Genetic analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.)

Drought is a major constraint for rice production and yield stability in rainfed ecosystems, especially when it occurs during the reproductive stage. Combined genetic and physiological analysis of reproductive-growth traits and their effects on yield and yield components under drought stress is important for dissecting the biological bases of drought resistance and for rice yield improvement in water-limited environments. A subset of a doubled haploid (DH) line population of CT9993-5-10-1-M/IR62266-42-6-2 was evaluated for variation in plant water status, phenology, reproductive-growth traits, yield and yield components under reproductive-stage drought stress and irrigated (non-stress) conditions in the field. Since this DH line population was previously used in extensive quantitative trait loci (QTLs) mapping of various drought resistance component traits, we aimed at identifying QTLs for specific reproductive-growth and yield traits and also to validate the consensus QTLs identified earlier in these DH lines using meta-analysis. DH lines showed significant variation for plant water status, reproductive-growth traits, yield and yield components under drought stress. Total dry matter, number of panicles per plant, harvest index, panicle harvest index, panicle fertility, pollen fertility, spikelet fertility and hundred grain weight had significant positive correlations with grain yield under drought stress. A total of 46 QTLs were identified for the various traits under stress and non-stress conditions with phenotypic effect ranging from 9.5 to 35.6% in this study. QTLs for panicle exsertion, peduncle length and pollen fertility, identified for the first time in this study, could be useful in marker-assisted breeding (MAB) for drought resistance in rice. A total of 97 QTLs linked to plant growth, phenology, reproductive-growth traits, yield and its components under non-stress and drought stress, identified in this study as well as from earlier published information, were subjected to meta-analysis. Meta-analysis identified 23 MQTLs linked to plant phenology and production traits under stress conditions. Among them, four MQTLs viz., 1.3 for plant height, 3.1 for days to flowering, 8.1 for days to flowering or delay in flowering and 9.1 for days to flowering are true QTLs. Consensus QTLs for reproductive-growth traits and grain yield under drought stress have been identified on chromosomes 1 and 9 using meta-QTL analysis in these DH lines. These MQTLs associated with reproductive-growth, grain yield and its component traits under drought stress could be useful targets for drought resistance improvement in rice through MAB and/or map-based positional analysis of candidate genes.