Genetic Prediction of Heterosis for Agronomic and Drought Tolerance Characters of Some Rice Genotypes by Molecular Markers and Multivariate Analysis Under Different Water Treatments

This investigation focused on assessing heterosis, genetic variability, and the key physiological and biochemical indicators associated with drought tolerance in rice at water-limited environments. Seven rice accessions were utilized in a half-diallel pattern, resulting in the development of twenty-one F1 hybrid combinations. Molecular divergence among the parental lines was analyzed through eleven SCoT polymorphism primers, generating 149 DNA fragments, out of which 71 were polymorphic, representing (47.6%) polymorphism. PIC value was 0.40, with SCoT-02, SCoT-08, and SCoT-09 showing the highest polymorphism. Genetic distances ranged from 0.81 to 0.90, with SK-101 and GZ-179 being the most divergent. Cluster separated the rice accessions into two main groups. Several hybrids, notably GZ-179×IET-1444, IET-1444×HR-5824, and SK-106×SK-107, displayed significant heterosis for yield-related traits across environments. Under normal circumstances, there was a strong correlation between marker-based genetic distance (GD) and heterosis, especially for sterility. Traits such as thousand-grain weight, weight panicle, sterility, and yield/plant-1 exhibited strong positive correlations with better-parent heterosis under water regime, indicating that SCoT-based genetic distance can predict hybrid performance under stress. Multivariate analyses (Bi-plot PCA and heatmap) revealed that grain yield was positively associated with photosynthetic rate, membrane stability, water-use efficiency, and proline content, while negatively correlated with oxidative stress indicators. PCA effectively discriminated drought-tolerant hybrids, especially GZ-179×IET-1444, IET-1444×HR-5824, and GZ-179×HR-5824, which combined superior photosynthetic capacity, membrane integrity, and biochemical resilience along highly production and related features.