Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation

Chris Duran, Nikki Appleby, David Edwards, Jacqueline Batley
2009 Current Bioinformatics  
Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and enable the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade and two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) now predominate applications in modern genetic analysis. The reducing cost of DNA sequencing has led to
more » ... encing has led to the availability of large sequence data sets derived from whole genome sequencing and large scale Expressed Sequence Tag (EST) discovery that enable the mining of SSRs and SNPs, which may then be applied to diversity analysis, genetic trait mapping, association studies, and marker assisted selection. These markers are inexpensive, require minimal labour to produce and can frequently be associated with annotated genes. Here we review automated methods for the discovery of SSRs and SNPs and provide an overview of the diverse applications of these markers. SSRs, also known as microsatellites, are stretches of DNA sequence consisting of short tandem repeats of mono-, di-, tri-, tetra-, penta-and hexa-nucleotides [7] . SSRs are widely distributed throughout genomes and have been found in all prokaryotic and eukaryotic genomes analysed to date [8, 9] . SSR perfect repeats are without interruptions, imper- Molecular Genetic Markers
doi:10.2174/157489309787158198 fatcat:xiookr4ueffgrohqfm67ct5una