You also want an ePaper? Increase the reach of your titles
YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.
16–17 June 2015<br />
Arnold Arboretum of Harvard University<br />
Boston, MA, USA<br />
Programme, <strong>abstract</strong>s and participants
35 th New Phytologist Symposium<br />
The genomes of forest trees: new<br />
frontiers of forest biology<br />
Arnold Arboretum of Harvard University, Boston, MA, USA<br />
16 – 17 June 2015<br />
Scientific Organizing Committee<br />
William Friedman (The Arnold Arboretum of Harvard University, Boston, USA)<br />
Andrew Groover (USDA Forest Service and University of California, Davis, USA)<br />
New Phytologist Organization<br />
Helen Pinfield-Wells (Deputy Managing Editor)<br />
Sarah Lennon (Managing Editor)<br />
Jill Brooke (Journal & Finance Administrator)<br />
Acknowledgements<br />
The 35 th New Phytologist Symposium is funded by the New Phytologist Trust<br />
New Phytologist Trust<br />
The New Phytologist Trust is a non-profit-making organization dedicated to the promotion<br />
of plant science, facilitating projects from symposia to open access for our Tansley reviews.<br />
Complete information is available at www.newphytologist.org<br />
Programme, <strong>abstract</strong>s and participant list compiled by Jill Brooke<br />
‘The genomes of forest trees: new frontiers of forest biology’ logo by A.P.P.S., Lancaster, UK<br />
Contact email: np-symposia@lancaster.ac.uk<br />
1
Table of Contents<br />
Information for Delegates .............................................................. 3<br />
Meeting Programme ...................................................................... 5<br />
Tour Groups ................................................................................... 8<br />
Discussion Session ....................................................................... 10<br />
Speaker Abstracts ........................................................................ 12<br />
Poster Abstracts ........................................................................... 28<br />
Participants.................................................................................. 56<br />
2
Information for Delegates<br />
Symposium location<br />
The <strong>35th</strong> New Phytologist Symposium will be held in the Weld Hill Research Building at The Arnold<br />
Arboretum of Harvard University in Boston.<br />
Please note that the Weld Hill Research Building is about a mile away from the main entrance to the<br />
Arboretum (Hunnewell Visitor Centre, off Arborway) so if you are travelling to the Arboretum by taxi<br />
you should ask to be taken to the Weld Hill Research Building, 1300 Centre Street, Boston, MA<br />
02131.<br />
Further directions and maps can be found on the Arboretum website:<br />
http://arboretum.harvard.edu/visit/weld-hill-directions/<br />
Map<br />
A map of the Arboretum is printed at the back of this <strong>book</strong>and can be viewed at<br />
http://arboretum.harvard.edu/wp-content/uploads/basic-map-b+w.pdf<br />
Catering<br />
Coffee breaks and lunch will be served in the lobby area just outside the lecture hall<br />
The conference dinner will be served in the lobby area just outside the lecture hall<br />
Accommodation<br />
If you are staying at the Holiday Inn in Dedham we have organised transportation on the 16 th and<br />
17 th June.<br />
Each day the bus will depart at from the Holiday Inn at 8:00. On the 16 th June it will return to the<br />
Holiday Inn at 20:00 and on the 17 th June it will return at 22:00.<br />
Posters<br />
Posters should be prepared so that they are no larger than A0 size, portrait orientation (118 cm high<br />
