Phenomics-assisted genetic dissection and molecular design of drought resistance in rice.

Dissecting the drought resistance (DR) mechanism and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change. Here, we selected a typical drought-avoidant (DA) variety IRAT109 and drought-tolerant (DT) variety Hanhui15 as the parents to develop a stable recombinant inbred line (RIL) population (F, 1,262 lines). The de novo assembled genomes of both parents were released. Through re-sequencing of the RIL population, a set of 1,189,216 reliable SNPs were obtained and used for constructing a dense genetic map. Using both aboveground and underground phenomic platforms and multimodal cameras, we captured 139,040 image-based traits (i-traits) of whole plant's phenotypes in response to drought stress throughout entire rice growth period and identified 32,586 drought-responsive quantitative trait loci (QTLs) including 2,097 unique QTLs. The QTLs related to panicle i-traits occurred on the middle of chromosome 8 over 600 times, while the QTLs related to leaf i-traits on the 5' end of chromosome 3 over 800 times, indicating potential effect of these QTLs on plant phenotypes. We chose three candidate genes (OsMADS50, OsGhd8, OsSAUR11) related to leaf, panicle, and root traits respectively and verified their functions in resisting drought. Gene OsMADS50 was found to negatively regulate DR by modulating leaf dehydration, grain size, and root downward growth. Furthermore, a total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were screened from 597 lines in RIL population under drought conditions in field experiments, and composite QTL region was highly overlapped (76.9%) with known DR gene region. Based on three candidate DR genes, we proposed the haplotype design suitable for different environments and breeding objectives. This study provides a valuable reference for multi-modal and time-series phenomic analyses, deciphers the genetic mechanism of DA and DT rice varieties, and offers a molecular navigation map for breeding DR variety.