Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants

Molecular markers are useful for a variety of purposes relevant to crop imp rovement. The most important of these uses is the indirect marker-assisted selection (MAS) exercised during plant breeding. For this purpose, molecula r markers need to be amenable to automation and high throughput approaches. However, the gel-based assays that are needed for most molecular markers a re time consuming and expensive, limiting their utility. The new generation molecular markers, called single nucleotide polymorphisms (SNPs) do not al ways need these gel-based assays. They are also the most abundant of all ma rker systems known so far, both in animal and plant genomes, A large number of SNPs have already been developed in the human genome, some of them prov ing useful for diagnosis of diseases, A beginning has also been made in the development and use of SNPs in higher plants, including some crop and tree species. Hopefully in future, they will be used in plants in a big way. Se veral approaches can be used for discovery of new SNPs and about a dozen di fferent methods are now available for SNP genotyping, Some of these methods are also suitable for automation and high throughput approaches. These met hods, in principle, make a distinction between a perfect match and a mismat ch (at the SNP site) between a probe of known sequence and the target DNA c ontaining the SNP site, The target DNA in most of these methods is a PCR pr oduct, except in some cases like 'invasive cleavage assay', and 'reduced re presentation shotgun (RRS)' devised and used recently. The different method s of SNP discovery and detection, along with examples of some known uses of SNPs in plant systems are described in this article.