Single nucleotide polymorphism (SNP)–Methods and applications in plant genetics: A review

An array of genetic markers viz. morphological, biochemical and DNA based has been used in various fields including plant genetics and crop improvement. A novel class of DNA markers namely single nucleotide polymorphisms (SNPs) has recently become highly preferred in genomic studies. They are single nucleotide base polymorphism in genomic DNA and are the most abundant class of markers. In recent times, various SNP databases have been constructed to assess the SNP data available in humans, animals and plants. Seeing the huge potential of SNPs in pharmacogenomics and crop genetics, various assays for their genotyping have been described, which include direct sequencing, mining from EST databases, cleavage assays, molecular beacons, etc. Each of these assays are having their own merits and demerits and the choice of assay depends on the objective of the study and availability of the resources. These assays utilize detection platforms that range from the conventional gel based detection to high throughput systems like microarrays, mass spectrometry and flow cytometry. SNPs have tremendous applications and prospects in crop genetics. They can be used in association studies, tagging of economic important genes, genotyping, diversity analysis and evaluation among the plant species.