Data from: Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome

The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints, but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the ‘environmental relevance’ of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study.

基因组内不同基因的种内多态性水平差异显著。诸多基因组学研究已探讨了基因多态性与重组率、表达模式等因素之间的关联。然而，基因的多态性不仅受其自身物理属性或功能约束的影响，还受到生物体所处环境中的自然选择作用的调控。具体而言，若功能分化的等位基因可帮助生物体适应不同环境，则空间异质性自然选择可维持位点特异性多态性。为验证该假说并评估环境选择塑造全基因组多态性模式的程度，我们将基因的‘环境相关性’定义为：在控制群体结构的前提下，环境因素所能解释的遗传变异占比。我们发现，环境相关性对不同基因的多态性模式存在显著影响。此外，环境相关性与基因多态性之间呈正相关，这与‘异质环境下的平衡选择可维持生态重要基因的遗传变异’的预期相符。对基因本体（Gene Ontology）注释结果的比较分析显示，环境相关性较高的基因在功能未知类别中显著富集。上述结果表明，环境因素在塑造全基因组多态性模式中发挥着重要作用，同时也为基因组学研究指明了新方向。