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.

No abstract

Drought is a major cause of yield loss in rain‐fed rice (Oryza sativa L.), grown on over 40 million ha in Asia. The objective of this study was to evaluate the effectiveness of direct selection for yield under drought stress in upland rice in populations derived from crosses between irrigated high‐yielding cultivars and upland‐adapted cultivars. Random F2:4 lines from five populations were screened for grain yield in fully irrigated lowland fields under nonstress conditions and in uplands under severe reproductive‐stage drought stress. Stress caused mean yield reduction of 64% across populations. Broad‐sense heritability for yield was not consistently lower in stress than in nonstress trials. Response to selection was evaluated in two crosses in subsequent seasons. Stress‐selected lines had a yield advantage of 25 to 34% over random lines when evaluated at stress levels similar to those in which they were selected. Yield gains under very severe stress occurred only in a population derived from a highly tolerant parent. Direct selection usually gave greater response under stress than indirect selection under nonstress conditions. Direct selection under dry‐season stress also gave response under naturally occurring wet‐season stress. These results support the hypothesis that selection for yield under reproductive‐stage drought stress is effective in rice, and that choice of donor is very important in breeding drought‐tolerant rice.

Rice double-haploid (DH) lines of an indica and japonica cross were grown at nine different locations across four countries in Asia. Genotype-by-environment (G x E) interaction analysis for 11 growth- and grain yield-related traits in nine locations was estimated by AMMI analysis. Maximum G x E interaction was exhibited for fertility percentage number of spikelets and grain yield. Plant height was least affected by environment, and the AMMI model explained a total of 76.2% of the interaction effect. Mean environment was computed by averaging the nine environments and subsequently analyzed with other environments to map quantitative trait loci (QTL). QTL controlling the 11 traits were detected by interval analysis using mapmaker/qtl. A threshold LOD of >/=3.20 was used to identify significant QTL. A total of 126 QTL were identified for the 11 traits across nine locations. Thirty-four QTL common in more than one environment were identified on ten chromosomes. A maximum of 44 QTL were detected for panicle length, and the maximum number of common QTL were detected for days to heading detected. A single locus for plant height (RZ730-RG810) had QTL common in all ten environments, confirming AMMI results that QTL for plant height were affected the least by environment, indicating the stability of the trait. Two QTL were detected for grain yield and 19 for thousand-grain weight in all DH lines. The number of QTL per trait per location ranged from zero to four. Clustering of the QTL for different traits at the same marker intervals was observed for plant height, panicle number, panicle length and spikelet number suggesting that pleiotropism and or tight linkage of different traits could be the possible reason for the congruence of several QTL. The many QTL detected by the same marker interval across environments indicate that QTL for most traits are stable and not essentially affected by environmental factors.

No abstract

BackgroundPlant roots are important organs to uptake soil water and nutrients, perceiving and transducing of soil water deficit signals to shoot. The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in roots of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress.ResultsGlobal gene expression analysis showed that about 55% of genes differentially expressed in roots of rice in response to drought stress treatments. The number of differentially expressed genes (DEGs) increased in NILs as the level of water deficits, increased from mild to severe condition, suggesting that more genes were affected by increasing drought stress. Gene onthology (GO) test and biological pathway analysis indicated that activated genes in the drought tolerant NILs IR77298-14-1-2-B-10 and IR77298-5-6-B-18 were mostly involved in secondary metabolism, amino acid metabolism, response to stimulus, defence response, transcription and signal transduction, and down-regulated genes were involved in photosynthesis and cell wall growth. We also observed gibberellic acid (GA) and auxin crosstalk modulating lateral root formation in the tolerant NILs.ConclusionsTranscriptome analysis on two pairs of NILs with a common genetic background (~97%) showed distinctive differences in gene expression profiles and could be effective to unravel genes involved in drought tolerance. In comparison with the moderately tolerant NIL IR77298-5-6-B-18 and other susceptible NILs, the tolerant NIL IR77298-14-1-2-B-10 showed a greater number of DEGs for cell growth, hormone biosynthesis, cellular transports, amino acid metabolism, signalling, transcription factors and carbohydrate metabolism in response to drought stress treatments. Thus, different mechanisms are achieving tolerance in the two tolerant lines.

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.

No abstract