Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1. Statistical analysis revealed that both SNPs were significantly associated with C18:1 (p = .0080 and .0003), validating the quantitative trait loci (QTLs) detected in GWAS. We subsequently selected VNN1 and LYPLA1 genes as candidate genes from each region on BTA9 and BTA14, respectively. We sequenced full-length coding sequence (CDS) of these genes in eight individuals and identified a nonsynonymous SNP T66M on VNN1 gene as a putative candidate polymorphism. The polymorphism was also significantly associated with C18:1, but the p value (p = .0162) was higher than the most significant SNP on BTA9, suggesting that it would not be responsible for the QTL. Although further investigation will be needed to determine the responsible gene and polymorphism, our findings would contribute to development of selective markers for fatty acid composition in the Japanese Black cattle of Hyogo.

In our previous study, we detected a QTL for the oleic acid percentage (C18:1) on BTA9 in Japanese Black cattle through a genome‐wide association study (GWAS). In this study, we performed whole‐genome resequencing on eight animals with higher and lower C18:1 to identify candidate polymorphisms for the QTL. A total of 39,658 polymorphisms were detected in the candidate region, which were narrowed to 1993 polymorphisms within 23 genes based on allele differences between the high and low C18:1 groups. We subsequently selected three candidate genes, that is, CYB5R4, MED23, and VNN1, among the 23 genes based on their function in fatty acid metabolism. In each candidate gene, three SNPs, that is, CYB5R4 c.*349G > T, MED23 c.3700G > A, and VNN1 c.197C > T, were selected as candidate SNPs to verify their effect on C18:1 in a Japanese Black cattle population (n = 889). The statistical analysis showed that these SNPs were significantly associated with C18:1 (p < 0.05), suggesting that they were candidates for the QTL. In conclusion, we successfully narrowed the candidates for the QTL by detecting possible polymorphisms located within the candidate region. It is expected that the responsible polymorphism can be identified by demonstrating their effect on the gene's function.

In this study, we focused on the STARD3 gene which is involved in cholesterol distribution and homeostasis in cells, and investigated the effects of the STARD3 gene polymorphism on carcass traits and fatty acid composition. We searched for polymorphisms in the STARD3 gene by whole-genome resequencing and selected a missense S396L from 280 detected polymorphisms. We genotyped S396L polymorphism for Japanese Black cattle population (n = 441) and then analyzed the effects on carcass traits and fatty acid composition. As a result, the polymorphism showed strong association with fatty acid composition (C14:0, C16:0, C18:1, SFA and MUFA) (p<0.0001). Although further research is warranted to clarify whether S396L directly impacts fatty acid composition, it is obvious that there is a novel QTL for fatty acid composition on BTA19 in the Japanese Black cattle. In conclusion, these results contribute to the identification of a novel causative mutation on BTA19 for fatty acid composition and development of a useful DNA marker for improving the beef quality of Japanese Black cattle.

We investigated the effect of the PLAG1 gene (on bovine chromosome 14) polymorphism on oleic acid percentage (C18:1) in four Japanese Black cattle populations (JB1: n = 900, JB2: n = 560, JB3: n = 456, JB4: n = 450). We genotyped the PLAG1 polymorphism (rs109231213) for four populations and then analyzed the effects on carcass weight (CW) and C18:1. This polymorphism was significantly associated with CW in these four populations (P<0.001), in agreement with previous reports. In addition, it also had a significant effect on C18:1 in JB1, JB2 and JB3 (P<0.05). However, considering that the effect of PLAG1 differed among populations, it was suggested that the PLAG1 polymorphism would not have a direct effect on C18:1 and would be in linkage disequilibrium (LD) with a causative mutation. Turkey-Kramer's honestly significant difference test revealed that the qq genotype had a higher percentage of C18:1 than the QQ genotype in JB1 and JB2 (1.62 and 2.23, respectively), while the qq genotype showed lower CW in all four populations. These results suggest that the PLAG1 gene polymorphism would be useful as a DNA marker for C18:1 in Japanese Black cattle populations; this H. Kigoshi et al. 2 information could contribute to the identification of a causative mutation on BTA14 for fatty acid composition.