Identification of genomic regions for salinity tolerance at germination stage of rice using doubled haploid mapping population

Seed germination is the most sensitive stage of rice for salinity stress. To map the genomic regions, a set of 117 doubled haploid (DH) lines derived from the F(1)s of salinity tolerant Pokkali and susceptible Savitri were used. Preliminary screening at 0, 4, 8, 12, 16 and 20 dsm(-1) of NaCl solution, Pokkali and Savitri showed significant variation of 78 % and 100%, respectively for seed germination. Based on this study, 117 DH lines were evaluated at 16 dsm(-1)NoCl, which exhibited variation in germination percentage, shoot length and root length. Bulked segregant analysis (BSA) was conducted by taking ten each extreme DH lines with 79 polymorphic SSR markers from 12 chromosomes to identify the genomic regions. Three markers, RM247, RM324 and RM283 were identified and found to be linked to four candidate genes, LOC_Os12g06560, LOC_Os12g06570, LOC_Os01g09550 and LOC_Os01g09560. Further research work is suggested to understand the tolerant mechanism of salinity at germination stage in rice.