Molecular Characterization of Genetic Diversity and Trait Association Analysis for Yield Improvement in Maize (Zea mays L.) Using SSR Markers

Abstract

A total of 11 maize inbred lines were crossed with 4 testers in a line × tester mating design (Kempthorne, 1957), generating 44 F₁ test crosses. These, along with 11 lines, 4 testers, and 5 checks (64 genotypes), were evaluated in a simple lattice design with two replications during Rabi 2022–23 to assess genetic variability, trait associations, and yield components. Molecular diversity analysis was carried out on 15 inbred lines along with testers using 26 SSR markers, of which 11 markers exhibited clear and reproducible polymorphism, generating 22 alleles with an average of 2.0 alleles per locus. Polymorphic Information Content (PIC) values ranged from 0.12 to 0.64, indicating moderate genetic diversity; the most informative markers included umc2170 (0.64), phi080 (0.61), and bnlg1036 (0.58). UPGMA clustering based on Jaccard’s similarity coefficient grouped the 15 inbred lines into two major clusters, revealing substantial genetic divergence useful for heterotic grouping and parental selection. Correlation analysis indicated that plant height, ear length, ear girth, kernels per row, kernel rows per ear, and 100-kernel weight were positively associated with grain yield. Path coefficient analysis identified ear girth and kernels per row as the traits exerting the strongest positive direct effects on yield. The combined molecular and phenotypic findings provide a robust basis for selecting genetically diverse and agronomically superior parents for developing high-yielding maize hybrids.