35th NPS abstract book

16–17 June 2015
Arnold Arboretum of Harvard University
Boston, MA, USA
Programme, abstracts and participants

35 th New Phytologist Symposium
The genomes of forest trees: new
frontiers of forest biology
Arnold Arboretum of Harvard University, Boston, MA, USA
16 – 17 June 2015
Scientific Organizing Committee
William Friedman (The Arnold Arboretum of Harvard University, Boston, USA)
Andrew Groover (USDA Forest Service and University of California, Davis, USA)
New Phytologist Organization
Helen Pinfield-Wells (Deputy Managing Editor)
Sarah Lennon (Managing Editor)
Jill Brooke (Journal & Finance Administrator)
Acknowledgements
The 35 th New Phytologist Symposium is funded by the New Phytologist Trust
New Phytologist Trust
The New Phytologist Trust is a non-profit-making organization dedicated to the promotion
of plant science, facilitating projects from symposia to open access for our Tansley reviews.
Complete information is available at www.newphytologist.org
Programme, abstracts and participant list compiled by Jill Brooke
‘The genomes of forest trees: new frontiers of forest biology’ logo by A.P.P.S., Lancaster, UK
Contact email: np-symposia@lancaster.ac.uk
1

Table of Contents
Information for Delegates .............................................................. 3
Meeting Programme ...................................................................... 5
Tour Groups ................................................................................... 8
Discussion Session ....................................................................... 10
Speaker Abstracts ........................................................................ 12
Poster Abstracts ........................................................................... 28
Participants.................................................................................. 56
2

Information for Delegates
Symposium location
The 35th New Phytologist Symposium will be held in the Weld Hill Research Building at The Arnold
Arboretum of Harvard University in Boston.
Please note that the Weld Hill Research Building is about a mile away from the main entrance to the
Arboretum (Hunnewell Visitor Centre, off Arborway) so if you are travelling to the Arboretum by taxi
you should ask to be taken to the Weld Hill Research Building, 1300 Centre Street, Boston, MA
02131.
Further directions and maps can be found on the Arboretum website:
http://arboretum.harvard.edu/visit/weld-hill-directions/
Map
A map of the Arboretum is printed at the back of this bookand can be viewed at
http://arboretum.harvard.edu/wp-content/uploads/basic-map-b+w.pdf
Catering
Coffee breaks and lunch will be served in the lobby area just outside the lecture hall
The conference dinner will be served in the lobby area just outside the lecture hall
Accommodation
If you are staying at the Holiday Inn in Dedham we have organised transportation on the 16 th and
17 th June.
Each day the bus will depart at from the Holiday Inn at 8:00. On the 16 th June it will return to the
Holiday Inn at 20:00 and on the 17 th June it will return at 22:00.
Posters
Posters should be prepared so that they are no larger than A0 size, portrait orientation (118 cm high
x 84 cm wide). Posters should be put up during registration (8:30–9:30 on 16 th June) and will be
displayed for the duration of the meeting. There will be two dedicated poster sessions at 18:15–
19:45 on Tuesday and 18:30–20:00 on Wednesday. Beer, wine and soft drinks will be served during
the poster sessions. Please stand by your poster at these sessions – there will be prizes for the best
poster presentations.
Weld Hill tour
On Tuesday afternoon there will be a short tour of the Weld Hill Building and the research resources
which are available. Tour guides will lead groups of 20 people around and answer questions. Please
see the back of your name badge for your Weld Hill tour group allocation.
Arboretum tour
On Wednesday morning please meet at Weld Hill Research Building and there will be a tour of the
Arboretum. Tour guides will lead groups of 25–30 people around. Note that the tour will involve
walking 1-2 miles on paved and unpaved paths. Please see the back of your name badge for your
Arboretum tour group allocation.
3

Discussion session
More information can be found about this on page 10. Please also refer to the back of your name
badge for your Discussion group allocation.
Internet access
Free wifi will be provided throughout the venue. The network is ArbPublic and the password is:
@rbor3tum!
Social media
We encourage all attendees to join in discussions on social media sites. Follow @NewPhyt on Twitter
and fb.com/NewPhytologist on Facebook for updates before, during and after the meeting. Please
use #35NPS in all of your tweets.
Contact
For further information, and in case of any emergencies, please contact Helen Pinfield-Wells. Email:
h.pinfield-wells@lancaster.ac.uk, np-symposia@lancaster.ac.uk; tel: +44 7966 966 450 389.
4

Meeting Programme
Tuesday 16 th June
08:30–09:30 Registration
09:30–09:45 Welcome, Introductions and Information
Session 1: Genome-enabled insights into forest biology, populations and adaptive traits
Chair: Ned Friedman
09:45–10:15 S1-1 David Neale
Comparative genomics of conifers
10:15–10:45 S1-2 Carl Douglas
Microevolution in Populus trichocarpa driven by introgression
10:45–11:15 Break
11:15–11:45 S1-3 Nathalie Isabel
Journey into the genome of white spruce: achievements, lessons and
challenges for the future
11:45–12:00 Selected poster abstract talk 1 – Ian MacLachlan P25
12:00–12:15 Selected poster abstract talk 2 – Megan Supple P41
12:15–12:45 S1-4 Steve DiFazio
Comparative and ecological genomics in the Salicaceae
12:45–13:45 Lunch
Session 2: Evolution
Chair: Andrew Groover
13:45–14:15 S2-1 William Friedman
The origins of big: homoplasious evolution of vascular cambia and
arborescence
14:15–14:45 S2-2 Catherine Kidner
Drivers of diversity in tropical forest trees
14:45–15:00 Selected poster abstract talk 3 – Amanda De La Torre P11
15:00–15:15 Selected poster abstract talk 4 – Alison Dawn Scott P37
15:15–16:15 Break and tour of Weld Hill Research Resources including
refreshment break
16:15–16:45 S2-3 Nathaniel Street
Comparative genomics of the quaking aspens Populus tremula and P.
tremuloides
5

16:45–17:00 Selected poster abstract talk 5 – Meng-Zhu Lu P24
17.00–17:15 Selected poster abstract talk 6 – Elizabeth Trippe P42
17:15–18:15 Keynote lecture Peter Crane
Ginkgo: An evolutionary and cultural biography
18:15–19:45 Poster session with wine and cheese
Wednesday 17th June
09:00–11:00 Tour of the Arnold Arboretum, including a refreshment break
Session 3: Molecular and computational approaches
Chair: Carl Douglas
11:00–11:30 S3-1 Kaisa Nieminen
Silver birch (Betula pendula): a novel model for forest tree genetics
11:30–12:00 S3-2 Taku Demura
Transcriptional switches controlling wood cell fates
12:00–12:15 Selected poster abstract talk 7 – Richard Buggs P2
12:15–12:30 Selected poster abstract talk 8 – Karl Fetter P16
12:30–13:30 Lunch
13:30–14:00 S3-3 Siobhan Brady
Regulation of xylem cell specification and secondary cell wall synthesis in
Arabidopsis thaliana
14:00–14:30 S3-4 Matthew Zinkgraf
Transcriptional networks regulating tension wood formation in Populus
14:30–15:00 Break
Session 4: Comparative, functional and ecological genomics
Chair: Catherine Kidner
15:00–15:30 S4-1 Jonathan Plett
Ectomycorrhizal fungi are playing JAZs during symbiosis formation in
Populus
15:30–16:00 S4-2 Jill Wegrzyn
Computational tools and resources for comparative tree genomics
16:00–16:30 Break and group photo
16:30–17:00 S4-3 Isabelle Henry
6

The how and Y of sex determination in persimmon
17:00–18:30 Discussion session led by Steve Strauss
See page 10 for more details
18:30–20:00 Poster session
20:00 Symposium Barbeque
7

Tour Groups
Tuesday (15:15–16:15)
Tour of Weld Hill Research Resources at the Arboretum
Group 1 Group 2 Group 3 Group 4
Joelle Amselem Lynda Delph Catherine Kidner Julia Quintana Gonzalez
Meghan Blumstein Steve DiFazio Elena Kramer Salim Hossain Reza
Justin Borevitz Pamela Diggle Andrew Leslie Jeanne Romero-Severson
Siobhan Brady Carl Douglas Brandon Lind Atef Sahli
Richard Buggs Yousry El-Kassaby Jennifer Lind-Riehl Bastian Schiffthaler
Lorinda Bullington Ingo Ensminger Rick Lindroth Alison Dawn Scott
Hilary Bultman Dejuan Euring Keith Lindsey Armand Seguin
Claudio Casola Danilo Fernando Meng-Zhu Lu Uzay Sezen
Vikram Chhatre Karl C. Fetter Ian MacLachlan Prabha Sharma
Chris Cole Elisabeth Fitzek Mitra Menon David Showalter
Bob Cook Ned Friedman Celia Michotey Steve Strauss
Janice Cooke Suzanne Gerttula David Neale Nathaniel Street
Peter Crane Daniel Gonzalez-Ibeas Kaisa Nieminen Megan Supple
Yohann Daguerre Jessica Guseman Natalia Pabon-Mora Elizabeth Trippe
Chris Dardick Ko Harada Geneviève Parent Daniel Uddenberg
Barnabas Daru Isabelle Henry Robin Paul Tao Wan
Amanda De La Torre Alistair Hetherington Helen Pinfield-Wells Jill Wegrzyn
Taku Demura Courtney Hollender Jonathan Plett Igor Yakovlev
Andrew Groover Nathalie Isabel Andrea Polle Sam Yeaman
Sudhir Khodwekar Ben Potter Matthew Zinkgraf
8

Tour Groups
Wednesday (9:00–11:00)
Tour of the Arnold Arboretum
Group 1 Group 2 Group 3
Joelle Amselem Danilo Fernando Geneviève Parent
Meghan Blumstein Karl C. Fetter Robin Paul
Justin Borevitz Elisabeth Fitzek Helen Pinfield-Wells
Siobhan Brady Suzanne Gerttula Jonathan Plett
Richard Buggs Daniel Gonzalez-Ibeas Andrea Polle
Lorinda Bullington Andrew Groover Ben Potter
Hilary Bultman Jessica Guseman Julia Quintana Gonzalez
Claudio Casola Ko Harada Salim Hossain Reza
Vikram Chhatre Isabelle Henry Jeanne Romero-Severson
Chris Cole Alistair Hetherington Atef Sahli
Bob Cook Courtney Hollender Bastian Schiffthaler
Janice Cooke Nathalie Isabel Alison Dawn Scott
Peter Crane Sudhir Khodwekar Armand Seguin
Yohann Daguerre Catherine Kidner Uzay Sezen
Chris Dardick Elena Kramer Prabha Sharma
Barnabas Daru Andrew Leslie David Showalter
Amanda De La Torre Brandon Lind Steve Strauss
Lynda Delph Jennifer Lind-Riehl Nathaniel Street
Taku Demura Rick Lindroth Megan Supple
Steve DiFazio Keith Lindsey Elizabeth Trippe
Pamela Diggle Meng-Zhu Lu Daniel Uddenberg
Carl Douglas Ian MacLachlan Tao Wan
Yousry El-Kassaby Mitra Menon Jill Wegrzyn
Ingo Ensminger Celia Michotey Igor Yakovlev
Dejuan Euring David Neale Sam Yeaman
Ned Friedman Kaisa Nieminen Matthew Zinkgraf
Natalia Pabon-Mora
9

Wednesday
Discussion Session
Discussion Session
STEVE STRAUSS 17:00–18.30
steve.strauss@oregonstate.edu
Steve will lead a period of discussion (1 hr 30 mins). There will be 7 groups (10–12 people per group)
each considering one of the below questions for 30–45 mins. Each group is assigned a chair and a
scribe so notes can be taken for reporting back to the symposium. Your discussion group is printed on
the back of your name badge and also below.
Groups will be called back to the main meeting room, and each group chair will give a brief report of its
main findings.
D1
D2
D3
D4
D5
D6
D7
Discussion Groups*
What are the big questions in tree genomics, and how far have
we come toward answering them?
What were the specific, key findings/conclusions from this
conference, and why?
What will be the key findings and impacts, and the most
surprising findings, from this area of work in the next 5–10 years?
What have been the societal impacts of tree genomics with
respect to conservation, breeding, biotechnology, and
management, if any? Are any essential/game changing vs.
incremental? What is needed to increase impact?
What is the state of the field re: human resources (e.g.,
development of scientific careers, intellectual capital, education,
outreach, help for struggling scientists and economies and
human/ethnic diversity)?
How can we better collaborate, communicate with funding
agencies, and increase our competitiveness?
What research is needed to better understand genome microand
macro-evolution? What species (angiosperm, gymnosperm
or other) should be prioritized for sequencing to provide better
phylogenetic coverage and interpretations of tree genomes?
Discussion Chair
Carl Douglas
Nathalie Isabel
Jill Wegrzyn
Steve DiFazio
Andrew Groover
Siobhan Brady
Catherine Kidner
10

D1 D2 D3 D4 D5 D6 D7
Chair Carl Douglas Janice Cooke Jill Wegrzyn Steve DiFazio Andrew Groover Siobhan Brady Catherine Kidner
Scribe Alison Dawn Scott Geneviève Brandon Lind Megan Supple Elizabeth Trippe Amanda De La Torre Ben Potter
Parent
Peter Crane Taku Demura Ned Friedman Isabelle Henry Kaisa Nieminen Jonathan Plett Nathaniel Street
Helen Pinfield- Matthew Zinkgraf Lynda Delph Alistair Hetherington Elena Kramer Keith Lindsey Andrea Polle
Wells
Meghan Blumstein Lorinda
Hilary Bultman Karl C. Fetter Sudhir Khodwekar
Ian MacLachlan
Bullington
Jennifer Lind-Riehl
Mitra Menon Salim Hossain Atef Sahli Bastian Schiffthaler David Showalter Celia Michotey Uzay Sezen
Reza
Joelle Amselem Chris Cole Barnabas Daru Danilo Fernando Ko Harada Natalia Pabon-Mora Prabha Sharma
Justin Borevitz Bob Cook Pamela Diggle Elisabeth Fitzek Courtney
Hollender
Robin Paul
Daniel
Uddenberg
Richard Buggs Nathalie Isabel Yousry El- Suzanne Gerttula Andrew Leslie Julia Quintana Gonzalez Tao Wan
Kassaby
Claudio Casola Yohann Daguerre Ingo Ensminger Daniel Gonzalez-Ibeas Rick Lindroth Jeanne Romero-Severson Igor Yakovlev
Vikram Chhatre Chris Dardick Dejuan Euring Jessica Guseman Meng-Zhu Lu Armand Seguin Sam Yeaman
11

Speaker Abstracts
* S=speaker abstract; P=poster abstract
Brady , Siobhan S3.3
Crane, Peter
Keynote Lecture
Demura, Taku S3.2
DiFazio, Stephen S1.4
Douglas, Carl S1.2
Friedman, William S2.1
Groover, Andrew
S3.4, P18
Henry, Isabelle S4.3
Isabel, Nathalie
S1.3, P35
Kidner, Catherine S2.2
Neale, David
S1.1, S4.2, P19, P22, P30
Nieminen, Kaisa S3.1
Plett, Jonathan
Strauss, Steven
Street, Nathaniel
Wegrzyn, Jill
Zinkgraf, Matthew
S4.1, P9
Discussion Session Leader
S2.3, P34, P36
S4.2, P19, P30
S3.4, P18
12

