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Updated: Oct 25, 2026

Genotyping of Plant and Animal Samples without Prior DNA Purification
Published on: September 24, 2012
Development and Validation of SNP Markers for Plant Genomic Studies
Kannan Shrinithi1, Tennyson Jebasingh2
1Department of Plant Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India.
Abstract:
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.
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Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

