Integrating phenotypic and SSR marker-based molecular diversity for prioritization of parental resources in elite maize (Zea mays L.) inbred lines

Genetic diversity provides an important basis for the effective utilization of maize germplasm and the identification of complementary parental resources for breeding. In the present study, 54 elite maize (Zea mays L.) inbred lines were characterized for 14 phenological, plant-architectural, cob, kernel and grain-productivity traits during the Kharif seasons of 2024 and 2025, together with 20 simple sequence repeat (SSR) markers. Phenotypic variation was assessed using analysis of variance, Mahalanobis’ generalized distance, Tocher clustering and principal component analysis, while molecular diversity was examined using Jaccard similarity, UPGMA clustering, principal coordinate analysis and Bayesian population-structure analysis. The inbred lines formed seven phenotypic clusters, with grain yield per plant (16.61%), test weight (14.47%), shelling percentage (9.07%), kernel rows per cob (8.27%), kernels per row (8.16%) and kernels per cob (7.97%) contributing most to phenotypic divergence. SSR analysis resolved the inbred panel into 12 molecular clusters, with the largest cluster comprising 29 lines. The markers showed variable polymorphism, with PIC values ranging from 0.02 to 0.70; bnlg180, phi96100, umc1685, phi299852 and bnlg371 were among the more informative markers. The first two principal coordinate axes explained 18.29% and 13.91% of the molecular variation, respectively, while STRUCTURE analysis indicated five inferred genetic groups (K = 5) with varying levels of admixture among the lines. Phenotypic and molecular classifications showed partial correspondence, indicating that the two approaches captured complementary dimensions of genetic variation within the breeding material. Integration of trait-specific agronomic performance with molecular relationships enabled the prioritization of G2, G5 and G39 for grain productivity; G13, G14, G28, G47, G48 and G49 for kernel and cob attributes; G26 for shelling efficiency; and G35 and G45 for earliness. Several prioritized lines also occupied differentiated molecular backgrounds, supporting their value as diverse parental resources. Overall, the integrated phenotypic and molecular assessment provided a practical basis for prioritizing genetically differentiated and agronomically valuable parental resources for strategic use in maize breeding.