ABSTRACTS - Eucalypt genetics: fundamental and applied research in a post-genome era - Eucalypt genetics conference 2019
←
→
Page content transcription
If your browser does not render page correctly, please read the page content below
EucGen19 Abstracts v3 15 February 2019
ABSTRACTS
Eucalypt genetics:
fundamental and applied research in a post-genome era
Hobart, Tasmania 18-21 February 2019Published by:
Biological Sciences, School of Natural Sciences
Life Science Building, College Road, Private Bag 55
University of Tasmania
Hobart, Tasmania 7001
AUSTRALIA
This publication and its individual abstracts can be cited in the following manner:
1. General
Jones RC, Steane DS, Tilyard P, Vaillancourt RE, Rymer PD, Andrew RL, Potts BM (Eds). 2019. ‘Eucalypt
genetics: fundamental and applied research in a post-genome era’. Abstracts of conference presentations
and posters. University of Tasmania, Hobart, Tasmania. 18-21 February.
2. Specific
Myburg AA, Wierzbicki MP, Candotti J, Lotter A, Henning S, Engelbrecht S, Reynolds M, O’Neill M, Pinard D,
Ployet R, Maloney V, Christie N, Hussey S, Naidoo S, Mizrachi E. 2019. Eucalyptus in the postgenomic era:
Leveraging the power of genetics and genomics to unravel the biology of development, defence and
adaptation in eucalypts. In ‘Eucalypt genetics: fundamental and applied research in a post-genome era’.
Jones RC, Steane DS, Tilyard P, Vaillancourt RE, Andrew RL, Rymer PD, Potts BM (Eds) P. 2. Abstracts of
conference presentations and posters. University of Tasmania, Hobart, Tasmania. 18-21 February.
Symposium organisers: Dr Rebecca Jones (University of Tasmania), Dr Dorothy Steane (University of
Tasmania), Prof. René Vaillancourt (University of Tasmania), Prof. Brad Potts (University of Tasmania), Dr
Paul Rymer (Western Sydney University), Dr Rose Andrew (University of New England).
We thank the following conference sponsors: Eucalypt Australia, Ian Potter Foundation, University of
Tasmania, ARC Training Centre for Forest Value, Greening Australia, and Gondwana Genomics.
Cover photo: Robert Wiltshire
Contents Pages
Talks (in order of presentation)
Theme 1: Comparative Genomics 2–7
Theme 2: Phylogenetics and Evolution 8 – 12
Theme 3: Population and Adaptation Genetics 13 – 23
Theme 4: Conservation and Restoration Genetics 24 – 30
Theme 5: Genetics of Complex Traits 31 – 42
Theme 6: Genetic Improvement 43 – 48
Posters (in poster order) 49 – 73
Page 1Eucalyptus in the postgenomic era: Leveraging the power of genetics and
genomics to unravel the biology of development, defence and adaptation in
eucalypts
Alexander A. Myburg, Martin P. Wierzbicki, Julia Candotti, Anneri Lotter, Stephan Henning, Stephan
Engelbrecht, Melissa Reynolds, Marja O’Neill, Desre Pinard, Raphael Ployet, Victoria Maloney, Nanette
Christie, Steven Hussey, Sanushka Naidoo, Eshchar Mizrachi
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute
(FABI), Genomics Research Institute (GRI), University of Pretoria, South Africa.
The completion of the Eucalyptus grandis reference genome (Myburg et al. 2014, Nature) has enabled the
creation of resources for genome-wide genetic analysis underpinning postgenomic research in eucalypts.
This includes large collections of transcriptome profiles, metabolomic and proteomic profiles and genome-
wide genotyping resources applied in natural and experimental populations. Our research programme has
used these technologies and genomic resources to study wood development and defence to pests and
pathogens in Eucalyptus. In particular, we have been able to combine the power of genetic segregation in
structured populations with genomic technologies to construct systems genetics models of growth,
development and wood chemistry in eucalypt hybrid populations. Candidate genes and pathways identified
in this approach are important targets for genetic engineering and we have produced the first gene edited
trees for functional analysis in a woody model system. Alongside this, we have embarked on the
construction of a Genome Diversity Atlas for eucalypt species grown for plantation forestry in South Africa.
This has provided robust genome reference collections informing genetic resource management and the
selection of genetic variation for adaptive and commercial traits. The genome diversity references are also
empowering admixture mapping in advanced (F2) generation interspecific hybrids to assess genomic
composition of trees planted in trials representing environmental variation (temperature, rainfall,
elevation, disease etc) in South Africa. More recently, we have expanded our genomic references for E.
grandis, an important hybrid partner for subtropical and temperate regions in South Africa. We are
assessing neutral and adaptive population structure of a large collection of E. grandis provenances using
SNP DNA marker analysis. This information forms the basis for a species-wide analysis of genome diversity
and population structure, as well as the genomic consequences of 100 years of selective breeding in South
Africa. Our work lays the foundation for the application of landscape genomics for improved genotype-by-
site matching and the development of an online informatics resource for breeders supporting gene
conservation efforts, genetic resource management and molecular breeding of eucalypts.
Page 2The sequenced genome of Corymbia citriodora subsp. variegata
Adam Healey1, Merv Shepherd2, Abdul Baten2, Graham King2, David Lee3, René Vaillancourt4, Jak Butler4,
Jules Freeman4, Brad Potts4, Dario Grattapraglia5, Orzenil da Silva5, Kerrie Barry6, Jeremy Schmutz1,6, Blake
Simmons6, Agnelo Furtado7, Robert Henry7
1
HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
2
Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia.
3
University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Qld 4558, Australia.
4
School of Natural Sciences, University of Tasmania, Hobart, TAS, 7001, Australia.
5
EMBRAPA Genetic Resources and Biotechnology, EPqB Final W5 Norte, Brasilia, 70770-917, Brazil.
6
Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
7
Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld. 4072,
Australia.
