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).
 |
|
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.
 |
|
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 Eucalyptus. Plant 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
