Understanding the Evolution of Defense Metabolites in Arabidopsis thaliana Using Genome-wide Association Mapping
Understanding the Evolution of Defense Metabolites in Arabidopsis thaliana Using Genome-wide Association Mapping
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DOI：
10.1534/genetics.109.108522
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发表时间：
2010-07-01
期刊：
影响因子：
3.3
通讯作者：
Kliebenstein, Daniel J.
中科院分区：
文献类型：
--
作者：
Chan, Eva K. F.;Rowe, Heather C.;Kliebenstein, Daniel J.
随着高通量基因分型和表型技术的改进和成本的下降，全基因组关联（GWA）研究正迅速成为剖析复杂数量性状的首选方法。拟南芥芥子油苷（GSL）次生代谢产物。可以作为一个模型系统来理解数量性状的基因组结构。GSL是在野生环境中对抗昆虫的关键防御，并且相对大量的克隆的控制GSL性状的数量性状基因座（QTL）允许将GWA与先前的QTL分析进行比较。为了更好地了解控制植物-昆虫互作的全物种基因组结构以及GWA和QTL研究的相对优势，我们利用96 A. 43个GSL表型，230，000个SNPs相似。我们的GWA分析确定了两个主要的多态位点控制GSL的变化（AOP和MAM）在自然种群中的大块的正相关，包括几十个基因。这些区块的积极协会显示了扩展的连锁不平衡（LD），我们假设已经出现了平衡或波动的选择性扫描在AOP和MAM基因座。这些潜在的清扫块可能与新的防御化学物质的形成有关，这些防御化学物质改变了植物在自然环境中的适应性。有趣的是，该GWA分析没有鉴定大多数先前鉴定的QTL，即使这些多态性存在于GWA群体中。这可能是部分解释的非随机分布的表型变异的人口亚群，人口结构和GSL的变化，这表明自然选择可以阻碍检测自然群体中的表型基因型协会。
With the improvement and decline in cost of high-throughput genotyping and phenotyping technologies, genome-wide association (GWA) studies are fast becoming a preferred approach for dissecting complex quantitative traits. Glucosinolate (GSL) secondary metabolites within Arabidopsis spp. can serve as a model system to understand the genomic architecture of quantitative traits. GSLs are key defenses against insects in the wild and the relatively large number of cloned quantitative trait locus (QTL) controlling GSL traits allows comparison of GWA to previous QTL analyses. To better understand the specieswide genomic architecture controlling plant-insect interactions and the relative strengths of GWA and QTL studies, we conducted a GWA mapping study using 96 A. thaliana accessions, 43 GSL phenotypes, and similar to 230,000 SNPs. Our GWA analysis identified the two major polymorphic loci controlling GSL variation (AOP and MAM) in natural populations within large blocks of positive associations encompassing dozens of genes. These blocks of positive associations showed extended linkage disequilibrium (LD) that we hypothesize to have arisen from balancing or fluctuating selective sweeps at both the AOP and MAM loci. These potential sweep blocks are likely linked with the formation of new defensive chemistries that alter plant fitness in natural environments. Interestingly, this GWA analysis did not identify the majority of previously identified QTL even though these polymorphisms were present in the GWA population. This may be partly explained by a nonrandom distribution of phenotypic variation across population subgroups that links population structure and GSL variation, suggesting that natural selection can hinder the detection of phenotype-genotype associations in natural populations.