Corresponding author email: ahealey@hudsonalpha.org
Eucalypts (genera Eucalyptus, Corymbia and Angophora) are the most widely planted hardwood trees in
the world, prized for their fast growth rate, timber and fibre quality, and environmental
adaptability. Corymbia (bloodwood taxa), having adapted to arid conditions and low quality soil types,
have become an important forestry resource, grown for timber and essential oil production. Given their
economic importance, the Corymbia genome consortium has sequenced the genome of C. citriodora
subspecies variegata (CCV). The high-quality CCV genome is a result of combining Illumina and long-read
PacBio technologies, along with a high-density DaRT-Seq genetic map to generate the 11 chromosome, 408
Mb assembly. Comparison of the CCV genome with Eucalyptus grandis found differing repeat content
among the two species, with several large structural chromosomal rearrangements. Syntenic and
orthologous gene analyses found 3981 shared eucalypt genes among the two species, as well as evidence
of the eudicot specific paleotetraploidy event. Unique to Corymbia were several gene families related to
pollen recognition and zinc-ion binding, as well as several gene families related to terpene synthesis and
abiotic/biotic stress response that underwent expansion through tandem gene duplication. These data
suggest that the genome of CCV has been shaped through adaptation to arid and stress-prone conditions
throughout its evolutionary history.
Page 3The rate and spectrum of somatic mutation in individual eucalypts
Robert Lanfear1, Reed Cartwright2, Adam Orr2, Alejandro Morales-Suarez3
1
Australian National University.
2
Arizona State University.
3
Macquarie University.
Corresponding author email: rob.lanfear@gmail.com
Despite the purported importance of somatic mutations to plant ecology and evolution we still lack basic
measurements about their rate and spectrum. I will describe our recent efforts in developing and applying
new methods to make these measurements in two species of Eucalyptus: E. melliodora, and E. pauciflora.
Page 4The clove (Syzygium aromaticum) genome
Sonia Ouadi1-2, Nicolas Sierro2, Simon Goepfert2, Manuel C. Peitsch2, Felix Kessler1, Nikolai V. Ivanov2
1
University of Neuchâtel, rue Emile-Argand 11, 2009 Neuchâtel, Switzerland.
2
PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
Corresponding author email: Nicolas.Sierro@pmi.com
Clove (Syzygium aromaticum) is a valuable tree native to Indonesia and belonging to the Myrtaceae family.
Its dried, unopened flower buds and essential oil are used commercially in a wide range of applications
within the pharmaceutical, cosmetic, food, and agricultural industries. The main bioactive component of
clove is eugenol, a phenylpropene with analgesic, antioxidant, anti-inflammatory, antimicrobial, and
antiviral activities. Despite its economic importance, few -omics resources are available for clove. Here, we
describe the next-generation sequencing strategy used to generate a first reference genome of S.
aromaticum and present assembly and annotation results.
The availability of a high-quality genome of S. aromaticum will enable comparative analysis with genomes
of other species in the Myrtaceae family. Combined with transcriptomic and metabolomic data, it will
provide insight into the biosynthesis of volatile and non-volatile compounds important for the quality of
clove products.
Page 5Eucalypt terpene synthases: Broad conservation overlays dynamic physical cluster
evolution
Jakob B. Butler1*, Jules S. Freeman1,2,3, Brad M. Potts1,3, René E. Vaillancourt1,3, Dario Grattapaglia4, Orzenil
B. Silva-Junior4, Blake A. Simmons5, Adam L. Healey5, Jeremy Schmutz6,7, Kerrie W. Barry7, David J. Lee8,
Robert J. Henry9, Graham J. King10, Abdul Baten10 and Mervyn Shepherd10
1
School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia.
2
Scion, Rotorua, New Zealand.
3
ARC Training Centre for Forest Value, University of Tasmania, Hobart, TAS 7001, Australia.
4
EMBRAPA Genetic Resources and Biotechnology, EPqB Final W5 Norte 70770-917, Brasilia, Brazil.
5
DOE Joint Bioenergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
6
Hudson-Alpha Institute for Biotechnology, Huntsville, AL, USA.
7
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA.
8
Forest Industries Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, Australia.
9
University of Queensland/QAAFI, Brisbane 4072, Australia.
10
Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
Corresponding author email: Jakob.Butler@utas.edu.au
Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the
terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The
Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in
terpene profiles. Eucalyptus grandis has the largest TPS gene family of plants currently sequenced, which is
largely conserved in the closely related E. globulus. The recent assembly of two Corymbia citriodora subsp.
variegata genomes presented an opportunity to examine the conservation of this important gene family
across more divergent eucalypt lineages. Manual annotation of the TPS gene family in C. citriodora subsp.
variegata revealed a similar overall number, and relative subfamily representation, to that previously
reported in E. grandis and E. globulus. Many of the TPS genes were in physical clusters that varied
considerably between Eucalyptus and Corymbia, with several instances of cluster translocation,
expansion/contraction and loss. Notably, there was greater conservation in the subfamilies involved in
primary metabolism than those involved in secondary metabolism. The potential contributions of selective
constraints, concerted evolution and stochastic processes to this variation are explored.
Page 6What makes a plant a tree: The defining attributes and consequences of woody
perennial habit
Gerald A. Tuskan
Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
What is a tree? We all know one when we see one but coming to a consensus on the parameters that
define a tree as a tree is challenging. It is generally accepted that a tree is a vascular plant that contains at
least one upright perennial stem which supports branches and leaves, where the stem and/or branches
display secondary growth and where the cell walls consisting primarily of cellulose, hemicellulose and
lignin. Tree forms have occurred and disappeared multiple times in the phylogenetic lineages of extant
woody and herbaceous taxa, i.e., trees are polyphyletic. Today, there may be as many of 100,000 different
plant species that satisfy the above criteria. The large stature, perennial habit, and long life expectancies
create genetic consequences that are unique to trees. Trees typically have slower rates of accumulated
mutations compared to the annual cousins, and yet the increase in reproductive biomass can result in
increased mutation rates per generation and higher degrees of genetic polymorphism at the population
level compared with herbaceous annuals. Large stature can result in increases the seed and pollen
dispersion ranges, leading to reduced population structure on a whole and lower local adaptation. The
perennial nature of woody plant root systems can lead to higher diversity of fungal and bacterial
microbiomes, leading to buffering of environmental fluctuations and acquired resistance to pathogens. At
the gene and genome levels trees are not substantially different from their herbaceous relatives. The
genomes of several sequenced tree species, e.g., Populus, Eucalyptus, Salix, Carya, and Quercus, suggest
that certain gene families have expanded in trees, e.g., NBS-LRR genes, and that this expansion often
occurred via tandem gene duplication. Despite the availability of fully sequenced tree genomes there are
several evolutionary questions surrounding woody perennial habit that remain unanswered. Issues related
to somatic mutations in independent vegetative lineages in a single tree lead to questions related to multi-
level selection within a single organism. These and other questions surrounding the genetics and evolution
of trees will be presented with supporting data from the Eucalyptus and Populus genomes.
