Major QTL for enhancing rice grain yield under lowland reproductive drought stress identified using an O. sativa/O. glaberrima introgression line

•A major QTL, qDTY3.2 was mapped on chromosome 3 with consistent effect on grain yield across three seasons under both stress and control conditions.•We observed the effect of qDTY3.2 increases with increase in level of stress.•A clear grain yield advantage was found between with QTL lines and without QTL lines.•qDTY3.2 is also governing canopy temperature and seedling dry weight under stress conditions.

Water stress is a major abiotic stress limiting the rice production and yield stability in rainfed conditions and getting worse with the predicted global climatic change. A Backcross inbred line (BIL) population derived from Swarna/WAB 450-I-B-P-157-2-1 was screened for grain yield under reproductive stage drought stress and irrigated conditions during DS2013, WS2012 and DS2012. A major qDTY3.2 with large and consistent effect on grain yield was mapped on chromosome 3 flanked by RM14303 and RM22 across three seasons under both stress and control conditions. qDTY3.2 explained a phenotypic variance of 29.5%, 18.8% and 31.8% under drought stress during DS13, WS12 and DS12, respectively. Apart from grain yield, qDTY3.2 is also account for variation in canopy temperature during flowering and seedling shoot dry weight and drought recovery under stress conditions. Lines with QTL showed a clear grain yield advantage over lines without QTL under both stress and control conditions. Due to the consistent effect of qDTY3.2 across diverse environments and varied level of stresses makes it an appropriate candidate for MAS. Introgression of such genomic regions in to elite drought susceptible backgrounds can lead to enhancement of grain yield level to a greater extent.