3 1 severe due to recent climate changes. To cope with this increased soil salinity, we need to 3 2 develop salt tolerant rice varieties that can maintaining higher yield. Rice landraces indigenous to 3 3 the coastal region of Bangladesh can be a great resource to study the genetic basis of salt 3 4 adaptation. In this study, we developed a reciprocal mapping population between a salt tolerant 3 5landrace Horkuch and a high yielding rice variety IR29. We applied a QTL analysis framework 3 6to identify genetic loci that contributes to salt adaptive responses for two different developmental 3 7 stages of salinity treatment. We identified 14 QTL for 9 traits and found most QTL are unique to 3 8 the specific developmental stage. Moreover, we discovered a significant effect of the 3 9 cytoplasmic genome on the QTL model for some important traits such as leaf total potassium 4 0 and filled grain number. This underscores the importance of considering cytoplasm-nuclear 4 1interaction for breeding programs. Along with that, we detected QTL co-localization for multiple 4 2 traits that highlights the constraint of multiple QTL selection for breeding program. Overall, in 4 3 this study we identified multiple QTL for different physiological and yield related traits for 4 4 salinity treatment for two different developmental stages of the rice plant. We detected a 4 5 significant contribution of cytoplasm-nuclear genome interaction for many traits. This study also 4 6 suggests the selection constraint of donor alleles due to the presence of QTL co-localization. 4 7