Page 7Progress in eucalypt phylogenetics
Michael J. Bayly
School of BioSciences, The University of Melbourne.
Corresponding author email: mbayly@unimelb.edu.au
This talk provides an overview of phylogenetic studies of Eucalyptus, Corymbia, Angophora and the related
genera Arillastrum, Allosyncarpia, Stockwellia and Eucalyptopsis that comprise tribe Eucalypteae. Some
relationships in the group are well-established, but many lower-level relationships (e.g., among related
species, series and sections) and key aspects of higher-level relationships (e.g., between Corymbia and
Angophora) remain poorly resolved or supported. There is widespread incongruence between
phylogenetic signals from plastid and nuclear DNA markers, attributed largely to hybridisation and
introgression, which presents challenges for resolving phylogenies, but provides useful insight into
evolutionary processes in eucalypts. Examples of such incongruence will be presented from recent studies
of co-occurring ash eucalypts (Eucalyptus subg. Eucalyptus) in south eastern Australia and bloodwoods
(Corymbia) in northern Australia. Greater sampling of genomes (especially nuclear genomes) and taxa is
needed to improve our understanding of eucalypt relationships.
Page 8A phylogenetic analysis of the eucalypts using targeted genes
Michael D. Crisp1, Carsten Kulheim1,4, Bokyung Choi1, Alicia Toon2, Robert D. Edwards3, Yen-Po Lin1,2, Karen
Meuesemann6, Minh Bui1, Lyn G. Cook2
1
Division of Ecology and Evolution, Research School of Biology, The Australian National University,
Canberra, ACT 2601, Australia.
2
The University of Queensland, School of Biological Sciences, Brisbane, QLD 4072, Australia.
3 Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington
D.C., USA.
4
Biology I, Evolution & Ecology, University of Freiburg, Hauptstrasse 1, D-79104, Freiburg, Germany.
5
Present address: School of Forest Resources and Environmental Science, Michigan Technological
University, Houghton, Michigan 49931-1295, USA.
Corresponding author email: mike.crisp@anu.edu.au
We will present a preliminary analysis of sequence data from nearly 200 targeted nuclear genes, plus part
of the chloroplast, from about 1500 samples representing most of the phylogenetic diversity across
Eucalyptus, Corymbia and Angophora, plus Myrtaceae outgroups. We identified and targeted low copy
exons using the annotated genome of E. grandis, two transcriptomes and two whole-genome shotgun
sequences of one Eucalyptus and four Melaleuca species. We will discuss preliminary results from testing
the phylogenetic informativeness of the selected loci, including conflict among gene trees (and between
chloroplast and nuclear genes), and minimisation of errors due to paralogy in some loci.
Page 9Herbivorous insect radiations on eucalypts
Lyn Cook
The University of Queensland
Eucalypts are heavily attacked by numerous insects, but these are not a random selection of taxonomic
groups: some common groups of insects are absent whereas others have undergone significant radiations
on eucalypts. Given the long evolutionary history of eucalypts in Australia (from Gondwanan times), it
might be expected that some of the diverse lineages of insects have co-radiated with them. Strict host-use
and co-diversification through deep time is rare in insects, where host shifts appear to be common. Here, I
use several groups of insects (including paropsine beetles, sawflies, scale insects and parasitoid wasps) to
assess whether long-term co-diversification or "switch-and-radiate" best explain insect radiations on
eucalypts.
Page 10Hybridisation and introgression in woodland Eucalyptus
Rose L. Andrew1, Jasmine K. Janes2, Justin O. Borevitz3
1
School of Environment and Rural Sciences, University of New England, Armidale, NSW, Australia
2
Biology Department, Vancouver Island University, Canada
3
Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT,
Australia
Corresponding author email: rose.andrew@une.edu.au
In Eucalyptus, hybridisation has been variously described as “a rather restricted phenomenon” and “fairly
common”. Perhaps both are true. I will discuss our work to resolve these views and to understand the
evolutionary role of hybridisation and subsequent gene flow between species (introgression) from
historical and contemporary perspectives. Our approach takes advantage of species with broadly
overlapping distributions, covering wide environmental gradients. Based on whole-genome shotgun
sequence data, multiple tests confirm major impacts of introgression on widespread members of the box-
ironbark group (Section Adnataria). We are starting to gain a deeper understanding of the complex
interactions of selection and demography in shaping divergence between Eucalyptus species.
Page 11Adaptive evolution of cpDNA in Eucalyptus: rbcL, a pivotal gene, shows nucleotide
signature of selection
Hossein Valipour Kahrood1, Antanas V. Spokevicius1, Philippe Rigault2, Andrew Hung3, Peter K. Ades1, Gerd
Bossinger1, Josquin F. G. Tibbits4
1
School of Ecosystem and Forest Sciences, University of Melbourne, Creswick, Victoria 3363, Australia.
2
GYDLE, 1135 Grande Allée Ouest, suite 220, Québec, QC G1S 1E7, Canada.
3
School of Science, RMIT University, Melbourne, Victoria 3000, Australia.
4
Biosciences Research Division - AgriBio, Victorian Government Department of Economic Development,
Jobs, Transport & Resources, Bundoora, Victoria 3083, Australia.
