Department of Animal and Dairy Science, University of Georgia Athens, GA, USA.
Instituto Nacional de Investigación Agropecuaria Las Brujas, Uruguay.
Front Genet. 2014 Oct 1;5:332. doi: 10.3389/fgene.2014.00332. eCollection 2014.
The purpose of this study was to determine if the set of genomic regions inferred as accounting for the majority of genetic variation in quantitative traits remain stable over multiple generations of selection. The data set contained phenotypes for five generations of broiler chicken for body weight, breast meat, and leg score. The population consisted of 294,632 animals over five generations and also included genotypes of 41,036 single nucleotide polymorphism (SNP) for 4,866 animals, after quality control. The SNP effects were calculated by a GWAS type analysis using single step genomic BLUP approach for generations 1-3, 2-4, 3-5, and 1-5. Variances were calculated for windows of 20 SNP. The top ten windows for each trait that explained the largest fraction of the genetic variance across generations were examined. Across generations, the top 10 windows explained more than 0.5% but less than 1% of the total variance. Also, the pattern of the windows was not consistent across generations. The windows that explained the greatest variance changed greatly among the combinations of generations, with a few exceptions. In many cases, a window identified as top for one combination, explained less than 0.1% for the other combinations. We conclude that identification of top SNP windows for a population may have little predictive power for genetic selection in the following generations for the traits here evaluated.
本研究旨在确定在多个世代的选择中，解释数量性状大部分遗传变异的基因组区域集合是否保持稳定。数据集包含了 5 代肉鸡体重、胸肉和腿评分的表型。该群体由 294632 只动物组成，经过质量控制后，还包括 41036 个单核苷酸多态性（SNP）的基因型，涉及 4866 只动物。使用单步基因组 BLUP 方法，对第 1-3、2-4、3-5 和 1-5 代进行了全基因组关联分析（GWAS），计算了 SNP 效应。对 20 个 SNP 的窗口进行了方差计算。检查了在各世代中解释遗传方差最大部分的前 10 个特征窗口。跨世代，前 10 个窗口解释了超过 0.5%但低于 1%的总方差。此外，窗口的模式在各世代之间并不一致。在各世代的组合中，解释最大方差的窗口变化很大，只有少数例外。在许多情况下，一个被确定为某一代组合的最佳窗口，对于其他组合的解释不到 0.1%。我们得出结论，对于所评估的性状，为一个群体确定最佳 SNP 窗口可能对后续世代的遗传选择几乎没有预测能力。
