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.
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