Genomic prediction for carcass traits in Japanese Black cattle using single nucleotide polymorphism markers of different densities.
Genomic prediction for carcass traits in Japanese Black cattle using single nucleotide polymorphism markers of different densities.
复制标题
使用不同密度的单核苷酸多态性标记对日本黑牛胴体性状进行基因组预测。
DOI：
10.1071/an15696
复制
发表时间：
2016
影响因子：
1.4
通讯作者：
Iwaisaki H.
中科院分区：
文献类型：
--
作者：
Ogawa S.;Matsuda H.;Taniguchi Y.;Watanabe T.;Kitamura Y.;Tabuchi I.;Sugimoto Y.;Iwaisaki H.
使用单核苷酸多态性（SNP）标记的育种值的基因组预测（GP）即使在系谱信息不可用时也可以进行，只要表型是已知的并且提供标记数据。虽然高密度SNP标记的使用对于准确的GP是期望的，但在某些情况下，较低密度的SNP可以表现良好。在本研究中，使用不同密度的SNP标记对日本黑牛的胴体重和大理石花纹评分进行了GP。将1791头具有表型数据的育肥牛和189头具有官方遗传评估育种值的育肥牛分别作为训练群体和验证群体。565 837个常染色体SNP的基因型数据是可用的，选择SNP以提供不同的等间隔的较低密度的SNP子集。基因组估计育种值（GEBV），获得了基因组最佳线性无偏预测纳入两种类型的基因组关系矩阵（G矩阵）。当使用565 837个SNPs时，GP准确性评估为GEBV和校正记录之间的相关性除以估计遗传力的平方根，胴体重约为0.85，大理石花纹评分约为0.60。所使用的G矩阵的类型在给定的SNP密度下对所检查的性状的结果没有实质性差异。当SNP密度降低到所有可用SNP密度的1/1000时，保留了约80%的GP准确性。这些结果表明，即使当使用较低密度的SNP面板时，GP也可能有益于日本黑幼种动物胴体性状的预选。
Genomic prediction (GP) of breeding values using single nucleotide polymorphism (SNP) markers can be conducted even when pedigree information is unavailable, providing phenotypes are known and marker data are provided. While use of high-density SNP markers is desirable for accurate GP, lower-density SNPs can perform well in some situations. In the present study, GP was performed for carcass weight and marbling score in Japanese Black cattle using SNP markers of varying densities. The 1791 fattened steers with phenotypic data and 189 having predicted breeding values provided by the official genetic evaluation using pedigree data were treated as the training and validation populations respectively. Genotype data on 565 837 autosomal SNPs were available and SNPs were selected to provide different equally spaced SNP subsets of lower densities. Genomic estimated breeding values (GEBVs) were obtained using genomic best linear unbiased prediction incorporating one of two types of genomic relationship matrices (G matrices). The GP accuracy assessed as the correlation between the GEBVs and the corrected records divided by the square root of estimated heritability was around 0.85 for carcass weight and 0.60 for marbling score when using 565 837 SNPs. The type of G matrix used gave no substantial difference in the results at a given SNP density for traits examined. Around 80% of the GP accuracy was retained when the SNP density was decreased to 1/1000 of that of all available SNPs. These results indicate that even when a SNP panel of a lower density is used, GP may be beneficial to the pre-selection for the carcass traits in Japanese Black young breeding animals.