Corresponding author email: avjs@unimelb.edu.au
Understanding the evolutionary processes affecting observed patterns of genetic variation within a species
can aid efforts to enhance conservation genetics and breeding programs in plants. This study tests for rate
acceleration, an indicator of positive selection, in chloroplast-encoded (cp-encoded) genes.
A dN/dS method was used to test neutral evolution hypotheses of 80 orthologous chloroplast genes in 39
Australian eucalypts, as well as in 136 individuals of the commercially important Eucalyptus globulus ssp.
globulus Labill. A combination of glasshouse experiments and protein structural modelling was used to
functionally investigate the signatures detected.
Across the 39 eucalypt species and intra-specifically in E. globulus, five sites (ndhD-454, ndhF-230, matK-
252, rbcL-142 and rbcL-251) in four cp-encoded genes showed consistent dN/dS signatures indicative of
positive selection. Functional glasshouse experiments and protein structural modelling provide evidence for
links between rbcL variants and photosynthetic net assimilation rates.
This study shows that genetic variation in rbcL, and other cp-encoded genes, are likely to play an important
role in adaptation to changing environments in the Australian eucalypts. We provide functional evidence
that mutations in rbcL may underlie adaptation to changing temperature in E. globulus and, as identical
mutations have been observed in many other species, may be universally important in plant adaptation.
Page 12Eucalypt genetics – diversity, differentiation and adaptation
Margaret Byrne
Department of Biodiversity, Conservation and Attractions, Western Australia.
Corresponding author email: margaret.byrne@dbca.wa.gov.au
Eucalypts are a key component of the Australian landscape and particularly our forest and woodland
ecosystems. Assessment of genetic diversity provides a foundation for management and conservation of
eucalypt species. Analysis of genetic diversity and differentiation has been undertaken for many years with
a range of genetic markers from allozymes to genomics. Most eucalypts show high levels of diversity even
in localised species. In conjunction with high diversity, most widespread species show very low levels of
population differentiation although this is higher in regional and localised species. Eucalypts have mixed
mating system with generally high levels of outcrossing. Although selfing is possible, many species show
reduced seed set on selfing due to post zygotic incompatibility systems. Seed dispersal is generally limited
while pollen dispersal can be extensive, particularly in open landscapes. Mallee eucalypts can have
extensive clonality with clonal patches covering up to 3000m2. A number of clonal species present as one or
a few clonal patches have also been shown to be hybrids, where persistence as a hybrid is facilitated by
clonality. Phylogenetic relationships in eucalypts at low taxonomic levels is challenging and population
genetic approaches can be useful in determining species relationships, as well as identifying major lineages
or cryptic speciation within widespread species. Recent analysis has also shown that tree versus mallee
habit can be taxonomically informative. Phylogeography has been a valuable means of identifying
evolutionary history in eucalypts with major signals of persistence through Pleistocene climatic change but
also evidence for refugia. With the advent of genomics, recent studies have focussed on understanding
patterns of adaptive variation within widespread eucalypts. Analysis of genomics widespread eucalypts has
shown signals of adaptation across climate gradients, and in some species this has also been supported by
associated analysis of ecophysiological and morphological traits. Further genomic analysis provides a means
of gaining much greater knowledge of eucalypt genetics in coming years.
Page 13Natural selection in action: The adaptive capacity of eucalypt populations
Brad M. Potts1, João Costa e Silva2, Peter A. Harrison1, Greg Dutkowski3, Tanya Bailey1, Akira Weller-Wong1
1
School of Natural Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart,
Tasmania, Australia.
2
Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda,
1349-017 Lisboa, Portugal.
3
PlantPlan Genetics, PO Box 1811, Mount Gambier, South Australia, 5290.
Corresponding author email: B.M.Potts@utas.edu.au
Global warming is leading to shifts in the distribution of plant and animal species globally. Sessile species,
such as forest trees, are among the most vulnerable to rapid climate change owing to their often-poor
dispersal and long-life histories. Already, extreme climate events causing heat and drought stress have
been linked to large-scale forest dieback. Ongoing climate change is expected to exacerbate such stresses,
and it has been argued that the rate of climate change may exceed the adaptive capacity of local
populations. Accordingly, conservation, restoration and forestry strategies are increasingly advocating
active translocation of species and provenances, and genetic enrichment of local populations. However,
there are little empirical data on the adaptive capacity of tree populations, and it is unclear whether large-
scale tree mortality is selectively filtering populations and leading to adaptive evolutionary change.
We present studies of the evolutionary capacity of three eucalypt species based on field progeny trials
established from open-pollinated seed collected from a wide range of wild populations. The first study
examined the response of 3-4-year-old Eucalyptus globulus to prolonged drought. The second involved
progeny of the endemic E. risdonii-tenuiramis complex and related variation in vegetative juvenility to 20-
year survival on an atypical wet site. The third study examined the growth of 4-5-year-old E. pauciflora at
multiple sites in the dry midlands of Tasmania. We show that genetic variation exists between and within
populations for the assessed fitness surrogates and functional traits. Genetic correlations or formal
selection analysis suggest that directional selection is acting directly or indirectly on diverse functional
traits. Cases of directional selection matching trends expected from historic climate-trait associations,
support the argument that the predicted changes in functional traits are adaptive and consistent with an
evolutionary response to climate-driven selection.
Page 14Eucalyptus genomes to phenomes to precision landscape regeneration
Justin Borevitz
Australian National University.
Tremendous untapped genetic diversity exists within and among the radiating lineages of Eucalyptus. They
have amazing tolerance to extreme climate, soil, and biotic challenges and are foundation species of
resilient ecosystems. I will outline a precision breeding and landscape regeneration approach to identify
and deploy adaptive genetic diversity to restore degraded ecosystems, ensure resilience in agriculture, and
reverse global warming (100B trees on 100M hectares, drawing down 1GtCO2/y).
Page 15Genomic assisted provenancing. A nice idea… but does it work?
