Evaluation of Morpho-Physiological and Yield-Associated Traits of Rice (<i>Oryza sativa</i> L.) Landraces Combined with Marker-Assisted Selection under High-Temperature Stress and Elevated Atmospheric CO₂ Levels

Rice (<i>Oryza sativa</i> L.) is an important cereal crop worldwide due to its long domestication history. North-Eastern India (NEI) is one of the origins of <i>indica</i> rice and contains various native landraces that can withstand climatic changes. The present study compared NEI rice landraces to a check variety for phenological, morpho-physiological, and yield-associated traits under high temperatures (HTs) and elevated CO₂ (eCO₂) levels using molecular markers. The first experiment tested 75 rice landraces for HT tolerance. Seven better-performing landraces and the check variety (N22) were evaluated for the above traits in bioreactors for two years (2019 and 2020) under control (T1) and two stress treatments [mild stress or T2 (eCO₂ 550 ppm + 4 °C more than ambient temperature) and severe stress or T3 (eCO₂ 750 ppm + 6 °C more than ambient temperature)]. The findings showed that moderate stress (T2) improved plant height (PH), leaf number (LN), leaf area (LA), spikelets panicle⁻¹ (S/P), thousand-grain weight (TGW), harvest index (HI), and grain production. HT and eCO₂ in T3 significantly decreased all genotypes’ metrics, including grain yield (GY). Pollen traits are strongly and positively associated with spikelet fertility at maturity and GY under stress conditions. Shoot biomass positively affected yield-associated traits including S/P, TGW, HI, and GY. This study recorded an average reduction of 8.09% GY across two seasons in response to the conditions simulated in T3. Overall, two landraces—Kohima special and Lisem—were found to be more responsive compared to other the landraces as well as N22 under stress conditions, with a higher yield and biomass increment. SCoT-marker-assisted genotyping amplified 77 alleles, 55 of which were polymorphic, with polymorphism information content (PIC) values from 0.22 to 0.67. The study reveals genetic variation among the rice lines and supports Kohima Special and Lisem’s close relationship. These two better-performing rice landraces are useful pre-breeding resources for future rice-breeding programs to increase stress tolerance, especially to HT and high eCO₂ levels under changing climatic situations.