The annotation of significant SNPs.

Loin muscle area (LMA) is an indicator of carcass composition and is related to weight gain, animal musculature and meat quality traits. Therefore, integrating multi-omics data to reveal candidate genes affecting LMA has attracted extensive attention. We used the combined analysis method of GWAS and RNA-seq to find the candidate genes that affect the size of LMA. The association of 770K SNPs with the LMA captured four significant SNPs within or near three genes. Additionally, seven overlapping genes regarding LMA were determined via the analysis of differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA). There is an overlapping gene (CD93) between the results of GWAS and DEGs. Through functional enrichment analysis of the above genes, candidate genes were identified as THBD, CD93, RIMS2, PLP1, SNCA, and NDUFS8, and it was found that they mainly affected the size of LMA by affecting muscle fiber diameter, muscle cell development, differentiation, and function. The findings provide valuable molecular insights into the mechanisms that influence LMA content in beef cattle.