x 84 cm wide). Posters should be put up during registration (8:30–9:30 on 16 th June) and will be<br />
displayed for the duration of the meeting. There will be two dedicated poster sessions at 18:15–<br />
19:45 on Tuesday and 18:30–20:00 on Wednesday. Beer, wine and soft drinks will be served during<br />
the poster sessions. Please stand by your poster at these sessions – there will be prizes for the best<br />
poster presentations.<br />
Weld Hill tour<br />
On Tuesday afternoon there will be a short tour of the Weld Hill Building and the research resources<br />
which are available. Tour guides will lead groups of 20 people around and answer questions. Please<br />
see the back of your name badge for your Weld Hill tour group allocation.<br />
Arboretum tour<br />
On Wednesday morning please meet at Weld Hill Research Building and there will be a tour of the<br />
Arboretum. Tour guides will lead groups of 25–30 people around. Note that the tour will involve<br />
walking 1-2 miles on paved and unpaved paths. Please see the back of your name badge for your<br />
Arboretum tour group allocation.<br />
3
Discussion session<br />
More information can be found about this on page 10. Please also refer to the back of your name<br />
badge for your Discussion group allocation.<br />
Internet access<br />
Free wifi will be provided throughout the venue. The network is ArbPublic and the password is:<br />
@rbor3tum!<br />
Social media<br />
We encourage all attendees to join in discussions on social media sites. Follow @NewPhyt on Twitter<br />
and fb.com/NewPhytologist on Face<strong>book</strong> for updates before, during and after the meeting. Please<br />
use #35<strong>NPS</strong> in all of your tweets.<br />
Contact<br />
For further information, and in case of any emergencies, please contact Helen Pinfield-Wells. Email:<br />
h.pinfield-wells@lancaster.ac.uk, np-symposia@lancaster.ac.uk; tel: +44 7966 966 450 389.<br />
4
Meeting Programme<br />
Tuesday 16 th June<br />
08:30–09:30 Registration<br />
09:30–09:45 Welcome, Introductions and Information<br />
Session 1: Genome-enabled insights into forest biology, populations and adaptive traits<br />
Chair: Ned Friedman<br />
09:45–10:15 S1-1 David Neale<br />
Comparative genomics of conifers<br />
10:15–10:45 S1-2 Carl Douglas<br />
Microevolution in Populus trichocarpa driven by introgression<br />
10:45–11:15 Break<br />
11:15–11:45 S1-3 Nathalie Isabel<br />
Journey into the genome of white spruce: achievements, lessons and<br />
challenges for the future<br />
11:45–12:00 Selected poster <strong>abstract</strong> talk 1 – Ian MacLachlan P25<br />
12:00–12:15 Selected poster <strong>abstract</strong> talk 2 – Megan Supple P41<br />
12:15–12:45 S1-4 Steve DiFazio<br />
Comparative and ecological genomics in the Salicaceae<br />
12:45–13:45 Lunch<br />
Session 2: Evolution<br />
Chair: Andrew Groover<br />
13:45–14:15 S2-1 William Friedman<br />
The origins of big: homoplasious evolution of vascular cambia and<br />
arborescence<br />
14:15–14:45 S2-2 Catherine Kidner<br />
Drivers of diversity in tropical forest trees<br />
14:45–15:00 Selected poster <strong>abstract</strong> talk 3 – Amanda De La Torre P11<br />
15:00–15:15 Selected poster <strong>abstract</strong> talk 4 – Alison Dawn Scott P37<br />
15:15–16:15 Break and tour of Weld Hill Research Resources including<br />
refreshment break<br />
16:15–16:45 S2-3 Nathaniel Street<br />
Comparative genomics of the quaking aspens Populus tremula and P.<br />
tremuloides<br />
5
16:45–17:00 Selected poster <strong>abstract</strong> talk 5 – Meng-Zhu Lu P24<br />
17.00–17:15 Selected poster <strong>abstract</strong> talk 6 – Elizabeth Trippe P42<br />
