This study was conducted to identify and map the quantitative trait locus (QTL) controlling Al tolerance in rice using molecular markers. A population of 171 F(6) recombinant inbred lines (RILs) derived from the cross of Oryza sativa (IR64), the Al susceptible parent, and Oryza rufipogon, the Al tolerant parent, was evaluated for Al tolerance using a nutrient solution with and without 40 ppm of active Al(+3). A genetic map, consisting of 151 molecular markers covering 1,755 cM with an average distance of 11.6 cM between loci, was constructed. Nine QTLs were dentified including one for root length under non-stress conditions (CRL), three for root length under Al stress (SRL) and five for relative root length (RRL). O. rufipogon contributed favorable alleles for each of the five QTLs for RRL, which is a primary parameter for Al tolerance, and individually they explained 9.0-24.9% of the phenotypic variation. Epistatic analysis revealed that CRL was conditioned by an epistatic effect, whereas SRL and RRL were controlled by additive effects. Comparative genetic analysis showed that QTLs for RRL, which mapped on chromosomes 1 and 9, appear to be consistent among different rice populations. Interestingly, a major QTL for RRL, which explained 24.9% of the phenotypic variation, was found on chromosome 3 of rice, which is conserved across cereal species. These results indicate the possibilities to use marker-assisted selection and pyramiding QTLs for enhancing Al tolerance in rice. Positional cloning of such QTLs introgressed from O. rufipogon will provide a better understanding of the Al tolerance mechanism in rice and the evolutionary genetics of plant adaptation to acid-soil conditions across cereal species.

Drought and submergence are the two major limiting factors that reduce rice production. In this study, the relevance of yield traits through path analysis under drought and submergence conditions to improve grain yield of rice, from dry season 2014-2015 and genotypic analysis using SSR markers was evaluated, during 2015-2016. Path analysis indicated that the number of panicles/clusters had the highest and a direct positive effect on the grain yield, followed by the number of filled-grain/panicle, and the harvest index compared to other component traits. These traits could be used as selection criteria for high yield and drought tolerance in populations of rice. There were two markers including RM201 (210-225 bp) and RM219 (210-215 bp) chosen to select parents in backcrossing because production of polymorphic bands relevant to submergence and drought tolerance genes. By the BC 1 F 1 and BC 2 F 1 generations of the cross OM6162/Swarnasub1//OM6162, primers RM201 and RM219 were identified drought and submergence tolerant individuals. These lines will be used in breeding programme for release of both drought and submergence tolerant with considerable yield in next step. Findings of this study are promising to develop rice cultivars tolerant to both drought and submergence, and may therefore help to reduce detrimental impacts from climate changes to rice production.