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Eucalyptus genomics: Linkage mapping, QTL analysis and population genomic studies

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Hudson, CJ (2012) Eucalyptus genomics: Linkage mapping, QTL analysis and population genomic studies. PhD thesis, University of Tasmania.

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Abstract

This thesis reports on genomic studies conducted in five of the most commercially
important species of Eucalyptus, all from subgenus Symphyomyrtus; E. globulus, E.
nitens (section Maidenaria), E. grandis, E. urophylla (section Latoangulatae) and E.
camaldulensis (section Exsertaria). These studies utilised Diversity Arrays Technology
(DArT), a microarray-based genotyping system which provides high-throughput
genome-wide genotyping. DArT markers, and in particular linkage maps constructed
with these markers, formed the basis for most of the research conducted in this thesis.
The DArT markers are highly transferable across species which facilitates the transfer
of information between studies and as sequences are available for most of the 7680
markers contained on the eucalypt genotyping array it is possible to place these markers
on the recently released E. grandis genome sequence.
A 1060 DArT and microsatellite marker linkage map was constructed in a large E.
globulus dwarf x tall ecotype out-crossed F2 family (n = 503) in Chapter 1. This is the
highest density linkage map produced for E. globulus and together with other high
density DArT maps constructed in E. grandis x E. urophylla it was used to assess
genome similarity (e.g. synteny and colinearity) between species through comparative
mapping. Despite the detection of two small putative translocations or duplications in
the inter-sectional comparison, these species showed very high synteny and colinearity
overall. This finding showed that it is possible to link the economically important E.
globulus to the E. grandis genome sequence.
The feasibility of constructing a multi-species composite linkage map for
Symphyomyrtus was explored in Chapter 2. Seven independently constructed linkage
maps (built in either E. globulus or E. grandis x E. urophylla mapping families) were
integrated into a single map containing a total of 4135 markers (3909 DArT markers,
218 microsatellite markers and 8 candidate genes). This composite map will, (1) serve
as a valuable reference map for Symphyomyrtus and related species, and (2) aid
comparative research by enabling the relative positions of markers and quantitative trait
loci (QTL) from different studies to be determined more easily.
Quantitative trait loci analyses were used to examine the genetic architecture underlying
differences between dwarf and tall E. globulus ecotypes in Chapter 3; with a particular
focus on vegetative and reproductive phase-change traits. A total of 22 significant and 11 suggestive QTL were detected for the nine traits examined. A highly significant QTL
was detected for vegetative phase-change (LOD 103, 62.8% phenotypic variation
explained). A micro-RNA gene known to regulate vegetative phase-change was found
near the peak of this QTL. It is hypothesised that a mutation in, or a deletion of, this
gene may be responsible for the heterochronic evolution of early phase-change in dwarf
ecotype populations and that this has allowed E. globulus to inhabit the exposed coastal
environments in which the dwarf ecotype occurs.
In Chapter 4, population genomic analyses were conducted using range-wide samples
(84 to 93 individuals per species) of E. globulus, E. nitens, E. grandis, E. urophylla and
E. camaldulensis. Genetic diversity parameters were calculated using a common set of
2207 markers. In each of ten pair-wise species comparisons, markers under putative
directional selection were identified using FST outlier analyses. These outlier markers
along with genetic diversity estimates were mapped on the composite map (Chapter 2)
to produce a ‘genomic atlas’. This identified several genomic ‘hot-spots’ of species
molecular differentiation and together with other genetic resources, such as the E.
grandis genome sequence and QTL positional information, offers the potential to
identify candidate genes underlying traits associated with species adaptation and
speciation.

Item Type: Thesis (PhD)
Keywords: eucalyptus - genomics - linkage mapping
Additional Information:

Copyright 2012 the Author

Date Deposited: 17 Aug 2012 04:48
Last Modified: 11 Mar 2016 05:53
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