The shade avoidance response is a set of developmental changes exhibited by plants to avoid shading by competitors, and is an important model of adaptive plant plasticity. While the mechanisms of sensing shading by other plants are well-known and appear conserved across plants, less is known about the developmental mechanisms that result in the diverse array of morphological and phenological responses to shading. This is particularly true for traits that appear later in plant development. Here we use a nested association mapping (NAM) population of Arabidopsis thaliana to decipher the genetic architecture of the shade avoidance response in late-vegetative and reproductive plants. We focused on four traits: bolting time, rosette size, inflorescence growth rate, and inflorescence size, found plasticity in each trait in response to shade, and detected 17 total QTL; at least one of which is a novel locus not previously identified for shade responses in Arabidopsis. Using path analysis, we dissected each colocalizing QTL into direct effects on each trait and indirect effects transmitted through direct effects on earlier developmental traits. Doing this separately for each of the seven NAM populations in each environment, we discovered considerable heterogeneity among the QTL effects across populations, suggesting allelic series at multiple QTL or interactions between QTL and the genetic background or the environment. Our results provide insight into the development and variation in shade avoidance responses in Arabidopsis, and emphasize the value of directly modeling the relationships among traits when studying the genetics of complex developmental syndromes.

避荫响应是植物表现出的一组发展变化，以避免竞争者遮荫，并且是适应植物可塑性的重要模型。虽然其他植物感测阴影的机制是众所周知的，并且在整个植物中看起来都是保守的，但对于导致对阴影的形态学和物候响应的多样化阵列的发育机制知之甚少。对于在植物发育后期出现的性状尤其如此。在这里，我们使用拟南芥的嵌套关联映射（NAM）种群解释晚期无性和生殖植物避光反应的遗传结构。我们着重研究了四个性状：抽time时间，莲座丛大小，花序生长速率和花序大小，发现每个性状对阴影的响应均具有可塑性，并检测了17个总QTL。至少其中之一是以前未鉴定出拟南芥中阴影反应的新基因座。使用路径分析，我们将每个共定位QTL分解为对每个性状的直接影响和通过对较早的发育性状的直接影响传递的间接影响。对每种环境中的七个NAM种群中的每一个分别进行此操作，我们发现了各个种群在QTL效应之间存在相当大的异质性，表明多个QTL的等位基因序列或QTL与遗传背景或环境之间的相互作用。我们的结果提供了对拟南芥中避荫反应的发展和变化的见识，并强调了在研究复杂的发育综合征的遗传因素时直接建立性状之间关系的价值。