Identification of QTLs for stagnant flooding tolerance in rice employing genotyping by sequencing of a RIL population derived from Swarna × Rashpanjor

In lowland rice ecosystems stagnant flooding or partial submergence has a significant negative impact on important yield attributing traits resulting in substantial grain yield reduction. Genetics of this stress is not yet studied intensively. Rashpanjor (IC 575321), a landrace from India, was identified and used as the tolerant donor for stagnant flooding and was crossed with high yielding variety Swarna to develop the RIL population for the present investigation. Yield and yield attributing traits of 180 F₂:₈ lines in rainfed non-stressed and stressed (stagnant flooding with 45 ± 5 cm standing water) conditions were recorded in the wet season of 2018 and stress susceptibility and tolerance indices of yield component traits were deduced. Homo-polymorphic high-quality SNPs between two parents derived from genotyping by sequencing were employed and 17 putative QTLs for plant height, shoot elongation, panicle number, grain weight, panicle length in control and stagnant flooding conditions were identified. Tolerance and susceptibility indexes for these traits were detected in chromosomes 1, 3, 4, 5, 6, 10, 11, and 12 with PVE ranging from 6.53 to 57.89%. Two major QTLs clusters were found for stress susceptibility index of grain and panicle weight on chromosome 1 and plant height in non-stress condition and stress tolerance index of elongation ability on chromosome 3. Putative functional genes present either in associated non-synonymous SNPs or inside the QTL regions were also predicted. Some of them were directly associated with ethylene biosynthesis and encoding auxin responsive factors for better adaptation under stagnant flooding and also coded for different transcription factors viz. NAC domain-binding protein, WRKY gene family, and MYB class known for ROS scavenging and production of metabolites to enhance tolerance to stagnant flooding.