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Drought regularly affects rainfed lowland and upland rice ecosystems in Malaysia. Three drought yield QTLs, viz qDTY 2.2 , qDTY 3.1 and qDTY 12.1 successfully pyramided into MRQ74 to increase its yield under reproductive stage drought stress (RS). Forty-eight genotypes comprising 39 pyramided lines (PLs) with different qDTYs combinations, four parents including MRQ74 (recipient) and five checks were evaluated for morpho-physiological traits under RS and non-stress (NS). This study aims to determine which traits influenced by individual qDTY and qDTY combinations and to gain better understanding of QTL interactions in enhancing grain yield (GY) under RS. Results showed plant height, number of panicles, root length, root weight, relative water content and 100-grain weight increased while chlorophyll content and GY decreased under RS compared to NS. No significant difference was observed in days to flowering, leaf rolling and grain length between selected PLs and MRQ74 under RS. Six PLs with yield advantage (YA) of 208.17–1751.63 kg ha−1 compared to MRQ74 in RS but yielded similar to MRQ74 under NS were further selected. Under RS, qDTY class analysis showed qDTY 12.1 individually and combination qDTY 12.1 + qDTY 2.2 produced the highest yield of 1521.77 and 1092.30 kg ha−1 respectively. qDTY 12.1 as single or combination with other qDTY is the best qDTY in stabilizing GY under RS. PL-77 with qDTY 12.1 is the best PL with YA of more than 1100 kg ha−1 compared to MRQ74 in both RS and NS conditions can be recommended for cultivation in normal and drought-prone areas.

Drought has been a major limiting factor for rice production. Drought yield QTLs (qDTYs, QTLs = quantitative trait loci) were pyramided into MRQ74 and MR219 to produce drought tolerant lines. In this study, new drought tolerant MRQ74 and MR219 pyramided lines (PLs) were evaluated under drought stress (RS) and non-stress (NS) conditions to evaluate the effects of different qDTYs combinations on morphological and agronomical traits. MRQ74 PLs having qDTY12.1 possessed the best root length (RL) under both RS and NS but the effect was only significant for MR219 PLs under RS. Some qDTYs combinations also found to have consistent effect on the same trait of both populations. PLs with only qDTY12.1 showed the highest grain yield (GY) under RS in both populations which means qDTY12.1 controlled RL and caused higher GY under drought condition. The interaction of major-effect qDTY12.1 with qDTY2.2 also shows significant effect on leaf rolling (LR) of both PL populations. These qDTYs proved to be beneficial in improving traits related to drought tolerance. Selected PLs with qDTY12.1 combinations also found to have better RL and root weight (RW) under RS. Improvement of morphological and agronomical traits led to higher GY of PLs. Therefore, qDTY12.1 either is present singly or in combination with other qDTYs was the best qDTY due to its consistent effect on morphological and agronomical traits and GY across populations under RS and NS.