Abstract
Development of molecular marker selection permits rapid and accurate identification of individuals that contain gene(s) for a specific trait like salt tolerance. Microsatellite markers are suitable for tagging and mapping of QTL/ gene associated with salt tolerance. SalTol is a major quantitative trait locus (QTL) for salinity tolerance in rice. Three F₂ breeding populations derived from the crosses viz. BRRI dhan40 (moderately tolerant)/ NSICRc106 (highly tolerant); BRRI dhan28 (highly susceptible)/ IR50184-3B-18-2B-1 (moderately tolerant); and Kajalshail (tolerant)/ PSBRc88 (tolerant) were used in validation studies. 20 SSR and two EST markers were used for the targeted mapping of the chromosomal region containing SalTol (49.6 to 87.1 cM) on chromosome 1. There was a good parallel among the linkage maps of the three populations to the previous QTL map that identified SalTol. SalTol QTL was detected only in population derived from BRRI dhan40/ NSICRc106 cross. The SSR marker RM8094 was the most tightly-linked marker (P<0.001) comparison to four other markers, RM1287, RM3412, RM493 and CP03970, which were also significantly associated with salinity tolerance (P<0.05). A F₃ population of population 1 was used to reconfirm these results and similar result was observed as in the F₂ population. The identified SalTol in population 1 was the same though the tolerant parent was unrelated to the tolerant parent (Pokkali) used for the previous population. No QTLs were detected at the SalTol locus in any of the other two populations. This indicates that the SalTol QTL could only be present in specific populations. To determine the usefulness of specific SSR markers associated with major QTL for salinity tolerance designated as ‘SalTol’, a collection of 115 diverse rice genotypes were phenotyped and genotyped using tightly-linked DNA markers viz. SSR RM1287, RM8094, RM3412, RM493, RM140 and two EST CP6224, CP03970 on chromosome 1. Among the seven markers, RM8094 produced the highest number of alleles (15) followed by RM187, RM3412 and RM493 (10). The polymorphic information content (PIC) values ranged from 0.54 to 0.89 with highest for RM8094, followed by RM493 and RM3412 (0.81), RM1287 and RM140 (0.77). It suggested that RM8094 markers could be useful for discriminating tolerant and susceptible genotypes and may be applicable for marker assisted selection. Out of 115 genotypes studied seven haplotypes were identified with reference to haplotype of IR66946-3R-178-1-1 (FL478), one of the most widely-used tolerant parents. Four genotypes had the same haplotype as of FL478. Of the seven different Pokkali seed accessions from different sources, Pokkali-1 (IRGC8948) was identified as the actual source that contributed the SalTol region in chromosome 1 segment of FL478. Genotypes from the haplotypes 1, 2, and 5 could be important for selecting alternative tolerant parents.