17:15–18:15 Keynote lecture Peter Crane<br />
Ginkgo: An evolutionary and cultural biography<br />
18:15–19:45 Poster session with wine and cheese<br />
Wednesday 17th June<br />
09:00–11:00 Tour of the Arnold Arboretum, including a refreshment break<br />
Session 3: Molecular and computational approaches<br />
Chair: Carl Douglas<br />
11:00–11:30 S3-1 Kaisa Nieminen<br />
Silver birch (Betula pendula): a novel model for forest tree genetics<br />
11:30–12:00 S3-2 Taku Demura<br />
Transcriptional switches controlling wood cell fates<br />
12:00–12:15 Selected poster <strong>abstract</strong> talk 7 – Richard Buggs P2<br />
12:15–12:30 Selected poster <strong>abstract</strong> talk 8 – Karl Fetter P16<br />
12:30–13:30 Lunch<br />
13:30–14:00 S3-3 Siobhan Brady<br />
Regulation of xylem cell specification and secondary cell wall synthesis in<br />
Arabidopsis thaliana<br />
14:00–14:30 S3-4 Matthew Zinkgraf<br />
Transcriptional networks regulating tension wood formation in Populus<br />
14:30–15:00 Break<br />
Session 4: Comparative, functional and ecological genomics<br />
Chair: Catherine Kidner<br />
15:00–15:30 S4-1 Jonathan Plett<br />
Ectomycorrhizal fungi are playing JAZs during symbiosis formation in<br />
Populus<br />
15:30–16:00 S4-2 Jill Wegrzyn<br />
Computational tools and resources for comparative tree genomics<br />
16:00–16:30 Break and group photo<br />
16:30–17:00 S4-3 Isabelle Henry<br />
6
The how and Y of sex determination in persimmon<br />
17:00–18:30 Discussion session led by Steve Strauss<br />
See page 10 for more details<br />
18:30–20:00 Poster session<br />
20:00 Symposium Barbeque<br />
7
Tour Groups<br />
Tuesday (15:15–16:15)<br />
Tour of Weld Hill Research Resources at the Arboretum<br />
Group 1 Group 2 Group 3 Group 4<br />
Joelle Amselem Lynda Delph Catherine Kidner Julia Quintana Gonzalez<br />
Meghan Blumstein Steve DiFazio Elena Kramer Salim Hossain Reza<br />
Justin Borevitz Pamela Diggle Andrew Leslie Jeanne Romero-Severson<br />
Siobhan Brady Carl Douglas Brandon Lind Atef Sahli<br />
Richard Buggs Yousry El-Kassaby Jennifer Lind-Riehl Bastian Schiffthaler<br />
Lorinda Bullington Ingo Ensminger Rick Lindroth Alison Dawn Scott<br />
Hilary Bultman Dejuan Euring Keith Lindsey Armand Seguin<br />
Claudio Casola Danilo Fernando Meng-Zhu Lu Uzay Sezen<br />
Vikram Chhatre Karl C. Fetter Ian MacLachlan Prabha Sharma<br />
Chris Cole Elisabeth Fitzek Mitra Menon David Showalter<br />
Bob Cook Ned Friedman Celia Michotey Steve Strauss<br />
Janice Cooke Suzanne Gerttula David Neale Nathaniel Street<br />
Peter Crane Daniel Gonzalez-Ibeas Kaisa Nieminen Megan Supple<br />
Yohann Daguerre Jessica Guseman Natalia Pabon-Mora Elizabeth Trippe<br />
Chris Dardick Ko Harada Geneviève Parent Daniel Uddenberg<br />
Barnabas Daru Isabelle Henry Robin Paul Tao Wan<br />
Amanda De La Torre Alistair Hetherington Helen Pinfield-Wells Jill Wegrzyn<br />
Taku Demura Courtney Hollender Jonathan Plett Igor Yakovlev<br />
Andrew Groover Nathalie Isabel Andrea Polle Sam Yeaman<br />
Sudhir Khodwekar Ben Potter Matthew Zinkgraf<br />
8
Tour Groups<br />
Wednesday (9:00–11:00)<br />
Tour of the Arnold Arboretum<br />
Group 1 Group 2 Group 3<br />
Joelle Amselem Danilo Fernando Geneviève Parent<br />
Meghan Blumstein Karl C. Fetter Robin Paul<br />
Justin Borevitz Elisabeth Fitzek Helen Pinfield-Wells<br />
Siobhan Brady Suzanne Gerttula Jonathan Plett<br />
Richard Buggs Daniel Gonzalez-Ibeas Andrea Polle<br />
Lorinda Bullington Andrew Groover Ben Potter<br />
Hilary Bultman Jessica Guseman Julia Quintana Gonzalez<br />
Claudio Casola Ko Harada Salim Hossain Reza<br />
Vikram Chhatre Isabelle Henry Jeanne Romero-Severson<br />