Speaker Abstracts
Session 1: Genome-enabled insights into forest biology,
populations and adaptive traits
Chair: Ned Friedman
Comparative genomics of conifers
S1.1
DAVID NEALE 9:45–10:15
dbneale@ucdavis.edu
Department of Plant Sciences, University of California, Davis, One Shields
Ave, Davis, CA 95616, USA
Conifers are an ancient and highly diverse group of seed plants. Much can be learned about the
evolution of form and function in conifers by comparative genome analysis. The logical starting
point for the development of ‘omics’ resources and comparative ‘omics’ analyses is the reference
genome sequence. In conifers, however, reference genome sequences were not obtainable until
only recently due to their very large genomes sizes (10 to nearly 40 Gb.). Next generation
sequencing technology and advanced assembly algorithms have made it possible to develop the first
generation reference genome sequences for a small number of conifers. Now that approaches to
generating reference genomes have been established, there will be rapid development of reference
sequences for many of the 400+ conifers and thus enabling powerful and informative comparative
genome analysis. In this presentation, I will describe the development of the first few conifer
reference genomes and the preliminary comparative ‘omic’ analyses done to date.
13

Microevolution in Populus trichocarpa driven by
introgression
S1.2
CARL J. DOUGLAS 1 , ADRIANA SUAREZ-GONZALES 1 , 10:15–10:45
CAMILLE CHRISTE 2 , ARMANDO GERALDES 1 , CHARLES
HEFER 1 , ATHENA D. MCKOWN 3 , SUBINOY BISWAS 4 ,
JUERGEN EHLTING 4 , ROBERT D. GUY 3 , SHAWN D.
MANSFIELD 5 , CHRISTIAN LEXER 2 and QUENTIN C.B.
CRONK 1
carl.douglas@ubc.ca
1 Department of Botany, University of British Columbia, Vancouver, BC,
Canada; 2 Unit of Ecology & Evolution, Department of Biology, University
of Fribourg, Fribourg, Switzerland; 3 Department of Forest and
Conservation Sciences, University of British Columbia, Vancouver, BC,
Canada 4 Department of Biology, University of Victoria, Victoria, BC
Canada; 5 Department of Wood Science, University of British Columbia,
Vancouver, BC, Canada
Introgression between closely related species can provide allelic variation underlying adaptation.
Populus trichocarpa and P. balsamifera are attractive sister species to study the effects of natural
hybridization on local adaptation in forest trees, since they diverged recently, are adapted to
contrasting environments in western and northern North America, and hybridize in contact zones.
Using genome-wide scans of population differentiation, based on extensive SNP genotype data from
collections of P. trichocarpa and P. balsamifera individuals, we showed that introgression from P.
balsamifera plays a role in shaping the landscape genomics of P. trichocarpa in northern and eastern
parts of its range and identified 396 candidate genes for local adaptation in P. trichocarpa. On
chromosomes 6 and 15, two genomic regions showed strong patterns of population structure and
association with latitude and a number of environmental variables. Several genes involved in light
signaling, secondary metabolism and transcriptional control (e.g., FAR1, FHY3, PRR5, COMT1, TTG1,
ANAC062) in these regions had SNPs associated with adaptive traits. In order to further address the
role of introgression from P. balsamifera in the microevolution of P. trichocarpa, we selected 25
pure P. trichocarpa, 25 pure P. balsamifera, and 68 admixed individuals, and used whole genome
resequencing data to carry out ancestry analysis. This revealed that the candidate region for local
adaptation on chromosome 15 introgressed from P. balsamifera into P. trichocarpa, and that these
balsamifera alleles are restricted to interior and northern populations of P. trichocarpa. We
implemented genomic and gene ontology enrichment tests to test for signals of selection and
overrepresented biological themes, respectively. To determine if introgressed alleles are functionally
different from P. trichocarpa alleles, we analyzed gene expression levels, and compared phenotypes
of admixed vs. pure P. trichocarpa individuals. Our results support the hypothesis that the
introgression of functionally distinct alleles from P. balsamifera contributes to local adaptation in P.
trichocarpa.
14

Journey into the genome of white spruce:
achievements, lessons and challenges for the future
S1.3
NATHALIE ISABEL 1,2 , JANICE COOKE 3 , NATHALIE PAVY 2 , 11:15–11:45
BETTY PELGAS 1,2 , BENJAMIN HORNOY 2 , JULIEN
PRUNIER 2 , JEAN BEAULIEU 1,2 , ARMAND SÉGUIN 1,2 ,
KERMIT RITLAND 4 , INANC BIROL 5 , JOERG BOHLMANN 6 ,
JOHN MACKAY 2,7 and JEAN BOUSQUET 2
nisabel@rncan-nrcan.gc.ca
1 Natural Resources Canada, Canadian Forest Service, Québec, QC, Canada;
2 Department of Wood and Forest Sciences, Université Laval, Québec, QC,
Canada; 3 Department of Biological Sciences, University of Alberta,
Edmonton, AB, Canada; 4 Department of Forest Sciences, University of
British Columbia, Vancouver, BC, Canada; 5 Michael Smith Genome
Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada; 6 Michael
Smith Laboratories, University of British Columbia, Vancouver, BC,
Canada; 7 Department of Plant Sciences, University of Oxford, Oxford, UK
Conifer forests are dominant across Canada, yield most of the wood used by the industry, and
provide numerous ecosystem services. Spruces account for sixty percent of the 650 million tree
seedlings planted each year. Changing environments, pressure to conserve forest lands, and demand
for sustainable forest management call for new approaches to increase forest productivity.
Reforestation conducted using seeds with superior growth, wood attributes and adaptability could
be part of the solution but it relies on the development of fast-track tree breeding and high
performance trees.
For more than forty years, tree improvement programs have resulted in tangible productivity gains,
but breeding cycles are long and gains per cycle modest. Around the new millennium, genomic
science was seen as a means of developing tools to characterize and help preserve the natural
genetic diversity of trees, and more rapidly develop new varieties for reforestation. This vision has
become particularly compelling in the context of environmental change and for the adoption of
better sustainable forest management practices.
Over the last decade, extensive genomic resources for white spruce have been developed by two
Genome Canada’s projects, Arborea and Treenomix. More recently, their complementary expertise
were brought together into a unified project, SMarTForests, to break new ground in spruce genome
sequencing, and to achieve efficient translation of results toward end-users from across Canada. The
SMarTForests’ goals were to develop tools to enhance forest health and productivity and to increase
the value recovered from forest plantations.
Accordingly, major achievements have been obtained. The white spruce giga-genome has been
sequenced, a gene map allowing interspecific and inter-generic comparisons has been constructed,
gene catalogue and large registries of high-quality SNPs for population genomics applications have
been set up, functional genomics studies have highlighted processes and networks of genes involved
in pest resistance, adaptation and wood formation, genomic selection models for wood properties
are being transferred to end-users, etc. However, we must be prepared to face new challenges and
new frontiers in this post-genomic era. Like for other conifers, the sheer size and diversity of the
spruce genome still represent significant challenges to further comprehend the mechanisms
underlying observed phenotypes in the forests. Also, given the environmental changes already
affecting boreal forests, genomics and its affiliated ‘omics’ sciences will certainly be key to proposing
valuable adaptation measures in an uncertain future.
15

Comparative and ecological genomics in the
Salicaceae
S1.4
STEPHEN P. DIFAZIO 1 , LUKE M. EVANS 1 , WELLINGTON 12:15–12:45
MUCHERO 2 , ELI RODGERS-MELNICK 3 , ALEJANDRO
RIVEROS-WALKER 1 , GANCHO T. SLAVOV 4 and GERALD A.
TUSKAN 2
spdifazio@mail.wvu.edu
1 Department of Biology, West Virginia University, Morgantown, West
Virginia, USA; 2 Plant Systems Biology Group, BioSciences Division, Oak
Ridge National Laboratory, Oak Ridge, Tennessee, USA; 3 Plant Biology
Department, Cornell University, Ithaca, NY USA; 4 Institute of Biological,
Environmental and Rural Sciences, Aberystwyth University, Aberystwyth,
UK
Broadly-distributed and ecologically dominant forest trees provide excellent model systems for
studying fundamental questions about the molecular bases of adaptive variation and the nature of
species boundaries. In particular, population resequencing has provided an integrated view of major
demographic events that have shaped standing neutral genetic variation, including population
bottlenecks and rapid range expansions following glacial maxima. Furthermore, departures from this
neutral backdrop provide characteristic signatures of natural selection. We have used whole genome
sequencing in Populus trees to investigate patterns of nucleotide variation across a broad geographic
area. In addition to the expected patterns of clinal latitudinal variation, the unprecedented
resolution afforded by whole genome sequencing has revealed subtle details about glacial refugia,
patterns of postglacial range expansion, and signatures of past gene flow and introgression.
Furthermore, comparative analysis across species has demonstrated differences in genome content
and organization that may have driven adaptive differentiation of species, and possible mechanisms
for the establishment and maintenance of species boundaries in sympatry. We have found that
there are gene content differences between species that are likely driven by differential loss and
retention of duplicated genes. Furthermore, the presence of polymorphic insertion/deletion
polymorphism in the population indicates that genome fraction is an ongoing process involved in the
continued differentiation of species. Increasingly accessible genomics approaches have already
caused radical shifts in approaches to studying adaptive variation in tree populations, and the
resulting insights will accelerate the domestication of these recalcitrant organisms and enhance our
ability to predict and possibly mitigate the effects of climate change.
16

Session 2: Evolution
Chair: Andrew Groover
The origins of big: homoplasious evolution of
vascular cambia and arborescence
S2.1
WILLIAM E. FRIEDMAN 13:45–14:15
ned@oeb.harvard.edu
Department of Organismic and Evolutionary Biology, Arnold Arboretum,
Harvard University
The presence of a vascular cambium can be traced to at least 407 million years ago, in plants just
slightly larger than their primary-body-only close relatives. The evolution of true arborescence and
forested ecosystems would wait another 20 million years, when a group of fern-like plants
(cladoxylopsids, now extinct) appear to have gained in height and circumference the key features of
trees. Over the course of an additional roughly 25 million years, a vascular cambium arose
independently among members of an additional four major lineages: progymnosperms,
heterospourous lycophytes, horsetails, and sphenophytes. Despite the multiple origins of a vascular
cambium and arborescence, and the dominance of these linages in ancient forests, only the vascular
cambium of the progymnosperms has persisted through time to the present, as expressed in seed
plants. All other ancient clades that produced a vascular cambium have since gone extinct (with but
one minor exception). The striking homoplasy of vascular cambia in (at least) six distinct clades of
vascular plants over the course of a geological ‘blink of an eye’ suggests that there may have been
compelling adaptive reasons for the evolutionary innovation of plants with larger bodies, although
interestingly, developmental aspects of cambial behavior clearly differ between these different
lineages. Regrettably, the question of whether the independent origins of cambia during the
Paleozoic in different lineages of vascular plants relied upon similar or dissimilar underlying genetic
‘toolkits’ may never be answered; an answer is precluded by the inconvenient fact of extinction.
17

Drivers of diversity in tropical forest trees
S2.2
CATHERINE KIDNER 2, 3 , JAMES NICHOLLS 3 , MARIA-JOSE 14:15–14:45
ENDARA 1 , GRAHAM STONE 3 , PHYLLIS COLEY 1 , THOMAS
KURSAR 1 and TOBY PENNINGTON 2
c.kidner@rbge.ac.uk
1 Royal Botanic Garden Edinburgh, UK; 2 University of Edinburgh, UK;
3 University of Utah, USA
The greatest diversity of tree species is found in tropical rain forests. It is notable that this diversity is
found even at very local levels. For example, within a 50 ha plot on Barro Colorado Island in Panama
303 tree species are found, including 16 species of a single genus – Inga. Inga species are found in
high abundance across all neotropical rain forests. It is a genus of 300 legume tree species which
radiated during the last 6 million years. We are investigating the role of herbivores in generating this
species diversity and maintaining species coexistence in local communities. We have developed a
hybrid capture protocol to resolve phylogenetic structure in the face of low sequence divergence
shown in widely used phylogenetic markers. Our new phylogeny allows us to analyse evolutionary
patterns in chemical diversity, herbivore load and gene expression as well as biogeographic patterns.
Results support the hypothesis that a key factor in Inga diversity is herbivore pressure leading to
divergence in secondary chemistry produced by variation in expression of biosynthetic enzymes.
18

Comparative genomics of the quaking aspens
Populus tremula and P. tremuloides
S2.3
YAO-CHENG LIN 1 , NICOLAS DELHOMME 2 , JING WANG 3 , 16:15–16:45
BASTIAN SCHIFFTHALER 2 , MANFRED GRABHERR 4 , NEDA
ZAMANI 4 , MARC P HÖPNNER 4 , CHANAKA
MANNAPPERUMA 2 , NIKLAS MÄHLER 5 , DAVID SUNDELL 2 ,
YVES VAN DE PEER 1,6 , TORGEIR R HVIDSTEN 5 , STEFAN
JANSSON 2, PÄR K INGVARSSON 3 and NATHANIEL R
STREET 1
nathaniel.street@umu.se
1 Department of Plant Systems Biology (VIB) and Department of Plant
Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium;
2 Umeå Plant Science Centre, Department of Plant Physiology, Umeå
University, SE-907 81, Umeå, Sweden; 3 Umeå Plant Science Centre,
Department of Ecology and Environmental Science, Umeå University, SE-
901-97, Umeå, Sweden; 4 Department of Medical Biochemistry and
Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;
5 Department of Chemistry, Biotechnology and Food Science, Norwegian
University of Life Sciences, 1432 Ås, Norway; 6 Genomics Research
Institute, University of Pretoria, Hatfield Campus, 0028 Pretoria, South
Africa
European and North American aspens, Populus tremula and P. tremuloides, are keystone species in
addition to being extensively used as model systems for forest tree research. To date, genomics
analyses in these species required use of the P. trichocarpa reference genome sequence. However,
this is often limiting due to poor sequence alignment rates. Given these limitations, we undertook
sequencing and assembly of the two aspen genomes in addition to re-sequencing 24 P. tremula and
22 P. tremuloides individuals and we are extending our sequencing to additional aspen species.
Analysis of kmer content and alignment of sequence reads to the P. trichocarpa reference revealed
rapid divergence of intergenic regions compared to the reference P. trichocarpa genome assembly in
addition to high rates of heterozygosity. We subsequently produced next generation sequencing
based de novo genome assemblies that were ab initio annotated. This resource allowed comparative
analysis to the reference assembly as well as among aspen species. To complement these analyses,
extensive RNA-Seq based transcript sequencing efforts were performed and used in combination
with large-scale transcriptomics studies at the Umeå Plant Science Centre. Whole genome alignment
and population level genotype data were used to identify regions of the aspen genome that have
rapidly diverged from the reference P. trichocarpa genome as well as to identify novel, aspen
specific features. We have focused on annotating and comparing both the protein coding and noncoding
gene space.
Assembling the aspen genome proved challenging as a result of extensive heterozygosity, driven by a
combination of both SNPs and INDELs, leading to frequent haplotype splitting. However, the gene
space is comprehensively represented, facilitating many comparative genomics analyses.
The developed resources have been integrated within the PlantGenIE.org web platform to allow the
wider community to benefit from and contribute to this genome project.
19

