Comprehensive genotyping analysis of single nucleotide polymorphisms responsible for beef marbling in Japanese Black cattle

Abstract Background Beef marbling is considered a desirable trait in the meat industry. Therefore, understanding the genetic factors that cause marbling is important. Previously, we performed a genome-wide association study to examine genetic factors associated with beef marbling in Japanese Black cattle and identified a candidate region between 10–30 Mbp on chromosome 7. We verified the effect of the SNPs in this region on beef marbling using linkage disequilibrium block analysis. We narrowed down the candidate region to a range of 15.8–16.1 Mbp. In this study, we comprehensively detected all of the SNPs in this region and verified their effects on beef marbling. Results Genome resequencing using four animals exhibiting high beef marbling standard (BMS) and four with low BMS revealed a total of 1,846 polymorphisms within the candidate region. Based on the annotation, we selected 13 SNPs exhibiting a moderate impact, as no high-impact SNPs were detected. All of the SNPs represented missense polymorphisms and were located in the following seven genes: RDH8 , ANGPTL6 , DNMT1 , MRPL4 , ICAM1 , ICAM3 , and ICAM5 . Finally, we determined the effects of these SNPs on the BMS of a Japanese Black cattle population ( n = 529). Analysis of variance revealed that the five SNPs were located in genes encoding the intercellular adhesion molecules ( ICAM1 , ICAM3 , and ICAM5 ), and showed a highly significant association compared with the remainder ( p < 0.01). The lowest p-value was observed for ICAM3_c.739G > A ( p = 1.18E-04). Previous studies have suggested that intercellular adhesion molecules (ICAM) may be an upstream factor that regulates adipocyte differentiation. Therefore, considering the polymorphism and putative gene function, we suggest that ICAM1 is potentially responsible for beef marbling. c.470C > G and/or c.994G > A on ICAM1 may be responsible for this quantitative trait locus. Conclusions Promising SNP candidates responsible for beef marbling were identified using extensive polymorphism verification in a previously reported QTL region. We aim to elucidate the mechanism of beef marbling in future studies by investigating how these polymorphisms alter protein structure and function.