Chris Cole Alistair Hetherington Atef Sahli<br />
Bob Cook Courtney Hollender Bastian Schiffthaler<br />
Janice Cooke Nathalie Isabel Alison Dawn Scott<br />
Peter Crane Sudhir Khodwekar Armand Seguin<br />
Yohann Daguerre Catherine Kidner Uzay Sezen<br />
Chris Dardick Elena Kramer Prabha Sharma<br />
Barnabas Daru Andrew Leslie David Showalter<br />
Amanda De La Torre Brandon Lind Steve Strauss<br />
Lynda Delph Jennifer Lind-Riehl Nathaniel Street<br />
Taku Demura Rick Lindroth Megan Supple<br />
Steve DiFazio Keith Lindsey Elizabeth Trippe<br />
Pamela Diggle Meng-Zhu Lu Daniel Uddenberg<br />
Carl Douglas Ian MacLachlan Tao Wan<br />
Yousry El-Kassaby Mitra Menon Jill Wegrzyn<br />
Ingo Ensminger Celia Michotey Igor Yakovlev<br />
Dejuan Euring David Neale Sam Yeaman<br />
Ned Friedman Kaisa Nieminen Matthew Zinkgraf<br />
Natalia Pabon-Mora<br />
9
Wednesday<br />
Discussion Session<br />
Discussion Session<br />
STEVE STRAUSS 17:00–18.30<br />
steve.strauss@oregonstate.edu<br />
Steve will lead a period of discussion (1 hr 30 mins). There will be 7 groups (10–12 people per group)<br />
each considering one of the below questions for 30–45 mins. Each group is assigned a chair and a<br />
scribe so notes can be taken for reporting back to the symposium. Your discussion group is printed on<br />
the back of your name badge and also below.<br />
Groups will be called back to the main meeting room, and each group chair will give a brief report of its<br />
main findings.<br />
D1<br />
D2<br />
D3<br />
D4<br />
D5<br />
D6<br />
D7<br />
Discussion Groups*<br />
What are the big questions in tree genomics, and how far have<br />
we come toward answering them?<br />
What were the specific, key findings/conclusions from this<br />
conference, and why?<br />
What will be the key findings and impacts, and the most<br />
surprising findings, from this area of work in the next 5–10 years?<br />
What have been the societal impacts of tree genomics with<br />
respect to conservation, breeding, biotechnology, and<br />
management, if any? Are any essential/game changing vs.<br />
incremental? What is needed to increase impact?<br />
What is the state of the field re: human resources (e.g.,<br />
development of scientific careers, intellectual capital, education,<br />
outreach, help for struggling scientists and economies and<br />
human/ethnic diversity)?<br />
How can we better collaborate, communicate with funding<br />
agencies, and increase our competitiveness?<br />
What research is needed to better understand genome microand<br />
macro-evolution? What species (angiosperm, gymnosperm<br />
or other) should be prioritized for sequencing to provide better<br />
phylogenetic coverage and interpretations of tree genomes?<br />
Discussion Chair<br />
Carl Douglas<br />
Nathalie Isabel<br />
Jill Wegrzyn<br />
Steve DiFazio<br />
Andrew Groover<br />
Siobhan Brady<br />
Catherine Kidner<br />
10
D1 D2 D3 D4 D5 D6 D7<br />
Chair Carl Douglas Janice Cooke Jill Wegrzyn Steve DiFazio Andrew Groover Siobhan Brady Catherine Kidner<br />
Scribe Alison Dawn Scott Geneviève Brandon Lind Megan Supple Elizabeth Trippe Amanda De La Torre Ben Potter<br />
Parent<br />
Peter Crane Taku Demura Ned Friedman Isabelle Henry Kaisa Nieminen Jonathan Plett Nathaniel Street<br />
Helen Pinfield- Matthew Zinkgraf Lynda Delph Alistair Hetherington Elena Kramer Keith Lindsey Andrea Polle<br />
Wells<br />
Meghan Blumstein Lorinda<br />
Hilary Bultman Karl C. Fetter Sudhir Khodwekar<br />
Ian MacLachlan<br />
Bullington<br />
Jennifer Lind-Riehl<br />
Mitra Menon Salim Hossain Atef Sahli Bastian Schiffthaler David Showalter Celia Michotey Uzay Sezen<br />
Reza<br />
