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Background  Availability of irrigation water is becoming a major limiting factor in rice cultivation. Production in rainfed areas is affected in particular by drought events, as these areas are commonly planted to high-yielding drought-susceptible rice ( Oryza sativa  L.) varieties. The use of bulk segregant analysis (BSA), taking grain yield (GY) as a selection criterion, has resulted in the identification of several large-effect QTL. A QTL mapping study was undertaken on a BC 1 F 3:4  population developed from the cross IR55419-04/2*TDK1 with the aim of identifying large-effect QTL in the background of TDK1, a popular variety from Lao PDR.    Results  The study identified three QTL— qDTY    3.1    (RM168-RM468),  qDTY    6.1    (RM586-RM217), and  qDTY    6.2    (RM121-RM541)—for grain yield under drought.  qDTY    3.1    and  qDTY    6.1   , showed consistent effect across seasons under lowland drought-stress conditions while  qDTY    6.1    and  qDTY    6.2    showed effect under both upland and lowland drought conditions. The test of QTL effect, conducted through a QTL class analysis, showed the complimentary nature of  qDTY    3.1    and  qDTY    6.1   . Both QTL showed specific patterns of effect across different maturity groups within the mapping population and higher stability for grain yield was seen across stress levels for lines with both QTLs as compared to those with single or no QTL.    Conclusions  The study offers a clear understanding of large-effect QTL for grain yield under drought and their effect as individual QTL and in various combinations. The study also opens up an opportunity to develop a drought-tolerant version of TDK1 through marker-assisted backcross breeding and has led to a large-scale QTL pyramiding program aiming to combine these QTL with  Sub1  in the background of TDK1 as recipient variety.

Multiple major QTL lead to stable yield performance of rice cultivars across varying drought intensities