Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines.

The detection of genetically modified (GM) maize events is an inevitable necessity under the strict regulatory systems of many countries. To screen for GM maize events, we developed a multiplex PCR system to specifically detect 29 GM maize events as well as the cauliflower mosaic virus 35S promoter, the Agrobacterium tumefaciens nos terminator, the Streptomyces viridochromogenes pat gene, and the endogenous zSSIIb maize reference gene. These targets were divided into five panels for screening and event-specific detection by multiplex (10-plex, 7-plex, 7-plex, 4-plex, and 5-plex) PCR. All amplification products were separated and visualized by fluorescence capillary electrophoresis (CE). By taking advantage of the high resolution, multiple fluorescence detection, and high sensitivity of CE, our system was able to identify all targets simultaneously with a limit of detection of 0.1%. The accurate identification of specific amplification peaks from different GM maize materials by CE confirmed the specificity of the system. To verify the practical applicability of this system, we analyzed 20 blind samples. We successfully identified five MON810, four TC1507, and three MIR162 samples. The detection of concomitant elements also verified the accuracy of this approach. Our system can, therefore, be used for the screening and detection of GM maize events. The system, which is easy to use, facilitates high-throughput detection with the help of a high-throughput platform and automated identification software. Multiplex PCR coupled with CE is, thus, very suitable for the detection of genetically modified organisms (GMOs) with a large number of detection targets. Additional multiplexed electrophoretic targets can be easily incorporated as well, thereby increasing the usefulness of this system as the number of GMO events continues to increase.

The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.

A DNA fingerprint database is an efficient, stable, and automated tool for plant molecular research that can provide comprehensive technical support for multiple fields of study, such as pan-genome analysis and crop breeding. However, constructing a DNA fingerprint database for plants requires significant resources for data output, storage, analysis, and quality control. Large amounts of heterogeneous data must be processed efficiently and accurately. Thus, we developed plant SNP database management system (PSNPdms) using an open-source web server and free software that is compatible with single nucleotide polymorphism (SNP), insertion–deletion (InDel) markers, Kompetitive Allele Specific PCR (KASP), SNP array platforms, and 23 species. It fully integrates with the KASP platform and allows for graphical presentation and modification of KASP data. The system has a simple, efficient, and versatile laboratory personnel management structure that adapts to complex and changing experimental needs with a simple workflow process. PSNPdms internally provides effective support for data quality control through multiple dimensions, such as the standardized experimental design, standard reference samples, fingerprint statistical selection algorithm, and raw data correlation queries. In addition, we developed a fingerprint-merging algorithm to solve the problem of merging fingerprints of mixed samples and single samples in plant detection, providing unique standard fingerprints of each plant species for construction of a standard DNA fingerprint database. Different laboratories can use the system to generate fingerprint packages for data interaction and sharing. In addition, we integrated genetic analysis into the system to enable drawing and downloading of dendrograms. PSNPdms has been widely used by 23 institutions and has proven to be a stable and effective system for sharing data and performing genetic analysis. Interested researchers are required to adapt and further develop the system.

Background: Dirigent genes play crucial roles in regulating plant architecture development and responses to environmental stress. However, the pan-genomic attributes of these genes remain poorly characterized. Method: The dirigent pan-gene family was reconstructed using the public genome assemblies from the 26 maize Nested Association Mapping project founder lines. Orthogroup classification based on multiple sequence alignment revealed both core and variable family members. Evolutionary pressures were assessed through Ka/Ks ratio analysis, and promoter regions were examined for cis-acting regulatory elements. Haplotype, transcriptomic and genome-wide association study (GWAS) analyses were integrated to explore genetic diversity and functional relevance. Results: Most dirigent members were under purifying selection, whereas a subset may have undergone positive selection. Promoter analysis demonstrated enrichment of stress- and phytohormone-responsive cis-acting regulatory elements, suggesting that regulatory divergence was associated with environmental adaptation. Haplotype analysis revealed allelic diversity among heterotic clusters, potentially contributing to heterosis. Integration with public genome-wide association study datasets identified candidate genes significantly associated with plant architecture and kernel-quality-related traits. Transcriptome profiles indicated that several dirigent genes were preferentially expressed in the roots, suggesting their involvement in root development and nutrient uptake. In addition, public gene expression data showed that certain dirigent genes are induced in response to salt stress, supporting their putative roles in abiotic stress tolerance. Conclusions: These findings provide insights into the molecular mechanisms underlying dirigent gene functions and reveal candidate genes with potential utility for improving maize performance and stress resilience through molecular breeding.

Maize, as an important dual-purpose grain and forage crop all over the world, exhibits extensive heritable and phenotypic diversity. Taking the breeding pa