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

Abstract

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 of 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 of linkage phase, and genotype concordance among the steers. The distribution of allele frequencies in the steers sampled in Hyogo differed from the others, showing >10% of the SNPs as monomorphic. Observed heterozygosity was lowest and degree of linkage disequilibrium was highest in Hyogo. Genotypes were more similar among Hyogo steers than between other steer pairs. These results show the genetic characteristics of the Japanese Black cattle populations inferred from genotype data on genome-wide SNPs obtained using a commercial chip.