Rice genes namely TPP7 ( Trehalose Phosphate Phosphatase 7), Sub1A ( Submergence 1a) and their interactions regulate tolerance to submergence at germination and seedling stage, respectively. Sequential stress of initial submergence during the germination and subsequent seedling stage water deficit stresses are not properly addressed in direct seeded rice cultivation. In our initial linkage disequilibrium and meta-QTL analysis, Sub1 locus and TPP7 genes co-segregated for tolerance to submergence at germination and seedling stage and were in linkage disequilibrium only in aus subpopulations of rice. Phenotypically, root traits were positively correlated (correlation coefficient = >0.8) with seedling growth in germination under submergence and also in subsequent water deficit stresses in recombinant inbred lines developed from N22 and Bhalum 2 cross. Further, favourable alleles of Sub1 in N22 and 3’-UTR allele of TPP7 in Bhalum 2 enhanced the root traits (>20 per cent) and seedling survival (>25 per cent), respectively in germination under submergence stress. Additionally, the interaction of N22 alleles of Sub1 and TPP7 significantly enhanced the culm diameter and root dry weight in submergence at germination stress. Interestingly, two QTLs with high additive effects associated with sixteen different traits for submerged germination and water deficit tolerance traits were identified within the genomic regions spanning Sub1 and TPP7 genes (~4 Mbp) in Chr09 indicative of genomic region effects on the trait response rather than Sub1 and TPP7. Further, favourable haplotype within the Sub1 and TPP7 genomic region had an epistatic effect on trait responses and enhanced the crown root number, root dry weight, and specific root area by 11.45%, 15.69%, and 33.15% respectively in flooded germination condition, indicative of haplo-allelic contribution in trait response. A wall-associated kinase 79 ( WAK79) and malectin-like receptor-like kinase 59 ( MRLK59) were identified as candidate genes, that through regulation of cell wall elongation might coordinate the ‘haplogenic model’ of quantitative trait response under flooded germination, recovery, and subsequent water deficit conditions and thus, favourable haplotypes could be employed in direct seeded rice improvement.