QTL analysis on rice genotypes adapted to acid sulfate soils in the Mekong river delta, Vietnam

Abstract

Three target points in acid sulfate soils have been identified as: 1) Aluminum (Al) toxicity; 2) Iron (Fe) toxicity; 3) Phosphorous (P)deficiency; and 4) Droughts at the seedling stage. The exploitation of gene pools from wild rice species fruitfully obtained a true introgression of desirable traits into high yielding varieties (HYVs), such as AS996 (IR64/Oryza rufipogon), which are tolerant to Al-toxicity, have short durations, high yields, and adaptability to acid sulfate soils. Major QTLs on chromosome 3 were detected to control Al-toxicity as identified through an analysis of the RIL population of IR64/O. rufipogon on control relative root length (RRL). RM232 was considered as a good marker linked to the target quantitative trait locus(QTL)on chromosome 3, then SR28 and OSR29 on chromosome 9 were also used.QTL mapping by 126 SSRs through 225 individuals of the F6 RILs population of AS996/OM2395 was carried out to find the P-uptake gene on chromosome 12. The promising genotype of OM4498 from the BC population of IR64/OMCS2000 was selected through MAS with RM235 and RM247 on chromosome 12 linked to QTL, which controls the P-deficiency tolerance. Based on the leaf bronzing index (LBI), SSR markers were used to select promising genotypes tolerant to iron-toxicity, such as RM315 and RM212 on chromosome 1, and RM252 and RM211 on chromosome 2. The intervals among RM315-RM212 on chromosome 1, RM6-RM240 on chromosome 2, and RM252-RM451 on chromosome 4, were continually studied through further fine mapping.A backcrossing mapping population that included 217 individuals of BC2F2, was set up from OM1490/WAB880-1-38-18-20-P1-HB to detect the QTLs relating to drought tolerance (DT). The QTL was located in the intervals between RM201-RM511 on chromosome 9. BAC clones 13A9 and 7O3 were used as pinpoints on the high solution map for new markers designed from their sequences. The markers became useful to help rice breeders possibly select the improved genotypes adapting to drought stress in the seedling stage.