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

Aoi ZODA; Shinichiro OGAWA; Hirokazu MATSUDA; Yukio TANIGUCHI; Toshio WATANABE; Yoshikazu SUGIMOTO; Hiroaki IWAISAKI

doi:10.5924/abgri.50.3

Original paper

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

Aoi ZODA, Shinichiro OGAWA , Hirokazu MATSUDA, Yukio TANIGUCHI, Toshio WATANABE, Yoshikazu SUGIMOTO, Hiroaki IWAISAKI

Author information

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

Keywords: allele frequency, Japanese Black cattle, linkage disequilibrium, population structure, single nucleotide polymorphism

JOURNAL OPEN ACCESS

2022 Volume 50 Issue 1 Pages 3-9

DOI https://doi.org/10.5924/abgri.50.3

Details

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.

Corresponding author

Register with J-STAGE for free!