Phenotypic and genome-wide association with the local environment of Arabidopsis
Phenotypic and genome-wide association with the local environment of Arabidopsis
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DOI：
10.1038/s41559-018-0754-5
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发表时间：
2019-02-01
影响因子：
16.8
通讯作者：
Assmann, Sarah M.
中科院分区：
文献类型：
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作者：
Ferrero-Serrano, Angel;Assmann, Sarah M.
环境对所有生物体施加了关键的选择力，植物的固着性使它们特别有助于研究遗传变异和环境适应之间的关系。在模式植物拟南芥中，表型和基因型变异的广泛信息是可用的，但在物种的原生范围内的环境变化的可比信息是缺乏的。在这里，我们编译了204个地理气候变量来描述拟南芥种质的当地环境，已知的收集地点涵盖了广泛的地理环境范围，并从1001基因组计划中完全测序了基因组。我们确定了与这些环境变量相关的候选适应性遗传变异，并通过与以前的实验研究进行比较来验证这种方法，并通过有针对性地确认异源三聚体G蛋白γ亚基AGG3在耐寒性中的作用，正如我们的环境全基因组关联研究（GWAS）新预测的那样。为了便于识别适应性变异，我们创建了拟南芥CLIMtools：基于网络的交互式数据库的环境x基因组协会和当地环境之间的相关性和131表型编译从以前的实验GWAS。我们的研究提出了一个广泛的分析当地环境，景观基因组学和拟南芥的表型变异，并说明了如何在silico GWAS的方法可以通知和补充实验表型组学研究。
The environment imposes critical selective forces on all living organisms, and the sessile nature of plants makes them particularly useful for investigating the relationship between genetic variation and environmental adaptation. In the model plant Arabidopsis thaliana, extensive information on phenotypic and genotypic variation is available, but comparable information on environmental variation within the native range of the species is lacking. Here, we compile 204 geoclimatic variables to describe the local environments of Arabidopsis accessions with known collection sites encompassing a wide geo-environmental range, and fully sequenced genomes from the 1001 Genomes Project. We identify candidate adaptive genetic variation associated with these environmental variables, and validate this approach through comparison with previous experimental studies, and by targeted confirmation of a role of the heterotrimeric G-protein gamma subunit, AGG3, in cold tolerance, as newly predicted from our environmental genome wide association study (GWAS). To facilitate identification of adaptive variation, we created Arabidopsis CLIMtools: interactive web-based databases of the environment x genome associations and correlations between the local environments and 131 phenotypes compiled from previous experimental GWASs. Our study presents an extensive analysis of the local environments, landscape genomics and phenotypic variation of Arabidopsis, and illustrates how 'in silico GWAS' approaches can inform and complement experimental phenomics studies.