Drought is a significant abiotic stress that has a significant impact on rice growth, production, and quality. Furthermore, water scarcity is expected to become increasingly severe and frequent as a result of climate change, particularly in arid environments. Therefore, the objective of this study was to assess the impact of water deficit on morphological, physiological and agronomic of eight rice varieties with different genetic backgrounds. In addition to apply two PCR-based molecular marker systems ISSR and SCoT to assess the genetic diversity among the studied rice varieties. The results revealed that, water shortage stress significantly reduced relative water content, total chlorophyll content, grain yield, and yield characteristics. While, it significantly increased proline content and antioxidant enzyme activity (CAT, APX, and SOD) compared to normal irrigation treatment. The combined analysis of variance demonstrated that the mean squares for environments, varieties, and their interaction were highly significant for all investigated traits, The evaluated genotypes exhibited varied responses to drought-stress conditions. The Puebla and Hispagran varieties possessed the highest performance for most of the evaluated parameters and surpassed the other tested genotypes under water-deficit conditions. Therefore, it could be exploited in rice breeding programs for water-deficit tolerance..
The ISSR primers produce 46 amplified bands with an average of 6.6 bands/primer and 49.64% polymorphism. The SCoT primers reveal 46 bands with a mean of 11.5 bands/primer and 57% polymorphism. Both marker systems were informative, and the average polymorphism information content (PIC) was 0.33 and 0.38 for ISSR and SCoT, respectively. The dendrogram generated by ISSR and SCoT markers combined data divided the varieties into two major clusters. Cluster I consisted of the genotype Sakha 106. Cluster II retained seven varieties, which were further divided into two sub-clusters; Sakha 101, Sakha 105, Sakha 106, Sakha 107 constituted the first subgroup, while Giza 177, Hispagran, and Puebla formed the second one. It could be concluded that, Puebla, Hispagran, and sakha 108, which recorded the highest desirable values for the majority of studied traits under water deficit stress, could be used as a doner in rice breeding programs to develop new promising lines under water shortage conditions.