Estimation of variance components for carcass traits in Japanese Black cattle using 50K SNP genotype data.
Estimation of variance components for carcass traits in Japanese Black cattle using 50K SNP genotype data.
复制标题
使用 50K SNP 基因型数据估计日本黑牛胴体性状的方差分量。
DOI：
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发表时间：
2014
期刊：
影响因子：
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通讯作者：
Y. Sugimoto
中科院分区：
文献类型：
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作者：
Toshio Watanabe;H. Matsuda;A. Arakawa;Takahisa Yamada;H. Iwaisaki;S. Nishimura;Y. Sugimoto
使用高密度单核苷酸多态性（SNP）基因型数据的基因组选择可以加速家畜动物的遗传改良。在这项研究中，我们试图估计方差分量的六个胴体性状的育肥日本黑牛使用SNP基因型数据。使用Illumina Bovine SNP 50 BeadChip对673头阉牛进行基因分型，并对冷胴体重量、眼肌面积、肋骨厚度、皮下脂肪厚度、估计产量百分比和大理石花纹评分进行表型分析。加性多基因方差和归因于对性状具有统计学显著影响的一组SNP的方差通过Gibbs抽样用两个模型估计：（i）具有所选SNP和加性多基因效应的模型;和（ii）仅具有多基因效应的模型。随着拟合的SNP效应数量的增加，归因于SNP的估计方差的比例变得更高。高相关性的育种值估计与模型包含的多基因效应单独和那些估计选择SNPs。在P ≥ 0.1时，与该性状相关的SNP无法解释总遗传方差的任何部分。我们的研究结果表明，对于日本黑牛的胴体性状，最多一半的总加性遗传方差可以解释的SNPs之间的100几十到几十个100。
Genomic selection using high-density single nucleotide polymorphism (SNP) genotype data may accelerate genetic improvements in livestock animals. In this study, we attempted to estimate the variance components of six carcass traits in fattened Japanese Black steers using SNP genotype data. Six hundred and seventy-three steers were genotyped using an Illumina Bovine SNP50 BeadChip and phenotyped for cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percent and marbling score. Additive polygenic variance and the variance attributable to a set of SNPs that had statistically significant effects on the trait were estimated via Gibbs sampling with two models: (i) a model with the chosen SNPs and the additive polygenic effects; and (ii) a model with the polygenic effects alone. The proportion of the estimated variance attributable to the SNPs became higher as the number of SNP effects that fit increased. High correlations between breeding values estimated with the model containing the polygenic effect alone and those estimated by chosen SNPs were obtained. No fraction of the total genetic variance was explained by SNPs associated with the trait at P ≥ 0.1. Our results suggest that for the carcass traits of Japanese Black cattle, a maximum of half of the total additive genetic variance may be explained by SNPs between 100 several tens to several 100s.