Single nucleotide polymorphisms (SNPs): a new paradigm in molecular marker technology and DNA polymorphism detection with emphasis on their use in plants

Abstract

Molecular markers are useful for a variety of purposes relevant to crop improvement. The most important of these uses is the indirect marker­ assisted selection (MAS) exercised during plant breeding. For this purpose, molecular markers need to be amenable to automation and high throughput approaches. However, the gel-based assays that are needed for most molecular markers are time con­ suming and expensive, limiting their utility. The new generation molecular markers, called single nucleo­ tide polymorphisms (SNPs) do not always need these gel-based assays. They are also the most abundant of all marker 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 proving 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. Several approaches can be used for discovery of new SNPs and about a dozen different methods are now available for SNP genotyping. Some of these methods are also suitable for automation and high throughput approaches. These methods, in prin­ ciple, make a distinction between a perfect match and a mismatch (at the SNP site) between a probe of known sequence and the target DNA containing the SNP site. The target DNA in most of these methods is a peR product, except in some cases like 'invasive cleavage assay', and 'reduced representation shotgun (RRS)' devised and used recently. The different methods of SNP discovery and detection, along with examples of some known uses of SNPs in plant sys­ tems are described in this article.