Ginkgo: An evolutionary and cultural biography
Keynote
PETER CRANE 17:15–18:15
peter.crane@yale.edu
School of Forestry and Environmental Studies, Yale University, 195
Prospect Street, New Haven, CT 06511, USA
Perhaps the world’s most distinctive tree, Ginkgo is a botanical oddity that has remained little
changed for more than two hundred million years. Once regarded as a conifer, Ginkgo was first
recognized as distinct in plant classifications of the early nineteenth century, a conclusion underlined
subsequent by the remarkable discovery in Ginkgo (and also in cycads) of motile sperm cells. Despite
its long geologic record and former widespread distribution, Ginkgo barely survived the Pleistocene
Ice Ages and today the only remaining putatively wild populations exist as relics in China.
Nevertheless, Ginkgo began its remarkable contemporary renewal and resurgence when people first
found it useful as a nut tree about a thousand years ago. Today Ginkgo is revered for its longevity,
beloved for the elegance of its leaves, valued as medicinal herb, and widely cultivated as one of the
world’s most popular street trees. It is also a source of artistic and religious inspiration. Scientifically
Ginkgo is the most widely known of all botanical ‘living fossils’ and the last survivor of a lineage that
was once much more diverse. Ginkgo may provide our best window into the genetics of the diverse
ancient seed plants that flourished between about 200 and 100 million years ago, but became
extinct during the later Mesozoic.
20

Session 3: Molecular and computational approaches
Chair: Carl Douglas
Silver birch (Betula pendula): a novel model for
forest tree genetics
S3.1
KAISA NIEMINEN 11:00–11:30
kaisa.nieminen@helsinki.fi
Natural Resources Institute Finland (Luke), Green Technology,
Jokiniemenkuja 1, FI-01301 Vantaa, Finland
The aim of our research is to understand molecular mechanisms controlling tree development. We
will explore natural variation in forest trees to identify novel genetic regulators of cambial activity,
wood formation and tree architecture. Our model is an important forestry tree, silver birch, whose
small diploid genome is being sequenced. This tree is monoecious, and already young seedlings can
be induced to flower. Birch brings the power of inbreeding and short generation times into tree
genetics, enabling exploitation of advanced crossing schemes for genetic analyses. With birch as our
model, our project represents a novel approach in tree genetics with potential for ground-breaking
insights into tree development. Besides its fascinating basic science aspect (what makes a tree a
tree?), this knowledge has immense applied value for forest tree breeding. Detailed knowledge
about the regulatory mechanisms controlling tree traits will provide us tools for the domestication of
forest trees. As wood represents a renewable source of lignocellulosic biomass, with potential for
conversion into timber, pulp, fuels, energy, and value-added chemicals, boosting its efficient
production in commercial forests is essential for sustainable management of natural resources.
21

Transcriptional switches controlling wood cell fates
S3.2
MISATO OHTANI 1,2 , BO XU 2 , MASATOSHI YAMAGUCHI 3 , 11:30–12.00
MINORU KUBO 2 , TAKU DEMURA 1,2
demura@bs.naist.jp
1 Graduate School of Biological Sciences, Nara Institute of Science and
Technology, Ikoma, Nara, Japan; 2 RIKEN Center for Sustainable Resource
Science, Yokohama, Kanagawa, Japan; 3 Institute for Environmental
Science and Technology, Saitama University, Saitama, Japan; 4 Center for
Frontier Science and Technology, Nara Institute of Science and
Technology, Ikoma, Nara, Japan
Wood has long been used for natural materials including pulp, timber, and wood products. Recently,
in addition, wood is also expected to be utilized as a sustainable and carbon-neutral resource for
bioenergy. Therefore, it is important to understand the process of wood formation for improving the
quality and quantity of wood and wood product. Hard wood contains two major cell types, fiber and
vessel, which have similar but distinct developmental processes. Recent considerable effort has
identified the regulatory genes for the differentiation of each cell type. Using Arabidopsis, we
showed that VASCULAR-RELATED NAC-DOMAIN6 (AtVND6) and AtVND7 are the transcriptional
switches for metaxylem and protoxylem vessels, respectively: overexpression of AtVND6 and
AtVND7 can induce the transdifferentiation of various types of cells into metaxylem and protoxylem
vessels, respectively, not only in Arabidopsis but also heterologously in poplar. Further researches
revealed that two genes (AtNST1 and AtNST3/SND1) belonging to the same gene family of AtVND6
and AtVND7 are the key regulators of fiber differentiation in Arabidopsis. Based on the phylogenetic
analysis, we also showed that 16 poplar genes (PtVNS1 to PtVNS16, of which 12 genes also called
PtrWND1A to PtrWND6B) were homologous to the VND and NST/SND genes. Moreover, the
functional analysis of these genes suggested that wood formation in poplar is regulated by the
cooperative functions of the PtVNS/PtrWND genes.
These transcriptional switches seem to be conserved in evolutionary history. We recently revealed
that the differentiation of water-conducting and supporting cells in moss Physcomitrella patens,
hydroid and stereid cells, respectively, is regulated by genes (PpVNS1 to PpVNS8) homologous to the
VND/NST/SND genes. Concomitant loss of function of PpVNS1, 6, and 7 failed to form normal
hydroid and stereid cells, suggesting conservation of the transcriptional between Arabidopsis and
moss.
22

Regulation of xylem cell specification and
secondary cell wall synthesis in Arabidopsis
thaliana
MALLORIE TAYLOR-TEEPLES, MIGUEL DE LUCAS, GINA
TURCO, ALLISON GAUDINIER, TED TOAL and SIOBHAN
M. BRADY
S3.3
13:30–14.00
sbrady@ucdavis.edu
Plant Biology, University of California-Davis, Davis, CA 95616, USA;
Arabidopsis root development provides a remarkably tractable system to delineate cell type-specific,
developmental gene regulatory networks and to study their functionality in a complex multicellular
model system over developmental time. We have mapped gene regulatory networks guiding two
aspects of vascular cell type development, specifically xylem cell specification and differentiation
and vascular proliferation. Together, these networks identify novel regulators of vascular
development and provide considerable insight into the combinatorial nature of root development at
cell type and temporal stage-resolution.
23

Transcriptional networks regulating tension wood
formation in Populus
S3.4
MATTHEW ZINKGRAF 1,2,4 , ANDREW GROOVER 2 , 14:00–14.30
SUZANNE GERTTULA 2 , SHAWN D. MANSFIELD 3 and
VLADIMIR FILKOV 4
mszinkgraf@fs.fed.us
1 Postdoctoral Research Fellow in Biology, National Science Foundation;
2 Pacific Southwest Research Station, Forest Service, Davis CA USA;
3 Department of Wood Science, University of British Columbia, Vancouver
BC Canada; 4 Computer Science Department, University of California –
Davis, Davis CA USA
Angiosperm trees respond to gravitational and mechanical stresses by producing tension wood,
which generates the tensile force necessary to reorient and reinforce woody stems. In this talk, we
present results from Populus tension wood experiments that integrate data from genome-wide gene
expression and transcription factor binding experiments with physiological and biochemical data.
Treatments included perturbation of ARBORKNOX2 expression and treatment with gibberellic acid.
Modules of genes were defined based on co-expression patterns across wood types, genotypes, and
gibberellic acid treatments. Modules were then tested for correlations with wood types, genotypes,
GA treatment, and various measures of wood chemistry attributes. Modules were identified that
have significant correlations with phenotypes, and enrichment for ARK2 binding. Modules were also
characterized by GO analysis, and modules were further annotated based on enrichment with key
processes that contribute to cambium function, secondary cell wall biosynthesis and hormone
regulation. We further show how these gene modules can be further dissected to identify candidate
regulatory genes responsible for control of specific traits. Together, these results present an
integrated view of the key changes in gene expression and transcription factor binding that influence
tension wood development and generation of the forces underlying the reorientation of woody
stems, and provide results and methods that can be applied for complex trait dissection in trees.
24

Session 4: Comparative, functional and ecological genomics
Chair: Catherine Kidner
Ectomycorrhizal fungi are playing JAZs during
symbiosis formation
S4.1
JONATHAN M PLETT 1,2 , YOHANN DAGUERRE 1 , IAN C 15:00–15.30
ANDERSON 2 , CLAIRE VENEAULT-FOURREY 3 and FRANCIS
MARTIN 1
j.plett@uws.edu.au
1 Labex ARBRE, Tree-Microbe Interactions’ department, INRA-Nancy,
Champenoux, France; 2 Hawkesbury Institute for the Environment,
University of Western Sydney, Richmond, NSW, Australia; 3 University of
Lorraine, Nancy, 54000, France
In forest ecosystems, ectomycorrhizal (ECM) fungi constitute a significant proportion of soil
microbial biomass where they form symbioses with tree roots, providing growth limiting nutrients
such as nitrogen and phosphorus to the tree in return for up to 20-30% of photosyntheticallyderived
carbon from their hosts. While colonization of roots by ECM fungi is a very invasive process
reminiscent of when pathogens take over plant tissues, in-growth of ECM fungal hyphae into roots is
typically characterized by a relatively low defense response on the part of the tree host. Our ongoing
research is beginning to uncover how the ECM fungus is able to avoid immune detection by
the plant: through the use of small secreted effector proteins. I will focus on our current
understanding of how one of these proteins, MiSSP7 encoded by the ECM fungus Laccaria bicolor,
enters poplar tree root cells and interacts with JAZ proteins – the co-receptors to the plant defense
hormone jasmonic acid (JA). Interaction between MiSSP7 and the JAZ proteins is essential for L.
bicolor colonisation of poplar roots and leads to a repression of one part of the JA signaling pathway.
I will cover our most recent findings concerning the role of JAZ proteins in poplar cellular biology as
well as our preliminary work characterizing the role of these proteins during the interaction between
Eucalyptus grandis and its ECM symbiont Pisolithus microcarpus.
25

Computational tools and resources for comparative
tree genomics
S4.2
JILL WEGRZYN 1,2 , EMILY GRAU 3 , HANS VASQUEZ- 15:30–16.00
GROSS 3 , TAEIN LEE 4, JODI HUMANN 4 , STEPHEN FICKLIN 4 ,
MARGARET STATON 5 , NATHAN HENRY 5 , DOREEN MAIN 4
and DAVID NEALE 3
jill.wegrzyn@uconn.edu
1 Department of Ecology and Evolutionary Biology, University of
Connecticut, Storrs, CT, USA; 2 Institute for Systems Genomics, University of
Connecticut, Storrs, CT, USA; 3 Department of Plant Sciences, University of
California at Davis, Davis, CA, USA; 4 Department of Horticulture,
Washington State University, Pullman, WA, USA; 5 Department of
Entomology and Plant Pathology, University of Tennessee, TN, USA
Full genome sequences are being generated for the first time for several conifer and hardwood
species. The recent influx of genomic resources from previously underserved tree species presents a
wealth of information and scientific opportunities to the research community. Recipients of this data
are often faced with navigating the complex landscape of online resources with conflicting genome
versions, incomplete annotations, and various levels of resolution. As is often the case with early
genome sequences and genomic sets that pre-date a full genome, the optimal data source and
associated metadata are difficult to obtain. This problem is magnified by the size of genomic
datasets which produce additional barriers once the user brings this information to a desktop
machine for analysis. In addition to genomic data, we are increasingly interested in associating
phenotypic and environmental metrics to geo-referenced trees. These datasets provide additional
computational challenges and reside in repositories even more diverse than those holding genomic
artefacts.
Here, we will describe two clade organism databases – TreeGenes
(http://dendrome.ucdavis.edu/treegenes) and the Hardwood Genomics Web
(http://www.hardwoodgenomics.org/). Aside from direct access to curated genomic resources, we
present two tools – GenSAS and CartograTree. GenSAS is a genome visualization tool that supports
moderate to large genome assemblies and guides researchers through the process of repeat
identification, gene prediction, structural annotation, and comparative genomics. CartograTree is an
interactive workspace that allows for geographical visualization and engagement of high
performance computing (HPC) resources. CartograTree merges genomic, phenotypic, and
environmental data to facilitate association studies in a variety of forest trees.
26

The how and Y of sex determination in
persimmon
S4.3
ISABELLE M. HENRY 1 , TAKASHI AKAGI 2 , RYUTARO TAO 2
and LUCA COMAI 1 16:30–17.00
imhenry@ucdavis.edu
1
Department of Plant Biology and Genome Center, University of California
Davis, Davis, USA; 2 Laboratory of Pomology, Graduate School of
Agriculture, Kyoto University, Kyoto, Japan
In approximately five percent of plant species, male and female flowers grow on separate trees. This
sexual system, called dioecy, is often associated with sex chromosomes. Dioecy has evolved multiple
times independently in different plant taxa, but the molecular mechanisms underlying sex
determination remain poorly understood. We have tackled these questions in diploid Caucasian
persimmon (Diospyros lotus). Using a combination of genomic and transcriptome sequencing, as well
as evolutionary analyses, we were able to identify a potential master regulator of sex in this species,
that we called OGI. Analyses of the genomic context surrounding OGI are consistent with those of Y-
sequences from other species. Further small RNA and sequence analyses suggest that OGI produces
small RNA that repress a homologous autosomal gene called MeGI. Heterologous transgenic
experiments in Arabidopsis and Nicotiana confirmed the repressive role of OGI on MeGI and the
feminizing role of MeGI, with transgenic plants exhibiting dosage-dependent phenotypes consistent
with a repression of androecium development. Phenotypic comparison between the transgenic
plants and male and female persimmon flowers provide clues about the potential mechanisms
underlying sex-specific flower development in diploid persimmon. Further analyses suggest that
MeGI promoter methylation, possibly triggered by the action of OGI smRNAs, might also play a role
in MeGI regulation. A model summarizing our current understanding of the mechanisms underlying
sex determination in diploid persimmon will be presented. The implications of this model to sex
determination in hexaploid persimmon, in which trees either bear only female flowers or both male
and female flowers, will be discussed as well.
27

Amselem, Joelle
Buggs, Richard
Bullington, Lorinda
Bultman, Hilary
Casola, Claudio
Chhatre, Vikram
Cole, Christopher
Cooke, Janice
Daguerre, Yohann
Daru, Barnabas
De La Torre, Amanda
El-Kassaby, Yousry
Ensminger, Ingo
Euring, Dejuan
Fernando, Danilo
Fetter, Karl
Fitzek, Elisabeth
Gerttula, Suzanne
Gonzalez-Ibeas, Daniel
Harada, Ko
Khodwekar, Sudhir
Lind, Brandon
Lind-Riehl, Jennifer
Lu, Meng-Zhu
MacLachlan, Ian
Menon, Mitra
Michotey, Celia
Pabon Mora, Natalia
Parent, Geneviève
Paul, Robin
Polle, Andrea
Potter, Ben
Quintana Gonzalez, Julia
Reza, Md Salim Hossain
Sahli, Atef
Schiffthaler, Bastian
Scott, Alison Dawn
Seguin, Armand
Sharma, Prabha
Showalter, David
Supple, Megan
28
Poster Abstracts
* P=poster abstract. Bold=presenting author
P1
P2
P3
P4
P5
P6, P16
P7
S1.3, P8
S4.1, P9
P10
P11
P12
P13
P14
P15
P16
P17
S3.4, P18
P19, P30
P20
P21
P22
P23
P24
P25
P26
P1, P27
P28
P29
P30
P14, P31
P32
P33
P34
P35
S2.3, P36
P37
S1.3, P38
P39
P40
P41

Trippe, Elizabeth
Uddenberg, Daniel
Yakovlev, Igor
Yeaman, Sam
P42
P43
P44
P45
29

