Application of Bioinformatics resources for mining of simple sequence repeats (SSRs) marker in plant genomes: An Overview

Abstract

In the case of plants, the prediction of simple sequence repeats (SSRs) is important for the purpose of gene mapping, biodiversity study and detection of genes with desired characters. In addition to this, due to their polymorphic nature and distribution throughout the genome, it is considered as an ideal marker in plants. However, the traditional methods for the detection of SSR-based polymorphism cause difficultly. As an alternative method, the bioinformatics approaches have been used extensively in the study of these molecular markers, in a economic way. The next generation sequencing (NGS) techniques generate a huge amount of genomic data which is stored in the public databases in the form of whole genome and EST. This provides the opportunity to implement the bioinformatics tools to predict and annotate the SSR associated with desired gene of the plants. Several computational programs along with the pipelines have been developed to detect the SSR sequences automatically by using the genomic information from the database. In this review, the application and availability of specific bioinformatics resources and the methods of application involved for SSR discovery have been presented by taking suitable examples from the literature.