Analysis of genomic region spanning Saltol using SSR markers in rice genotypes showing differential seedlings stage salt tolerance

Micro satellite markers located in the Saltol QTL of 5 Mb region (10.4–15.6 Mb) in chromosome 1 confering seedling stage salt tolerance were used to evaluate 94 rice genotypes. Out of 21, eight SSR markers at Saltol region of Chromosome were found polymorphic. Based on the phenotypic screening, 94 genotypes were grouped as highly tolerant (20), tolerant (18) moderately tolerant (32), sensitive (19) and highly sensitive (5). The marker RM3412 appears to be diagnostic of salinity tolerance and associate to salinity tolerance at seedling stage as it is closely linked to SKC gene. Based on Saltol markers study, CSR 31, CSR 38, CSR 41, CSR 32, Wild 11, CSR 18, Azgo, Pant Dhan 4, Trichi 1, CSR 10 and IR64426-4B-11-1 could not be identified as tolerant genotypes though had expressed tolerant to highly tolerant phenotype to salinity stress at seedling stage, suggesting that QTLs other than Saltol might be controlling their salinity tolerance. It is suggested that these genotypes could serve as potentially novel germplasm and could be exploited for the development of new breeding lines with high level of salinity tolerance by pyramiding of the Saltol and other QTLs.