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

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 Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. When the number of assumed clusters was 2, from Hyogo prefecture were clearly separated others. This indicates usefulness SNP for clarifications difference genetic constitutions each prefecture. Next, genomic predictions traits conducted a statistical model including proportions as partial linear regressions. Genomic breeding values predicted by without covariates likely to be divided into part explaining remaining part. result shows possibility that accuracy prediction depends degree information population structure.