Poster Abstracts
Poster abstracts are ordered alphabetically by presenting author (underlined).
P1
Oak genome sequencing project: genomic data and bioinformatic resources
to study oak tree adaptation
J. AMSELEM 1 , J.M. AURY 2 , N. FRANCILLONNE 1 , T. ALAEITABAR 1 , C. DA SILVA 2 , S. DUPLESSIS 3 ,
F. EHRENMANN 4 , C. KLOPP 5 , K. LABADIE 2 , T. LEROY 4 , I. LESUR 4 , T. LETELLIER 1 , I. LUYTEN 1 ,
C. MICHOTEY 1 , C. BODENES 4 , G. Le PROVOST 4 , F. MURAT 7 , P. FAIVRE RAMPANT 6 , A. KREMER 4 , F.
MARTIN 3 , J. SALSE 7 , H. QUESNEVILLE 1 and C. PLOMION 4
1 INRA, UR1164, URGI, Unité de Recherche Génomique Info, route de Saint-Cyr – RD 10, 78026
Versailles, France; 2 CEA, Institut de Génomique (IG), Genoscope, 2 rue Gaston Crémieux, 91057 Evry,
France; 3 INRA-Université́ de Lorraine, UMR1136, Interactions Arbres/Micro-organismes, 54280
Champenoux, France; 4 INRA, UMR1202, BIOGECO, 69 route d’Arcachon, 33610 Cestas, France; 5 INRA,
MIAT, Plateforme bioinformatique Toulouse Midi-Pyrénées, 24 chemin de Borde-Rouge, 31326
Auzeville Castanet-Tolosan, France; 6 INRA, URGV, Plant Genomics Research, 2 rue Gaston Crémieux,
91057 Evry, France; 7 INRA/UBP UMR1095, Laboratoire Génétique, Diversité́ et Ecophysiologie des
Céréales, Site de Crouël 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
The large, complex and highly heterozygous genome of pedunculate oak (Quercus robur) was
sequenced using a whole-genome shotgun approach. Roche 454 GS-FLX sequence reads were
assembled into contigs and combined with Illumina reads from paired-end and mate-pair libraries to
build a total of 17,910 scaffolds (> 2 kb; 1.34 Gb total size; N50=260 kb). Half of the genome was
aligned to a high-density linkage map.
We will present the results of the structural (Transposable Elements (TEs), genes) and functional
annotations of automatically predicted genes. These data were obtained using robust pipelines (i)
REPET to de novo detect, classify and annotate TEs (ii) Eugene to integrate ab initio and similarity
gene finding softwares (iii) A functional annotation pipeline, based on Interproscan to search for
patterns/motifs and Blast based comparative genomics. We also set up a dedicated integrated
genome annotation system based on GMOD based web interfaces (WebApollo/JBrowse and
Intermine) to make these data available under a user-friendly environment. This system allows
experts of different gene families to curate/validate automatically predicted genes. All together
these resources provide a framework to study the two key evolutionary processes that explain the
remarkable diversity found within the Quercus genus: local adaptation and speciation.
30

P2
Genome sequencing of Fraxinus species to identify loci relevant to ash
dieback and emerald ash borer
E. SOLLARS 1,2 , L. J. KELLY 1 , B. CLAVIJO 3 , D. SWARBRECK 3 , J. ZOHREN 1 , D. BOSHIER 4 , J. CLARK 5 , S.
LEE 6 , J. KOCH 7 , J. E. CARLSON 8 , E. D. KJAER 9 , L. R. NIELSEN 9 , W. CROWTHER 1 , S. J. ROSSITER 1 , A.
JOECKER 2 , S. AYLING 3 , M. CACCAMO 3 and R. J. A. BUGGS 1
1 School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road,
London, E1 4NS, UK; 2 Qiagen Aarhus, Silkeborgvej 2, Prismet, 8000 Aarhus C., Denmark; 3 The
Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK; 4 Department of Plant
Sciences, University of Oxford, Oxford, OX1 3RB, UK; 5 The Earth Trust, Little Wittenham, Abingdon,
Oxfordshire, OX14 4QZ, UK; 6 Forest Research, Northern Research Station, Roslin, Midlothian, EH25
9SY, UK; 7 U.S.D.A. Forest Service, Northern Research Station, Delaware, OH 43015, USA; 8 Department
of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802,
USA; 9 Department of Geosciences and Natural Resource Management, University of Copenhagen,
Rolighedsvej 23, 1958 Frederiksberg C, Denmark
Fraxinus (ash) species are highly threatened by emerald ash borer (EAB) in North America and ash
dieback (ADB) in Europe. Their future may depend on genomically assisted breeding for low
susceptibility to these threats. We have produced a de novo reference genome from a lowheterozygosity
British F. excelsior (European ash) tree (N50 = 99Kbp, Total length = 875Mbp; see
www.ashgenome.org), and sequenced 38 further trees from this species across Europe, including a
Danish tree with low susceptibility to ADB, which we are comparing. We are now sequencing the
genomes of 35 other Fraxinus species from around the world. Genome size in Fraxinus varies from
750Mbp to 4Gbp (1C-values), encompassing diploid, tetraploid and hexaploid taxa. Preliminary
evidence suggests that Asiatic Fraxinus species have low susceptibility to EAB and ADB, which we are
testing with genus-wide experimental EAB inoculation experiments in Ohio, and genus-wide field
exposure to ADB in Britain. We aim to find loci relevant to low susceptibility to ADB and EAB by
detecting genes in the genus Fraxinus that have phylogenies incongruent with the typical genus
phylogeny, but congruent with patterns of low susceptibility among species. If successful, this
method will be applicable to other tree pest/pathogen interactions.
31

P3
Using direct amplification and next-generation sequencing technology to
explore foliar endophyte communities in experimentally inoculated western
white pines
L. S. BULLINGTON 1 and B. G. LARKIN 1
1 MPG Operations, LLC, 1001 S Higgins Suite A3, Missoula, MT 59801, USA
Fungal endophytes can influence survivability and disease severity of trees. Here we characterized
the endophyte community in Pinus monticola (western white pine), an important species in the
northwest USA, largely decimated by pathogenic fungi. We also assessed the ability to successfully
inoculate seedlings with desirable endophytes, with the long-term goal of providing a protective
microbiome and added defense from pathogens. We inoculated P. monticola seedlings in the field
with potential pathogen antagonists and fungi isolated from healthy mature trees. Following
inoculations we used direct amplification and next generation sequencing to characterize fungal
endophyte communities, and explore interspecific competition, diversity, and co-occurrence
patterns in needle tissues. Negative co-occurrence patterns between inoculated fungi and potential
pathogens, as well as many other species, indicate early competitive interactions. Our results
support the role of competitive interactions in early endophyte community assemblage and show
that inoculations influence endophyte community development and tree health.
P4
Linking Populus genes to ecologically important traits and associated insect
communities
H. BULTMAN 1, 2 , L. HOLESKI 3 , P. INGVARSSON 4 and R. L. LINDROTH 1, 2
1 ,2 Departments of Zoology and Entomology, University of Wisconsin-Madison, 1630 Linden Drive,
Madison, WI 53706, USA; 3 Department of Biological Sciences, Northern Arizona University, 617 S.
Beaver St., Flagstaff, AZ 86011, USA; 4 Department of Ecology and Environmental Sciences, Umeå
University, Linnaeus väg 6, Umeå, SE-901 87, Sweden
Community genetics aims to link intraspecific genetic variation in one organism to the diversity and
composition of communities of interacting organisms. Populus genetics shape the community of
insects that colonize the trees, although the particular genes involved have not been identified. To
address this void, we have established a genetic mapping population (‘WisAsp’) of 515 aspen
(Populus tremuloides) replicated genotypes to identify the genes associated with tree traits that
influence communities of associated insects. Thus far, we have found substantial genotypic variation
in both tree traits (e.g., growth, phytochemistry and phenology) and insect communities (e.g.,
species richness) that colonize the trees. We have also found that insect communities vary across
aspen genotypes at a nearby garden with a subset of nine genotypes from WisAsp (PerMANOVA F =
2.02, P < 0.002). Phytochemical levels helped explain the variation in insect communities, indicating
that tree traits can serve to shape insect communities. In the future we will use genome-wide
association mapping to identify Populus genes underlying tree traits and insect communities. This
work will advance community genetics by linking plant genes to tree traits that effect variation in
dependent insect communities.
32

P5
An ancient trans-kingdom horizontal transfer of Penelope-like retroelements
from insects to conifers
X. LIN 1 , N. FARIDI 1, 2 , C. CASOLA 1
1 Department of Ecosystem Science and Management, Texas A&M University, College Station, TX
77843, USA; 2 USDA Forest Service Southern Research Station, Saucier, MS 77843, USA
Penelope-like elements, or PLEs, represent a class of retroelements represented by two main types:
EN(+)PLEs, which encode the unique combination of a reverse transcriptase (RT) domain and a GIY-
YIG endonuclease (EN) domain; and EN(-)PLEs, encoding only a RT domain. While members of the
second type occur in a variety of eukaryotes, EN(+)PLEs have thus far been detected only in animal
genomes. In this work, we have investigated the evolutionary history of conifers EN(+)PLEs, which
we have named Dryads, recently discovered in loblolly pine. In phylogenies of PLE sequences,
Dryads form a monophyletic group placed within a major animal EN(+)PLE lineage. Furthermore,
Dryads are closely related to a clade of EN(+)PLEs primarily found in insects. Bioinformatics surveys
revealed no EN(+)PLEs in 625 fully sequenced non-metazoan and non-conifer genomes from twelve
major eukaryotic lineages. Additionally, PCR assays indicate that Dryads are absent in non-conifer
gymnosperms, including Ginkgo biloba and several cycads and gnetales. These findings indicate that
Dryads emerged following an ancient horizontal transfer of Penelope-like elements from an insect
group to a common ancestor of conifers in the late Paleozoic, and suggest that retroelements
horizontal transfers might have played an important role in the expansion of the very large conifers
genomes.
P6
Detecting local selection in spatially heterogeneous environments: clues from
simulations and empirical data from a widespread boreal tree, Populus
balsamifera
V. E. CHHATRE 1 , M. C. FITZPATRICK 2 and S. R. KELLER 1
1 Dept. of Plant Biology, University of Vermont, Burlington, VT 05405, USA; 2 Appalachian Laboratory,
University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA
Most widely distributed tree species inhabiting spatially heterogeneous environments experience
varying strengths and types of ecological selection, often giving rise to strong local adaptation.
Frequentist and Bayesian approaches to detect genomic responses to selection along environmental
gradients typically assume linear responses, even though empirical allele frequencies often vary nonlinearly
along environmental gradients. Here, we compare the power of several existing methods in
SNP-environment association analysis (BayeScEnv, Bayenv2 and LFMM), as well as two more recent
biodiversity modelling techniques – Generalized Dissimilarity Modeling (GDM) and Gradient Forests
(GF), at detecting non-linear selection in population genomic datasets. We tested these methods
using two approaches. First, we used spatially explicit simulations of 1000 loci in 30 populations
arrayed in a linear stepping stone model with varying amounts of migration. Selection was applied to
one locus in the form of differential mortality increasing either linearly or non-linearly along the
gradient, and both false positive and false negative rates were calculated across replicate
simulations of each scenario. Second, we compared the performance of the different methods on an
empirical SNP data set from the widely distributed tree Populus balsamifera, consisting of ~1100
trees from 90 populations genotyped at 297 candidate SNPs from the flowering time network
controlling adaptive phenology.
33

P7
Distributed control constrains evolution of a major growth/defense pathway
in Aspens
C. T. COLE 1 , V. H. GUO DECKER 2 , B. R. ALBRECTSEN 2,3 and P. INGVARSSON 2
1 Division of Science & Mathematics, University of Minnesota, Morris, MN 56267, USA; 2 Plant Science
Center, Umeå University, 6 Linnaeus Vag, Umeå, 90187, Sweden; 3 University of Copenhagen,
Thorvaldsenvej 40, DK 1871 Frederiksberg C, Denmark
Aspens and their relatives (Populus spp.) are classical foundation species for major biomes across the
northern hemisphere. Trade-offs between aspen growth and defense, as well as interactions with
fungi, insects, mammals, and birds, are strongly influenced by products of the phenylpropanoid
pathway (PPP), which produces lignin as well as condensed tannins (CTs) and salicinoids. In Populus,
the PPP is a pleiotropic, highly branching pathway of enzymes from multi-gene families.
We investigated whether regulation of the PPP is focused on a single step or distributed throughout
the pathway, and assessed how that pattern of control has affected the pattern of selection on the
pathway.
Both intrinsic (genotype) and extrinsic (nutrient) factors altered expression levels of 8 enzyme genes
throughout the CT pathway, rather than at a single control point; this ‘distributed control’ was
evident as highly correlated expression levels throughout the pathway. Comparing the sequences
for 10 PPP enzymes (25 genes from 12 individuals) with P. trichocarpa showed that selection
constrains divergence of genes throughout the pathway, acting most strongly on upstream genes.
This signature of negative selection appeared despite the presence of multiple genes in most
families.
P8
Could host species and environmental factors affect mountain pine beetle
dynamics?
J. E. K. COOKE 1 , A. ARANGO-VELEZ 1 , C. I. CULLINGHAM 1 , E. MAHON 1 , M. MEENTS 1 , B. J. COOKE 2
and D. W. COLTMAN 1
1 University of Alberta, Department of Biological Sciences, Edmonton, AB, T6G 2E9, Canada; 2 Natural
Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, AB, T6H 3S5,
Canada
The current outbreak of mountain pine beetle (MPB) in western North America has impacted more
than 28 million hectares of pine forests. Lodgepole pine is the primary species that has been
impacted. In recent years, MPB has undergone range expansion from central British Columbia
across northern Alberta, where lodgepole pine hybridizes with a new host, jack pine. We used
population genetics to refine this hybrid zone, and demonstrate that population structures of
lodgepole and jack pine are influenced by introgression. We are testing the hypotheses that
lodgepole and jack pine exhibit differing responses to MPB and pathogenic fungal associates such as
Grosmannia clavigera, and that water limitation compromises these responses. G. clavigerainduced
lesion development was slower in jack pine than lodgepole pine, and lesion development in
both species was delayed by water deficit. Microarray analyses identified thousands of pine genes
responding to G. clavigera infection. There are substantial differences in lodgepole and jack pine
transcriptomic responses to G. clavigera, and water limitation alters these transcriptomic responses.
Some differentially expressed genes also showed signatures of selection in population genomic
analyses. Collaborations with modellers are enabling us to connect insights from these genomic
analyses to models of MPB population dynamics.
34

