"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana.
"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana.
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DOI：
10.1371/journal.pgen.1005597
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发表时间：
2015-10
期刊：
影响因子：
4.5
通讯作者：
Nordborg M
中科院分区：
文献类型：
--
作者：
Sasaki E;Zhang P;Atwell S;Meng D;Nordborg M
了解遗传变异如何与环境相互作用对于理解适应至关重要。特别是，植物的生命周期与当地的环境信号紧密协调，通过复杂的相互作用与遗传变异（G × E）。G x E的机制基础几乎完全未知。我们收集了瑞典173个拟南芥自交系在两种生长温度（10°C和16°C）下的开花时间数据，观察到大量的G x E变异。为了确定这种变异背后的遗传多态性，我们使用SNP和局部方差分量进行了全基因组扫描。基于SNP的扫描确定了在两种环境中具有共同效应的几个变体，但没有发现G x E效应的痕迹，而使用局部方差分量的扫描发现了两者。此外，G x E效应似乎集中在基因组的一小部分（0.5%）中。我们的结论是，在这项研究中，G × E效应主要是由于大量的等位基因或单倍型在少数位点，其中许多对应于以前确定的开花时间基因。许多性状都受到遗传变异与环境相互作用的影响，称为G × E变异。例如，在农业中，不同的品种在不同的环境中是最佳的。在进化中，G x E对于局部适应也至关重要。然而，鉴定G x E的基因已被证明是极具挑战性的。使用模式植物拟南芥的近交系的集合，我们meausured开花时间在两个温度制度下，并扫描基因组的多态性负责在这个性状的变化。虽然大部分变异是由于G x E，但使用SNP进行的全基因组扫描仅显示了直接的遗传效应（G），未能显示任何显著的G x E关联。相比之下，使用多态性的局部窗口扫描基因组表明，几乎所有观察到的变异都可以用2%的基因组来解释。以前确定的开花时间基因在这些地区的强烈过度，我们的研究结果是兼容的模型下，G x E主要是由于在一个相对较少的基因座的许多等位基因。
Understanding how genetic variation interacts with the environment is essential for understanding adaptation. In particular, the life cycle of plants is tightly coordinated with local environmental signals through complex interactions with the genetic variation (G x E). The mechanistic basis for G x E is almost completely unknown. We collected flowering time data for 173 natural inbred lines of Arabidopsis thaliana from Sweden under two growth temperatures (10°C and 16°C), and observed massive G x E variation. To identify the genetic polymorphisms underlying this variation, we conducted genome-wide scans using both SNPs and local variance components. The SNP-based scan identified several variants that had common effects in both environments, but found no trace of G x E effects, whereas the scan using local variance components found both. Furthermore, the G x E effects appears to be concentrated in a small fraction of the genome (0.5%). Our conclusion is that G x E effects in this study are mostly due to large numbers of allele or haplotypes at a small number of loci, many of which correspond to previously identified flowering time genes. Many traits are influenced by genetic variation in interaction with the environment, so called G x E variation. In agriculture, for example, different varieties are optimal in different environments. In evolution, G x E is also crucial for local adaptation. Identifying the genes underlying G x E has proven extremely challenging, however. Using a collection of inbred lines of the model plant Arabidopsis thaliana, we meausured flowering time under two temperature regimes, and scanned the genome for polymorphisms responsible for variation in this trait. Although most of the variation is due to G x E, genome-wide scans using SNPs only revealed direct genetic effects (G), and failed to reveal any significant G x E associations. In contrast, scanning the genome using local windows of polymorphism suggested that almost all the observed variation can be explained by 2% of the genome. Previously identified flowering time genes are strongly overrepresented in these regions, and our results are compatible with a model under which G x E is mainly due to many alleles at a relatively small number of loci.