Department of Plant Biology, University of California Davis, Davis, California, USA.
PLoS Genet. 2012;8(3):e1002589. doi: 10.1371/journal.pgen.1002589. Epub 2012 Mar 15.
Shade avoidance is an ecologically and molecularly well-understood set of plant developmental responses that occur when the ratio of red to far-red light (R:FR) is reduced as a result of foliar shade. Here, a genome-wide association study (GWAS) in Arabidopsis thaliana was used to identify variants underlying one of these responses: increased hypocotyl elongation. Four hypocotyl phenotypes were included in the study, including height in high R:FR conditions (simulated sun), height in low R:FR conditions (simulated shade), and two different indices of the response of height to low R:FR. GWAS results showed that variation in these traits is controlled by many loci of small to moderate effect. A known PHYC variant contributing to hypocotyl height variation was identified and lists of significantly associated genes were enriched in a priori candidates, suggesting that this GWAS was capable of generating meaningful results. Using metadata such as expression data, GO terms, and other annotation, we were also able to identify variants in candidate de novo genes. Patterns of significance among our four phenotypes allowed us to categorize associations into three groups: those that affected hypocotyl height without influencing shade avoidance, those that affected shade avoidance in a height-dependent fashion, and those that exerted specific control over shade avoidance. This grouping allowed for the development of explicit hypotheses about the genetics underlying shade avoidance variation. Additionally, the response to shade did not exhibit any marked geographic distribution, suggesting that variation in low R:FR-induced hypocotyl elongation may represent a response to local conditions.
遮光回避是一组在生态学和分子水平上都得到很好理解的植物发育反应，当由于叶片遮荫而导致红光与远红光的比例（R:FR）降低时，就会发生这种反应。在这里，对拟南芥进行了全基因组关联研究（GWAS），以鉴定这些反应之一的变异体：下胚轴伸长增加。该研究包括四种下胚轴表型，包括在高 R:FR 条件下（模拟阳光）的高度、在低 R:FR 条件下（模拟遮荫）的高度，以及下胚轴对低 R:FR 反应的两个不同指数。GWAS 结果表明，这些性状的变异受许多小至中等效应的位点控制。鉴定出一个已知的 PHYC 变体，该变体导致下胚轴高度的变异，并对显著相关基因的列表进行了先验候选物的富集，这表明该 GWAS 能够产生有意义的结果。使用元数据（如表达数据、GO 术语和其他注释），我们还能够鉴定候选从头基因中的变体。我们四种表型之间的显著模式使我们能够将关联分为三组：那些不影响遮光回避而影响下胚轴高度的关联、那些以高度依赖的方式影响遮光回避的关联，以及那些对遮光回避进行特定控制的关联。这种分组允许对遮光回避变异的遗传基础提出明确的假设。此外，对遮光的反应没有表现出任何明显的地理分布，这表明低 R:FR 诱导的下胚轴伸长的变异可能代表对当地条件的反应。
