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

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  • ZODA Aoi
    Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
  • OGAWA Shinichiro
    Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Current affiliation: Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
  • MATSUDA Hirokazu
    Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Current affiliation: Wagyu Registry Association, Kyoto 604-0845, Japan
  • TANIGUCHI Yukio
    Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
  • WATANABE Toshio
    National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan Current affiliation: Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, Gunma 371-0121, Japan
  • SUGIMOTO Yoshikazu
    Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
  • IWAISAKI Hiroaki
    Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Current affiliation: Satoyama Division, Sado Island Center for Ecological Sustainability, Niigata University, Niigata 952-0103, Japan

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  • ゲノムワイドな一塩基多型マーカーを用いた 黒毛和種集団における遺伝的特性把握の試み

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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.

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