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.

Evolutionarily Distinct BAHD N-acyltransferases are Responsible for Natural Variation of Aromatic Amine Conjugates in Rice

“…Unlike complex quantitative traits (such as flowering time) for which little epistasis has been detected (Buckler et al, 2009;Morris et al, 2013;Zuo and Li, 2014), variation in levels of metabolites, especially specialized metabolites, is predominately controlled by epistasis in both RILs (Kliebenstein et al, 2002;Loudet et al, 2003;Calenge et al, 2006;Lisec et al, 2008;Rowe et al, 2008;Gong et al, 2013) and natural populations (Chan et al, 2011;Chen et al, 2014;Sauvage et al, 2014;Dong et al, 2015;Matsuda et al, 2015). Similar results were observed between some of the loci identified in our study (Supplemental Figure 5 and Supplemental Table 3).…”

“…Eleven rice phenolamides in this study refer to different combinations of CoA-thioesters and amine moieties. combined metabolite-based linkage and association studies have provided powerful forward-genetic strategies for dissecting the genetic and biochemical bases of metabolism in plants (Riedelsheimer et al, 2012;Gong et al, 2013;Chen et al, 2014;Wen et al, 2014Wen et al, , 2015Alseekh et al, 2015;Matsuda et al, 2015). As for the BAHD family of enzymes in rice, OsAT1 has been reported to be involved in responses to rice blight and blast (Mori et al, 2007).…”

Metabolome Analysis of <i>Oryza sativa</i> (Rice) Using Liquid Chromatography-Mass Spectrometry for Characterizing Organ Specificity of Flavonoids with Anti-inflammatory and Anti-oxidant Activity

“…25,29) There are two primary types of rice grown in the world (i.e., the Indica and Japonica varieties). The Habataki cultivar is an Indica variety with higher yields, while the Koshihikari cultivar is a Japonica variety of better quality.…”

“…[15][16][17][18][19][20] Such metabolites exhibit properties beneficial to humans, including anti-tumor, 21) anti-inflammatory, 22) and anti-oxidant activities. 8) To improve the quality of rice plants, the organ-specific metabolic networks of primary and specialized metabolites were recently investigated using metabolite profiling based on liquid chromatography (LC)-MS. 19,[23][24][25][26][27][28] Metabolome-genome-wide association studies on rice have been increasingly attracting attention. 25,29) There are two primary types of rice grown in the world (i.e., the Indica and Japonica varieties).…”

Technical Challenges in Mass Spectrometry-Based Metabolomics

“…erefore, reporting and creating databases of tandem mass spectrum data of rare biological metabolites is important for enriching metabolome annotation data as performed by HMDB and ReSpect (http://spectra.psc.riken.jp/). 28) Although MS/MS spectra-based identi cation of biomarker metabolites and plant secondary metabolites has been reported, [29][30][31][32] structural elucidation of unknown metabolites from MS and MS/MS data is still a di cult task owing to lack of diversity in the measured MS/MS data in the databases and poor methodology for searching the similarity. 33,34) It should be noted that one of the most straightforward ways for certain identi cation of the metabolite structure is still the spectroscopic analysis of isolated metabolites.…”