DNA marker development and assay execution: a practice-oriented perspective

DNA markers serve as indispensable tools in molecular biology, enabling precise identification of genetic traits, assessment of genetic diversity, and implementation of marker-assisted selection across a wide range of organisms. This review presents a comprehensive, practice-oriented framework for DNA marker development and assay execution, encompassing primer design, PCR optimization, validation, and downstream data analysis. Emphasis is placed on the selection of informative genomic regions, evaluation of polymorphism through gel and capillary electrophoresis, and standardization of assay conditions to ensure reproducibility. The workflow integrates troubleshooting protocols and quality control measures to enhance genotyping accuracy and reliability. Applications of DNA markers in crop improvement, functional genomics, and biodiversity conservation are highlighted, demonstrating their versatility in plant breeding, phylogenetic analysis, and conservation of genetic resources.