Quantitative trait locus mapping for salt tolerance at maturity stage in indica rice using replicated F2 population

Salinity is one of the major abiotic stresses limiting rice production worldwide. A quantitative trait locus (QTL) mapping study was conducted to identify genomic regions involved in salt tolerance in rice (Oryza sativa L.) using F2 population derived from the cross of indica rice cultivars IR36 (salt susceptible) and Pokkali (salt tolerant). Plant material was phenotyped for morphological and yield-related traits at maturity stage under saline and normal conditions. Plant material was screened for polymorphism using five hundred and fifty-three simple sequence repeat markers, out of which one hundred and eleven were found polymorphic. Six QTLs for different agronomic traits, associated with salt tolerance, were identified. Phenotypic variance explained (R-2) values of QTLs ranged from 11.52 to 81.56 %. Genomic regions having strong correlation with salt tolerance were identified on chromosomes 2, 3, 7, and 8. These genomic regions can be targeted for positional cloning and identification of genes involved in salt tolerance in rice. Identified markers, associated with salt tolerance, can be used in marker-assisted breeding for developing salt-tolerant rice cultivars.