Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity

A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French Arabidopsis thaliana population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.

Methods
This dataset contains measurements of defensive metabolites in genotyped accessions of Arabodopsis thaliana, the genotypes used for genome-wide association (GWA) mapping of these metabolites, and the output of GWA analyses. For the TOU-A population, metabolites were extracted and quantified from full rosettes using high pressure liquid chromatography and mass spectrometry (HPLC-MS/MS). The raw HPLC-MS/MS output files have been deposited here, along with the output of linear mixed models of metabolite variation across accessions. For other populations, metabolite abundances were obtained from prior publications and associated repositories, as described here in the README file and in the methods section of the manuscript associated with this dataset (doi:10.1098/rstb.2020.0512). GWA mapping of each metabolite in each population was conducted using the GEMMA package (doi:10.1038/ng.2310), and all output files have been deposited here. Scripts used for the analysis of the current dataset are available at https://github.com/peterlaurin/TOUA_Glucosinolate_GWAS.

植物全基因组关联分析（Genome-Wide Association Studies, GWAS）得出了一项看似矛盾的结论：尽管代谢物谱的调控背后存在复杂的生物合成途径，但其变异通常仅定位到少量基因座。这一差异可能部分源于地理多样性作图群体所带来的局限性。会通过稀释因果变异的加性效应而干扰GWAS的代谢通路特性（例如等位基因异质性、基因异质性与上位性），其干扰强度会随着作图群体的地理分布范围扩大而加剧。我们据此提出假说：单一场所的种群可揭示更多的关联基因座。我们以法国拟南芥（Arabidopsis thaliana）群体（样带跨度小于1公里）为对象，针对硫代葡萄糖苷——一类已通过功能与遗传作图手段被深入研究的防御性代谢物——开展代谢物谱分析与GWAS，验证了该假说。针对两类不同的硫代葡萄糖苷，我们在生物合成相关基因座上发现的关联位点数量，多于此前使用大陆尺度作图群体开展的GWAS研究。新关联位点对应的候选基因，其在TOU-A群体中的观测效应与既往功能遗传及生化表征结果一致。本地群体可作为地理多样性作图群体的补充，从而更完整地揭示代谢性状的遗传结构。

方法
本数据集包含拟南芥已基因型鉴定生态型的防御性代谢物检测数据、用于这些代谢物全基因组关联（GWA）作图的基因型数据，以及GWA分析结果。针对TOU-A群体，我们从完整莲座叶中提取代谢物并采用高效液相色谱-串联质谱（High Performance Liquid Chromatography-Tandem Mass Spectrometry, HPLC-MS/MS）进行定量分析。原始HPLC-MS/MS输出文件已随不同生态型间代谢物变异的线性混合模型分析结果一并上传至本数据集。对于其他群体，代谢物丰度数据来源于已发表文献及相关数据库，详见本数据集的README文件及关联论文的方法部分（doi:10.1098/rstb.2020.0512）。本研究中各群体的各代谢物的GWA作图均采用GEMMA包完成（doi:10.1038/ng.2310），所有输出文件已上传至本数据集。本数据集的分析脚本可通过https://github.com/peterlaurin/TOUA_Glucosinolate_GWAS获取。