Validation of a major QTL for salinity tolerance on chromosome 1 of rice in three different breeding populations

The effect of a major quantitative trait locus (QTL) for salinity tolerance in rice, designated as SalTol in a previous study, was tested using three F2 breeding populations. The populations were derived from the following F1 hybrids: 'BRRI dhan40' (susceptible)/ 'IR61920-3B-22-2-1' (highly tolerant); 'BRRI dhan28' (highly susceptible)/ 'IR50184-3B-18-2B-1' (moderately tolerant); and 'Kajalsail' (tolerant)/ 'IR52713-2B-8-2B-1-2' (tolerant). Targeted mapping of the chromosome region containing SolTol (49.6 to 87.1 cM) on chromosome 1 was conducted using 20 SSR and two EST markers. Comparisons of linkage maps of the three populations were very similar to the previous QTL map that identified SolTol. A QTL was only detected for 'BRRI dhan40'/ 'IR61920-3B-22-2-1' population. The SSR marker RM8094 was the most tightly-linked marker (P<0.001); four other markers, RM1287, RM3412, RM493 and CP03970, were also significantly associated with salinity tolerance (P<0.05). An F-3 population of the cross 'BRRI dhan40'/ 'IR61920' was used to reconfirm this result. This was interesting because the tolerant parent in this population was not related to the tolerant parent used for the original mapping population. QTLs were not detected at the SalTol locus for either of the other two populations. This was consistent with the phenotypes of the parents used to construct these populations, and indicates that the SolTol QTL may only be effective in specific populations