Bioinformatics tools for development of fast and cost effective simple sequence repeat (SSR), and single nucleotide polymorphisms (SNP) markers from expressed sequence tags (ESTs)

Abstract

The development of current molecular biology techniques has led to the generation of huge amount of gene sequence information under the expressed sequence tag (EST) sequencing projects on a large number of plant species. This has opened a new era in crop molecular breeding with identification and/or development of a new class of useful DNA markers called genic molecular markers (GMMs). These markers represent the functional component of the genome in contrast to all other random DNA markers (RMMs). Many recent studies have demonstrated that GMMs may be superior to RMMs for use in the marker assisted selection, comparative mapping and exploration of functional genetic diversity in the germplasms adapted to different environment. Therefore, identification of DNA sequences which can be used as markers remains fundamental to the development of GMMs. Amongst others; bioinformatics approaches are very useful for development of molecular markers, making their development much faster and cheaper. Already, a number of computer programs have been implemented that aim at identifying molecular markers from sequence data. A revision of current bioinformatics tools for development of genic molecular markers is, therefore, crucial in this phase. This mini-review mainly provides an overview of different bioinformatics tools available and its use in marker development with particular reference to SNP and SSR markers.