Marker based haplotype diversity of Saltol QTL in relation to seedling stage salinity tolerance in selected genotypes of rice

A major QTL for seedling stage salt tolerance, Saltol has been mapped on chromosome 1 in rice. The present study was carried out to characterise the haplotype diversity in the Saltol region using 20 simple sequence repeat markers, and it association with seedling stage salt tolerance under controlled condition (ECe of 12 dSm(-1)) in 23 diverse rice germplasm including land races, wild germplasm and improved-varieties. Genotypes from kaipad ecosystem of Kerala showed salt tolerance and haplotypes of Saltol similar to Pokkali, whereas salt tolerant wild rices possessed different haplotypes and therefore may be novel sources for salt tolerance. Altogether, 14 different haplotypes were observed in 23 rice genotypes based on critical markers linked to Saltol QTL using Pokkali as the reference. The haplotypes possessing Pokkali alleles at both the markers, RM8094 and RM3412 could discriminate the salt tolerant genotypes from the susceptible genotypes and hence could be useful in marker-assisted selection.