Genetic diversity analysis in eggplant (Solanum melongena L.) using Mahalanobis D² analysis, Principal Component Analysis (PCA) and Start Codon Targeted (SCoT)

This study evaluated morpho-molecular diversity among 34 eggplant (Solanum melongena L.) accessions using 10 morphological descriptors, 16 quantitative traits and 15 SCoT to parent selection and broadening the breeding base effectively. Mahalanobis D² analysis grouped the accessions into five clusters, with the greatest inter-cluster divergence between Clusters V and IV. PCA identified five components (eigenvalues >1) explaining 75.65 % of the total variance, with PC1 contributing 38.3 %. High-performing and genetically diverse accessions such as Kashi Uttam, Kashi Green Round, CHBR-2, BUB-18-12 and BUB-18-27 were identified through PCA biplot. SCoT markers amplified 4-10 loci/primer (mean: 6.13), all polymorphic, with SCoT-20, SCoT-13, SCoT-17 and SCoT-25 being the most informative based on PIC values. UPGMA clustering grouped accessions into three clusters (A:14, B:15, C:5), while population structure analysis identified two sub-populations (A:26, B:10). SCoT analysis revealed significant molecular variability. The lack of unique clustering across morphological and molecular data highlights the importance of integrated approaches. Crosses among divergent clusters are recommended to enhance genetic gain and cultivar development.