Dorothy Steane1,2, Peter Harrison1, Joao Costa e Silva3, Tanya Bailey1, Archana Gauli4, René Vaillancourt1,
Brad Potts1
1
University of Tasmania and ARC Centre for Forest Value.
2
CSIRO Land and Water.
3
University of Lisbon, Portugal.
4
University of Hamburg, Germany.
The world’s forests are being challenged by environmental change due to global warming; increasing
exposure to exotic competitors, pests and diseases; and human population pressures. How we take
genomics beyond knowledge discovery to aid the development and implementation of adaptation
strategies to such change in the required time frame is a major challenge. Since the beginning of the
genomics revolution we have been exploring pathways to fulfil this objective.
While identification of causal genes underlying adaptation followed by mass screening of germplasm would
be ideal and will have applications in monitoring population change, it is not practical for broad-scale
implementation of restoration and conservation strategies. To this end, we have been investigating a
generalised approach that can be applied in many species. We use population genomics to identify and
weight the key environmental drivers that have shaped local adaptation. First, reduced representation
genome-wide scans are used to identify a suite of markers showing signals of adaptation to climate. The
environmental variables most closely aligned with the variation in this putative adaptive space are then
identified. The major environmental correlates are used to develop spatially explicit and biologically-
relevant fitness surfaces for contemporary and future climate projections. In the absence of better
information, the models can be used as transfer functions to guide seed source choice or identify
components of native gene pools most at risk of future maladaptation.
We are now validating our approach using functional trait and performance data for Eucalyptus pauciflora
(subg. Eucalyptus, sect. Cineraceae). This hot-off-the-press presentation reports on correlations between
putatively adaptive genomic variation across the native distribution of E. pauciflora in Tasmania, historical
climate and early-life growth and performance traits in common garden field trials.
Page 16Genomic variation and trait differentiation reveal signatures of selection in an
Australian foundation tree
Paul D. Rymer1, Collin A. Ahrens1, David T. Tissue1, Margaret Byrne2, Giles Hardy4, Richard A. Mazanec2,
Katinka X. Ruthroff4
1
Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag
1797, Penrith, NSW 2751, Australia.
2
Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked
Bag 104, Bentley Delivery Centre, Western Australia, Australia.
3
Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch
University, Murdoch, WA 6150, Australia.
4
Kings Park and Botanic Garden, Western Australian Department of Biodiversity, Conservation and
Attractions, Perth 6005, WA.
Corresponding author email: p.rymer@westernsydney.edu.au
The climate of southwestern Australia has already shifted and will continue to change in the future, making
some plant species vulnerable to novel conditions. This rapid change in climate will likely create a mismatch
between genotype and environment. Therefore, understanding the evolutionary capacity and patterns of
local adaptation of a foundation species is critical for the maintenance of the species and the collective
biodiversity associated with it. Collections of the co-dominant tree Corymbia calophylla (marri) were used
to study its adaptive potential by applying landscape genomics, glasshouse, and common garden
methodologies. We identified 475, 143, and 124 SNPs associated with maximum temperature of the
warmest month, mean annual precipitation, and aridity index, respectively, indicative of many alleles of
small effect. Non-synonymous SNPs were identified within coding and regulatory regions of genes that
regulate stress response to thermal and water stress. Quantitative genetic estimates of growth and disease
resistance traits revealed heritable patterns of regional adaptation, where populations from cool/wet
climates grew faster and were more resistant to pathogens. These traits suggest genetic adaptation to
extreme environments. The presence of high recombination rates, substantial gene flow, standing variation
within genes, and phenotypic plasticity demonstrate that marri is equipped with the genomic tools to adapt
to future climates. However, generation times for trees are often long and overlapping, so it is difficult to
imagine a scenario where adaptive response can occur fast enough to meet the pressures from rapid
climate change. Therefore, it is critical to maintain the many roles of marri through proactive approaches
such as assisted gene migration that increase local genetic variation associated with environment.
Page 17Genomic diversity, divergence, and isolation-by-landscape in woodland Eucalyptus
(section Adnataria)
Kevin Murray1, Jasmine Janes2, Justin Borevitz1, Rose Andrew2
1
ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, Australia.
2
University of New England, Armidale, Australia.
Corresponding author email: kevin.murray@anu.edu.au
An understanding of the processes which drive current genetic variation across the landscape can
illuminate how a species has adapted to tolerate current environments and can assist a species’
management under rapid environmental change. Using low-coverage whole-genome sequencing, we re-
sequenced the genomes of 400 individuals across two Eucalyptus species from section Adnataria (E.
sideroxylon and E. albens). We confirmed previous findings of high genetic diversity and found little
genome-wide divergence between species. We found signs of ongoing inter-species gene flow and
discovered many cryptic hybrids. We found little or no signal of discrete population structure, and varying
extents of genome-wide isolation by landscape among species. These results lay the ground work for the
gene-level investigation of adaptation to the Australian landscape in key Australian tree species.
Page 18Differential expression between two Eucalyptus species under experimental
temperature and water manipulations
Collin A. Ahrens, David T. Tissue, Guomin Huang, Paul D. Rymer
Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag
1797, Penrith, NSW 2751, Australia.
Corresponding author email: c.ahrens@westernsydney.edu.au
Some Eucalyptus species occupy a broad range of climates. To do this, plants must develop physiological
and genetic mechanisms to optimise their performance in their local climates (i.e. local adaptation). To
understand this process of local adaptation, we perform climate manipulations on two dominant eucalypts
(E. tereticornis and E. grandis) to identify differentially expressed genes using RNA sequencing. A reciprocal
transplant experiment was conducted under controlled glasshouse conditions with cool and warm
temperatures (E) for tropical and temperate populations (G) to identify locally adapted genes (GxE). In
addition, we applied a water limitation treatment to characterise genes important for stress response.
These genes were linked to plant growth and physiological traits measured in the glasshouse. Together,
these experiments reveal the underlying genetic mechanisms that contribute to local adaptation and
highlight putatively adaptive genes enabling species to respond to climatic variability.
