Inferring genetic characteristics of Japanese Black cattle populations using genome-wide single nucleotide polymorphism markers

This study attempted to infer the population structure of Japanese Black cattle by using genotype data on 33,063 genomewide single nucleotide polymorphism (SNP) markers totally 4,348 fattened steers slaughtered at carcass markets in Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. We evaluated allele frequency, heterozygosity, linkage disequilibrium, correlation phase, concordance among steers. The distribution frequencies sampled Hyogo differed from others, showing >10% SNPs as monomorphic. Observed heterozygosity was lowest degree disequilibrium highest Hyogo. Genotypes were more similar than between other steer pairs. These results show genetic characteristics populations inferred genome-wide obtained a commercial chip.