Validation of <i>SalTol</i> Linked Markers and Haplotype Diversity on Chromosome 1 of Rice

Abstract

To determine the usefulness of SSR markers associated with a major QTL for salinity tolerance designated as collection of 115 diverse rice genotypes was phenotyped and genotyped using tightly linked DNA markers. These markers include five SSRs, RM1287, RM8094, RM3412, RM493 and RM140, and two EST markers, CP6224 and CP03970, on chromosome 1. Among the seven markers, the highest number of alleles (15) was found in RM8094, followed by 10 in RM187, RM3412 and RM493. The polymorphic information content (PIC) values ranged from 0.54 to 0.89. The highest PIC value (0.89) was found for RM8094, followed by RM493 and RM3412 (0.81) and RM1287 and RM140 (0.77). The marker RM8094 was useful for discriminating between tolerant and susceptible genotypes and therefore may be useful for marker-assisted selection. Seven haplotypes were identified among the 115 genotypes using the haplotype of IR66946-3R-178-1-1 (FL478) – the most widely used tolerant parent – which was used as a reference haplotype. Four genotypes had the same haplotype as FL478 and Pokkali-1. Of the seven different Pokkali seed sources tested, Pokkali-1 (IRGC 8948) contributed the SalTol region on the chromosome 1 segment of FL478. Genotypes from the haplotypes (in comparison with FL478) 1, 2 and 5 may be important for selecting alternative tolerant parents.