Development and Validation of SNP Markers for Plant Genomic Studies.

One of the most useful techniques for studying genetic variations in plants is single-nucleotide polymorphisms (SNPs), which are useful in developing molecular markers for genetic research. In this chapter, the development and validation of SNP markers using targeted resequencing and in silico analysis of genomic resources for plant genomic research and breeding are included. Key steps include genomic DNA isolation, whole-genome resequencing, raw read processing, reference-based alignment, SNP detection, and stringent filtering to identify high-confidence variants. The importance of cross-platform validation, experimental genotyping, and array evaluation is also discussed. Overall, standardized SNP development pipelines provide a robust framework for genetic diversity analysis, linkage mapping, association studies, and marker-assisted selection, thereby accelerating crop improvement programs.