Molecular Marker Development Using Bioinformatic Tools

Abstract

Availability of molecular markers is essential for various genetic and breeding applications such as assessment of genetic diversity, construction of linkage map, genetic purity testing, QTL mapping, and marker-assisted selection. Prior to in silico approaches, DNA markers were developed through experimental approaches, which were skill oriented, time consuming, and expensive. Moreover, it resulted in the development of few hundred markers involving a substantial amount of time. The advent of next-generation sequencing technologies has led to the sequencing of whole nuclear as well as organellar genomes and the transcriptome projects have resulted in the accumulation of huge amounts of expressed sequence tags (ESTs) and/or cDNA sequences. Such an ocean of DNA sequence information, including genome survey sequences (GSS), expressed sequence tags (ESTs), full-length cDNAs, and complete nuclear and organellar genome sequences, serves as a vital resource for the identification of target motifs such as simple sequence repeats (SSRs), insertions-deletions (In-Dels), and single-nucleotide polymorphisms (SNPs) through in silico approaches leading to the rapid development of DNA-based markers, which otherwise would be time consuming through conventional experimental approaches. This review discusses the development of DNA markers such as SSR, SNP, In-Del, and intron length polymorphisms using various bioinformatic tools.