Abstract
BackgroundRice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge.Methodology/Principal FindingsTwo pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the −QTL BILs and IR64, four major-effect QTL - one each on chromosomes 2, 4, 9, and 10 - were identified. Meta-analysis of transcriptome data from the +QTL/−QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha−1 over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia.Conclusions/SignificanceGiven the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL combinations in different genetic backgrounds to maximize yield advantage under drought.
Highlights
Among cereals, rice (Oryza sativa L.) is the most drought-sensitive crop
We report physiological differences in backcross inbred lines (BILs) that were genetically similar but showed contrasting responses in yield under drought
Four quantitative trait loci (QTL) for Grain Yield under Drought Identified To define the QTL regions responsible for improved grain yield under drought in BILs derived from and IR646Aday Sel cross [22] (Table S1), we used Affymetrix Rice Chip analysis to identify genome polymorphism. This approach was chosen after attempts to characterize the QTL regions with SSR markers did not reveal sufficient polymorphism between the parents
Summary
Rice (Oryza sativa L.) is the most drought-sensitive crop. Even a mild drought stress during the reproductive stage results in severe yield losses [1,2,3]. Most of the semi-dwarf highyielding varieties developed during the green revolution era were meant for irrigated ecosystems and are highly susceptible to drought [4]. Deep root growth, which may increase water uptake during progressive soil drying, is suggested to be a likely mechanism to confer increased yield under drought. There is little direct evidence in the literature of deep root growth conferring a yield advantage under drought [10]. A drought-yield effect of QTLs for deep roots and improved soil penetration [11,12,13,14] is yet to be confirmed. Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress.
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