P9
PtJAZ5 and PtJAZ5 complexes in Populus trichocarpa and their roles in the
ectomycorrhizal development
Y. DAGUERRE, S. WITTULSKY, J. PLETT, R. SCHELLENBERGER, A. VAYSSIERES, A. KOHLER, C.
VENEAULT-FOURREY and F. MARTIN
Labex ARBRE, Tree-Microbe Interactions’ Department, INRA-Nancy, 54280 Champenoux, France
Roots of most trees form symbiosis with mutualistic soil-borne fungi. The crosstalk between the two
partners is fundamental for the establishment and maintenance of beneficial relationships.
However, little is known about how symbiosis is initiated. We showed that the ectomycorrhizal
basidiomycete Laccaria bicolor relies on Mycorrhizal-induced Small Secreted Proteins (MiSSP) to
establish the interaction. In particular MiSSP7 interacts with the jasmonic acid (JA) co-receptors
PtJAZ5 and PtJAZ6 of P. trichocarpa, blocking JA signaling and promoting mutualism. JAZ proteins are
known to interact with NINJA and TOPLESS proteins as well as bHLH transcriptional factor in
Arabidopsis leaves. Using Y2H and BiFC assays, we aim identifying the proteins interacting with
PtJAZ6 and PtJAZ5 in P. trichocarpa roots. First results show that PtJAZ5 and PtJAZ6 form homo- and
heterodimers and interact with at last one bHLH transcriptional factor. Next step will be the
identification of genes targeted by this transcription factor, using ChipSeq assay in order to fully
understand mechanism underlying ectomycorrhizal ontogenesis.
P10
A molecular phylogenetic analysis of tree diversity hotspots in southern
Africa
B. H. DARU, M. VAN DER BANK and T. J. DAVIES
Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
Biodiversity hotspots have important roles in conservation prioritisation, but efficient methods for
selecting among them remain debated. In this study, we assembled the most comprehensive dated
molecular phylogeny for the southern Africa’s tree flora along with their geographical distribution to
map and contrast regional hotspots of species richness and phylogenetic diversity. In addition, we
evaluated the efficiency of hotspots in capturing complementary areas of species richness and
phylogenetic diversity. We then explored the environmental factors influencing the distribution of
these diversity metrics in southern Africa. We showed that the different hotspots did not overlap,
but captured different conservation currencies. Areas selected using complementarity are even
more dispersed, but capture rare diversity that is overlooked by the hotspot approach. An
integrative approach that considers multiple facets of biodiversity is needed if we are to maximise
the conservation of tree diversity in southern Africa.
35

P11
Gene expression and natural selection shape the evolution of protein-coding
genes in Picea
A. R. DE LA TORRE 1, 2 , Y-C. LIN 3 , .Y. VAN DE PEER 3, 4 and P. INGVARSSON 1, 2
1 Department of Ecology and Environmental Science, Umeå University, Linneaus väg 6, SE-901 87
Umeå, Sweden; 2 Umeå Plant Science Centre, Umeå, Sweden; 3 Department of Plant Systems Biology,
VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark
927, 9052 Ghent, Belgium; 4 Genomics Research Institute, University of Pretoria, Hatfield Campus,
Pretoria 0028, South Africa
The role of natural selection on the evolution of gene expression levels remains largely unknown in
non-model species. In this study, we use the first two fully sequenced representatives of the
gymnosperm plant clade (Picea abies and Picea glauca) to test for the evidence of expressionmediated
selection. We used whole-genome gene expression data (>50,000 genes) to study the
relationship between gene expression, codon bias, rates of sequence divergence, protein length,
pathway position and gene duplication. We found that gene expression correlates with rates of
sequence divergence and codon bias for translational efficiency. A strong correlation between gene
expression and gene duplication was found, with genes in large multi-copy gene families having, on
average, a lower expression level and breadth, lower codon bias, and higher rates of sequence
divergence than single-copy gene families. A correlation between pathway position and gene
duplication was also found. Single-copy genes encoded essential biological functions and were under
strong selective pressures to maintain their copy number in Picea. In contrast, large paralogous gene
families had great expression divergence and higher levels of tissue-specific genes. Our study
highlights the importance of gene expression and natural selection in shaping the evolution of
protein-coding genes in Picea species.
P12
Forest tree improvement: the shift from quantitative genetics to quantitative
genomics
Y. A. EL-KASSABY and J. KLÁPŠTĚ
Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British
Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
Traditional and Next Generation Sequencing technologies increased the availability of sequence data
for model and non-model forest tree species. This in turn transformed quantitative genetics from
the pedigree-based founded on the utilization of Sewell Wright’s coefficient of relationship between
individuals (Wright S. 1922; Amr Nat 56:330-338) to a genomic-based realized kinship method for
estimating individuals’ breeding values and traits’ heritability and genetic correlation. This
substantial shift literally changed quantitative genetics to quantitative genomics and led to the
development of innovative methods such as the pedigree-free and the unified single-step (a
combination of pedigree and genomic realized kinship) evaluation approaches where the classical
Best Linear Unbiased Predictor (BLUP) is replaced by the Genomic Best Linear Unbiased Predictor
(GBLUP). The advantages of quantitative genomics offered opportunities for obtaining more precise
genetic parameters, better partition of the genetic variance, and even breeding without structured
pedigree. Examples from unstructured black cottonwood and white spruce open-pollinated
populations will be presented to demonstrate the unsurpassed potential of incorporating sequence
data in classical breeding.
36

P13
A catalogue of putative unique transcripts reveals tissue specific
transcriptome responses during the winter-spring transition in Eastern white
pine (Pinus strobus)
I. ENSMINGER and C. RASHEED-DEPARDIEU
Department of Biology, University of Toronto Mississauga, Mississauga Road, Mississauga, ON L5L
1C6, Canada
In the present study we report a catalog of putative unique transcripts enriched for genes associated
with freezing tolerance from Eastern white pine (EWP), a conifer native to Northern America. EWP
seedlings were exposed to a simulated transition from winter to spring and summer in controlled
environments in order to generate a catalogue of unique transcripts representing the EWP
transcriptome during various seasons and in different tissues. 44 libraries were generated including
needle, bud, stem and root tissues of pine seedlings. 1,118,287,330 raw reads were obtained using
the Illumina HiSeq 2000 sequencing platform. The EWP transcriptome was sequentially assembled
using a de-Bruijn graph and overlap-layout-consensus assemblers. This de novo assembly generated
a set of 339,371 putative unique transcripts. Functional characterization of transcripts included
BLAST searches against NR, PLAZA 2.5 and UNIPROT databases and mapping against GO, KEGG and
InterPro databases. We discuss the quality of the reference transcriptome using assembly statistics
as well as functional and comparative analysis with assembled transcriptomes of five other conifer
species. The present draft assembly and annotation of the EWP transcriptome provides a resource
for further gene expression analysis, comparative genomic studies and will further improve the
molecular understanding of frost tolerance in conifers.
P14
N-responsive gene expression of cell wall modification and dynamic changes
in wood anatomy in the elongation zone of poplar
D. J. EURING and A. POLLE
Department of Forst Botany and Tree Physiology, Georg-August Universität, Büsgenweg 2,
Göttingen, 37077, Germany
Nitrogen (N) is an important nutrient, often limiting plant productivity and yield. Fast growing trees,
such as poplars are increasingly used as a feedstock for wood production and biofuel generation. It
is therefore critical to understand how N availability affects growth and wood formation of poplar. In
this study, we characterized N-responsive dynamic changes in wood anatomy along the elongation
zone of poplar and identified an N-responsive cell wall modification gene expression network in the
elongation zone (first two internodes). Anatomical and biochemical analysis revealed increased cell
wall thickness and secondary metabolites in the elongation zone. The finding of an N-responsive cell
wall hub may have wider implications for the improvement of tree N use efficiency and opens new
perspectives on the enhancement of wood composition as a feedstock for biofuels.
37

P15
How has our understanding of the conifer sexual reproductive process
advanced in the age of genomics?
D.D. FERNANDO
Department of Environmental and Forest Biology, State University of New York College of
Environmental Science and Forestry, One Forestry Drive, Syracuse, NY 13210, USA
The long generation time and lengthy reproductive process in conifers are major barriers to
functional genomics and genetic improvement. Therefore, our understanding of conifer sexual
reproduction has also been mostly confined to comparative evolutionary genomics. This approach
has provided insights on the divergence of sequences related to angiosperm genes involved in
flowering time and floral organ identities, embryo formation, and other genes expressed in the
sporophyte phase of the reproductive stage. My lab is focused on the analysis of genes expressed in
the haploid phase of the reproductive stage, particularly male gametophyte development. We have
identified and characterized genes using various genomic and proteomic approaches including
microRNA analysis. We have described several conserved miRNAs in mature and germinated loblolly
pine pollen and many of these are differentially expressed indicating that male gametophyte
development is regulated at the miRNA level. This presentation/poster will focus on some of our
unpublished results on the correlation between conserved miRNA genes and their respective target
sequences. We have also introduced novel miRNA genes into pollen tubes through Agrobacterium
transformation and interesting phenotypes were obtained. We are developing a microgenomic
approach to validate transformed pollen tubes. The main goal of my lab is to understand the
molecular mechanism underlying conifer pollen germination which is necessary to be able to
facilitate germination and tube growth so as we may be able to bypass incompatibility barriers and
thus create novel hybrids or prevent germination as a gene containment strategy.
38

P16
Local adaptation to environment is observed from genome-wide SNP data in
Populus balsamifera (L.)
K. C. FETTER, V. E. CHHATRE and S. R. KELLER
Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Dr., Burlington, VT
05401, USA
Populus balsamifera has a large geographic range and local populations occupy distinct locations
along strong environmental gradients of climate and photoperiod. Range-edge populations,
particularly southern populations, may contain high levels of standing genetic diversity and harbor
unique alleles adapted to longer, warmer, and drier growing seasons, environments that may
become more widespread in the future. At the same time, southern populations are likely to be at
greater risk of extirpation from climate change. In this study, we characterize the population
structure and diversity of southern range-edge versus range-core populations, and identify genomic
regions associated with local adaptation. We analyzed 534 individuals collected from 63 core and
range-edge populations, and obtained genome-wide SNP data from >150K loci using genotype-bysequencing
at 48-plex. Population structure was estimated using Bayesian clustering
(fastSTRUCTURE) and discriminant analysis of principal components (DAPC). Tests for local
adaptation manifest as F ST outliers and SNP-environmental associations were estimated with
Bayescan, BAYENV, and LFMM. We find genomic regions suggesting novel, locally adapted loci in
range-edge populations that likely contribute to their fitness in warmer, drier environments. Loci
adapted to longer growing seasons and warm, dry environments may be useful for integrating into
poplar breeding programs under future climates.
P17
Oakcoding: a nuclear DNA barcode for evolutionary studies in oaks
E. FITZEK 1 , E. GUICHOUX 2 , R. PETIT 2 and A. HIPP 1
1 The Morton Arboretum, Herbarium, 4100 Illinois Route 53, Lisle, IL 60532, USA; 2 Platforme Genome
Transcriptome, 69 Route d’Arcachon INRA, Site de Pierroton/Btmt ARTIGA CESTAS, 33610 France
Oaks (Quercus, Fagaceae) are keystone species in forests and savannas across the northern
hemisphere. They are a model genus for studying tempo and rate of hybridization. Single-nucleotide
polymorphisms (SNP) genotyping is increasingly used to study population structure and hybridization
rates within a population. The goal of OAKCODING is to develop a single-multiplex (40 SNPs) as an
easy-to-use genotyping tool to distinguish a set of the most common North American white oaks.
Secondly, these SNPs will help to distinguish them from the Eurasian white oaks with which they can
hybridize in cultivation. An existing RADseq dataset for 69 samples representing the eastern North
American and Eurasian white oaks was utilized to identify species-specific SNPs. RADami, pyRAD,
STACKS and custom scripts were used to generate a list of potential SNPs and screen 10-plex (total of
344 SNPs) on ca. 200 DNA extractions to evaluate barcoding success rate using the SEQUENOM
(INRA, Pierroton). Currently, we have 26 verified SNPs that will count towards OAKCODING and are
specific to Quercus michauxi, Q. lyrata and Q. bicolor. We then propose to utilize this toolkit to study
hybridization patterns in a unique and old (> 90 years old) oak taxonomic collection at The Morton
Arboretum.
39

P18
Visualizing molecular changes associated with gravitropism and tension wood
formation in Populus
S. GERTTULA, H. BRUMER 2 , S. MANSFIELD 2 , M. ZINKGRAF 1 and A. GROOVER 1,3
1 US Forest Service, Pacific Southwest Research Station, Davis CA, USA; 2 University of British Columbia,
Vancouver BC, Canada; 3 Department of Plant Biology, University of California Davis, USA
Woody species have evolved specialized mechanisms for responding to gravity. In angiosperms, the
upper surface of a leaning stem develops tension wood in which a strong tensile force is generated
and used to counteract the force of gravity. Here, confocal imaging was used to visualize molecular
events occurring during graviperception and tension wood development in wild type and trees
transformed with ARBORKNOX2 (ARK2), a Class I Homeobox transcription factor. When ARK2
transcript levels are lowered, gravibending is compromised, while elevated ARK2 transcript levels
enhance gravibending. Immunolocalization against the poplar ptPIN3 auxin transport protein shows
that ptPIN3 undergoes dynamic polar relocalization events in response to gravity perception with
differences among the genotypes. Arabinogalactan proteins (AGPs), key markers of tension wood,
were visualized using an AGP specific antibody (JIM14) and showed strong labelling in developing
tension wood fibers. JIM14 labelling appeared in fibers closer to or further from the cambium
depending on the genotype. Xyloglucan endotransglycosylase (XET) activity has been proposed to
play an important role in force generation of tension wood fibers. XET activity was visualized after
incubation of wood tissue sections with a rhodamine-labelled XXXG oligomer. XET activity was strong
in developing tension wood fibers. Similar to JIM14 labelling, XET labelling occurred in fibers closer
to the cambium in ARK2 overexpressing plants. Together, these imaging techniques provide new
insights and tools for the study of graviperception, gravitropism, and wood development in
angiosperm trees.
40

P19
Survey of the sugar pine (Pinus lambertiana) transcriptome by deep
sequencing
D. GONZALEZ-IBEAS 1 , P. J. MARTINEZ-GARCIA 2 , R. FAMULA 2 , C. A. LOOPSTRA 3 , J. PURYEAR 3 , D.
NEALE 2 and J. L. WEGRZYN 1
1 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA:
2 Department of Plant Sciences, University of California Davis, Davis, CA, USA: 3 Department of
Ecosystem Science and Management, Texas A&M University, College Station, TX, USA
While rapid progress has been made in characterizing the genomes of angiosperms, the same is not
true for gymnosperms, in part due to their size and complexity. The advent of high-throughput
sequencing technologies has enabled complete genomes in a few economically important conifer
species. In this study, we present a comprehensive transcriptome of one of the largest conifer
genomes, sugar pine. Thirty-one tissue-specific RNA libraries have been constructed, including
needle, root, stem, pollen, cone, strobili, and embryonic tissues. Short read technologies (Illumina
MiSeq and HiSeq) and the Pacific Biosciences Iso-Seq reads which result from size-selected libraries
ranging from 1,000 to over 6,000 bp, have been included to combat many of the existing challenges
in transcriptome assembly. A description of the contribution of each technology is presented, in
terms of transcript length and coverage, mapping rate on the genome, and transcriptome
completeness. Two different approaches for protein coding region identification have been
compared to deal with the different type of technologies, and transcriptome composition has been
analysed per library. The assembly, which has been used to scaffolding and annotate the full genome
assembly, represents the first comprehensive survey of the sugar pine transcriptome.
P20
Phylogeography and genetic structure of two closely related species,
Dryobalanops aromatica and D. beccarii (Dipterocarpaceae) in Sundaland
K. HARADA, F. G. DWIYANTI, L. CHONG, B. DIWAY, Y. F. LEE, I. Z. SIREGAR, A. SBIAKTO, I.
NINOMIYA, K. KAMIYA
Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
Dipterocarps predominate the lowland evergreen forest in Sundaland and characterize the east
Malaysian tropical rain forest. Two congenic dipterocarp species, Dryobalanops aromatica Gaertn. F.
and D. beccarii Dyer were examined for their phylogeographic history and genetic structure by using
nuclear microsatellite markers. Bayesian model-based clustering analysis showed that the species
were clearly differentiated although hybridization probably occurred in two sympatric populations.
D. aromatica could be divided into two genetically distinct groups: Malay-Sumatra and Borneo. An
isolation with migration analysis using IMa program estimated the time of divergence of the two
population groups to be 7,300–3,600 years ago, i.e. after the last glacial maximum. This analysis also
suggested that the ancestral population was much larger than today’s populations. This supports the
idea that the present tropical rainforest is in a refugial state, and also suggests that the savanna
corridor that is hypothesized to have covered the central part of the exposed Sundaland during the
last glacial period, if it existed, was not contiguous but rather permeated by forest in some places.
41

