This study was conducted (1) to identify, map and validate the QTL located on chromosome 1 ( Saltol ) responsible for salinity tolerance in rice at seedling stage, (2) to find the most important SSR allelic combination in the Saltol region by haplotype diversity, (3) to identify other QTLs responsible for salinity tolerance in the FL478 line, and (4) to compare the genetic variation for salinity tolerance at seedling and reproductive stages in rice at International Rice Research Institute (IRRI) during 2005 - 2007. Ten SSR and EST-SSR markers were used to isogenic lines (BC 3 F 4 ) derived from IR29 × Pokkali and one QTL was found in Saltol region at salinity levels 12 and 16 dSm -1 , which explained 18 and 24% of phenotypic variation respectively for scoring. According to this research the location of Saltol was found in the interval around 1.2 cM on chromosome 1 that includes RM8094, RM3412 and CP6224, further fine mapping on this region, can facilitate the isolation of genes responsible for salinity tolerance. Haplotype diversity for 36 rice genotypes by 8 SSR markers located in the Saltol region, reference to Pokkali revealed 18 different haplotypes. Haplotypes with allele marker same with pokkali for RM8094 were tolerant to salinity, so this marker could discriminate the tolerant genotypes and hence could be useful for marker assisted selection of Saltol QTL. Since RM8094 showed the highest number of alleles (14) and PIC value (0.88) also this markers was the most effective markers for evaluation of genetic diversity studies. For detecting the other QTLs belonged to the traits attributed to salinity tolerance 2350 BC 3 F 4 lines derived from IR29/FL478 were used. Significant differences among BC families were found for scoring, sodium and potassium concentration and their ratio. The result showed the low ratio for Na + /K + in IR29 is mainly through low amount of Na + rather than high amount of K + . Genotyping with 500 extreme individuals showed the highest and the lowest number of QTLs respectively for Na + and K + . The result of interval mapping showed in addition to chromosome 1 there are major QTLs on chromosomes 6, 8, 10 and 12 for salinity tolerance at seedling stage in rice. In the Saltol region one QTL was found for Na + concentration while for the other traits the QTLs were found in the upper part of Saltol region. Major QTLs responsible for
