Zinc (Zn) is an essential micronutrient required for plants to perform various metabolic functions, and plant responses to Zn deficiency have been extensively studied. However, excessive levels of Zn in soil can induce toxic effects in plants, posing a substantial challenge to global agricultural productivity. Consequently, elucidating the response mechanisms of crop plants to excessive Zn toxicity is currently of great significance. In this study, seedlings of maize inbred line B73 were exposed to excessive Zn treatment, and transcriptomic profiling of the roots was conducted at 0, 2, 6, 12, 24, and 48 h post-treatment. In addition to changes in the expression of genes encoding zinc-regulated, iron-regulated transporter-like protein (ZIP), metal tolerance protein (MTP), and yellow stripe-like (YSL) transporter family members involved in Zn transport, we observed that differentially expressed genes (DEGs) were significantly enriched in the phenylpropanoid–lignin metabolic pathway across all treatment stages, including the early (2 and 6 h), middle (12 and 24 h), and late (48 h) stages of Zn treatment. Among the 11 core structural enzyme-encoding genes involved in monolignols biosynthesis from phenylalanine in this pathway, the expression of eight of them was altered by Zn treatment. Additionally, genes encoding peroxidase (POD), which are responsible for the polymerization of monolignols into lignin, demonstrated extensive changes across all treatment stages, particularly at the late stage. The expression levels of these key enzyme genes were further validated using quantitative real-time PCR. Correspondingly, the activity of POD enzymes and the lignin content both significantly increased in Zn treated roots. These findings suggest that the phenylpropanoid–lignin metabolic pathway plays a crucial role in maize root responses to excessive Zn stress.

The DIR (Dirigent) gene family plays a multifaceted role in plant growth, development, and stress responses, making it one of the key gene families for plant adaptation to environmental changes. However, research on ZmDIRs in maize remains limited. In this study, we identified a member of the maize DIR gene family, ZmDIR5, whose promoter region contains numerous elements associated with responses to abiotic stresses. ZmDIR5 is upregulated in response to waterlogging, salt, and drought stresses, and its protein is localized in the endoplasmic reticulum. Subsequent studies revealed that ZmDIR5-EMS (ethyl methane sulfonate) mutant lines exhibited reduced growth compared to WT (wild-type) plants under waterlogging, salt, and drought stress conditions. The mutant lines also demonstrated a relatively higher accumulation of malondialdehyde and reactive oxygen species, lower synthesis of proline and total lignans, and decreased antioxidant enzyme activity under these stress conditions. Additionally, the mutant lines displayed impaired sodium and potassium ion transport capabilities, reduced synthesis of abscisic acid and zeatin, and decreased expression of related genes. The mutation of ZmDIR5 also inhibited the phenylpropanoid biosynthesis pathway in maize. These results indicate that ZmDIR5 serves as a positive regulator of maize tolerance to waterlogging, salt, and drought stresses.

Drought and salt stresses are major abiotic factors limiting maize yield. Lignin, a key cell wall component, plays a crucial role in boosting plant stress resistance. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme at the late stage of lignin biosynthesis; however, a systematic study of its functions in abiotic stress responses and its potential for genetic improvement in maize remains lacking. In this study, we conducted the first comprehensive, multi-dimensional analysis of the maize ZmCAD gene family, including gene identification, evolutionary relationships, protein interaction networks, and stress-responsive expression patterns. We identified 9 ZmCAD members that showed significant functional divergence in evolution, structure, and expression patterns. Expression analysis revealed complex, tissue-specific responses of ZmCAD genes to drought and salt stress, with ZmCAD6 strongly induced by drought. Importantly, through haplotype analysis of 157 waxy maize inbred lines, we successfully identified an elite haplotype (H3) of ZmCAD6 that is significantly associated with improved drought tolerance in maize. This study not only clarifies the functional differentiation mechanisms of the ZmCAD gene family but also provides the identified elite ZmCAD6-H3 haplotype as a valuable genetic resource and precise target for molecular breeding aimed at enhancing drought tolerance in maize.

Melon (Cucumis melo L.) is a significant horticultural crop valued for its aroma and health-promoting compounds. However, the genetic similarity among numerous varieties poses challenges for identification and breeding. ‘Dongfangmi No.4’ is an F₁ hybrid derived from a cross between two Hami melon inbred lines, ‘M06-1-3’ and ‘M15-3’. This study utilized resequencing data derived from the bi-parents of ‘Dongfangmi No.4’ to identify 557,878 insertion and deletion (InDel) variations across the entire genome. Thirty-nine highly polymorphic InDel markers were screened to conduct a genetic analysis of 40 representative cultivated varieties, with marker MS108 specifically distinguishing ‘Dongfangmi No.4’ from the other 39 cultivated varieties. Genetic analysis revealed a high level of genetic diversity within the population (average observed heterozygosity Ho = 0.313, Shannon index I = 0.528), and polymorphic information content (PIC) analysis indicated that 54% of the markers (21/39) were highly polymorphic. Principal component analysis (PCA) and clustering demonstrated significant genetic differentiation between cantaloupe and Hami melons, as well as between cantaloupe and honeydew. In contrast, the genetic boundaries between Hami melons and honeydew were obscured due to frequent germplasm exchange. Ultimately, seven core InDel markers were selected to construct the DNA fingerprinting map, successfully achieving complete differentiation of 40 varieties. This marker system provides an effective molecular tool for melon variety identification, intellectual property protection, and breeding.

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.

Objectives: To facilitate the innovation and efficient utilization of specialty maize germplasm, this study aimed to systematically evaluate a panel of 222 inbred lines. The objective was to comprehensively characterize phenotypic variation, genetic diversity, and genotype–phenotype associations to screen for representative germplasm resources. Methods: We integrated Best Linear Unbiased Prediction (BLUP) values derived from multi-environment field trials with high-density whole-genome single-nucleotide polymorphism (SNP) data. Population structure and genetic diversity were analyzed, Mantel tests were conducted to assess genotype–phenotype correspondence, and a genome-wide association study (GWAS) was performed to identify significant loci. Results: The population exhibited substantial phenotypic variation, particularly in plant height and tassel traits, with distinct morphological differentiations among specialty types. Genetic diversity analyses revealed varying diversity levels among subpopulations. While Mantel tests indicated a weak overall genotype–phenotype correspondence, specific traits showed significant associations with genetic distance. GWAS successfully identified significant loci associated with plant height and tassel traits. Furthermore, population structure analysis revealed distinct genetic stratification corresponding to specialty types, albeit with a certain degree of admixture. Conclusions: By integrating multi-dimensional phenotypic and genomic profiles, a panel of highly diverse and representative candidate germplasm was identified. These findings provide a crucial theoretical basis for specialty maize breeding and the optimized utilization of germplasm resources.