Genetic Dissection of Component Traits for Salinity Tolerance at Reproductive Stage in Rice

Rice is highly sensitive to salt stress at flowering stage. With the objective of detection of quantitative trait loci (QTLs) in multi-environment for this stage, 180 backcross-derived lines (BC3F5) from salt tolerant donor Pokkali (AC41585) and recurrent parent IR 64 were subjected to evaluation in saline (EC = 8 dSm−1) and non-saline environments in wet season of 2014 and 2015 employing a novel phenotyping protocol. Nine multi-environmental consistent QTLs for spikelet degeneration, K+ concentration in flag leaf, stress susceptibility index for grain (SSI-Grain) and spikelet sterility (SSI-STE) on chromosomes1, 2, 3, 4 and 11 with 17–42% phenotypic variances were detected. Among several digenic epistatic interactions, one was associated with the main effect QTL (qSSI-STE-11-1) over the years. Similarly genotype × environment interaction associated with two additive QTLs, qDEG-S-2-2 and qSSI-STE-2-1 had positive effect on the resultant phenotype. Functional genes encoding calmodulin-binding protein and potassium transporter were predicted inside the consistent QTLs. Detected stable QTLs, associated markers, predicted genes and derived introgression lines with these QTLs could be utilized in future breeding programme.