475), phospholipid catabolic process (GO:0009395) and lipid catabolic process (GO:0016042). These results contribute to improving the knowledge of the genetic architecture of carcass quality traits in Angus beef cattle and may contribute to genetic evaluations.