IC4R012-Metabolomics-2012-22229385

Project Title

• Dissection of genotype–phenotype associations in rice grains using metabolome quantitative trait loci analysis

The Background of This Project

• As metabolic state is modulated by heritable factors,the genetic control of metabolic traits has been a major focus in the field of plant metabolic research. However, the relationship between genotype and metabolomic traits(m-traits) is not straightforward, because m-traits are under complex influences of quantitative trait loci (QTL) (Fernie and Schauer, 2009; Kliebenstein, 2009; Peleg et al., 2009).Furthermore, the metabolic composition of plant tissues is dynamically affected by environmental factors through post-translational interactions involving entire metabolic networks (Chan et al., 2010; Kerwin et al., 2011). Recent progress in metabolomics and QTL mapping techniques has made it possible to investigate the effect of genetic background on m-trait levels for a wide variety of metabolites.Metabolome QTL (mQTL) analyses have been performed for Arabidopsis and tomato (Solanum lycopersicum) using metabolomic techniques such as GC–MS and LC–MS, from which a better understanding of the genetics of plant metabolism has emerged (Keurentjes et al., 2006; Schauer et al., 2006, 2008; Lisec et al., 2008, 2009; Rowe et al., 2008).
• In this study, an mQTL analysis was performed for rice grains. An understanding of the genetic background of m-traits in rice (Oryza sativa) grain would provide a foundation for improvement of the nutritional quality of one of the world’s most important food crops.To address these issues, a large-scale metabolome dataset, including a wide variety of rice metabolites, was obtained using an analytical platform that covers primary and secondary metabolites. Based on this dataset, the genetic backgrounds representing natural variations in rice metabolism were investigated by analysis of broad-sense heritability, metabolite–metabolite correlation, QTL mapping and identification of putative causative genes from a candidate mQTL region.

Plant Culture & Treatment

• The plant population consisted of 85 back-crossed inbred lines derived from the cross Sasanishiki/Habataki//Sasanishiki///Sasanishiki (Sasanishiki · Habataki) (Nagata et al., 2002b). Seeds from the experimental lines were grown in a paddy field at the National Institute of Agrobiological Sciences (Tsukuba, Japan) in 2005 and 2007, employing similar cultivation schedules. The seeds of the 2005 and 2007 harvests were used for metabolome analysis. One hundred dehulled seeds obtained from whole seeds harvested from 10 independent plants were ground to a fine powder using an MM300 mixer mill (Retsch, http://www.retsch.com/) at 20 Hz for 2 min in a stainless steel grinding vessel. The powder was divided between small sample tubes (50–100 mg) under nitrogen, and the samples were stored at )80�C until analysis.

Labs working on this Project

• RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan,
• QTL Genomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, Japan, and
• Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan

Corresponding Author

• Kazuki Saito：ksaito@psc.riken.jp