Four target points in acid sulfate soils have been addressed as (1) aluminum toxicity, (2) iron toxicity, (3) phosphorous deficiency, (4) drought at seedling stage. The exploitation of gene pool trom wild rice species ftuitfully obtained a true introgression of desirable traits into high yielding varieties (HYVs) such as AS996 (IR64/ Oryza rufipogon) which is tolerant to aluminum toxicity, short duration, high yield, adaptability to acid sulfate soils. Major QTLs in chromosome 3 were detected to be control aluminum toxicity through analysis of RIL population of IR64 / O. rufipogon on control relative root length (RRL). RM232 was considered as good marker linked to the target QTL on chromosome 3, then SR28, OSR 29 on chromosome 9 were also used. QTL mapping by 126 SSRs through 225 individuals of F 6 RILs population of AS996 / OM2395 was carried out to find the P-uptake gene on chromosome 12. Promising genotype OM4498 trom BC population of IR64 / OMCS2000 was selected through MAS with RM235 and RM247 on chromosome 12 linked to the QTL, which controls to P deficiency tolerance. Based on leaf bronzing index (LBI), SSR markers were used to select promising genotypes tolerant to iron toxicity as RM315, RM212 on chromosome I, RM252 and RM211 on chromosome 2. The intervals between RM315 and RM212 on chromosome I, RM6 and RM240 on chromosome 2, and RM252 and RM451 on chromosome 4 will be continuo sly studied through further fine mapping. A backcrossing mapping population including 217 individuals BC2F2, was set up trom OMI490 / WAB880-1-38-18-20-PI-HB to detect the QTLs relating to drought tolerance. The QTL \yas located in the interval between RM20 I and RM5ll on chromosome 9. BAC clones 13A9 and 703 were used to pinpoint in the high solution map with new markers designed trom their sequences. The markers became useful to help rice breeders possibly select the improved genotypes adapting to drought stress in seedling stage.