Morpho-molecular profiling of rice (Oryza sativa L.) germplasm for submergence tolerance using SSR markers

Rice (Oryza sativa L.) is a primary staple for more than half of the world's population, ranking as the third most-consumed cereal globally and a key contributor to food security. However, climate change is intensifying abiotic stresses, including prolonged flooding during the monsoon season (late June - September), which can drastically reduce rice yield. This submergence stress poses significant challenges in many rice-growing regions worldwide, particularly in low-lying areas of South and Southeast Asia. In Pakistan, where rice is the second most-consumed staple, flooding similarly threatens production. In this study, twenty rice genotypes (3 international lines, 17 national basmati and non-basmati cultivars) were evaluated in a triplicate manner for submergence tolerance. Phenotypic data related to yield and related traits were recorded during 2023-2024 at the Rice Research Institute, Kala Shah Kaku (Pakistan), under natural stagnant flood conditions. Survival percentage and key physiological parameters such as plant height, tiller numbers, and other yield related traits were assessed after complete submergence, and differences were analyzed by ANOVA (P < 0.05). The cultivars KSK-282, ELT-53, and KSK-133 exhibited significantly higher survival rates than others. Molecular validation using five SSR markers linked to the SUB1 QTL revealed that markers RM 7481, RM 23869, and RM 23865 distinguished tolerant from sensitive genotypes. Notably, PK-SUB-15-35 carried the SUB1 allele and showed the highest tolerance. These identified tolerant varieties and associated genetic markers provide valuable resources for breeding programs aimed at improving rice resilience to flooding.