Phenotypic and Saltol-based molecular characterization of rice germplasm under salinity stress at seedling stage

Abstract This study integrated phenotypic and molecular characterization to identify salinity-tolerant rice germplasm for breeding. A total of 231 rice genotypes were evaluated under hydroponic conditions using Yoshida’s nutrient solution. Salt injury score (SES), shoot length (SL), root length (RL), shoot dry weight (SDW), chlorophyll content (CC), and Na⁺/K⁺ ratio were assessed. Salinity level, genotype, and their interaction significantly affected the measured traits, indicating substantial phenotypic variation in response to salinity stress. Under salinity stress, SL, RL, SDW, and CC declined by 60.8%, 46.6%, 82.0%, and 22.0%, respectively, whereas the Na⁺/K⁺ ratio increased from 0.23 under control conditions to 5.27. Twelve test genotypes, together with three tolerant checks, were classified as tolerant (mean SES < 4.5). G47 (IR21LT1066) and G73 (IR21LT1673) recorded lower mean SES values than the tolerant check CSR 28, while the Tanzanian landrace Kangaga (G94) was identified as a promising indigenous germplasm for further investigation of salinity tolerance. Of the 231 phenotypically evaluated genotypes, 188 were characterized using the 1 K-RiCA platform, of which 20 carried the tested favourable Saltol-associated haplotype. Only one phenotypically tolerant genotype, G66 (IR21LT1545), possessed the tested favourable Saltol-associated haplotype. The weak correspondence between the tested favourable Saltol-associated haplotype and phenotypic tolerance suggests that additional genetic loci or complementary physiological mechanisms may contribute to seedling-stage salinity tolerance. The identified tolerant genotypes provide valuable donor resources for breeding rice with improved adaptation to salinity-prone environments.