Mapping of QTLs controlling Na⁺, K⁺ and Cl^- ion concentrations in salt tolerant indica rice variety CSR27

Soil salinity and sodicity are major constraints to rice production in about twenty per cent of the irrigated crop land. Inbuilt genetic tolerance to salinity is the most economical and environmentally sustainable way to solve this problem. A mapping population of 200 F2 plants and their corresponding F3 families, derived from a cross between a salt tolerant indica rice variety CSR27 and a salt sensitive variety MI48 were used to map QTLs for salt tolerance. Seventeen different parameters, including seedling salt injury score, Na+, K+, Cl- concentrations and Na+/K+ ratio in leaf and stem tissues at vegetative and reproductive stages were mapped. A framework linkage map was constructed using 79 SSR and EST markers distributed over the twelve rice chromosomes at an average interval of 20.7cM and total map distance of 1634.5 cM. Twenty five major QTLs, each explaining more than ten per cent of the trait phenotypic variance, were mapped on chromosomes 1, 2, 3 and 8. These included one QTL for seedling salt injury score, nine for Na+ concentration, three for K+ concentration and four for Cl-concentration in leaf and stem tissues at vegetative and reproductive stages. The Na+/K+ ratio, an important ion balancing parameter for the salt tolerance, was controlled by eight QTLs explaining phenotypic variance in the range of 42.88-52.63%. Four QTL intervals were robust with major effect and having QTLs for multiple salt tolerance parameters that might be governed by common or tightly linked genes. One major QTL for multiple salt tolerance parameters on chromosome 8 and three major QTLs for Cl- ion concentration are novel for this study. The QTLs identified here will serve as a base for fine mapping, gene tagging and marker assisted selection for salt tolerance in rice.