Computational identification and analysis of single-nucleotide polymorphisms and insertions/deletions in expressed sequence tag data of Eucalyptus

Abstract

Molecular markers are widely employed in plant research and breeding as genes of scientific and agronomic importance can be isolated solely on the basis of their position on the genetic map. In plant genetic research, molecular markers are also being used for population and evolutionary studies (Bomblies andWeigel 2007). Single nucleotide polymorphism (SNP) markers have gained much interest, becoming the marker of choice in genetic analysis in the scientific and breeding community (Gupta et al. 2001). For myriad crop plant species, large numbers of expressed sequence tags (ESTs) have been generated which could serve as valuable source for SNP identification and analysis. The emergence of many novel molecular markers is changing and accelerating the process of analysing mutations in plantmolecular biology research. SNPs represent the most frequent type of genetic polymorphism and thus provide a high density of markers near the locus of interest. SNPs are highly stable, reliable and have a fine resolution (Syvanen 2001). The development of high throughput methods for the detection of SNPs and small indels (insertion/deletion) has led to a revolution in their use as molecular markers (Novaes et al. 2008).