OsLSC6 regulates leaf sheath color and cold tolerance in rice revealed by metabolite genome wide association study

Abstract

Abstract Plant metabolites including anthocyanins played an important role in the growth of plants, as well as in regulating biotic and abiotic stress responses to the environment. Here we report comprehensive profiling of 3315 metabolites and a further metabolic-based genome-wide association study (mGWAS) based on 292,485 SNPs obtained from 311 rice accessions, including 160 wild and 151 cultivars. We identified hundreds of common variants affecting a large number of secondary metabolites with large effects at high throughput. Finally, we functionally identified a novel gene named OsLSC6 (Oryza sativa leaf sheath color 6) which encoded a UDP 3-O-glucosyltransferase, and involved in the anthocyanin biosynthesis of Cyanidin-3-Galc (sd1825) responsible for leaf sheath color, and results in significant different accumulation of sd1825 between wild (purple) and cultivars (green). The knockout transgenic experiments results showed that OsLSC6 regulated the biosynthesis and accumulation of sd1825, controlled the purple leaf sheath. Our further research revealed that OsLSC6 also confers resistance to cold stress during the seedling stage in rice. And we identify that a SNP in OsLSC6 is responsible for the leaf sheath color and chilling tolerance, supporting the importance of OsLSC6 in plant adaption. Our study demonstrates that metabolites-to-genes analysis by mGWAS could provide a powerful complementary tool for functional gene identification and OsLSC6 is a vital regulator during anthocyanin biosynthesis and abiotic stress responses, which promising candidate in future rice breeding and improvement.