Joelle Amselem Chris Cole Barnabas Daru Danilo Fernando Ko Harada Natalia Pabon-Mora Prabha Sharma<br />
Justin Borevitz Bob Cook Pamela Diggle Elisabeth Fitzek Courtney<br />
Hollender<br />
Robin Paul<br />
Daniel<br />
Uddenberg<br />
Richard Buggs Nathalie Isabel Yousry El- Suzanne Gerttula Andrew Leslie Julia Quintana Gonzalez Tao Wan<br />
Kassaby<br />
Claudio Casola Yohann Daguerre Ingo Ensminger Daniel Gonzalez-Ibeas Rick Lindroth Jeanne Romero-Severson Igor Yakovlev<br />
Vikram Chhatre Chris Dardick Dejuan Euring Jessica Guseman Meng-Zhu Lu Armand Seguin Sam Yeaman<br />
11
Speaker Abstracts<br />
* S=speaker <strong>abstract</strong>; P=poster <strong>abstract</strong><br />
Brady , Siobhan S3.3<br />
Crane, Peter<br />
Keynote Lecture<br />
Demura, Taku S3.2<br />
DiFazio, Stephen S1.4<br />
Douglas, Carl S1.2<br />
Friedman, William S2.1<br />
Groover, Andrew<br />
S3.4, P18<br />
Henry, Isabelle S4.3<br />
Isabel, Nathalie<br />
S1.3, P35<br />
Kidner, Catherine S2.2<br />
Neale, David<br />
S1.1, S4.2, P19, P22, P30<br />
Nieminen, Kaisa S3.1<br />
Plett, Jonathan<br />
Strauss, Steven<br />
Street, Nathaniel<br />
Wegrzyn, Jill<br />
Zinkgraf, Matthew<br />
S4.1, P9<br />
Discussion Session Leader<br />
S2.3, P34, P36<br />
S4.2, P19, P30<br />
S3.4, P18<br />
12
Speaker Abstracts<br />
Session 1: Genome-enabled insights into forest biology,<br />
populations and adaptive traits<br />
Chair: Ned Friedman<br />
Comparative genomics of conifers<br />
S1.1<br />
DAVID NEALE 9:45–10:15<br />
dbneale@ucdavis.edu<br />
Department of Plant Sciences, University of California, Davis, One Shields<br />
Ave, Davis, CA 95616, USA<br />
Conifers are an ancient and highly diverse group of seed plants. Much can be learned about the<br />
evolution of form and function in conifers by comparative genome analysis. The logical starting<br />
point for the development of ‘omics’ resources and comparative ‘omics’ analyses is the reference<br />
genome sequence. In conifers, however, reference genome sequences were not obtainable until<br />
only recently due to their very large genomes sizes (10 to nearly 40 Gb.). Next generation<br />
sequencing technology and advanced assembly algorithms have made it possible to develop the first<br />
generation reference genome sequences for a small number of conifers. Now that approaches to<br />
generating reference genomes have been established, there will be rapid development of reference<br />
sequences for many of the 400+ conifers and thus enabling powerful and informative comparative<br />
genome analysis. In this presentation, I will describe the development of the first few conifer<br />
reference genomes and the preliminary comparative ‘omic’ analyses done to date.<br />
13
Microevolution in Populus trichocarpa driven by<br />
introgression<br />
S1.2<br />
CARL J. DOUGLAS 1 , ADRIANA SUAREZ-GONZALES 1 , 10:15–10:45<br />
CAMILLE CHRISTE 2 , ARMANDO GERALDES 1 , CHARLES<br />
HEFER 1 , ATHENA D. MCKOWN 3 , SUBINOY BISWAS 4 ,<br />
JUERGEN EHLTING 4 , ROBERT D. GUY 3 , SHAWN D.<br />
MANSFIELD 5 , CHRISTIAN LEXER 2 and QUENTIN C.B.<br />
CRONK 1<br />
carl.douglas@ubc.ca<br />
1 Department of Botany, University of British Columbia, Vancouver, BC,<br />
Canada; 2 Unit of Ecology & Evolution, Department of Biology, University<br />
of Fribourg, Fribourg, Switzerland; 3 Department of Forest and<br />
Conservation Sciences, University of British Columbia, Vancouver, BC,<br />
Canada 4 Department of Biology, University of Victoria, Victoria, BC<br />
Canada; 5 Department of Wood Science, University of British Columbia,<br />
Vancouver, BC, Canada<br />
Introgression between closely related species can provide allelic variation underlying adaptation.<br />
