title: Estimation of variance and genomic prediction using genotypes imputed from low-density marker subsets for carcass traits in Japanese black cattle.
abstract: The influence of genotype imputation using low-density single nucleotide polymorphism (SNP) marker subsets on the genomic relationship matrix (G matrix), genetic variance explained, and genomic prediction (GP) was investigated for carcass weight and marbling score in Japanese Black fattened steers, using genotype data of approximately 40,000 SNPs. Genotypes were imputed using equally spaced SNP subsets of different densities. Two different linear models were used. The first (model 1) incorporated one G matrix, while the second (model 2) used two different G matrices constructed using the selected and remaining SNPs. When using model 1, the estimated additive genetic variance was always larger when using all SNPs obtained via genotype imputation than when using only equally spaced SNP subsets. The correlations between the genomic estimated breeding values obtained using genotype imputation with at least 3,000 SNPs and those using all available SNPs without imputation were higher than 0.99 for both traits. While additive genetic variance was likely to be partitioned with model 2, it did not enhance the accuracy of GP compared with model 1. These results indicate that genotype imputation using an equally spaced low-density panel of an appropriate size can be used to produce a cost-effective, valid GP.
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Shinichiro
authors.initials: S
authors.lastname: Ogawa
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Matsuda
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Yukio
authors.initials: Y
authors.lastname: Taniguchi
authors.affiliation: National Livestock Breeding Center, Nishigo, Fukushima, Japan.
authors.forename: Toshio
authors.initials: T
authors.lastname: Watanabe
authors.affiliation: Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Nishigo, Fukushima, Japan.
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Sugimoto
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Iwaisaki
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D003362:Cost-Benefit Analysis; D063427:Food Quality; D014644:Genetic Variation; D023281:Genomics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D016014:Linear Models; D008297:Male; D008460:Meat / Q000032:analysis / Q000191:economics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011237:Predictive Value of Tests; D019655:Quantitative Trait, Heritable
keywords: Japanese Black cattle; carcass trait; genomic prediction; genotype imputation; variance component