Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects

Molecular Breeding, Nov 2017

TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY 3.1 , qDTY 6.1 , and qDTY 6.2 , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2–3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY 3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY 6.1 and qDTY 6.2 , respectively. QTL class analysis also showed that lines with a combination of qDTY 3.1 and qDTY 6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs.

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Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects

Mol Breeding Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects Shalabh Dixit 0 1 Anshuman Singh 0 1 Nitika Sandhu 0 1 Aditi Bhandari 0 1 Prashant Vikram 0 1 Arvind Kumar 0 1 0 P. Vikram International Maize and Wheat Improvement Center (CIMMYT) , Km. 45, Carretera México-Veracruz, El Batán, 56237 Texcoco, CP , Mexico 1 A. Singh Rani Lakshmi Bai Central Agriculture University , Jhansi , India 2 International Rice Research Institute (IRRI) , DAPO Box 7777, Metro Manila , Philippines TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY3.1, qDTY6.1, and qDTY6.2, that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2-3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY6.1 and qDTY6.2, respectively. QTL class analysis also showed that lines with a combination of qDTY3.1 and qDTY6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs. Rice; Drought; Yield; Submergence; QTL; MABB Introduction Drought and flooding are considered to be two of the most important abiotic stresses that affect rice production globally. A total of approximately 40 million hectares of rice area are affected by different forms of the two stresses occurring at different crop stages. Under natural conditions, both of these stresses are expected to occur at different levels in the topographic sequence. However, in rainfed rice ecosystems, these two stresses are often observed to occur in the same area within a growing season. This combination of stresses is especially relevant in South and Southeast Asia where rainfed rice ecosystems are major natural disaster hotspots prone to drought and flood risks (Dilley et al. 2005) . For example, in eastern India, the onset of the monsoon may bring heavy rains in July–August that cause flash floods at the vegetative stage of the rice crop. However, early withdrawal of the monsoon or prolonged dry phases at the reproductive stage may cause considerable yield loss due to drought. Similarly, in the Mekong River basin in Southeast Asia, rainfed areas in countries such as Lao PDR, Thailand, Vietnam, and Cambodia are prone to submergence and drought within or across seasons and locations. Among these countries, Lao PDR is likely the most affected by drought and flood. The rainfed lowland ecosystem dominates rice cultivation in the country and is highly prone to natural disasters. In 2004, rainfed lowlands accounted for about 75% of the total area and 78% of the production (www.irri.org). Although floods are a common phenomenon in this region due to the presence of the Mekong River, an increase in drought incidences has also been observed in the past two decades (Komany 2004) . TDK1 is a popular rice variety that is cultivated in a large part of the rainfed lowland ecosystems in Lao PDR. A submergence-tolerant version of this variety (TDK1-Sub1) has been developed which provides considerable tolerance to flash floods; however, both TDK1 and TDK1-Sub1 are highly susceptible to drought. SUB1 is a major quantitative trait locus (QTL) derived from landrace FR13A that provides tolerance of 2– 3 weeks of complete submergence (Septiningsih et al. 2014) . This QTL was found to account for 69% of the phenotypic variance in the original identification study (Xu and Mackill 1996) and has been used extensively in marker-assisted backcross breeding (MABB) programs to improve mega-varieties with tolerance of submergence (Neeraja et al. 2007; Septiningsih et al. 2014; Toledo et al. 2015) . Similar to the advances made in submergence tolerance, considerable progress has also been made in understanding the genetics of grain yield under drought conditions in the past decade at the International Rice Research (...truncated)


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Shalabh Dixit, Anshuman Singh, Nitika Sandhu, Aditi Bhandari, Prashant Vikram, Arvind Kumar. Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects, Molecular Breeding, 2017, pp. 143, Volume 37, Issue 12, DOI: 10.1007/s11032-017-0737-2