Genetic control of yield under reproductive‐stage drought stress was studied in a population of 436 random F3–derived lines from a cross between the upland rice (Oryza sativa L.) cultivars Vandana and Way Rarem. Screening was conducted under upland conditions at IRRI during the dry seasons of 2005 and 2006. Lines were evaluated in drought stress and nonstress trials in both years to identify QTL contributing to drought resistance. For QTL detection, a set of random lines and the highest and lowest‐yielding lines under both stress and nonstress conditions were genotyped by 126 SSR markers. A QTL (qtl12.1) with a large effect on grain yield under stress was detected on Chromosome 12 in both years. The whole population was genotyped for additional markers on Chromosome 12, allowing QTL localization to a 10.2 cM region between SSR markers RM28048 and RM511. Under stress conditions, the locus also increased harvest index, biomass yield, and plant height while reducing the number of days to flowering. Under nonstress conditions, qtl12.1 did not significantly affect any trait. The additive effect of this QTL on grain yield under stress was 172 kg ha−1 per year over the 2 yr of testing, representing 47% of the average yield under stress and explaining 51% of the genetic variance. The yield‐increasing allele was derived from the susceptible parent, Way Rarem, suggesting an epistatic effect. This is the first QTL reported in rice having a large and repeatable effect on grain yield under severe drought stress in the field.

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Upland rice, produced by smallholder farmers, is the lowest-yielding rice production system. Drought stress is the most severe abiotic constraint in upland rice. Improving productivity of rice in the upland ecosystem is essential to meet rice food security needs of impoverished upland communities. Breeding drought-resistant upland rice is therefore an increasingly important goal. Numerous secondary characters have been suggested to help plant breeders in their selections. Most of these traits are not used in selection, as they are not practical for selection purposes, exhibit low heritability, or are not highly correlated with grain yield. The use of managed drought stress, where drought stress can be imposed at specific periods, has been shown to increase the heritability of yield under stress to values similar to those obtained for yield in well-watered conditions. It has now been demonstrated that drought-tolerant upland rice can be bred by directly selecting for yield in stress environments. The use of molecular markers to perform selection may eventually provide plant breeders with more efficient selection methods. To date, many quantitative trait loci (QTL) for drought resistance have been identified in rice, but few are suitable for use in marker-assisted selection. However, large-effect drought resistance QTL have now been identified and may enable effective use of marker-assisted selection for drought resistance.

A large-effect QTL for grain yield under drought conditions (qtl12.1) was reported in a rice mapping population derived from Vandana and Way Rarem. Here, we measured the effect of qtl12.1 on grain yield and associated traits in 21 field trials: ten at IRRI in the Philippines and 11 in the target environment of eastern India. The relative effect of the QTL on grain yield increased with increasing intensity of drought stress, from having no effect under well-watered conditions to having an additive effect of more than 40% of the trial mean in the most severe stress treatments. The QTL improved grain yield in nine out of ten direct-seeded upland trials where drought stress was severe or moderate, but no effect was measured under well-watered aerobic conditions or under transplanted lowland conditions. These trials confirm that qtl12.1 has a large and consistent effect on grain yield under upland drought stress conditions, in a wide range of environments.

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Selective genotyping of one or both phenotypic extremes of a population can be used to detect linkage between markers and quantitative trait loci (QTL) in situations in which full-population genotyping is too costly or not feasible, or where the objective is to rapidly screen large numbers of potential donors for useful alleles with large effects. Data may be subjected to 'trait-based' analysis, in which marker allele frequencies are compared between classes of progeny defined based on trait values, or to 'marker-based' analysis, in which trait means are compared between progeny classes defined based on marker genotypes. Here, bidirectional and unidirectional selective genotyping were simulated, using population sizes and selection intensities relevant to cereal breeding. Control of Type I error was usually adequate with marker-based analysis of variance or trait-based testing using the normal approximation of the binomial distribution. Bidirectional selective genotyping was more powerful than unidirectional. Trait-based analysis and marker-based analysis of variance were about equally powerful. With genotyping of the best 30 out of 500 lines (6%), a QTL explaining 15% of the phenotypic variance could be detected with a power of 0.8 when tests were conducted at a marker 10 cM from the QTL. With bidirectional selective genotyping, QTL with smaller effects and (or) QTL farther from the nearest marker could be detected. Similar QTL detection approaches were applied to data from a population of 436 recombinant inbred rice lines segregating for a large-effect QTL affecting grain yield under drought stress. That QTL was reliably detected by genotyping as few as 20 selected lines (4.5%). In experimental populations, selective genotyping can reduce costs of QTL detection, allowing larger numbers of potential donors to be screened for useful alleles with effects across different backgrounds. In plant breeding programs, selective genotyping can make it possible to detect QTL using even a limited number of progeny that have been retained after selection.

Molecular marker loci responding to selection under drought stress were monitored in a rice breeding population obtained by crossing a tolerant parent (Apo) to a susceptible parent (IR64). The 40 highest-yielding lines under stress and nonstress conditions obtained after two cycles of divergent selection under drought stress and non-stress conditions, respectively were genotyped using 72 polymorphic and widely distributed SSR markers. Ten loci (RM572, RM6703, RM71, RM3387, RM5686, RM520, RM510, RM256, RM269 and RM511) showing highly significant allele frequency differences between the two sets were identified. Favorable alleles at eight of these loci came from the tolerant parent, and at two (RM3387 and RM510) from the susceptible parent (IR64). Effects of these loci on grain yield were tested in five independent experiments covering a range in soil moisture levels. Results showed that at six loci (RM572, RM6703, RM520, RM256, RM269, and RM511), Apo alleles had highly significant effects on grain yield in at least three of the four stress trials but only two of these loci (RM572 and RM511) also affected grain yield under non-stress conditions. In all these cases, the effects of loci generally increased with stress level. Apo alleles at these loci seem to enhance yield under stress mainly by increasing harvest index and reducing flowering delay. Large-effect quantitative trait loci (QTLs) affecting grain yield under upland drought stress have already been found previously in other populations near RM6703, RM520, and RM511. Thus, these regions appear to be important in explaining genetic variation for upland drought tolerance in rice.

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