P21
Nuclear microsatellite markers for population studies in sugar maple (Acer
saccharum Marsh.)
S. KHODWEKAR and O. GAILING
School of Forest and Environmental Sciences, Michigan Technological University, 1400 Townsend
Drive, Houghton, MI 49931, USA
A set of seven new nuclear microsatellite markers (nSSRs) was developed for sugar maple (Acer
saccharum Marsh.) using paired-end Illumina sequencing. Out of 96 primers screened in a panel of
six unrelated individuals, seven markers amplified polymorphic products. The utility of these
markers, in addition to six already published microsatellites, for genetic variation and gene flow
studies is assessed. Out of the seven newly developed markers three amplified multiple fragments
and were interpreted as dominant (absence/presence) markers, while four markers amplified a
maximum of two amplification products per sample. The six published microsatellites and three of
the four newly developed markers showed regular segregation in an open-pollinated single tree
progeny. Observed heterozygosity (H o ) and expected heterozygosity (H e ) in 48 individuals from one
population ranged from 0.436 to 0.917 and from 0.726 to 0.894, respectively. Paternity analyses in
the program CERVUS at co-dominant markers showed effective dispersal of pollen in the sugar
maple population. The absence of fine-scale Spatial Genetic Structure (SGS) suggested effective
dispersal of both seeds and pollen.
P22
The genetic architecture of fitness-related traits within whitebark pine (Pinus
albicaulis)
B. M. LIND 1 , P. E. MALONEY 2 , D. R. VOGLER 3 , D. B. NEALE 4 and A. J. ECKERT 5
1 Integrative Life Sciences or 5 Department of Biology, Virginia Commonwealth University, Life
Science Building 126, 1000 West Cary Street, Richmond, VA 23284, USA; 2 Department of Plant
Pathology and Tahoe Environmental Research Center or 4 Department of Plant Sciences, University of
California, One Shields Avenue, Davis, CA 95616, USA; 3 USDA, Forest Service, Pacific Southwest
Research Station, Institute of Forest Genetics, 2480 Carson Road, Placerville, CA 95667, USA
For populations of forest trees, fitness-related traits associated with survival, especially during
seedling and juvenile stages, are indicative of total lifetime fitness and are composed of phenotypic
traits related to growth, phenology, resource allocation patterns, water-use efficiency, and disease
resistance. As expected of traits having strong influence on fitness, these traits are often correlated
with environmental conditions. Yet, climate models predict redistribution of environmental variables
currently structuring standing genetic variation of such phenotypic traits, which could lead to
discordance between the environmental optima of tree populations and concurrent environmental
conditions. Temperature and precipitation gradients within the southern range of whitebark pine
(Pinus albicaulis, WbP) are predicted to be acutely impacted by climate change, thus necessitating
the preservation of heritable genetic variation for continued adaptation. Recently we have shown
WbP populations from Lake Tahoe Basin, California (LTB) to have heritable genetic variation
(h2=0.0608–0.7787) for fitness-related traits associated with survival. Here, we describe the genetic
architecture of local adaptation within WbP through results from genomic interrogation of these
traits using ddRADseq. Specifically, using tens-of-thousands of SNPs, we will discuss population
structure among 6 WbP populations within the LTB, and the links between genotype and phenotype
and those of genotype and environment.
42

P23
Sequence characterization of a CONSTANS-like gene in North American red
oaks
J. F. LIND-RIEHL and O. GAILING
Forest Resources and Environmental Sciences, Michigan Technological University, 1400 Townsend Dr,
Houghton, MI 49931, USA
Oaks (Quercus spp.) provide a model system to study local adaptation since they maintain species
identity despite frequent interfertile hybridization. Genome scans between two European white oak
species have found a largely homogenized genome resulting from interspecific gene flow. However,
a few genomic areas showed high interspecific differentiation thought to be involved in the
maintenance of species identity through divergent selection. Quercus rubra and Q. ellipsoidalis, two
interfertile North American oak species, show differences in flowering time and adaptations to
drought. Previously, we discovered a genic microsatellite nearly fixed on alternative alleles in each
species. This locus has a putative function as CONSTANS-like gene, which is thought to be involved in
flowering time and growth. To further elucidate the basis of this differentiation we have begun
sequencing the coding region of this gene in individuals from both species. Our initial findings
indicate that the differences in allele frequencies are the result of sequence variability in the
microsatellite motif that encodes a poly-Q repeat potentially involved in transcription regulation or
protein stabilization. We plan to continue this work by sequencing additional areas around the
microsatellite to determine whether or not surrounding areas display variations associated with
species differences.
P24
Identifying microRNAs involved in Regeneration of Secondary Vascular
System in 4 Populus tomentosa Carr.
F. TANG 1 , H. WEI 2 and M-Z LU 1
1 State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091,
China; 2 School of Forestry Resources and Environment Science, MTU, USA
Wood formation is a complex developmental process governed primarily by a regulatory
transcription network. MicroRNAs can exert regulatory roles over transcription of their target genes
involved in plant growth and development. We used the regeneration of the secondary vascular
system established in Populus tomentosa to harvest tissues generated from differentiating xylem in
a time series for small RNA high-throughput sequencing. 209 known and 189 novel miRNAs were
identified and Degradome sequencing analysis was then performed and 223 and 126 genes were
obtained. GO enrichment of these target genes revealed that the targets of 15 miRNAs were
enriched in the auxin signaling pathway, cell differentiation, meristem development and pattern
specification process, which were main biological events during the regeneration of secondary
vascular system. This study provides the basis for further analysis of these miRNAs to gain insight
into their regulatory roles in wood development in trees.
43

P25
The effects of selective breeding on adaptive phenotypic traits in the interior
spruce (Picea engelmannii x P. glauca) of western Canada
I. R. MACLACHLAN 1 , T. WANG 1 , A. HAMANN 2 , P. SMETS 1 , J. TUTYEL 1 and S. N. AITKEN 1
1 Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main
Mall, Vancouver, BC, V6T 1Z4, Canada; 2 Department of Renewable Resources, University of Alberta,
751 General Services Building, Edmonton, AB, T6G 2H1, Canada
The AdapTree project is quantifying phenotypic and genomic architectures of local adaptation to
climate in interior spruce (Picea glauca (Moench) Voss x P. engelmannii Parry ex Engelm.) to inform
future provincial climate-based seed transfer policies. In Western Canada, reforestation using
seedlots from selective breeding programs is increasing rapidly, but the impacts of selective
breeding on climate-relevant phenotypic traits in current and future climates remain unclear. To
address this knowledge gap, we established a large seedling common garden (n = 2880 individuals)
representing 254 natural seedlots and 18 selectively bred seedlots from provenances across British
Columbia and Alberta. We have made detailed assessments of growth, phenology and cold
hardiness traits. Our analyses compare trait means, climatic clines and trait-trait correlations
between natural and corresponding selectively bred seedlots. All seedlings are currently being
genotyped using the AdapTree 50K interior spruce SNP array.
Growth traits show large differences between seedlot types within breeding zones resulting from
selective breeding. Clines in growth traits along provenance climate gradients are steeper in
selectively bred material than natural populations, indicating that selection for timber volume has
increased the strength of local adaptation. However, trade-offs between gains in growth from
selection and phenology or cold hardiness traits are weak enough to suggest that the same assisted
gene flow prescriptions can be used for selectively bred and natural reforestation seedlots to preadapt
planted forests to new climates.
P26
Population genetics of freeze tolerance in Populus balsamifera across the
growing season and its implications for future climate adaptation
M. MENON, W. BARNES and M. OLSON
Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Biological
Sciences, Texas Tech University, Lubbock, TX, USA
Protection against freeze damage during the growing season influences the northern range limits of
many plant species. Winter survival strategies have been extensively studied in perennials, but few
have addressed them and their genetic basis during the growing season. We examined intraspecific
phenotypic variation in growing season freeze resistance across latitude and its molecular basis in
Populus balsamifera. Foliar tissues exhibited latitudinal and seasonal cline in freeze tolerance but
not freeze avoidance. The timing and rate of initiating freeze tolerance rather than the depth of
freeze tolerance is likely to be a trait under strong selection in P. balsamifera. Of the 46 SNPs
surveyed across the 6 CBF homologs, only CBF2_619 exhibited latitudinal differences consistent with
increased freeze tolerance in the north and also caused a conformational change in the predicted
protein structure. All 6 CBF genes were cold inducible, but showed varying patterns of expression
across the growing season. CBF genes only contributed to some amount of variation in freeze
tolerance indicating the role of other regulatory pathways and genes in nature. Overall, our study
suggests the role of both coding and regulatory variations as important contributors to clinal
adaptation and migration responses to historical climate shifts.
44

P27
Forest tree GnpIS: an information system dedicated to forest tree genetics,
genomics and phenomics
C. MICHOTEY 1 , C.ANGER 2 , F. EHRENMANN 4 , O. ROGIER 3 , V. JORGE 3 , C. POMMIER 1 , C. BASTIEN 3 , C.
PLOMION 4 , C. PICHOT 5 , H. QUESNEVILLE 1 and D. STEINBACH 1
1 INRA, UR1164 - URGI (Unité de Recherche en Génomique-Info), route de Saint-Cyr – RD 10, 78026
Versailles cedex, France ; 2 INRA, UE0995 - GBFOR (Génétique et Biomasse Forestière ORléans), 2163
avenue de la Pomme de Pin, CS 40001 Ardon, 45075 Orléans cedex, France; 3 INRA, UR0588 - AGPF
(Amélioration, Génétique et Physiologie Forestières), 2163 avenue de la Pomme de Pin, CS 40001
Ardon, 45075 Orléans cedex, France ; 4 INRA, UMR1202 - BIOGECO (BIOdiversité, GEnes et
COmmunautés), 69 route d’Arcachon, 33612 Cestas cedex, France; 5 INRA, UR0629 - URFM (Ecologie
des Forêts Méditerranéennes), 228 route de l’Aérodrome, 84914 Avignon, France
GnpIS is a multispecies integrative information system dedicated to plants and fungi pests. It
integrates and links genetic, genomic, phenomic and environmental data into a single environment,
allowing researchers to store, query and explore information from different angles. The Ecology
division of the French National Institute for Agricultural Research (INRA) uses GnpIS as its referential
information system to manage forest tree genetic, genomic and phenomic data.
The forest tree resources are accessible through the GnpIS web portal
(https://urgi.versailles.inra.fr/gnpis/). Its main entry point is a google-like search for data discovery.
This bird’s eye view allows navigation through the data with specific querying tools. It is regularly
improved with new functionalities answering specific needs raised by scientists and is released
several times a year. Data are supplied by local sources (files, databases …) produced and managed
by research teams working on forest trees.
Pine, spruce and oak data have been already integrated into this forest information system and we
are giving access to poplar genetic, phenomic and genomic data
(https://urgi.versailles.inra.fr/Species/Forest-trees/Database-overview). Integration of the data
produced within the common garden network (over 1,000 trials with genotypes gathered from ~15
species) is in progress.
45

P28
A developmental and genetic study of petal-less neotropical poppy trees
N. PABÓN-MORA 1* , C. ARANGO OCAMPO 1 , J. F. ALZATE 2 and F. GONZÁLEZ 3
1 Instituto de Biología, Universidad de Antioquia, AA 1226; 2 Centro de Secuenciación Genómico
Nacional, Universidad de Antioquia, AA 1226; 3 Instituto de Ciencias Naturales, Universidad Nacional
de Colombia, AA 7495
Flowers of most Papaveraceae (760 spp.) exhibit a dimerous groundplan with 2 deciduous sepals, 4
petals, many stamens and 2-8 carpels. The genera Bocconia (9 spp.) and Macleaya (2 spp.) are
atypical in their tree- or shrubby habit, and in having perianth-less flowers. By comparing flower
development in B. frutescens, M. cordata and its closely related species Stylophorum diphyllum, we
show that petal-to-stamen homeosis occurs early in development, but different ontogenetic
pathways underlie petal-loss in Bocconia and Macleaya. In order to explore the genetic basis of
apetaly, we generated a floral transcriptome of B. frutescens and identified all MADS-box
transcription factors that are part of the ABCE genetic model of floral development. We present data
on the evolution of these genes in the Ranunculales and their expression in dissected floral organs,
leaves and fruits in B. frutescens We also propose that the lack of expression of an AP3-3 ortholog is
responsible for such apetaly, as it occurs in species of Ranunculaceae. We identified local
duplications in FUL-like and PI genes likely resulting in pseudogenization and neofunctionalization,
respectively. Based on the number of copies and patterns of expression, we propose a modified
ABCE model for the petal-less poppy trees.
P29
Microevolutionary patterns of a resistance mechanism in white spruce
G.J. PARENT 1 , I. GIGUÈRE 1 and J.J. MACKAY 1, 2
1 Centre d’étude de la Forêt, Département des Sciences du Bois et de la Forêt, Université Laval, G1A
1V6, Québec, Canada; 2 Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
The accumulation of two foliar acetophenone compounds (piceol and pungenol) plays a key role in
the defense of white spruce (Picea glauca) against spruce budworm (SBW, Choristoneura
fumiferana). Variability in the expression of a beta-glucosidase, PGβGLU-1, responsible for their
release was linked to SBW resistance. This novel resistance mechanism is constitutive, genetically
transmissible and variable in the natural white spruce population. We were interested in
characterizing its microevolutionary patterns to better understand its importance. Levels of Pgβglu-1
transcripts and toxic acetophenones were measured in white spruce from multiple provenances and
preliminary results indicated a clear geographic pattern. Foliage expression of Pgβglu-1 was lower in
provenances south of the 48th parallel. This result may be accounted for by lower selection pressure
exerted by SBW associated with a reduced survival rate at the southern limit of its distribution.
However, concentrations of piceol and pungenol in white spruce foliage did not follow the
geographic pattern found for gene expression. This suggests that control of these specific
acetophenone compounds may also be affected by other factors than the expression of Pgβglu-1.
We are currently working to find other members of the biochemical pathway and regulatory
network through association testing and other genome analysis methods.
46

P30
Strategies for classifying repeats in conifer genomes
R. PAUL 1 , K. PRATT 1 , K. STEVENS 2 , D. GONZALEZ-IBEAS 1 , C. A. LOOPSTRA 3 , A. V. ZIMIN 4 , A. HOLTZ-
MORRIS 6 , M. KORIABINE 6 , J. A. YORKE 4, 5 , M. W. CREPEAU 2 , D. PUIU 7 , S. L. SALZBERG 7 , P. J. DE
JONG 6 , C. H. LANGLEY 2 , D.B. NEALE 3 and J. L. WEGRZYN 1
1 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA;
2 Department of Evolution and Ecology, University of California, Davis, CA, USA; 3 Department of
Ecosystem Science and Management, Texas A&M University, College Station, TX, USA; 4 Institute for
Physical Sciences and Technology, and 5 Departments of Mathematics and Physics, University of
Maryland, College Park, MD, USA; 6 Children’s Hospital Oakland Research Institute, Oakland, CA,
USA; 7 Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns
Hopkins University, Baltimore, MD, USA
Conifers are dominant life forms in temperate and boreal forests with important applications
towards wood production, carbon sequesterization, and renewal energy. Interspersed repeats
constitute up to 85% of these large, complex conifer genomes (20-40 gigabases). Characterizing
these repeats is a challenge due to extensive retrotransposon proliferation and the highly diverged
nature of the sequences. We have developed a pipeline that both identifies and characterizes the
repeat content through a combination of de novo and library based strategies. The homology-based
strategy provides comparisons against the plant component of Repbase while de novo identification
combined structural and alignment methods via RepeatModeler. The final resolution considers
alignment quality as well as manual and semi-automated repeat family classifications. This pipeline
was used to evaluate the repetitive content of the Pinus lambertiana (sugar pine) genome which is
estimated to be 79%. Over 1570 families were uniquely identified de novo and 1693 were previously
characterized in other plants. Future work includes identifying unclassified repeats via conserved
domains and machine learning strategies. Analysis of these diverged retrotransposon families in
sugar pine and the other sequenced conifers (Pinus taeda and Pseudotsuga menziesii) will help
explain evolutionary patterns as well as gene-duplication events.
47

