Fusarium ear rot (FER), caused by F. verticillioides, is a devastating disease in maize, leading to substantial yield losses and mycotoxin contamination. Therefore, revealing the molecular mechanisms underlying FER resistance is essential for crop breeding. Here, we performed integrated transcriptomic and metabolomic analyses on two maize inbred lines with contrasting FER resistance: the resistant line ZL30-12 (ZL30) and the susceptible line 92C0468U (92C). Following F. verticillioides inoculation, ZL30 exhibited sustained inhibition of fungal colonization and fumonisin accumulation, whereas 92C showed progressive disease development and elevated fumonisin levels. Both transcriptomic and metabolomic analyses converged on the phenylpropanoid pathway, with DEGs enriched in phenylpropanoid metabolism and DAMs enriched in phenylpropanoid biosynthesis, highlighting its central role in resistance. Further integrative analysis revealed that the lignin biosynthetic process, a key branch of phenylpropanoid metabolism, plays an important role in resistance. Several key DEGs (ZmPAL, ZmHCT, peroxidases, and ZmCOMT) and DAMs (sinapic acid, sinapaldehyde, coniferin, cinnamic acid, and caffeic acid) were differentially regulated between the two lines. Correlation analysis revealed a significant correlation between ZmCOMT expression and sinapic acid accumulation. RT-qPCR validation confirmed the expression patterns of key lignin-associated genes. The elevated activation of lignin biosynthesis in ZL30, via time-dependent induction of key genes (ZmPAL, ZmHCT, and peroxidases), suggests an increase in lignin accumulation, which likely reinforces cell wall integrity and restricts fungal invasion, thereby contributing to FER resistance. Collectively, these findings provide insights into the molecular mechanisms of FER resistance and identify key lignin-associated genes as promising targets for maize breeding.

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.