Populus trichocarpa and P. balsamifera are attractive sister species to study the effects of natural<br />
hybridization on local adaptation in forest trees, since they diverged recently, are adapted to<br />
contrasting environments in western and northern North America, and hybridize in contact zones.<br />
Using genome-wide scans of population differentiation, based on extensive SNP genotype data from<br />
collections of P. trichocarpa and P. balsamifera individuals, we showed that introgression from P.<br />
balsamifera plays a role in shaping the landscape genomics of P. trichocarpa in northern and eastern<br />
parts of its range and identified 396 candidate genes for local adaptation in P. trichocarpa. On<br />
chromosomes 6 and 15, two genomic regions showed strong patterns of population structure and<br />
association with latitude and a number of environmental variables. Several genes involved in light<br />
signaling, secondary metabolism and transcriptional control (e.g., FAR1, FHY3, PRR5, COMT1, TTG1,<br />
ANAC062) in these regions had SNPs associated with adaptive traits. In order to further address the<br />
role of introgression from P. balsamifera in the microevolution of P. trichocarpa, we selected 25<br />
pure P. trichocarpa, 25 pure P. balsamifera, and 68 admixed individuals, and used whole genome<br />
resequencing data to carry out ancestry analysis. This revealed that the candidate region for local<br />
adaptation on chromosome 15 introgressed from P. balsamifera into P. trichocarpa, and that these<br />
balsamifera alleles are restricted to interior and northern populations of P. trichocarpa. We<br />
implemented genomic and gene ontology enrichment tests to test for signals of selection and<br />
overrepresented biological themes, respectively. To determine if introgressed alleles are functionally<br />
different from P. trichocarpa alleles, we analyzed gene expression levels, and compared phenotypes<br />
of admixed vs. pure P. trichocarpa individuals. Our results support the hypothesis that the<br />
introgression of functionally distinct alleles from P. balsamifera contributes to local adaptation in P.<br />
trichocarpa.<br />
14
Journey into the genome of white spruce:<br />
achievements, lessons and challenges for the future<br />
S1.3<br />
NATHALIE ISABEL 1,2 , JANICE COOKE 3 , NATHALIE PAVY 2 , 11:15–11:45<br />
BETTY PELGAS 1,2 , BENJAMIN HORNOY 2 , JULIEN<br />
PRUNIER 2 , JEAN BEAULIEU 1,2 , ARMAND SÉGUIN 1,2 ,<br />
KERMIT RITLAND 4 , INANC BIROL 5 , JOERG BOHLMANN 6 ,<br />
JOHN MACKAY 2,7 and JEAN BOUSQUET 2<br />
nisabel@rncan-nrcan.gc.ca<br />
1 Natural Resources Canada, Canadian Forest Service, Québec, QC, Canada;<br />
2 Department of Wood and Forest Sciences, Université Laval, Québec, QC,<br />
Canada; 3 Department of Biological Sciences, University of Alberta,<br />
Edmonton, AB, Canada; 4 Department of Forest Sciences, University of<br />
British Columbia, Vancouver, BC, Canada; 5 Michael Smith Genome<br />
Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada; 6 Michael<br />
Smith Laboratories, University of British Columbia, Vancouver, BC,<br />
Canada; 7 Department of Plant Sciences, University of Oxford, Oxford, UK<br />
Conifer forests are dominant across Canada, yield most of the wood used by the industry, and<br />
provide numerous ecosystem services. Spruces account for sixty percent of the 650 million tree<br />
seedlings planted each year. Changing environments, pressure to conserve forest lands, and demand<br />
for sustainable forest management call for new approaches to increase forest productivity.<br />
