qDTY 1.1 , a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds

Abstract

BackgroundDrought is one of the most important abiotic stresses causing drastic reductions in yield in rainfed rice environments. The suitability of grain yield (GY) under drought as a selection criterion has been reported in the past few years. Most of the quantitative trait loci (QTLs) for GY under drought in rice reported so far has been in the background of low-yielding susceptible varieties. Such QTLs have not shown a similar effect in multiple high- yielding drought-susceptible varieties, thus limiting their use in marker-assisted selection. Genetic control of GY under reproductive-stage drought stress (RS) in elite genetic backgrounds was studied in three F3:4 mapping populations derived from crosses of N22, a drought-tolerant aus cultivar, with Swarna, IR64, and MTU1010, three high-yielding popular mega-varieties, with the aim to identify QTLs for GY under RS that show a consistent effect in multiple elite genetic backgrounds. Three populations were phenotyped under RS in the dry seasons (DS) of 2009 and 2010 at IRRI. For genotyping, whole-genome scans for N22/MTU1010 and bulked segregant analysis for N22/Swarna and N22/IR64 were employed using SSR markers.ResultsA major QTL for GY under RS, qDTY1.1, was identified on rice chromosome 1 flanked by RM11943 and RM431 in all three populations. In combined analysis over two years, qDTY1.1 showed an additive effect of 29.3%, 24.3%, and 16.1% of mean yield in N22/Swarna, N22/IR64, and N22/MTU1010, respectively, under RS. qDTY1.1 also showed a positive effect on GY in non-stress (NS) situations in N22/Swarna, N22/IR64 over both years, and N22/MTU1010 in DS2009.ConclusionsThis is the first reported QTL in rice with a major and consistent effect in multiple elite genetic backgrounds under both RS and NS situations. Consistency of the QTL effect across different genetic backgrounds makes it a suitable candidate for use in marker-assisted breeding.

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

“…Comparing the current results with previous studies, we found that QSnp1b affecting SpNP, detected in the region of 38493222-39565366 on chromosome 1 in this study, was mapped together with qDTY 1.1 affecting grain yield detected in N22 Â Swarna, N22 Â IR64, and N22 Â MTU1010 populations under drought stress (Vikram et al 2011), the QTL controlling leaf rolling, and relative water content (Price et al 2002b), as well OsCOIN (Liu et al 2007); OsNAC6 (Nakashima et al 2007); AP59 ); ARAG1 (Zhao et al 2010); OsTIFY11a (Ye et al2009); OsNAC045 (Xiao et al 2007;Zheng et al 2009 as QRvd1, QRvd1 and QDlr1 for root volume, root growth rate in volume, and number of days to leaf rolling under drought conditions (Yue et al 2006). The QTL QGyp2a for GYP detected in the region of 10693848-11540193 on chromosome 2 was mapped together with qDTY 2.1 affecting grain yield (Venuprasad et al 2009;Dixit et al 2012), the QTL for osmotic adjustment (Robin et al 2003), and the QRgvd2 for root growth rate in volume under drought conditions (Yue et al 2006).…”

“…The identification and introgression of QTLs for grain yield under reproductive-stage drought stress from landraces and wild progenitor species into elite rice varieties is a fast-track approach in breeding drought-tolerant rice varieties (Vikram et al 2011). However, very few DT rice varieties have been developed using MAS and released to farmers.…”

“…However, very few QTLs are actively targeted in breeding programs because most QTLs have not been validated in different genetic backgrounds and environments (Price et al 2002b;Yue et al 2008), which may also have hampered the pace of DT breeding. Nevertheless, several major DT QTLs, such as qDTY 12.1 (Bernier et al 2007;Mishra et al 2013), qDTY 1.1 (Vikram et al 2011), qDTY 6.1 (Venuprasad et al 2012), and the QTL closely associated with the markers EM11-11 ) and RM410 (Gu et al 2012) have been identified and used for developing DT varieties via MAS. Through functional and comparative genomic studies, many stressresponsive transcription factors were recently shown to affect DT (Liu et al 2007;Lu et al 2009;Ye et al2009;Zhao et al 2010;Jeong et al 2013).…”

Does Morphological and Anatomical Plasticity during the Vegetative Stage Make Wheat More Tolerant of Water Deficit Stress Than Rice?

“…Such comparative analysis should target key morphological, physiological, anatomical, and agronomic traits throughout the crop growth cycle, as water deficit stress occurs at both early (vegetative stage) and late (reproductive stage) seasons in rice (Pandey et al, 2007). Extensive research efforts are currently ongoing to reduce the impact of water deficit stress during the reproductive stage in rice (Venuprasad et al, 2008;Verulkar et al, 2010;Vikram et al, 2011;Kumar et al, 2014) and in wheat (Olivares-Villegas et al, 2007;Lopes and Reynolds, 2010;Pinto et al, 2010). Therefore, our study focused on stress during the vegetative stage to identify key checkpoints that determine whole-plant responses of representative rice cultivars adapted to lowland, upland/aerobic, or water deficit conditions and of wheat cultivars with moderate to high water deficit tolerance.…”

The effects of drought on rice cultivation in sub-Saharan Africa and its mitigation: A review

“…A large-effect QTL qDTY1.1 has been identified as having an effect on grain yield under severe lowland reproductive-stage drought across F3-derived populations developed from a cross between N22 and Swarma, N22 and IR64 and N22 and MTU1010 (Vikram et al, 2011). This QTL has also been reported in CT9993-5-10-1-M/IR62266-42-6-2 and Apo/IR64 populations Venuprasad et al, 2012a).…”