IC4R011-Metabolomics-2015-25267402

Project Title

• Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

The Background of This Project

• Recently, metabolomics studies revealed that the composition of secondary metabolites in plants is an inherently variable phenotype, as genetic polymorphisms cause large qualitative and quantitative variations in metabolic phenotypes (metabolotypes) among cultivars and ecotypes (Chan et al., 2010a; Saito and Matsuda, 2010; Weigel, 2012; Carreno-Quintero et al., 2013).Recently, metabolomics studies revealed that the composition of secondary metabolites in plants is an inherently variable phenotype, as genetic polymorphisms cause large qualitative and quantitative variations in metabolic phenotypes (metabolotypes) among cultivars and ecotypes (Chan et al., 2010a; Saito and Matsuda, 2010; Weigel, 2012; Carreno-Quintero et al., 2013).
• In this study, GWAS was conducted by analyzing the aerial part of 175 Japanese diverse rice (Oryza sativa) cultivar seedlings using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the non-targeted analysis of known and unknown metabolites (Bottcher et al., 2008;Matsuda et al., 2009). The analysis revealed that there are two types of genetic architectures responsible for the natural variations in the composition of secondary metabolites in the rice population. While the small number of mQTLs

tightly associated with levels of one-third of analyzed metabolites, levels of other one-third of metabolites were under the smaller effect of multiple QTL.

Plant Culture & Treatment

• A Japanese rice collection of 175 accessions were used in this study (Table S1) (Yonemaru et al., 2012). The Sasanishiki/Habataki chromosome segment substitution lines (CSSLs, 39 accessions) were also used (Ando et al., 2008). Seeds were sterilized in 10% sodium hypochloric acid solution by vacuum infiltration for 1 h,and then immersed in aqueous 2% PPMTM solution (Nacalai Tesque, Kyoto, Japan, http://www.nacalai.co.jp/) at 28°C for 1 day in darkness. Seeds were sown in wet commercial fertilized soil (Bonsol II; Sumitomo Chemical, Tokyo, Japan, http://www.sumitomochem.co.jp/), and maintained under a 12-h light (28°C)/12-h dark(20°C) cycle for germination. Plants were kept under constant subirrigation conditions with tap water. After 2 weeks of growth, the entire aboveground (or aerial) part of one seedling was collected,weighed, and frozen in liquid nitrogen for analysis. Samples were stored at �80°C until analysis.

Labs working on this Project

• 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,
• National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan, and
• Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, Japan

Corresponding Author

• Kazuki Saito:ksaito@faculty.chiba-u.jp