Reforestation conducted using seeds with superior growth, wood attributes and adaptability could<br />
be part of the solution but it relies on the development of fast-track tree breeding and high<br />
performance trees.<br />
For more than forty years, tree improvement programs have resulted in tangible productivity gains,<br />
but breeding cycles are long and gains per cycle modest. Around the new millennium, genomic<br />
science was seen as a means of developing tools to characterize and help preserve the natural<br />
genetic diversity of trees, and more rapidly develop new varieties for reforestation. This vision has<br />
become particularly compelling in the context of environmental change and for the adoption of<br />
better sustainable forest management practices.<br />
Over the last decade, extensive genomic resources for white spruce have been developed by two<br />
Genome Canada’s projects, Arborea and Treenomix. More recently, their complementary expertise<br />
were brought together into a unified project, SMarTForests, to break new ground in spruce genome<br />
sequencing, and to achieve efficient translation of results toward end-users from across Canada. The<br />
SMarTForests’ goals were to develop tools to enhance forest health and productivity and to increase<br />
the value recovered from forest plantations.<br />
Accordingly, major achievements have been obtained. The white spruce giga-genome has been<br />
sequenced, a gene map allowing interspecific and inter-generic comparisons has been constructed,<br />
gene catalogue and large registries of high-quality SNPs for population genomics applications have<br />
been set up, functional genomics studies have highlighted processes and networks of genes involved<br />
in pest resistance, adaptation and wood formation, genomic selection models for wood properties<br />
are being transferred to end-users, etc. However, we must be prepared to face new challenges and<br />
new frontiers in this post-genomic era. Like for other conifers, the sheer size and diversity of the<br />
spruce genome still represent significant challenges to further comprehend the mechanisms<br />
underlying observed phenotypes in the forests. Also, given the environmental changes already<br />
affecting boreal forests, genomics and its affiliated ‘omics’ sciences will certainly be key to proposing<br />
valuable adaptation measures in an uncertain future.<br />
15
Comparative and ecological genomics in the<br />
Salicaceae<br />
S1.4<br />
STEPHEN P. DIFAZIO 1 , LUKE M. EVANS 1 , WELLINGTON 12:15–12:45<br />
MUCHERO 2 , ELI RODGERS-MELNICK 3 , ALEJANDRO<br />
RIVEROS-WALKER 1 , GANCHO T. SLAVOV 4 and GERALD A.<br />
TUSKAN 2<br />
spdifazio@mail.wvu.edu<br />
1 Department of Biology, West Virginia University, Morgantown, West<br />
Virginia, USA; 2 Plant Systems Biology Group, BioSciences Division, Oak<br />
Ridge National Laboratory, Oak Ridge, Tennessee, USA; 3 Plant Biology<br />
Department, Cornell University, Ithaca, NY USA; 4 Institute of Biological,<br />
Environmental and Rural Sciences, Aberystwyth University, Aberystwyth,<br />
UK<br />
Broadly-distributed and ecologically dominant forest trees provide excellent model systems for<br />
studying fundamental questions about the molecular bases of adaptive variation and the nature of<br />
species boundaries. In particular, population resequencing has provided an integrated view of major<br />
demographic events that have shaped standing neutral genetic variation, including population<br />
bottlenecks and rapid range expansions following glacial maxima. Furthermore, departures from this<br />
neutral backdrop provide characteristic signatures of natural selection. We have used whole genome<br />
