Unveiling Genetic Loci for Root Morphology and Salt Response at Rice Seedling Stage via Genome-Wide Association Studies

Rice (<i>Oryza sativa</i> L.) is a salt-sensitive crop, where even moderate soil salinity (electrical conductivity ≥ 3.5 dS/m) can cause significant yield reduction. During the seedling stage, the underdeveloped root system has limited capacity for salt uptake and translocation, making root system architecture (RSA) a crucial trait for enhancing salinity tolerance. In this study, we used 165 individuals from the 3K Rice Genome Project to comprehensively measure multidimensional root morphological traits at the early seedling stage under salt stress, thereby overcoming the limitations of conventional methods that mainly rely on root length and biomass. We identified 78 quantitative trait nucleotides (QTNs) associated with eight root morphological traits through genome-wide association studies (GWAS) of 3VmrMLM. Among these, 12 QTNs co-localized within genomic regions of previously cloned salt tolerance-related genes. Additionally, six salt-tolerant lines were selected based on significantly increased root volume (RV) and surface area (SA), suggesting that their adaptive mechanism under salinity involves optimized spatial root distribution rather than radial thickening. Our findings show that high-resolution root scanning-based phenotyping provides a reliable platform for screening and breeding salt-tolerant rice varieties, offering valuable indicators for assessing seedling-stage salt tolerance.