Rice (Oryza sativa L.) is a crucial global food crop, although it is extremely susceptible to drought stress owing to its adaption to wetland environments. This study assessed nine enhanced rice lines possessing qDTY3.1 and qDTY2.1, significant quantitative trait loci (QTLs) for drought resistance during the flowering stage, under both flooded and drought stress conditions. The experiment was performed on agricultural land at Kandaswami Kandar’s College during the Rabi season of 2023–2024. Physiological characteristics, including relative leaf water content (RLWC), proline accumulation, and total chlorophyll content (TCC), as well as the internal structure of the flag leaf, were evaluated and correlated with the seed setting rate (SS%). Elevated SS% had a positive correlation with proline accumulation in RL-1, RL-12, RL-21, RL-27, RL-29, and RL-33, whereas RLWC shown a positive association with SS% in RL-10, RL-12, RL-27, RL-29, and RL-33. Only RL-24 and RL-33 demonstrated a robust correlation between total chlorophyll content and SS%. Anatomical investigation indicated that enhanced rice lines RL-1, RL-9, RL-10, RL-27, and RL-29, characterized by an increased quantity of vascular bundles, also exhibited superior SS% under drought stress. RL-12, RL-27, and RL-29 exhibited correlations with both RLWC and proline accumulation for SS%, whereas RL-33 was associated with all three physiological factors. Moreover, RL-24 and RL-33 demonstrated enhanced SS% under drought stress, exceeding both parental lines. The results highlight the varied drought response mechanisms of the enhanced rice lines, placing them into four distinct groups. This study offers significant insights for future breeding initiatives focused on improving drought resistance in rice farming, hence supporting consistent rice production in water-scarce conditions.
