Homozygosity region analysis using commercial single nucleotide polymorphism markers in Japanese Black cattle population

We previously reported that 4,237 of 33,063 single nucleotide polymorphism (SNP) markers genotyped by commercial SNP chips were monomorphic in Japanese Black fattened steers slaughtered at carcass market in Hyogo prefecture. Here we investigated their distribution and extracted their neighboring genes. Genomic regions were detected as candidate homozygous regions where ≥ 2 of these SNPs were consecutively located, and the genes located within the regions were extracted. The 672 homozygous regions detected were widely distributed throughout the genome. The 608 extracted genes included ones previously studied as candidate genes for the degree of marbling in Japanese Black cattle. Gene ontology enrichment analysis (GO analysis) of the extracted genes found many significant GO terms related to lipids and lipid metabolism (P <0.05). Network analysis of the genes belonging to the significant term“ nucleotide binding (GO: 000166)” in the STRING database suggested several connections (edges) among the genes. The results could be useful to characterize the Japanese Black cattle, especially the Hyogo subpopulation.