P31
Wood formation in the real world
N. Q. NGUYEN 1 , D. JANZ 1 , C. CARSJENS 1 , G. LOHAUS 1 , T. IVEN 2 , I. FEUSSNER 2 and A. POLLE 1
1 Dept. for Forest Botany and Tree Physiology, Georg-August Universität Göttingen, Büsgenweg 2,
37077 Göttingen, Germany; 2 Dept. for Plant Biochemistry, Georg-August Universität Göttingen,
Justus von Liebig Weg 11, 37077 Göttingen, Germany
In temperate ecosystems, wood formation of deciduous tree species undergoes seasonal
fluctuations, usually with the production of larger vessels early and the formation of smaller vessel
lumina, more fibers and thicker cell walls towards the end of the growth phase. The transcriptional
networks and hormonal regulation underlying wood formation of non-model trees has barely been
studied. Here, we investigated the formation of beech wood (Fagus sylvatica L.). Although beech is a
key stone species in temperate European forests, genomic information is lacking. To increase our
knowledge on wood formation of beech, we used RNA sequencing of the developing xylem of
mature field grown trees located at two field sites. The transcriptomic data were related to the
hormonal status and wood anatomy employing weighted gene correlation network analysis.
Thereby, co-regulated genes and hormones were assigned to the formation of specific cell types.
Our analysis suggests that ABA (abscisic acid) is a main player in seasonal acclimation of the wood
structure balancing vessel lumina and fibre numbers.
P32
What are the drivers of non-coding plastome variation in the New Zealand
tree flora?
B. C. M. POTTER, A. J. DRUMMOND, R. D. NEWCOMB and W. G. LEE
School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1010, New
Zealand
The native tree flora of New Zealand is diverse (ca. 320 species), highly endemic (over 90%), and
situated on a landmass with a deep history of geographic isolation in the southern Pacific (ca. 80
Ma.). As a result this region provides an excellent system for the study of forest tree genetics, as the
lineages have estimable island colonisation ages, display a range of generation times and seed
dispersal strategies, and encompass a broad array of phylogenetic diversity – from tree ferns to tree
daisies. To better understand the drivers of non-coding chloroplast variation in forest trees, targeted
sequencing was performed (e.g. trnQ-rps16, rpL32-trnL, psbA-trnH, rpoB-trnC, and trnL-trnF) on
numerous accessions of a broad selection of 20 widespread species. The results show a direct
correlation between lineage age and genetic variation in some taxa (e.g. Nothofagus spp., Nestegis
spp., Rhopalostylis sapida), highlighting the importance of the temporal driver. However, in other
species the opposite pattern was recovered, with a recently colonised tree (Geniostoma
ligustrifolium) representing the most genetically variable species – potentially owing to its rapid
generation time. While one of the most ancient species in the flora (Agathis australis) was found to
be one of the least variable – possibly owing to a slow-down in the evolutionary rate of the
araucarian plastome. These findings are discussed along with directions for further research.
48

P33
Transcriptome sequencing reveals new insights into the interaction of
European chestnut with the causal agent of chestnut blight
J. QUINTANA 1, 2 , I. MERINO 1 , A. CONTRERAS 1 , G. OROZCO 1 , A. VINUESA 1 , F.O. ASIEGBU 2 and L.
GÓMEZ 1
1 Center for Plant Biotechnology and Genomics, Polytechnic University, 28223 Pozuelo de Alarcón,
Spain; 2 Department of Forest Sciences, Helsinki University, Latokartanonkaari 7, FIN- 00014, Finland
European chestnut is a multipurpose tree with a diversification history tightly linked to human
management. Nonetheless, several diseases have diminished its natural range and economic impact.
Chestnut blight, caused by the ascomycete Cryphonectria parasitica, is a prominent example. Here
we present the first transcriptome reconstruction of European chestnut after challenge with this
pathogen. Four libraries were constructed and an Illumina HiSeq2000 platform was used to generate
over 90 million reads. De novo assembly produced 104,310 contigs. Extensive analysis on the
functional annotation of Differentially Expressed Transcripts (DEGs) revealed that JA/ET-mediated
signalling pathways are crucial to fine-tune defense response. The large number of DEGs encoding
transcription factors evidences a deep transcriptional reprograming, which leads to the upregulation
of several genes encoding for proteins with potential antimicrobial activity. Our results represent a
valuable source of information to be used in programs aimed to develop resistant cultivars.
P34
Functional genomics of developmental programmed cell death in the Norway
spruce embryo-suspensor
S. H. REZA 1 , N. DELHOMME 2 , N. R. STREET 2 , O. NILSSON 3 , H. TUOMINEN 2 , E. A. MININA 1 and P. V.
BOZHKOV 1
1 Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and
Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden; 2 Umeå Plant Science Centre,
Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden; 3 Umeå Plant Science
Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural
Sciences, 901 83 Umeå, Sweden
In Norway spruce (Picea abies) the embryo-suspensor is composed of several layers of terminally
differentiated cells, originating from asymmetric cell divisions in the embryonal mass. While the cells
in the upper layer of the suspensor (i.e. adjacent to the embryonal mass) are in the commitment
phase of PCD, the cells in the lower layers exhibit a gradient of successive stages of vacuolar cell
death towards the basal end of the suspensor where hollow walled cell corpses are located. The goal
of this study is to find out a critical subset of genes, required for vacuolar cell death in the Norway
spruce embryo-suspensor. We performed deep sequencing of RNA isolated from the suspensors and
the embryonal masses of embryogenic cell line 88:22 and identified 136 up- and 31 down-regulated
transcripts in the suspensors. Up-regulated transcripts were enriched with cell death-related genes
and genes encoding proteins involved in catabolic processes. Our next goal is to investigate the role
of these genes in the cell death and embryo development using reverse genetics.
49

P35
Population-scale characterisation of copy number variations in the gene
space of Picea glauca
A. SAHLI 1 , I. GIGUÈRE 1 , J. PRUNIER 1 , N. ISABEL 2 , J. BEAULIEU 1 , J. BOUSQUET 1 and J. MACKAY 1, 3
1 Center for Forest Research and Institute for Systems and Integrative Biology, Université Laval, 1030,
avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada; 2 Natural Resources Canada, Canadian
Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., Stn. Sainte-Foy, Quebec City, QC, G1V
4C7, Canada; 3 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
3RB, UK
Copy number variations (CNVs) are large genetic variations present in the genome of every
multicellular organism examined so far. They are believed to play an important role in the evolution
and adaptation of species. In plants, little is known about the characteristics of CNVs. Here, we used
SNP-array intensity data for pedigrees and trees sampled from natural populations to scan the gene
space of Picea glauca for CNVs. We were particularly interested in the characterisation of CNVs
abundance, inheritance modalities, frequency spectrum and functional impact. Our findings
indicated that CNVs affect a small proportion of the gene space (less than 5%) and are
predominantly bi-allelic copy number losses. CNVs were found to follow the Mendelian inheritance
and many resulted from spontaneous mutations. The CNV frequency spectrum suggests that they
are mostly under purifying selection and that few genes may be under positive or balancing
selection. The functional annotation of CNV genes shows enrichment in genes involved in response
to environment, growth and development regulation processes. This study represents a first report
on CNVs in conifer trees at the genome and population scale and contributes to our understanding
of the genomic basis of evolution and population diversity in forest trees.
P36
Assembly challenges of the highly heterogeneous and repetitive genomes of
Populus tremula and Populus tremuloides
Y.-C. LIN, J. WANG, N. DELHOMME, B. SCHIFFTHALER, N. MÄHLER, D. SUNDELL, C.
MANNAPERUMA, K.M. ROBINSON, Y. VAN DE PEER, P. INGVERSSON, T.R. HVIDSTEN, S. JANSSON
and N.R. STREET
Department of Plant Physiology, Umeå University, Artedigränd 7, 90736 Umeå, Sweden; Department
of Biostatistics, Norwegian University of Life Sciences, Universitetstunet 3, 1432 Ås, Norway;
Department of Bioinformatics and Systems Biology, University of Ghent, Technologiepark 927, 9052
Ghent, Belgium
The European and American aspens, Populus tremula and Populus tremuloides, are ecological keystone and
scientific model forest tree species. Currently, most of the sequencing-based analyses of these species are
based on the genome assembly of the black cottonwood P. trichocarpa, a distant relative. This affects
alignment rates, especially for nongenic analyses. The aspen science community in particular, but also the
plant science community as a whole, would therefore benefit from genome assemblies of these two aspens.
These, currently undergoing, are challenging, as their genomes are highly heterozygous and repetitive, causing
extensive assembly fragmentation. Here, we first demonstrate the need for assemblies of P. tremula and P.
tremuloides by evaluating sequence alignment to the existing P. trichocarpa reference. We further present our
refined genome assembly strategies, leading to better assemblies of these two genomes. In parallel to this
genomic effort, we also present our de-novo transcriptome assembly of P. tremula, based on a comprehensive
RNA-Seq tissue catalog. Integrating these together, we assess the completeness of the genomes and their gene
spaces in our assemblies. This, ultimately, allows us to conduct a comparative genomics analysis that gives
insight into three members of the genus Populus, discussing their biological key differences and similarities.
50

P37
Unraveling the polyploid origin of coast redwood (Sequoia sempervirens)
with Bayesian concordance analysis
A. D. SCOTT, N. STENZ and D. A. BAUM
Department of Botany, University of Wisconsin - Madison, 430 Lincoln Drive, Madison, WI 53706,
USA
Coast redwood (Sequoia sempervirens) stands out as not only one of the tallest, longest-lived trees,
but as the only hexaploid conifer. As whole genome duplication is rare in gymnosperms, a better
understanding of the causes of polyploidy in Sequoia may clarify why polyploidy has played a
relatively minimal role in gymnosperm evolution. We sequenced transcriptomes from Sequoia,
Sequoiadendron, and Metasequoia, and estimated phylogenetic trees for 3,605 genes. Bayesian
concordance analysis of 3,045 low-copy genes suggests Sequoiadendron is the closest relative of
Sequoia for ~80% of the genome. Gene trees with multiple homeologs in coast redwood consistently
show monophyly of those homeologs. This suggests that hexaploidy is a result of autopolyploidy or,
that if hybridization did occur, it involved only species that are more closely related to Sequoia than
either Sequoiadendron or Metasequoia. Our analyses suggest a polyploid origin for Sequoia ~24 mya
(homeolog divergence at K s ~ 0.0168), in apparent contradiction to the fossil record.
P38
Who’s who? Finding the CESA genes in White Spruce encoding the secondary
wall specific cellulose synthase
I. DUVAL 1 , D. LACHANCE 1 , I. GIGUÈRE 2 , M-J. MORENCY 1 , G. PELLETIER 1 , J. J. MACKAY 2, 3 and A.
SÉGUIN 1*
1 Natural Resources Canada, Laurentian Forestry Centre, Québec QC G1V 4C7, Canada; 2 Centre
d’Étude de la Forêt, Université Laval, Québec (QC), G1V A06, Canada; 3 Department of Plant Sciences,
University of Oxford, Oxford, OX1 2RB, UK
Phylogenetic analyses of CESA genes have shown specific divergence within the gene family for
either primary or secondary wall development. In Picea glauca (white spruce) the PgCESA3 gene has
been principally associated to developing xylem. Tissue specific gene expression analyses using a
PgCESA3 promoter-GUS reporter construct revealed localised expression associated to secondary
wall formation. We also obtained evidences that specific spruce MYB transcription factors are
implicated in the regulation of PgCESA3 gene promoter by using a tissue culture based system and a
transactivation approach. Furthermore, using electrophoretic mobility shift assay (EMSA) we
confirmed that PgMYB12 directly binds in vitro to the PgCESA3 promoter. Overall, functional
genomic tools and global expression data for white spruce is a powerful assets for delineating the
evolution and dynamics of complex gene families such as CESA.
51

P39
Conifer’s comparative genomics – a novel topic for global collaborative, open
access, policy adoption
P. SHARMA and P. L. UNIYAL
Department of Botany, University of Delhi, Delhi 110007, India
Gymnosperms comprise 83 genera, and about 1000 species worldwide and 47 species in 14 genera
occur in India. Conifers form dominant component of vegetation in Western Himalaya. The data on
phenological studies in conifers reflects that the phenotype and thus the genotype have strong
affinities with the existing environment. However, the research data on the phenologiy of conifers in
India relating the concept of speciation and evolution is very meager. The importance of
comparative-genomic approaches for understanding functions in an evolutionary framework should
be highlighted, which may expose much novel information. There is an enormous variation in the
morphology in the populations of Taxus in Himachal Pradesh. I invite people for a comparative
genomics approach by pooling the data for research. I wish to put forward my step in this direction
for the collaborative work in comparative genomic approaches for this study with the forest tree
genomics.
P40
Transcriptional responses of resistant and susceptible ash species under
attack by emerald ash borer
D.N. SHOWALTER, R.C. HANSEN, D.A. HERMS, S. WIJERATNE, A. WIJERATNE and P. BONELLO
Department of Plant Pathology, The Ohio State University, 201 Kottman Hall, 2021 Coffey Road,
Columbus, OH 43210, USA; Department of Food, Agricultural, and Biological Engineering,
Department of Entomology, and Molecular and Cellular Imaging Center, Ohio Agricultural Research
and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691, USA
The alien, invasive wood boring beetle known as emerald ash borer (EAB, Agrilus planipennis
Fairmaire) is devastating North American ash (Fraxinus spp.) populations in urban and natural forest
settings. A critical part of landscape-scale, long-term management will be deployment of host
resistance traits, which are present in coevolved Asian ash species, but have not yet been
characterized. In an effort to understand ash defense responses against EAB, we are comparing
transcription, hormone signaling, and phenolic secondary metabolism in phloem and cambial tissue
from resistant Asian and susceptible North American ash before and immediately after EAB attack.
Qualitative comparisons of species-specific transcriptomes are revealing sequences in resistant or
susceptible species for which no orthologous transcription is detected in the other species.
Quantitative comparisons are identifying orthologous transcripts differentially expressed between
species, either constitutively or following EAB-attack. Genes of interest with support from signaling
and defense metabolite analysis may be useful targets for ash resistance breeding programs and
improve understanding of the genetic basis of angiosperm defenses against wood boring insects.
Species-specific transcriptome data will assist ongoing assembly and annotation of Fraxinus
genomes.
52

