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Hot new tool for genetic studies

Dr Dorothy Steane
School of Plant Science
University of Tasmania

DArT data (click for larger image).

A research team comprising scientists from UTAS/CRC, Brazil and South Africa have developed a set of highly polymorphic DNA markers that have diverse applications in a range of genetic studies in Eucalyptus.  An array of 7700 Diversity Arrays Technology (DArT) markers has been developed in collaboration with an Australian biotechnology company, DArT P/L.

For the gene-jockeys out there, DArT markers can be described as “cloned RFLPs”.  Based on restriction site polymorphisms, they are dominant markers, yielding binary (ie, presence/absence) data.  The markers provide genome-wide screening of genetic variation.  About 30% of the markers occur within known gene regions.  Only a very small proportion of the markers represent chloroplast and mitochondrial DNA; the majority come from the nuclear genome.

The big advantages of DArT markers over others such as RAPDs, RFLPs, AFLPs and SSRs are that (i) the streamlined automated screening process allows rapid high-density genotyping of large numbers of samples (94 at a time) at a relatively low cost ($50 per sample for thousands of binary data points); (ii) the markers are cloned so that if you find that particular markers are of special interest to you (e.g., they are linked to a particular phenotypic trait or they are characteristic of a particular species or group of species) you can get the DNA sequence of the clone and compare it to various databases, including the E. grandis whole genome sequence.  This will greatly accelerate the process of gene discovery.

The Eucalyptus DArT markers were originally intended for use in association genetics and genetic linkage mapping (CRC Project 2) but the markers are also proving to be highly informative for population genetics and studies of phylogeny (i.e., evolution) of eucalypts.  During the development of the DArT array, trial phylogenetic analyses using over 8000 DArT markers across 94 species of Eucalyptus resolved relationships among subgenera, sections and species.  Species-level studies also detected genetic subdivision within species that are known to have geographically disjunct populations (e.g., E. urophylla, E. camaldulensis, E. globulus and E. cladocalyx).  The markers also successfully differentiated pure species from hybrids.  The general congruence of the results with those obtained from traditional morphology-based classifications or from ITS, AFLP or SSR data gives us confidence that genome-wide genotyping with DArT will allow rapid and relatively inexpensive resolution of previously intractable phylogenetic questions within Eucalyptus.

Three manuscripts describing the development and application of the new markers are currently being prepared.

Biobuzz issue ten, December 2009