Analysis of genetic diversity and validation of salt stress responsive candidate genes at early seedling stage of rice varieties for salt tolerance

Abstract In the present investigation of genetic diversity related to salinity tolerance in rice at the early seedling stage, ten salt stress responsive candidate genes were employed to screen a collection of eighteen rice varieties with two tolerant (Pokkali, CSR-36) and two sensitive (IR-29, IR-64) as checks. The microsatellite repeat motifs found in the six salt stress responsive candidate genes (OsHKT1;5, SNAC1, CDMK, CCC, SHMT1, SHMT2) revealed a comparatively higher alleles number per locus, ranged from 3 (OsHKT1;5) to 12 (SHMT1). The remaining four salt stress responsive candidate genes (OsHKT1;1, OsHKT1;3, OsHKT2;3, OsHKT2;4) produced a significantly smaller number of alleles because they lacked microsatellite. The polymorphism percentage was found to be lowest in the cases of OsHKT1;5 and CDMK (00.00%) and highest in the case of SHMT1 (75.00%). Amplification profiles dependent similarity indices, together with hierarchical classification and spatial distribution patterns, clearly distinguished 18 varieties according to their tolerance to salt stress. The results of the hierarchical classification of the varieties were fully supported by principal coordinate analysis. Microsatellite including six salt stress responsive candidate gene (OsHKT1;5, SNAC1, CDMK, CCC, SHMT1, SHMT2) as well as microsatellite lacking four salt stress responsive candidate gene (OsHKT1;1, OsHKT1;3, OsHKT2;3, OsHKT2;4) specific markers based genetic profiling facilitated clear discrimination between salt stress sensitive and tolerant varieties, validating their utility for differentiation. The identified salt tolerant varieties, along with validated markers, can be influential in developing salt tolerant rice varieties through targeted breeding programs.