Natural variation of DROT1 confers drought adaptation in upland rice

Abstract Upland rice is a distinct ecotype that grows in aerobic environments and tolerates drought stress. However, the genetic basis of its drought resistance is unclear. Here, using an integrative approach combining a genome-wide association study with analyses of introgression lines and transcriptomic profiles, we identify a gene, DROUGHT1 ( DROT1 ), encoding a COBRA-like protein that confers drought resistance in rice. DROT1 is specifically expressed in vascular bundles and is directly repressed by ERF3 and activated by ERF71, both drought-responsive transcription factors. DROT1 improves drought resistance by adjusting cell wall structure by increasing cellulose content and maintaining cellulose crystallinity. A C-to-T single-nucleotide variation in the promoter increases DROT1 expression and drought resistance in upland rice. The potential elite haplotype of DROT1 in upland rice could originate in wild rice ( O. rufipogon ) and may be beneficial for breeding upland rice varieties.