title: Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism.
abstract: Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications.
authors.affiliation: RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan; Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, Japan.
authors.forename: Fumio
authors.initials: F
authors.lastname: Matsuda
authors.forename: Ryo
authors.initials: R
authors.lastname: Nakabayashi
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Yang
authors.forename: Yozo
authors.initials: Y
authors.lastname: Okazaki
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Yonemaru
authors.forename: Kaworu
authors.initials: K
authors.lastname: Ebana
authors.forename: Masahiro
authors.initials: M
authors.lastname: Yano
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D002853:Chromatography, Liquid; D056726:Genetic Association Studies; D014644:Genetic Variation; D055442:Metabolome; D012275:Oryza / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D064209:Phytochemicals / Q000737:chemistry / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D053719:Tandem Mass Spectrometry
chemical_list: D064209:Phytochemicals
keywords: Oryza sativa; genome-wide association study; metabolome analysis; natural variation; secondary metabolites