Identification of potential biomarkers associated with meat tenderness in Hanwoo (Korean cattle): an expression quantitative trait loci analysis

Abstract

Abstract Meat tenderness is considered the most important trait contributing to beef quality, level of consumer satisfaction, willingness to pay premium prices, and industry profit. Genomic selection method would be helpful for genetic improvement of traits with low heritability and are difficult to measure. The identification of genes that affect beef tenderness can promote efficient genomic prediction in breeding programs. We performed statistical analysis of associations between longissimus dorsi muscle tenderness and gene expression in 20 Hanwoo cattle, using Warner-Bratzler shear force (WBSF) and RNAseq data, respectively. We found 166 core genes with significant regression coefficient. In expression quantitative trait loci (eQTL) analysis, using the core genes and 777,962 SNPs for 20 individuals, we found 6 core genes (ASAP1, CAPN5, ELN, SUMF2, TTC8, and MGAT4A) regulated by 16 cis-eQTL SNPs. The variants within 5 kb of the transcription start site or transcription termination site of these core genes were significant (p < 0.01). Notably, we found that a cis-eQTL SNP of the ELN gene contained an MFZ1 binding site in its putative promoter region. These findings provide a useful information for genomic prediction using additive and non-additive genetic effects in prediction model.