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Sample Set Information

Title Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism
Description 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 Fumio Matsuda, Ryo Nakabayashi, Zhigang Yang, Yozo Okazaki, Jun-ichi Yonemaru, Kaworu Ebana, Masahiro Yano, Kazuki Saito
Reference Matsuda F et al. (2014) The Plant Journal Jan;81(1):13-23

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The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Sample Preparation Details Information

Title Sample Preparation
Description 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, at 28°C for 1 day in darkness. Seeds were sown in wet commercial fertilized soil (Bonsol II; Sumitomo Chemical, Tokyo, Japan,, 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℃ until analysis.

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