Molecular marker discovery and genetic map visualisation

The bulk of variation at the nucleotide level is often not visible at the phenotypic level. However, this variation can be exploited using molecular genetic marker systems. Molecular genetic markers represent one of the most powerful tools for genome analysis and permit the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods and the availability of large amounts of sequence data for automated marker discovery. Two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) are the principal markers currently applied in modern genetic analysis. This are supplemented with anonymous marker systems such as Amplified Fragment Length Polymorphisms (AFLPs; Vos et al. 1995), and Diversity Array Technology (DArT; Jaccoud et al. 2001). The reducing cost of DNA sequencing has led to the availability of large sequence data sets that enable the mining of sequence based markers, such as SSRs and SNPs, which may then be applied to diversity analysis, genetic trait mapping, association studies, and marker assisted selection.