Unravelling salt tolerance in rice through multiphase evaluation integrating morpho-physiological, biochemical and molecular insights

• Salt tolerance assessment was conducted on 120 rice genotypes at both the seedling and reproductive stages under two salinity stress levels. • Seven highly salt-tolerant landraces were identified as potential genetic resources for further studies and breeding programmes. • Morpho-physiological, biochemical, and molecular analyses were performed, including gene expression studies of key salt-responsive genes. • A proposed model was developed to elucidate the salt stress signalling pathway in rice. • A novel, low-cost field-based screening approach was introduced for validating salt tolerance response of the selected genotypes at the reproductive stage. Salinity stress significantly hampers rice productivity, necessitating the need to identify salt-tolerant genotypes for sustainable cultivation in this climate-changing scenario. This study evaluated 120 diverse rice landraces (including two checks) under hydroponic conditions at two salinity levels (EC 6 and EC 12 dS/m) to assess seedling-stage tolerance. Considerable phenotypic variation was detected across all assessed traits, with noticeable reductions in observed traits under stress conditions. Hierarchical clustering and PCA demarcated distinct tolerance groups, with genotypes such as Kalomota, Okhrajhama, Bhutmuri, Tapan 2, Radhashree, etc., exhibiting superior salt tolerance. Standard evaluation scoring (SES) further categorized genotypes into five tolerance levels, emphasizing the observed phenotypic classification. Biochemical profiling revealed that tolerant genotypes maintained significantly increased chlorophyll content and proline accumulation under salinity stress, while the Na + /K + ratio remained relatively stable. Antioxidant enzyme assays demonstrated differential enzymatic responses. qRT-PCR analysis of key salt-responsive genes indicated strong upregulation of OsCAMK1, OsDREB2A, OsV-ATPase , and OsABT in tolerant genotypes. To validate seedling-stage tolerance at the reproductive phase, a novel low-cost screening approach was employed under natural field conditions, confirming that identified highly tolerant genotypes exhibited stable grain yield and minimal reductions in yield-contributing traits under moderate (EC 6 dS/m) and severe (EC 12 dS/m) salt stress. Overall, Okhrajhama, Bhutmuri, Radhashree, Tapan 2, Gheus, Khejurchari, and Kalomota exhibited the highest levels of salt tolerance. The integration of multifaceted morpho-physiological, biochemical, and molecular analyses provides critical insights into salt tolerance mechanisms and offers a robust framework for breeding stress-resilient rice cultivars for salinity-prone agroecosystems.