Identification and characterization of quantitative trait loci for drought resistance in upland rice (Oryza sativa L.)

Breeding improved drought-resistant upland rice cultivars could be accelerated if suitable quantitative trait loci (QTL) with large and consistent effects on grain yield under drought conditions in the desired genetic backgrounds were identified. Experiments were performed with the aim of identifying, characterizing and validating a QTL with the potential to be used in marker-assisted selection. A population from the cross Vandana/Way Rarem was field tested during two consecutive years. A large-effect QTL (qtl12.1) for grain yield under reproductive-stage drought was identified. This locus had an additive effect equivalent to 47% of the trial mean yield over two years and had a very low level of QTL x year interaction. The favorable effect was contributed by Way Rarem, the drought-susceptible parent. A subset of lines was subsequently tested in a total of 21 trials, in order to confirm the effect of qtl12.1 under a wider range of environments, stress intensities and stress timing. The QTL had a very consistent effect across trials, as it improved grain yield in 9 out of 10 moderately to severely drought-stressed trials. The locus had no effect under well-watered conditions. The results from those trials confirm that qtl12.1 is a drought-specific locus that is consistent across environments. Physiological experiments on a subset of lines having contrasting genotypes at qtl12.1 revealed that the Way Rarem-derived allele of qtl12.1 improves grain yield under drought mainly through a slight improvement (7 to 9 %) in plant water uptake under water-limited conditions. Such an increase in water uptake could explain the large effect on grain yield observed under field conditions. This improvement of plant water uptake is likely associated with improved root architecture. Finally, QTL mapping for drought resistance was also performed in an IR55419-04/Way Rarem population evaluated under similar conditions as the Vandana/Way Rarem population. This revealed that qtl12.1 had no effect on grain yield under stress in the IR55419-04/Way Rarem population, suggesting QTL x genetic background interaction for qtl12.1.