Department of Evolution and Ecology, University of California, Davis, California 95616
Center for Population Biology, University of California, Davis, California 95616.
Genetics. 2019 Mar;211(3):989-1004. doi: 10.1534/genetics.118.301786. Epub 2019 Jan 24.
Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci-a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation. Here, we develop methods that do just this, using principal components of the relatedness matrix to detect excess divergence consistent with polygenic adaptation, and using a conditional test to control for confounding effects due to population structure. We apply these methods to inbred maize lines from the United States Department of Agriculture germplasm pool and maize landraces from Europe. Ultimately, these methods can be applied to additional domesticated and wild species to give us a broader picture of the specific traits that contribute to adaptation and the overall importance of polygenic adaptation in shaping quantitative trait variation.
数量性状的适应通常通过许多基因座上等位基因频率的微妙变化发生——这一过程称为多基因适应。虽然已经开发出许多方法来检测人类群体中的多基因适应，但我们在许多其他系统中缺乏明确的策略。特别是，有机会开发新的方法，利用具有基因组数据和常见花园特征测量的数据集，系统地检测对适应很重要的数量性状。在这里，我们使用相关矩阵的主成分来检测与多基因适应一致的过度分歧，并使用条件检验来控制由于群体结构造成的混杂效应，开发了正是这样的方法。我们将这些方法应用于美国农业部种质库的自交玉米系和欧洲的玉米地方品种。最终，这些方法可以应用于其他驯化和野生物种，以更全面地了解有助于适应的特定性状，以及多基因适应在塑造数量性状变异方面的总体重要性。
