Genetic, Physiological, and Gene Expression Analyses Reveal That Multiple QTL Enhance Yield of Rice Mega-Variety IR64 under Drought

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.

Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress

“…The effect of qDTY 2.3 under both RS and NS makes it an important candidate for use in MAB to increase yield under both RS and NS conditions. Bernier et al [44] reported the stability of qDTY 12.1 across different environments; qDTY 2.2 and qDTY 4.1 together have been reported to contribute to increase GY under both RS and NS conditions [43]. In both cases, the increase in GY was high under RS and low under NS, which was also observed in the present study.…”

“…Similarly, qDTY 2.2 has earlier been identified to be contributed by Aday Sel, another traditional drought-tolerant donor from India, and has shown a high effect in the IR64 background. In previous studies, qDTY 2.2 , qDTY 4.1 , qDTY 9.1 , and qDTY 10.1 contributed by donor Aday Sel have shown an effect in the IR64 background, [43]. In the present study, qDTY 2.2 showed effect in the MTU1010 background and not in IR64 background, indicating the importance of interaction between QTL allele and genetic background in determining the effect of a QTL region.…”

The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat

“…Other drought resistant QTLs have also been reported in rice. Multiple QTLs were reported in the rice mega-variety IR64 that enhance the yield under drought conditions (Swamy et al, 2013). Combinations/pyramiding of transgenic plants and QTL drought resistant varieties by marker-assist selection (MAS) may promote drought tolerance.…”

Ratooning as a management strategy for lodged or drought‐damaged rice crops

“…Genotypes showing the highest levels of ratoon crop productivity included both relatively drought-susceptible as well as drought-tolerant released varieties based on previous evaluations (Torres & Henry, 2018). Interestingly, genotypes Binuhangin and IR87707-445-B-B-B (released as the variety DRR 42 in India) have both stood out as having high grain yield under drought in previous reports (Swamy et al, 2013;Torres, McNally, Vera Cruz, Serraj, & Henry, 2013) and have shown some similarities in their physiology in terms of low canopy temperature and deep root growth compared with other genotypes (Henry et al, 2015;Torres & Henry, 2018). However, this study revealed Binuhangin and IR87707-445-B-B-B to have much different ratooning ability,…”