Investigating rice adaptation to drought and salt stress through large-scale screening and genetic analysis

Rice (Oryza sativa) is one of the most important staple crops worldwide, providing food for over half of theglobal population. However, its cultivation is increasingly threatened by abiotic stresses such as drought and soilsalinity, both of which are exacerbated by climate change. Water scarcity and soil salinization are becomingmajor constraints for rice cultivation, particularly in Mediterranean and coastal regions, where salinity intrusionand unpredictable rainfall patterns are severely impacting yield stability. As rice is highly sensitive to both waterdeficit and salt stress, identifying tolerant genotypes is crucial for ensuring food security and sustainableproduction. To address these challenges, within the Pheno.gen project we are investigating the genetic and physiologicalmechanisms underlying rice adaptation to abiotic stresses, focusing on both drought and salinity tolerance. Thisstudy integrates high-throughput phenotypic screening with molecular analyses to identify stress-resilientgenotypes and genetic loci associated with stress responses. For drought tolerance, we are conducting a large-scale screening of the NEURICE collection, which comprises281 japonica accessions cultivated in Mediterranean regions. Here, we present preliminary data fromaccessions grown in a hydroponic system using Hoagland solution, either under standard conditions or exposedto 20% polyethylene glycol (PEG-6000), which induces osmotic stress by lowering the water potential of thegrowth medium. After seven days of treatment, phenotypic traits such as plant height, chlorophyll content, andrelative water content (RWC) were measured to evaluate their response to stress. These parameters providekey insights into plant vigor and physiological adaptation under water-limiting conditions. Beyond the identification of specific drought-tolerant varieties, this study aims to integrate phenotypic data withgenotypic information from a large number of japonica accessions to perform a genome-wide association study(GWAS). This approach will enable the identification of genetic loci associated with water stress response,providing valuable information for future breeding programs through marker-assisted selection. In parallel, we are investigating salinity tolerance using a population of introgression lines (ILs) derived from across between the salt-sensitive cultivar Vialone Nano and the wild rice O. rufipogon (PI 347745), which hasshown superior salt tolerance in previous studies. A BC3F4 IL population was developed using Vialone Nano asthe recurrent parent, generating a valuable genetic resource for dissecting the genetic basis of salt tolerance.Here, we present preliminary results obtained from ILs grown hydroponically under control conditions orexposed to 80 mM NaCl, a concentration known to induce salt stress in rice. Phenotypic responses were assessed through visual scoring (SES), morphometric measurements (root andshoot fresh and dry biomass, shoot/root biomass ratio, plant height), and physiological analyses (leaf watercontent and photosynthetic efficiency) to determine variations in stress tolerance. Analysis of the phenotypicdata with respect to SNPs generated by low pass sequencing of the ILs is currently underway for theidentification of wild rice loci possibly affecting salt tolerance. By combining phenotypic, physiological, and molecular analyses, this research aims to improve ourunderstanding of the genetic mechanisms underlying rice adaptation to water stress and salinity. Theidentification of tolerant genotypes and the associated genetic loci will provide essential tools for breedingprograms focused on enhancing rice resilience to abiotic stresses. Ultimately, this work contributes to the broader goal of developing climate-resilient rice varieties that can sustainproduction in increasingly unpredictable environments. The findings from this study will not only benefit breedingprograms but also support policy decisions aimed at mitigating the impact of climate change on global riceproduction.