Page 19The genetic landscape of adaptive variation in native Eucalyptus grandis
Marja M. O’Neill1, S. Melissa Reynolds1, David J. Lee2, Juan J. Acosta3, Justin O. Borevitz4 and Alexander A.
Myburg1
1
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute
(FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria 0028, South
Africa.
2
Forest Industries Research Centre, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD
4558, Australia.
3
Department of Forestry and Environmental Resources, Camcore, North Carolina State University, PO Box
7626, Raleigh, NC, NC 27695, USA.
4
Research School of Biology and Centre for Biodiversity Analysis, ARC Centre of Excellence in Plant Energy
Biology, Australian National University, Canberra, ACT 0200, Australia.
Corresponding author email: zander.myburg@fabi.up.ac.za
Extant genomes tell the tale of millennia of abiotic and biotic pressures that have moulded populations
through natural selection. With the availability of powerful genomic resources for eucalypts, we can begin
to decipher the genetic landscape of adaptive variation using population genomics, which relies on the
principle that regions of the genome affected by selection for adaptive traits would have different patterns
of inheritance compared to selectively neutral regions. We use this premise to investigate the population
structure and patterns of genetic differentiation in terms of neutral and adaptive evolutionary forces in the
natural species range of Eucalyptus grandis. E. grandis and its interspecific hybrids have been the most
successful hardwood species for forest tree breeding in South Africa for more than 80 years. Despite its
commercial importance, little is known about the genetic diversity in the natural range, the genetic
variation maintained in breeding programmes, and the traits and genes underlying genotype by
environment interactions (GEI). Using the EUChip60K DNA marker chip, we profiled ~64 000 single
nucleotide polymorphisms (SNPs) of which ~26 000 were informative in 596 E. grandis individuals from the
natural range in Australia. We used outlier detection and environmental association analysis to identify SNP
markers with inheritance patterns that deviate from the genomic surrounds to define the neutral and
adaptively enriched genetic spaces. These were interrogated using multivariate and Bayesian approaches to
uncover population differentiation. This study represents the first step towards deciphering the genomic
intricacies that underpin GEI in E. grandis.
Page 20Uncovering the adaptive capacity of Australia’s red gums
John Whale, Paul D. Rymer, Collin A. Ahrens, David T. Tissue
Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag
1797, Penrith, NSW 2751, Australia.
Corresponding author email: J.Whale@westernsydney.edu.au
Local adaptation is the process in which organisms develop optimal characteristics to persist in their local
environment through natural selection and is common among trees. However, climate change may alter
this balance between genotype and environment, putting species at risk of decline. Eucalypts often show
patterns of local adaptation and are synonymous with the Australian landscape. The red gums (section:
Exsertaria) are common along Australia’s east coast, traversing temperature and rainfall gradients. In this
study, we characterise the genomic variation in four red gum species from contrasting biomes: two
widespread (Eucalyptus blakelyi, E. tereticornis) and two restricted (E. glaucina, E. parramattensis). We
focus on addressing three hypotheses: (1) Widespread species have greater adaptive capacity than
restricted species; (2) hot and dry sites harbour greater adaptive variants than southern/coastal sites; (3)
regions of geographic overlap have greater introgression and shared adaptive variants among
populations/species. The findings of this study emphasise the importance of standing genetic variation and
gene flow for local adaptation within and among species. As climate change continues to impact
ecosystems throughout Australia, it is important to consider and implement adaptive management
strategies informed by genomic analyses.
Page 21A population-genomic and taxonomic study of Eucalyptus argophloia and E.
bosistoana
Seol-Jong Kim1,2, Clemens Altaner2, Luis Apiolaza2, Tammy Steeves1, Pieter B Pelser1
1
School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
2
School of Forestry, University of Canterbury, Christchurch, New Zealand.
Corresponding author email: seoljong.kim@pg.canterbury.ac.nz
The New Zealand Dryland Forests Initiative (NZDFI) aims to create plantations of high-value Eucalyptus
timber species in dry environments on the east coasts of New Zealand. This would enable the sustainable
production of naturally durable hardwood in New Zealand as a substitute for CCA treated pine and
unsustainably harvested tropical hardwoods. For this purpose, Australian seed collections of five promising
Eucalyptus species have been used since 2009 to establish progeny trials in New Zealand to select desirable
growth and wood properties for the New Zealand environment. As part of this effort, we recently started to
generate Single Nucleotide Polymorphism (SNP) data to understand how genomic and environmental
variation interact to influence commercially important traits of selected Eucalyptus species in the NZDFI
progeny trials experiments. For this, we joined the ‘Eucalyptus 65kSNP Axiom array production and
deployment initiative’ and preliminary investigations are underway to determine the utility of the new SNP
chip. The specific goals of this project are to 1) resolve the taxonomic delimitation of two morphologically
similar species (E. argophloia and E. bosistoana), 2) understand the population structure of E. bosistoana, 3)
reconstruct the pedigree of E. argophloia and E. bosistoana trials, and 4) inform the conservation
management of E. argophloia (Vulnerable) and E. bosistoana (Near Threatened) in Australia.
Page 22A genetic investigation of two rare, fragmented Eucalyptus species endemic to
Victoria
Eleanor Fox, Fiona Hogan, Wendy Wright, Nick Schultz
School of Health and Life Sciences, Federation University Australia.
Corresponding author email: e.fox@federation.edu.au
Eucalyptus yarraensis (Yarra Gum) and Eucalyptus strzeleckii (Strzelecki Gum) are endemic to Victoria and
are both listed as ‘Vulnerable’ under the Commonwealth Environment Protection and Biodiversity
Conservation (EPBC) Act 1999. Strzelecki gum is also listed as ‘Threatened’ under the Victorian Flora and
Fauna Guarantee Act 1988 (FFG Act). The distributions of both species are considered to be severely
fragmented post-European colonisation as a result of urbanisation, agricultural expansion and
development.
