Quantitative Trait Loci Associated with Drought Tolerance at Reproductive Stage in Rice

Abstract

Drought is a major constraint to rice (Oryza sativa) yield and its stability in rainfed and poorly irrigated environments. Identifying genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and development of more drought tolerant cultivars. Quantitative trait loci (QTL) for grain yield and its components and other agronomic traits were identified using a subset of 154 doubled haploid lines derived from a cross between two rice cultivars, CT9993-510 to 1-M and IR62266-42 to 6-2. Drought stress treatments were managed by use of a line source sprinkler irrigation system, which provided a linearly decreasing level of irrigation coinciding with the sensitive reproductive growth stages. The research was conducted at the Ubon Rice Research Center, Ubon, Thailand. A total of 77 QTL were identified for grain yield and its components under varying levels of water stress. Out of the total of 77 QTL, the number of QTL per trait were: 7-grain yield (GY); 8-biological yield (BY); 6-harvest index (HI); 5-d to flowering after initiation of irrigation gradient (DFAIG); 10-total spikelet number (TSN); 7-percent spikelet sterility (PSS); 23-panicle number (PN); and 11-plant height (PH). The phenotypic variation explained by individual QTL ranged from 7.5% to 55.7%. Under wellwatered conditions, we observed a high genetic association for BY, HI, DFAIG, PSS, TSN, PH, and GY. However, only BY and HI were found to be significantly associated with GY under drought treatments. QTL flanked by markers RG104 to RM231, EMP2_2 to RM127, and G2132 to RZ598 on chromosomes 3, 4, and 8 were associated with GY, HI, DFAIG, BY, PSS, and PN under drought treatments. The aggregate effects of these QTL on chromosomes 3, 4, and 8 resulted in higher grain yield. These QTL will be useful for rainfed rice improvement, and will also contribute to our understanding of the genetic control of GY under drought conditions at the sensitive reproductive stage. Close linkage or pleiotropy may be responsible for the coincidence of QTL detected in this experiment. Digenic interactions between QTL main effects for GY, BY, HI, and PSS were observed under irrigation treatments. Most (but not all) DH lines have the same response in measure of productivity when the intensity of water deficit was increased, but no QTL by irrigation treatment interaction was detected. The identification of genomic regions associated with GY and its components under drought stress will be useful for marker-based approaches to improve GY and its stability for farmers in drought-prone rice environments.In rainfed lowland areas, one of the major abiotic constraints depressing rice (Oryza sativa) production is water stress, including deficit (drought) or excess water (flood; O' Toole and Chang, 1979;Herdt, 1991;Lin and Shen, 1993). Drought stress is a serious limiting factor to rice production and yield stability in rainfed rice areas (Dey and Upadhyaya, 1996). The occurrence of drought can be as...

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

“…The result indicated that the flowering time of all tested cultivars was significantly delayed by drought regime in both LDs and SDs (Supplemental Figure S10), suggesting that drought-delayed flowering response may have already existed prior to genetic divergence of indica and japonica cultivars. Rice is more susceptible to drought sensitivity during reproductive stages (Lanceras et al, 2004), so we hypothesize that rain-fed ancestors of contemporary rice species may have postponed the transition from vegetative phase to reproductive phase as they sensed temporary water deficits and reduced water consumption. Such a drought avoidance strategy may enable rice to enhance survival by postponing blossoming until the upcoming rainy season.…”

Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

“…A total of 80 QTLs for flowering time detected under well-watered conditions were collected from ten papers (Li et al 1995;Yano et al 1997;Lafitte and Courtois 1999;Lin et al 2000;Maheswaran et al 2000;Yamamoto et al 2000;Yu et al 2002;Hittalmani et al 2003;Lanceras et al 2004;Dong et al 2004). A total of 59 QTLs for plant height were collected from ten papers (Li et al 1995;Lafitte and Courtois 1999;Hemamalini et al 2000;Yu et al 2002;Courtois et al 2003;Hittalmani et al 2003;Lanceras et al 2004;Xu et al 2004;MacMillan et al 2006;Gomez et al 2006). All the QTLs are compiled in TropgeneDB.…”

Drought-tolerance QTLs commonly detected in two sets of reciprocal introgression lines in rice

“…The use of quantitative trait locus (QTL) mapping has contributed to a better understanding of the genetic basis of DT-related traits. An increasing number of QTLs related to drought response have been reported, and these include QTLs for osmotic adjustment (Robin et al 2003), grain yield and yield components (Lanceras et al 2004;Xu et al 2005;Wang et al 2013), stay-green (Jiang et al 2004), canopy temperature, leaf rolling and leaf drying (Yue et al 2005), carbon isotope discrimination (D 13 C) (Takai et al 2009;Xu et al 2009), photosynthesis parameters (Gu et al 2012), and root morphology and other root-related traits such as root penetration ability (Price et al 2002a;Babu et al 2003). The earlier approach to improve grain yield under reproductive-stage drought stress through selection based on secondary traits such as root architecture, leaf water potential, panicle water potential, osmotic adjustment, relative water content, etc.…”

“…Drought can occur at any stage during the rice-growing season, due to inadequate irrigation, uneven distribution of rainfall, variation in rainfall patterns from one year to another or inadequate rainfall in large areas (Zhang 2007). The reproductive stage (from panicle initiation to flowering) is recognised as the most critical stage at which drought stress can directly affect grain yield (Lanceras et al 2004;Venuprasad et al 2009). Therefore, enhancement of drought tolerance (DT) in rice is becoming an important strategy to stabilise rice production in areas with rainfed agriculture.…”