Genetic Diversity, Population Structure and Parental Panel Optimization in Elite Popcorn (Zea mays L.) Inbred Lines Revealed by SSR Markers

This study provides a genome-wide assessment of genetic diversity, fixation status, and population structure in 77 elite Korean popcorn (Zea mays L.) inbred lines using 100 SSR markers. The mean number of alleles per locus was 2.99, with an expected heterozygosity (He) of 0.373 and a mean polymorphic information content (PIC) of 0.321, indicating moderate but structured diversity within a relatively narrow breeding base. The low observed heterozygosity (Ho = 0.053) and high fixation index (F = 0.875) confirmed the advanced homozygosity of these inbred lines, although residual heterozygosity ranged from 2.00% to 12.12% among lines. Population structure analyses using Bayesian STRUCTURE (K = 2), principal coordinate analysis (PCoA), and UPGMA clustering consistently revealed two major genetic groups with substantial admixture and hierarchical substructure. Chromosome 6 exhibited complete fixation (F = 1.000), coinciding with previously reported popping-related QTL hotspots, thereby suggesting the possible role of directional selection during elite line development. For hybrid seed purity verification, 16–35 informative codominant SSR markers were identified for each F1 hybrid combination, with umc2309 consistently polymorphic between the parental lines of all five tested commercial hybrid combinations. In addition, breeding-oriented subset optimization using PowerCore, CoreHunter, and their intersection retained 100% allele coverage while increasing the mean genetic distance by up to 16.0% and mean diversity indices by approximately 11%. These results demonstrate that redundancy within elite popcorn germplasm can be reduced without losing allelic representation, thereby improving parental discrimination, hybrid purity control, and breeding efficiency. Collectively, this study establishes a practical molecular framework for germplasm management, parental line discrimination, hybrid purity testing, and future popcorn breeding programs in South Korea.