This project will map the locations of populations of Strzelecki Gum and Yarra Gum across Victoria, and
investigate their genetic diversity and connectivity. Genetic sequencing methods developed using Diversity
Arrays Technology (DArT) will subsequently be used to assess the genetic characteristics of Eucalyptus seed
stock used in commercial revegetation projects.
Preliminary results will be presented indicating the potential of the study to contribute to the conservation
strategy for both of these species. Data from this project will inform future restoration projects which
involve Yarra Gum and Strzelecki Gum. The study will also contribute to our knowledge of how landscape
contributes to patterns of genetic variation in fragmented tree populations, informing our understanding of
the effects of fragmentation on a range of rare or threatened plant species.
Page 23Genetics to inform restoration and conservation of eucalypts
Jason Bragg
Royal Botanic Gardens and Domain Trust, Sydney.
Corresponding author email: Jason.Bragg@rbgsyd.nsw.gov.au
At the RBG Sydney, we’re undertaking a large multispecies landscape genetic study, with the goal of
informing genetic provenancing for ecological restoration (the ‘Restore and Renew’ project). I will give an
overview of this highly collaborative project, with particular reference to eucalypts, and the value of an
available reference genome to this kind of research. We are also undertaking genetic studies of a number
of species that are threatened, including eucalypts, and I will describe the approaches that we are
developing to design conservation populations based on genetic information.
Page 24Eucalyptus melliodora – past, present and future Linda Broadhurst Centre for Australian National Biodiversity Research, CSIRO National Research Collections Australia, GPO Box 1700 Canberra ACT 2601. Corresponding author email: Linda.Broadhurst@csiro.au Yellow Box (Eucalyptus melliodora A.Cunn. ex Schauer) is a foundation tree of Box-Gum Grassy Woodlands (BGGW) which were once extensively distributed from western Victoria, through New South Wales and into south eastern Queensland. However, agricultural expansion since European settlement has cleared and converted millions of hectares of eucalypt woodlands and forests across southern Australia, fragmenting many communities. For example, only 10% of pre-European BGGW remain with more than half of this distribution occurring as patches of
Utilising genomics to assess restoration efforts: How do patterns of genomic and
adaptive diversity in revegetated stands of Grey Box (Eucalyptus microcarpa)
compare to natural stands?
Rebecca Jordan1,2, Shannon K Dillon3, Suzanne M Prober4, Ary A Hoffmann1
1
Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia 3052.
2
Current address: CSIRO Land & Water, Sandy Bay, Tasmania, Australia, 7005.
3
CSIRO Agriculture, Black Mountain, ACT, Australia.
4
CSIRO Land & Water, Floreat, WA, Australia.
Revegetation plantings are a key component of conservation management. However, under ongoing
climate change, the simple presence of plant species does not necessarily equate to the long term survival
of populations. Rather, conservation and restoration need to capture genomic diversity to ensure
populations can adapt and evolve to future changes. Next-generation genomic approaches are enabling
assessments of genomic diversity in unprecedented detail. Using the test case of Eucalyptus microcarpa, we
present an example of how genomic approaches can be applied to investigate genomic diversity in
revegetation plantings. Eucalyptus microcarpa is an important revegetation species across south-eastern
Australia, mitigating loss from agricultural clearing. We used DArTseq, a reduced representation genomic
approach, to assess how well current revegetation plantings capture both neutral and adaptive genomic
diversity and how these compare to natural patterns of diversity across the landscape. Lower diversity and
greater differentiation in revegetation sites suggest that, at the landscape level, not all variation is being
captured in these plantings. Finer-scale, chromosome-level assessments show that differences in diversity
vary across the genome. Through this case-study, we demonstrate how genomics can provide deeper
insight for restoration under climate change; moving beyond general genetic diversity towards comparisons
of neutral and adaptive genomic diversity and thus adaptive potential. We show the power of genomics to
provide in-depth knowledge that may assist in improving seed sourcing strategies and evolutionary-
resilience of future revegetation efforts.
Page 26Population genomics and hybridisation of Eucalyptus tetrapleura: examining
genetic swamping in a rare ironbark
Susan Rutherford, Marlien van der Merwe, Peter G. Wilson, Rob Kooyman and Maurizio Rossetto
National Herbarium of New South Wales, Royal Botanic Garden Sydney.
Corresponding author email: Susan.Rutherford@rbgsyd.nsw.gov.au
Hybridisation is a complex process that has important evolutionary consequences. In the case of rare
species, a comprehensive understanding of inter-specific hybridisation can be critical for their conservation
and management. Eucalyptus tetrapleura is a rare species of ironbark that is restricted to a 40 km × 100 km
area around Grafton on the North Coast of New South Wales. Commonly known as the ‘square-fruited
ironbark’, E. tetrapleura is distinctive in that it has four ribs on the sides of its buds and fruits. In recent
years, the central populations of E. tetrapleura have been cleared to facilitate upgrades to one of the major
highways along eastern Australia. This has led to increased habitat fragmentation, and there are now
concerns that the species is at risk of genetic swamping by more common ironbark relatives. In this study,
we investigated the population genetics and patterns of gene flow in E. tetrapleura. We used DArTseq to
genotype samples collected from across the known distribution of E. tetrapleura, as well as leaf material
collected from co-occurring ironbark species. We found that while E. tetrapleura formed a distinct
evolutionary lineage, there was evidence of gene flow between this species and other ironbarks (e.g. E.
fibrosa and E. siderophloia). Furthermore, many populations that had been identified as E. tetrapleura
based on morphology were of hybrid origin, and the range of the species was much smaller than previously
thought. Overall, our findings demonstrate how genomic methods can improve our understanding of
admixture across closely related lineages, which can be used to inform the restoration of rare species.
Page 27The interplay of hybridisation and selection has shaped the evolutionary response
to climate change in a group of endemic Tasmanian eucalypts
Rebecca C. Jones, Peter A. Harrison, Corey J. Hudson, Cate Hirst, Alex Matthews, Romuald Rouger, Sascha
L. Wise, Julianne M. O’Reilly-Wapstra, Robert J. E. Wiltshire, René E. Vaillancourt, Brad M. Potts
School of Natural Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart,
Tasmania, Australia.
