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Improvement in salt tolerance at reproductive stage is very important for enhancing the grain yield and highly desirable to sustain production in saline areas. In the present study, 140 F₂ populations derived from PS5, which is saline sensitive and CSR10, saline tolerant rice variety. We evaluated 140 F₂ for salinity tolerance at reproductive stage for 18 different morphological, biochemical and physiological traits. We used 436 rice HvSSR markers which covers 12 chromosomes of rice. The linkage map has been created with 100 polymorphic markers and 140 F₂ mapping population. We identified 39 QTLs which explained 3–45% phenotypic variance at LOD score 2.6–15.2. Significant QTLs were identified for sodium content, potassium content, sodium/potassium ratio in roots and leaves including qNaL-1.2, qNa/KL-1.3, qKR-1 and qNa/KL-1.2 with R² of 45%, 42%, 35% and 32%, respectively, on chromosome 1. We identified novel QTL qGY-2 for grain yield on chromosome 2 along with QTL for stress tolerant index on chromosome 6, a noteworthy QTL for salt susceptible index of grain yield was recognized with 45% of phenotypic variation. We also identified four novel QTLs for chlorophyll content and one locus for proline content in leaves under salinity. Validation of these QTLs in fixed mapping population (RILs) and further fine mapping of these QTLs may be advantageous for marker-assisted breeding programs that led to development and commercial cultivation of reproductive stage salt-tolerant rice varieties.

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