Genotyping is a key step in molecular breeding. Due to its cost-effectiveness, accuracy, and flexibility, genotyping by target sequencing (GBTS) has become a preferred technology for medium-density genotyping. In this study, a new GBTS array for fresh edible maize was developed using resequencing data from 477 lines. The array contains 5759 SNPs evenly distributed across the maize genome, with average minor allele frequency (MAF) and polymorphism information content (PIC) values of 0.40 and 0.36, respectively. These SNPs are closely associated with 1566 functional genes. Cluster analysis of 198 maize lines based on the GBTS array was consistent with their pedigree relationships. Furthermore, 277 fresh waxy maize lines were genotyped and used for genomic selection analyses of hundred-kernel weight, kernel length, and kernel width. Comparative evaluation of different models indicated that Ridge Regression Best Linear Unbiased Prediction (rrBLUP) was the optimal model, with prediction accuracies of 0.33, 0.64, and 0.36, respectively. Additional analyses using different marker densities based on the rrBLUP model showed that prediction accuracy did not increase when the number of markers exceeded 2000, indicating that this array provides sufficient marker density for genetic analysis and genomic selection. Overall, this array provides a useful tool for genetic studies of fresh edible maize and facilitates the application of genomic selection in breeding programs.

Postharvest sucrose depletion severely limits the organoleptic quality and commercial value of sweet corn during ambient storage. To characterize the temporal transcriptional responses associated with cultivar-dependent sugar loss, ears of two supersweet corn hybrids, ‘Shenketian 811’ (SKT) and ‘Overland’ (AFL), were stored under monitored ambient conditions (24–26 °C) for 7 days. Kernel sugars, total soluble solids, whole-ear respiration rates, and transcriptomic profiles were assessed at five time points. Sucrose concentration declined from 77.9 to 30.9 μg mg⁻¹ fresh weight in SKT and from 80.3 to 20.3 μg mg⁻¹ fresh weight in AFL. Weighted gene co-expression network analysis (WGCNA), followed by within-cultivar module–trait analysis, identified one module positively and one negatively associated with sucrose concentration in both cultivars. Subsequent gene-level correlation analysis of the 1071 genes in these modules identified 571 non-redundant sucrose-associated genes, which were enriched in carbon metabolism, glycolysis/gluconeogenesis, the citrate cycle, and starch and sucrose metabolism. Pairwise differential-expression analysis further identified 194 genes showing recurrent storage-responsive or cultivar-dependent expression, of which five genes involved in sucrose cleavage or sucrose–starch interconversion were prioritized. Notably, the cell-wall invertase gene ZmINVCW1 exhibited a sustained AFL-biased expression pattern, which was validated by RT-qPCR, while total cell wall invertase activity was also significantly higher in AFL at multiple sampling points. This time-resolved analysis characterizes recurrent transcriptional responses associated with cultivar-dependent sucrose loss and provides a focused framework for further functional studies of postharvest sucrose retention.

Sweet corn is widely cultivated for fresh consumption and processing, and kernel size and weight are important yield-related traits. However, the genetic architecture of these traits in sweet corn remains poorly understood. In this study, the SHL01 × SHL03 recombinant inbred line (RIL) population was used to investigate the genetic basis of kernel size and weight-related traits using a high-density SNP-based genetic map. Quantitative trait loci (QTL) mapping was conducted in two environments and using the best linear unbiased estimates (BLUEs), followed by candidate-region association analysis to identify candidate genes. A total of 11 unique QTLs were identified from 12 detection records across the two environments and the BLUE dataset. Among them, seven unique QTLs, corresponding to eight detection records, were located on chromosome 7. Several QTLs were located near previously reported loci for kernel-related traits, suggesting a partially shared genetic basis between sweet corn and field corn. Candidate-region association analysis further characterized the major QTL regions and highlighted five potential candidate genes. Among them, Zm00001d020325 (HAK23), encoding a putative potassium transporter, was supported by functional annotation and available expression information, but its haplotypes were not significantly associated with HKW. In contrast, haplotypes defined by variants in neighboring Zm00001d020323 differed in HKW, with the GG haplotype showing the highest mean value. Because these analyses were conducted in overlapping populations, the haplotype results are exploratory. Together, these findings characterize genomic regions associated with mature-kernel traits in sweet corn and identify candidates for further validation.