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Genome-wide markers provide multi-purpose data for Eucalyptus studies

Two research papers were published recently reporting the development and testing of a set of genome-wide markers for Eucalyptus.  Diversity Arrays Technology (DArT) markers were developed by an international team of eucalypt researchers led by UTAS researcher Assoc Prof René Vaillancourt (CRC project 2) and coordinated by Dr Dorothy Steane (CRC projects 2 and 4).  The developmental methods were reported by Sansaloni et al. (2010) and the markers will be described fully (e.g., DNA sequences and map locations of the mar­kers) in a paper that is currently in preparation (Petroli et al., in prep.).  The markers were designed primarily for use in genetic linkage mapping and association studies, and several such studies are currently underway.  In fact, the DArT markers were fundamental to the final assembly of the Eucalyptus grandis genome sequence and have also provided the means to create a high-resolution “consensus” linkage map for Eucalyptus (Hudson et al., unpub. data).
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Figure 1: This distance network derived from 7052 DArT markers shows the separation of the seven species of Eucalyptus used in the development of the DArT markers.  The markers have the potential to differentiate closely related species as well as sections and subgenera.  They can also identify geographic disjunctions within a species.


In addition to these exciting developments, the UTAS team in charge of developing the markers was interested in exploring the use of DArT markers for population genetic analysis.  Steane et al. (2011) conducted pilot studies during the developmental phase of the markers that demonstrated the utility of the markers for (i) differentiating species from one another and (ii) identifying population structure within a range of species.  These studies have been extended by CRC-affiliated UTAS PhD student Corey Hudson, who genotyped much larger numbers of samples with the final DArT array (comprising 7700 markers).  All trials so far have shown that DArT markers can be used to differentiate clearly one species of Eucalyptus from another (Figure 1), opening the way for the development of PCR-based diagnostic tools for species identification.  Within species, DArTs are highly effective at identifying geographic population structure, especially in species with disjunct distributions.  For example, Steane et al. (2011) showed that E. globulus samples clustered on the basis of race, and the races clustered in the same geographic lineages that have been identified­ previously using microsatellite data (Steane et al. 2006) (Figure 2).  Between them, Hudson (unpub. data) and Steane et al. (2011) obtained similar results for geographically disjunct populations of E. nitens, E. grandis, E. camaldulensis and E. urophylla.Figure 2: This Splitstree network based on 4684 DArT markers shows how E. globulus samples from various quantitative genetic races cluster into genetic lineages that correlate with geographic distribution.  These lineages are also found using other neutral molecular markers such as microsatellites.
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Figure 2: This Splitstree network based on 4684 DArT markers shows how Eucalyptus globulus samples from various quantitative genetic races cluster into genetic lineages that correlate with geographic distribution.  These lineages are also found using other neutral molecular markers such as microsatellites.


References

Petroli CD, Sansaloni CP, Carling J, Hudson C, Steane DA, Myburg AA, Vaillancourt RE, Kilian A, Grattapaglia D (in prep.) A high-density sub-centiMorgan DArT/microsatellite genetic linkage map for species of Eucalyptus based on 2,450 markers.


Sansaloni CP, Petroli CD, Carling J, Hudson C, Steane DA, Myburg AA, Grattapaglia D, Vaillancourt RE, Kilian A (2010) A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in EucalyptusPlant Methods 6:16 (doi:10.1186/1746-4811-6-16) [read]


Steane DA, Nicolle D, Sansaloni CP, Petroli C, Carling J, Kilian A, Myburg AA, Vaillancourt (2011) Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping.  Molecular Phylogenetics and Evolution 59: 206-224. [read]


Biobuzz issue fourteen, May 2011
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