title: Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.
abstract: 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.
authors.affiliation: 1] National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China. [2].
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: 1] National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China. [2].
authors.forename: Yanqiang
authors.initials: Y
authors.lastname: Gao
authors.affiliation: 1] National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China. [2].
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.affiliation: 1] National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China. [2].
authors.forename: Liang
authors.initials: L
authors.lastname: Gong
authors.affiliation: 1] National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China. [2].
authors.forename: Kai
authors.initials: K
authors.lastname: Lu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Xianqing
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Huaxia
authors.initials: H
authors.lastname: Dong
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Wan
authors.initials: W
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Lejing
authors.initials: L
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Sibin
authors.initials: S
authors.lastname: Yu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Gongwei
authors.initials: G
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Xingming
authors.initials: X
authors.lastname: Lian
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Luo
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D008040:Genetic Linkage; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D055442:Metabolome; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D040641:Quantitative Trait Loci