Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism

Wei Chen, Yanqiang Gao, Weibo Xie, Liang Gong, Kai Lu, Wensheng Wang, Yang Li, Xianqing Liu, Hongyan Zhang, Huaxia Dong, Wan Zhang, Lejing Zhang, Sibin Yu, Gongwei Wang, Xingming Lian, Jie Luo
Nature Genetics 2014, 46 (7): 714-21
Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.

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