P41
Landscape genomics for climate adaptation in Eucalyptus trees
M. A. SUPPLE, J. BRAGG, R. ANDREW, A. NICOTRA, M. BYRNE, L. BROADHURST and J. O. BOREVITZ
The Australian National University, Canberra, ACT 2601, Australia
The rapid pace of climate change is threatening the survival of many species. Especially vulnerable
are long lived species with slow migration rates, which have limited ability to move with favorable
climatic conditions. Extensive reforestation projects are ongoing across Australia, providing the
opportunity to assist migration of potentially adaptive alleles. Eucalyptuses, which are foundation
species in forests and woodlands across Australia, are focal species of the reforestation effort. We
are using landscape genomic techniques to identify alleles associated with various climate conditions
in two Eucalyptus species. Using genotype by sequencing methods, we have genotyped hundreds of
samples across the distributions of each species. Each sampling location is associated with numerous
climate variables, enabling us to identify specific alleles associated with specific climatic conditions.
This association is suggestive of adaptation, which we can test experimentally in climate controlled
growth chambers. Populations harboring alleles that are potentially adaptive to predicted future
climates can be used as sources of seeds for reforestation, thereby assisting migration of the
adaptive alleles.
P42
Comparative analysis of pollen transcriptomes reveals distinct sucrose
utilization mechanisms in angiosperm trees
E. D. TRIPPE 1 , L.J. XUE 2, 3 , X. GU 1 , V. MICHELIZZI 2, 3 , V. E. JOHNSON 2, 3 , B. NYAMDARI 2, 3 , S.A.
HARDING 2, 3 1, 2, 3
and C. J. TSAI
1 Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 2 Warnell School of
Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA; 3 Department of
Genetics, University of Georgia, Athens, GA 30602, USA
Carbohydrate allocation is an important fundamental process during reproduction, and is best
understood in herbaceous annuals. Woody perennials exhibit distinct flowering phenology
(precocious versus serotinous flowering), but the genetic underpinning is poorly understood. We
found that flowering phenology is linked to pollen expression of distinct sucrose transporter (SUT)
family members. Plasma membrane SUTs are dominant in the pollen of herbaceous annuals, as well
as woody perennials with serotinous flowering, such as grapevine and Eucalyptus. In contrast, early
flowering Populus, willow and oak pollen show high transcript levels of tonoplast-localized SUT.
Additionally, our analysis reveals differential expression of vacuolar and cell wall invertases between
pollen of early- and late-flowering trees. The observation of differential compartmentalization of
sucrose transport and processing enzymes suggests alternative carbohydrate utilization mechanisms
in pollen during angiosperm evolution. Comparative gene co-expression analysis is underway to
identify other molecular candidates that are involved in different carbohydrate allocation pathways
during reproduction.
53

P43
Molecular control of vasculature development in Norway spruce
D. UDDENBERG, P. RAMACHANDRAN and A. CARLSBECKER
Department of Organismal Biology, Physiological Botany, Uppsala University and the Linnean Centre
for Plant Biology, PO Box 7080, SE 75007 Uppsala, Sweden
The wood forming vascular tissues are vital for water and nutrient transport, as well as mechanical
support thus enabling plants to stand upright and to grow large. Tissue-specific transcriptomics of
the seedling root of the model plant Arabidopsis thaliana has been instrumental in identifying
genetic control mechanisms for vascular patterning and xylem differentiation. Moreover, class III
HD-ZIP transcription factors and their interactome have emerged as key regulators of xylem
formation and cambium activity in angiosperms. While the molecular control of angiosperm vascular
development is well understood, at least for certain model plants, we know little about this in
woody perennials such as the conifers.
We aim at developing the Norway spruce seedling root as a model system to elucidate the molecular
regulation of conifer vasculature development. To do so, we will generate tissue-specific expression
profiles using high throughput RNA sequencing following micro-dissection. We have also identified a
set of Norway spruce HD-ZIP III genes together with their regulatory miRNAs and precursors. To
elucidate their role in conifer vasculature development we will in depth characterize their
endogenous expression patterns and transgenic assays will reveal their function.
P44
Genome-wide identification and profiling of novel and conserved miRNAs in
somatic embryos of Norway spruce during formation of an epigenetic
memory
I. A. YAKOVLEV and C. G. FOSSDAL
Norwegian Forest and Landscape Institute, PO Box 115, 1431, Ås, Norway
Epigenetic memory in Norway spruce permanently affect the timing of bud burst and bud set, vitally
important adaptive traits, in this long-lived forest species. MicroRNAs (miRNAs), a class of small noncoding
RNA molecules have recently drawn attention for their prominent role in development and
epigenetic regulations.
We prepared 18 small RNA libraries from embryogenic tissues of two individuals at three stages of
maturation grown up in vitro at three culturing temperatures (18, 23 and 28°C). Obtained libraries
were sequenced in duplicate on PGM (Ion Torrent) system and analyzed using CLC genomic
workbench.
In this study, we report the identification of more than 1600 novel and conserved miRNAs in Norway
spruce derived from 1050 precursors. Precursors could be transcribed from around 3400 miRNA
genes. We found high amount of isomiRs and high redundancy of putative miRNA genes in released
Norway spruce genome v1. Based on identified miRNAs we studied their expression patterns in
dependence on the temperature prevailing during SE growth and leading to establishing of
epigenetic marks. Distinct temperature dependent expression patterns were determined for most of
analyzed miRNAs. miRNAs are targeting the large amounts of spruce genes with a wide range of
functions, including genes involved in epigenetic regulation.
54

P45
Contrasting genomic signatures of local adaptation in lodgepole pine (Pinus
contorta) and interior spruce (Picea glauca x Picea engelmannii)
S. YEAMAN, K. A. HODGINS, K. LOTTERHOS, H. SUREN, T. WANG, P. SMETS, K. NURKOWSKI, J. A.
HOLLIDAY, L. H. RIESEBERG, M. C. WHITLOCK and S. N. AITKEN
Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall,
Vancouver, BC, V6T 1Z4, Canada
Understanding the genomic basis of local adaptation is a central question in evolutionary biology,
with important applications to forestry management. Common garden studies in both lodgepole
pine (Pinus contorta) and interior spruce (Picea glauca x Picea engelmannii) have shown
considerable local adaptation, yet the genomic basis of this adaptation is poorly understood. Here,
we use targeted resequencing of a large fraction of the exome to characterize the genomic basis of
adaptation in hundreds of individuals of each species, sampled along wide geographical and climatic
gradients. We use a combination of GWAS and environment association analyses to identify regions
of the genome with signatures that are strongly consistent with local adaptation. By examining
comparing these signatures among species for thousands of SNPs within 11,833 orthologous genes,
we explore the extent of parallelism and gene re-use in local adaptation.
55

Participants
Amselem, Joelle INRA joelle.amselem@versailles.inra.fr
Blumstein, Meghan Harvard University blumstein@fas.harvard.edu
Borevitz, Justin
The Australian National justin.borevitz@anu.edu.au
University
Brady, Siobhan
University of California, sbrady@ucdavis.edu
Davis
Buggs, Richard
Queen Mary University r.buggs@qmul.ac.uk
of London
Bullington, Lorinda MPG Operations LLC lbullington@mpgranch.com
Bultman, Hilary
University of Wisconsin, hlbultman@wisc.edu
Madison
Casola, Claudio Texas A&M University ccasola@tamu.edu
Chhatre, Vikram University of Vermont vchhatre@uvm.edu
Cole, Christopher
Cook, Bob
University of Minnesota,
Morris
colect@morris.umn.edu
4cooki4@gmail.com
Cooke, Janice University of Alberta janice.cooke@ualberta.ca
Crane, Peter Yale University peter.crane@yale.edu
Daguerre, Yohann INRA de Nancy yohann.daguerre@nancy.inra.fr
Dardick, Chris
USDA ARS Appalachian chris.dardick@ars.usda.gov
Fruit Research Station
Daru, Barnabas University of Pretoria darunabas@gmail.com
De La Torre, Amanda Umea Plant Science amandarodltc@gmail.com
Centre
Delph, Lynda Indiana University ldelph@indiana.edu
Demura, Taku
Nara Institute of Science demura@bs.naist.jp
and Technology
DiFazio, Stephen West Virginia University spdifazio@mail.wvu.edu
Diggle, Pamela University of Connecticut pamela.diggle@uconn.edu
Douglas, Carl
El-Kassaby, Yousry
University of British
Columbia
University of British
Columbia
carl.douglas@ubc.ca
y.el-kassaby@ubc.ca
56

Ensminger, Ingo University of Toronto ingo.ensminger@utoronto.ca
Euring, Dejuan Büsgen-Institut dning@gwdg.de
Fernando, Danilo State University of New fernando@esf.edu
York
Fetter, Karl University of Vermont kfetter@uvm.edu
Fitzek, Elisabeth The Morton Arboretum elisha.fitzek@gmail.com
Friedman, William Harvard University ned@oeb.harvard.edu
Gerttula, Suzanne USDA Forest Service 35sgerttula@gmail.com
Gonzalez-Ibeas, Daniel University of Connecticut gonzalez.ibeas@gmail.com
Groover, Andrew US Forest Service agroover@fs.fed.us
Guseman, Jessica USDA Jessica.Guseman@ars.usda.gov
Harada, Ko Ehime University kharada@agr.ehime-u.ac.jp
Henry, Isabelle
University of California, imhenry@ucdavis.edu
Davis
Hetherington, Alistair University of Bristol alistair.hetherington@bristol.ac.uk
Hollender, Courtney USDA Courtney.Hollender@ars.usda.gov
Isabel, Nathalie
Natural Resources nisabel@rncan-nrcan.gc.ca
Canada
Khodwekar, Sudhir Michigan Technological sdkhodwe@mtu.edu
University
Kidner, Catherine University of Edinburgh c.kidner@rbge.ac.uk
Kramer, Elena Harvard University ekramer@oeb.harvard.edu
Leslie, Andrew Brown University Andrew_Leslie@brown.edu
Lind, Brandon
Virginia Commonwealth lindb@vcu.edu
University
Lind-Riehl, Jennifer Michigan Technological jflind@mtu.edu
University
Lindroth, Richard University of Wisconsin, richard.lindroth@wisc.edu
Madison
Lindsey, Keith University of Durham keith.lindsey@durham.ac.uk
Lu, Meng-Zhu
MacLachlan, Ian
Chinese Academy of
Forestry
University of British
Columbia
lumz@caf.ac.cn
ian.maclachlan@forestry.ubc.ca
57

Menon, Mitra University of Virginia mm4kx@virginia.edu
Michotey, Celia INRA celia.michotey@versailles.inra.fr
Neale, David
University of California, dbneale@ucdavis.edu
Davis
Nieminen, Kaisa
Natural Resources kaisa.nieminen@helsinki.fi
Institute Finland
Pabon Mora, Natalia Universidad de Antioquia lucia.pabon@udea.edu.co
Parent, Geneviève Université Laval genevieve.parent.5@ulaval.ca
Paul, Robin University of Connecticut robin.paul@uconn.edu
Pinfield-Wells, Helen New Phytologist h.pinfield-wells@lancaster.ac.uk
Plett, Jonathan
University of Western j.plett@uws.edu.au
Sydney
Polle, Andrea University of Göttingen apolle@gwdg.de
Potter, Ben University of Auckland bmyl026@aucklanduni.ac.nz
Quintana Gonzalez, Julia Helsinki University julia.quintana@helsinki.fi
Reza, Md Salim Hossain Swedish University of salim.hossain.reza@slu.se
Agricultural Sciences
Romero-Severson, University of Notre Dame jromeros@nd.edu
Jeanne
Sahli, Atef Université Laval atef.sahli.1@ulaval.ca
Schiffthaler, Bastian Umeå Plant Science bastian.schiffthaler@umu.se
Center
Scott, Alison Dawn University of Wisconsin, adscott4@wisc.edu
Madison
Seguin, Armand
Natural Resources armand.seguin@nrcan.gc.ca
Canada
Sezen, Uzay University of Connecticut uzay@uga.edu
Sharma, Prabha University Of Delhi sharmaprabha3@gmail.com
Showalter, David The Ohio State University showalter.53@osu.edu
Strauss, Steven Oregon State University steve.strauss@oregonstate.edu
Street, Nathaniel Umeå University nathaniel.street@umu.se
Supple, Megan
The Australian National megan.supple@anu.edu.au
University
Trippe, Elizabeth University of Georgia elizabeth.trippe25@uga.edu
58

Uddenberg, Daniel Uppsala University daniel.uddenberg@ebc.uu.se
Wan, Tao
Fairylake Botanical wantao1983@gmail.com
Garden
Wegrzyn, Jill University of Connecticut jill.wegrzyn@uconn.edu
Yakovlev, Igor
Norwegian Forest and yai@skogoglandskap.no
Landscape Institute
Yeaman, Sam
University of British yeaman@zoology.ubc.ca
Columbia
Zinkgraf, Matthew USDA Forest Service mszinkgraf@fs.fed.us
59

HUNNEWELL
VISITOR CENTER
A RBORWAY
G ATE
Magnolias
Dawn
Redwoods
Tulip Trees
Lindens
L ARZ A NDERSON
B ONSAI C OLLECTION
Dana Greenhouses
(No Public Access)
Linden Path
L EVENTRITT
S HRUB & V INE
G ARDEN
Cork Trees
Meadow Road
Willow Path
Willows
Horsechestnuts
Maples
Arborway/Route 203
F OREST H ILLS
G ATE
Faulkner
Hospital
C ENTRE S TREET
G ATE
Centre Street
Hickories
Walnuts
Elms
Birches
Bussey Hill Road
Lilacs
B USSEY H ILL
Ashes
B RADLEY
R OSACEOUS
Faxon
Pond C OLLECTION
Rehder
Pond
Dawson
Pond
Cherries
Forest Hills Road
VFW Parkway
Weld Hill Research
& Administration Building
(No Public Access)
Centre Street
W ELD H ILL
Weld Street
Hebrew
Rehabilitation
Center
Walter Street
Conifer Path
Firs
Larches
Honey Locusts
Spruces
Conifer Path
W ALTER S TREET
G ATE
B USSEY S TREET
G ATE
P ETERS H ILL
G ATE
Pines
P ETERS H ILL
Hemlock Hill Road
Bussey Street
Valley Road
Peters Hill Road
Yews
Crabapples
Oaks
Oak Path
Junipers
Mountain Laurels
Pears
Azaleas
Chinese Path
Rhododendron Path
South Street
E XPLORERS
G ARDEN
Dove Tree
Stewartias
Beech Path
Rhododendrons
Beech Path
S OUTH S TREET
Beeches G ATE
H EMLOCK H ILL
P OPLAR
G ATE
South Street
Blackwell Footpath
B U S
N
S E Y
B R O O
K M E A
D O W
M AP K EY
Valley Road
W ASHINGTON
S TREET
G ATE
Walnuts
Oak Path
Oaks
Public Restrooms
Visitor Information
Washington Street
City Street (traffic)
Entrance Gate
Access Road (paved)
Plant Collection
Walking Path (unpaved)
Main Road (paved)
Forest Hills
MBTA Station
Orange Line
Peters Hill Road
Drinking Fountain
WALTER S TREET
B URYING G ROUND
M ENDUM S TREET
G ATE
Oaks
Hawthorns
Hunnewell Building Hours
April–October
Weekdays: 9:00am–5:00pm
Weekends: 10:00am–5:00pm
November–March
Weekdays: 9:00am–4:00pm
Weekends: noon–4:00pm
Visitor Center Hours
April–October, 10:00am–5:00pm
November–March, noon–4:00pm
Closed Wednesdays
Closed holidays
www.arboretum.harvard.edu
617-524-1718
mi.
mi. mi. mi.
.25 km. .50 km. .75 km.