Detection of QTLs and Candidate Polymorphisms for Percentage of Oleic Acid Through GWAS and Post-GWAS Analysis in Japanese Black Beef

Abstract

Fatty acid composition is a key trait affecting meat quality in Japanese Black cattle. In this study, a genome-wide association study (GWAS) was conducted on Hyogo population of Japanese Black cattle (n = 432) for the percentage of oleic acid (C18:1). Quantitative trait loci (QTLs) were detected on chromosomes 6 and 19 (BTA6 and BTA19). Focusing on the QTL on BTA6, we conducted a detailed search for candidate polymorphisms. Using whole-genome resequencing data (n = 42), all polymorphisms were detected within 83 genes located on the candidate region (chr6: 55–83 Mbp). Based on variant annotations and linkage disequilibrium coefficients with the most significantly associated single nucleotide polymorphism from GWAS (top SNP), 93 variants were extracted as potential causal polymorphisms. Validation revealed that four variants, located within four different genes, had p values comparable to the top SNP. Among them, CWH43 emerged as a strong candidate, as it regulates the intracellular Mn²⁺ concentrations, which influence fatty acid metabolism. Notably, the SNP in CWH43 was located upstream of the gene, suggesting a possible regulatory role in gene expression. These findings provide important insights into the genetic basis of fatty acid composition and support the identification of functional polymorphisms in Japanese Black cattle.