A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response.
A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response.
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DOI：
10.1371/journal.pgen.1002589
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Maloof JN
中科院分区：
文献类型：
--
作者：
Filiault DL;Maloof JN
避荫是植物在遮荫条件下，当红光与远红光的比值（R∶FR）降低时所产生的一系列生态学和分子生物学上已被充分理解的发育反应。在这里，拟南芥的全基因组关联研究（GWAS）被用来确定这些反应之一的变异：增加下胚轴伸长。研究了高R∶FR条件下（模拟阳光）、低R∶FR条件下（模拟遮荫）的4种下胚轴表型，以及2种不同的下胚轴表型对低R∶FR的反应指数。GWAS结果表明，这些性状的变异是由许多小到中等效应的位点控制的。一个已知的PHYC变异有助于下胚轴高度的变化进行了鉴定和列表中的显着相关的基因丰富的先验的候选人，这表明该GWAS是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，我们还能够识别候选从头基因中的变体。我们的四个表型之间的显着性模式，使我们能够将协会分为三组：那些影响下胚轴高度不影响避荫，那些影响避荫的高度依赖的方式，和那些施加特定的控制避荫。这种分组允许发展明确的遗传学假说的避荫变异。此外，遮荫的反应没有表现出任何明显的地理分布，表明低R∶ FR诱导下胚轴伸长的变化可能代表了对当地条件的反应。这项工作的目标是确定遗传变异的基础上的一个良好的表征环境的反应，延长拟南芥下胚轴（幼苗茎）响应遮荫，也被称为避荫。我们进行了一个全基因组关联研究与四个表型：绝对下胚轴高度的植物生长在模拟阳光和阴影和两个措施的高度如何响应遮荫。通过这项研究，我们证实了先前的发现，即两种光感受器的变异与下胚轴高度变异相关。我们还发现了与先前确定的避荫基因中的遗传变异的关联，以及与通常不被认为是避荫途径一部分的基因中的变异的关联。通过检查与每个基因相关的四种表型中的哪一种的模式，我们能够区分在下胚轴高度变化中具有一般作用的遗传变异和特异性参与避荫反应的变异。我们还发现，避荫与地理没有广泛的联系，这表明这种特性的变化可能是由于当地的光质量差异。
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. The goal of this work was to identify genetic variants underlying a well-characterized environmental response, the elongation of Arabidopsis thaliana hypocotyls (seedling stems) in response to shade, otherwise known as shade avoidance. We performed a genome-wide association study with four phenotypes: absolute hypocotyl height of plants grown in both simulated sun and shade and two measures of how height responded to shade. With this study, we confirmed previous findings that variants in two photoreceptors were associated with hypocotyl height variation. We also found associations with genetic variants in previously-identified shade avoidance genes, as well as with variants in genes not typically considered part of the shade avoidance pathway. By examining patterns of which of the four phenotypes were associated with each gene, we were then able to discriminate between genetic variants that have a general role in hypocotyl height variation and variants that are specifically involved in the shade avoidance response. We also found that shade avoidance was not broadly associated with geography, suggesting that variation in this trait may be due to local differences in light quality.
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影响因子：
11.6
作者：
Aukerman, MJ;Hirschfeld, M;Sharrock, RA
通讯作者：
Sharrock, RA
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
4.5
作者：
Baxter I;Brazelton JN;Yu D;Huang YS;Lahner B;Yakubova E;Li Y;Bergelson J;Borevitz JO;Nordborg M;Vitek O;Salt DE
通讯作者：
Salt DE
影响因子：
4.5
作者：
Brachi B;Faure N;Horton M;Flahauw E;Vazquez A;Nordborg M;Bergelson J;Cuguen J;Roux F
通讯作者：
Roux F
影响因子：
7.4
作者：
Devlin, PF;Yanovsky, MJ;Kay, SA
通讯作者：
Kay, SA