Genomic prediction for carcass traits in Japanese Black cattle considering mixed structure of subpopulations

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

doi:10.5924/abgri.50.31

Original paper

Genomic prediction for carcass traits in Japanese Black cattle considering mixed structure of subpopulations

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

Author information

Aoi ZODA [Japan]
Graduate School of Agriculture, Kyoto University [Japan]
Shinichiro OGAWA [Japan] Corresponding author
Graduate School of Agriculture, Kyoto University [Japan]
Graduate School of Agricultural Science, Tohoku University [Japan]
Hirokazu MATSUDA [Japan]
Graduate School of Agriculture, Kyoto University [Japan]
Wagyu Registry Association [Japan]
Yukio TANIGUCHI [Japan]
Graduate School of Agriculture, Kyoto University [Japan]
Toshio WATANABE [Japan]
National Livestock Breeding Center [Japan]
Maebashi Institute of Animal Science, Livestock Improvement Association of Japan [Japan]
Yoshikazu SUGIMOTO [Japan]
Shirakawa Institute of Animal Genetics [Japan]
Hiroaki WAISAKI [Japan]
Graduate School of Agriculture, Kyoto University [Japan]
Sado Island Center for Ecological Sustainability, Niigata University [Japan]

Keywords: carcass traits, genomic prediction, Japanese Black cattle, population structure, single nucleotide polymorphism

JOURNAL OPEN ACCESS

2022 Volume 50 Issue 2 Pages 31-38

DOI https://doi.org/10.5924/abgri.50.31

Details

Abstract

We performed Bayesian clustering analysis using STRUCTURE software with genotype data on 33,063 commercial single nucleotide polymorphism (SNP) markers in 4,348 Japanese Black fattened steers slaughtered at carcass markets in Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. When the number of the assumed clusters in STRUCTURE was 2, the steers from Hyogo prefecture were clearly separated from the others. This indicates the usefulness of the STRUCTURE analysis with commercial SNP markers for the clarifications of the difference of the genetic constitutions of each prefecture. Next, genomic predictions for carcass traits were conducted using a statistical model including the proportions of the clusters as partial linear regressions. Genomic breeding values predicted by the model without the STRUCTURE covariates were likely to be divided into the part of explaining the STRUCTURE analysis and the remaining part. This result shows the possibility that the accuracy of genomic prediction depends on the degree of information of the genomic population structure.

Corresponding author

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