Corresponding author email: Rebecca.Jones@utas.edu.au
Climatic changes in the Pleistocene were responsible for dramatic redistributions and extinctions of plant
species worldwide. On the island of Tasmania, increases in temperature following the end of the last glacial
would have seen upslope migration of climatically suitable species from lowland glacial refugia and
expansion of eucalypt dominated forests and woodlands in the central highlands region. We integrate
multiple lines of evidence (chloroplast and nuclear DNA markers, quantitative genetic analysis and common
garden experiments) to argue that the complex patterns of variation in and among three endemic
Tasmanian eucalypt species (E. gunnii [subsp. gunnii and subsp. divaricata], E. archeri and E. urnigera) in
the central highlands region represents the interplay of strong diversifying natural selection and inter- and
intra-specific hybridization. The central highland region is characterised by low chloroplast haplotype
diversity, extensive haplotype sharing between taxa and high nuclear marker genetic diversity compared
with refugial, low-altitude regions. Molecular markers provide evidence that: (i) the central highlands were
colonised from multiple refugia; (ii) there was extensive hybridisation between the species of this complex
following their post-glacial upslope expansion; (iii) subsp. divaricata, a form of E. gunnii adapted to dry cold
habitats, and now experiencing severe decline, could be of hybrid origin, and (iv) there has been a deep
evolutionary history of hybridisation and species resurrection in the complex. Evidence for strong selective
filtering of the products of intra-and interspecific hybridisation comes from (i) the highland populations
being virtually indistinguishable by neutral markers but strongly differentiated in quantitative traits (i.e.
QST > FST), and (ii) 40-year-old reciprocal plantings signalling local adaptation at a holistic level. We conclude
that hybridisation has provided diversity for the evolution of novel adaptations and argue that since
hybridisation was a natural response to past climate change, it will be an important evolutionary
mechanism during the Anthropocene, highlighting the importance of maintaining species interactions
under future climate change.
Page 28Using genetics to delineate current and future adaptive seed zones for restoration,
conservation and forestry
Peter A. Harrison1, Dorothy Steane1,2, René Vaillancourt1, Margaret Byrne3, Suzanne Prober2, Elizabeth
McLean4, Brad Potts1
1
School of Natural Sciences & ARC Training Centre for Forest Value, University of Tasmania.
2
CSIRO Land and Water.
3
Department of Biodiversity, Conservation and Attractions, Western Australia.
4
School of Biological Sciences, University of Western Australia.
Corresponding author email: P.A.Harrison@utas.edu.au
Global change (land-use and climate) has negatively impacted numerous species, resulting in ecosystem
degradation. Such change is likely to intensify in the coming decades. Central to managing and halting
further ecosystem degradation and maintaining ecosystem productivity is an understanding of the capacity
of populations to withstand change and, in worse case scenarios, how climate adaptation strategies such as
assisted gene flow can be used to enhance future outcomes. These issues are particularly relevant to long-
lived trees species. In the case of species being managed for conservation, ecological restoration or
forestry, the identification of seed zones based on adaptive characteristics is important to guide seed
transfer strategies. We here employ molecular and quantitative genetics to model and predict the key
components of adaptive variation and associated climatic drivers. Indices representing the latter are used
to delineate adaptive seed zones under current and future climates to (i) detect critical seed sources that
are likely to be resilient to future climates, (ii) identify populations at risk of future climate maladaptation,
and (iii) identify future climate refuges important for ex situ conservation. Two eucalypt species were
studied using markers that exhibited signals of divergent selection associated with home-site climate
variation. We used genome-wide molecular markers in one case (Eucalyptus tricarpa) and seedling traits in
the other (Eucalyptus ovata). Indices of predicted adaptive differences among populations were most
closely aligned with a climate index reflecting home-site aridity. Mapping of these climate indices provided
a spatial model of the contemporary adaptive surfaces for each species and thus a framework for seed zone
delineation. Mapping based on future climate surfaces allowed forecasting of future adaptive surfaces.
This genetics-informed approach for identifying climatic drivers of adaptation allows rapid development of
frameworks for guiding climate-adjusted provenancing and prioritising in situ conservation efforts.
Page 29Developing guidelines for habitat restoration in a changing climate
Sacha Jellinek1, 2, Elisa Raulings1, Alistair Philipps1
1
Greening Australia, Melbourne, Victoria.
2
Latrobe University, Bundoora, Victoria.
Corresponding author email: Sjellinek@greeningaustralia.org.au
Climate change is having measurable impacts on our land, water and biodiversity. In line with climate-
driven impacts on the natural environment, there is a pressing need to understand and plan for the climate
impacts on restored habitats and develop guidelines to implement and monitor climate adapted plantings
and nursery sites. These areas have the potential to improve habitat resilience of native flora and fauna
within the wider landscape and provide empirical data to develop effective adaptive management
strategies in the face of uncertainty. By including a diversity of species and seed provenances in
revegetation projects, we can maximise the resilience of plantings to climate change and other
environmental stressors.
In Victoria guidelines are being developed to help restore native, biodiverse habitats under a changing
climate. Some of the key questions of this project will focus on selecting a diversity of species for
restoration and nursery development, seed provenance, genetic profiling and climate trajectories for
different regions of Victoria. The establishment of future climate plots will (a) validate the ‘climate
readiness’ of different provenances (identified through genetic and climate modelling), (b) act as seed
production areas that provide climate ready sources of seed for future restoration projects (helping
overcome the current risks of seed shortages), (c) identify how diverse ecological plantings influence faunal
communities in different climatic landscapes, and (d) provide demonstration sites for the public and
restoration industry.
This presentation will outline the development of these guidelines and discuss how information from
stakeholders, experts and practitioners within Victoria and nationally is being used to guide their
development. We will also discuss examples of where climate plots are already being implemented, and
some of the learnings about how to source seed from different provenances, the importance of
stakeholder engagement, and monitoring habitat changes into the future.
Page 30You can also read
