Estimation of variance and genomic prediction using genotypes imputed from low-density marker subsets for carcass traits in Japanese black cattle.
Estimation of variance and genomic prediction using genotypes imputed from low-density marker subsets for carcass traits in Japanese black cattle.
复制标题
使用从日本黑牛胴体性状低密度标记子集推算的基因型估计方差和基因组预测。
DOI：
10.1111/asj.12570
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发表时间：
2015
影响因子：
2
通讯作者：
Iwaisaki H.
中科院分区：
文献类型：
--
作者：
Ogawa S.;Matsuda H.;Taniguchi T.;Watanabe T.;Sugimoto Y.;Iwaisaki H.
利用约40000个SNP的基因型数据，研究了利用低密度单核苷酸多态性（SNP）标记亚群对基因组关系矩阵（G矩阵）、遗传变异解释和基因组预测（GP）进行基因型估算对日本黑育肥牛胴体重和大理石纹评分的影响。使用不同密度的等间隔SNP亚群进行基因型估算。使用了两种不同的线性模型。第一个（模型1）包含一个G矩阵，而第二个（模型2）使用两个不同的G矩阵，使用选择的和剩余的snp构建。当使用模型1时，当使用通过基因型插入获得的所有SNP时，估计的加性遗传方差总是比仅使用间隔等的SNP子集时更大。在这两个性状中，使用至少3000个snp进行基因型代入的基因组育种估计值与使用所有可用snp而不进行代入的基因组育种估计值的相关性均大于0.99。虽然加性遗传方差可能会被模型2分割，但与模型1相比，它并没有提高GP的准确性。这些结果表明，使用适当大小的等间距低密度面板进行基因型插入可用于产生具有成本效益的有效GP。
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.