SSR-Based Genetic Diversity, Population Structure, and Marker–Trait Associations for Popping-Related Traits in Popcorn Germplasm

Background/Objectives: Popcorn (Zea mays L. var. everta) is an important specialty maize type; however, the genetic variation underlying popping-related quality traits remains insufficiently characterized in breeding. Methods: In this study, 18 popcorn inbred lines were analyzed using 25 simple sequence repeat (SSR) markers distributed across all 10 maize chromosomes, and 16 lines were further evaluated for popping performance and image-based flake morphology. Results: Substantial phenotypic variation was observed among the tested lines, with expansion volume ranging from 173.33 to 343.33 mL and expandability ranging from 16.79- to 32.46-fold. Image-based analysis of 957 popped kernels revealed continuous variation in flake circularity, indicating that flake morphology represents a quantitative trait rather than a strictly discrete classification. SSR analysis detected 2 to 11 alleles per locus, with polymorphism information content values ranging from 0.05 to 0.85, indicating moderate-to-high genetic diversity among the tested lines. Principal component analysis (PCA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and population structure analysis revealed clear genetic differentiation and heterogeneous genetic backgrounds within the germplasm collection. Marker–trait association analysis identified several putative SSR loci associated with expansion efficiency, flake morphology, pericarp retention, and popping dynamics. Notably, marker M18 was putatively associated with both expansion volume and expandability. Conclusions: Based on these results, a conceptual framework was proposed in which popping-related traits were organized into partially independent but interconnected functional modules. Overall, this study provides SSR-based genetic information for popcorn germplasm characterization and offers preliminary marker resources for quality-oriented popcorn breeding.