sequencing in Populus trees to investigate patterns of nucleotide variation across a broad geographic<br />
area. In addition to the expected patterns of clinal latitudinal variation, the unprecedented<br />
resolution afforded by whole genome sequencing has revealed subtle details about glacial refugia,<br />
patterns of postglacial range expansion, and signatures of past gene flow and introgression.<br />
Furthermore, comparative analysis across species has demonstrated differences in genome content<br />
and organization that may have driven adaptive differentiation of species, and possible mechanisms<br />
for the establishment and maintenance of species boundaries in sympatry. We have found that<br />
there are gene content differences between species that are likely driven by differential loss and<br />
retention of duplicated genes. Furthermore, the presence of polymorphic insertion/deletion<br />
polymorphism in the population indicates that genome fraction is an ongoing process involved in the<br />
continued differentiation of species. Increasingly accessible genomics approaches have already<br />
caused radical shifts in approaches to studying adaptive variation in tree populations, and the<br />
resulting insights will accelerate the domestication of these recalcitrant organisms and enhance our<br />
ability to predict and possibly mitigate the effects of climate change.<br />
16
Session 2: Evolution<br />
Chair: Andrew Groover<br />
The origins of big: homoplasious evolution of<br />
vascular cambia and arborescence<br />
S2.1<br />
WILLIAM E. FRIEDMAN 13:45–14:15<br />
ned@oeb.harvard.edu<br />
Department of Organismic and Evolutionary Biology, Arnold Arboretum,<br />
Harvard University<br />
The presence of a vascular cambium can be traced to at least 407 million years ago, in plants just<br />
slightly larger than their primary-body-only close relatives. The evolution of true arborescence and<br />
forested ecosystems would wait another 20 million years, when a group of fern-like plants<br />
(cladoxylopsids, now extinct) appear to have gained in height and circumference the key features of<br />
trees. Over the course of an additional roughly 25 million years, a vascular cambium arose<br />
independently among members of an additional four major lineages: progymnosperms,<br />
heterospourous lycophytes, horsetails, and sphenophytes. Despite the multiple origins of a vascular<br />
cambium and arborescence, and the dominance of these linages in ancient forests, only the vascular<br />
cambium of the progymnosperms has persisted through time to the present, as expressed in seed<br />
plants. All other ancient clades that produced a vascular cambium have since gone extinct (with but<br />
one minor exception). The striking homoplasy of vascular cambia in (at least) six distinct clades of<br />
vascular plants over the course of a geological ‘blink of an eye’ suggests that there may have been<br />
compelling adaptive reasons for the evolutionary innovation of plants with larger bodies, although<br />
interestingly, developmental aspects of cambial behavior clearly differ between these different<br />
lineages. Regrettably, the question of whether the independent origins of cambia during the<br />
Paleozoic in different lineages of vascular plants relied upon similar or dissimilar underlying genetic<br />
‘toolkits’ may never be answered; an answer is precluded by the inconvenient fact of extinction.<br />
17
Drivers of diversity in tropical forest trees<br />
S2.2<br />
CATHERINE KIDNER 2, 3 , JAMES NICHOLLS 3 , MARIA-JOSE 14:15–14:45<br />
ENDARA 1 , GRAHAM STONE 3 , PHYLLIS COLEY 1 , THOMAS<br />
KURSAR 1 and TOBY PENNINGTON 2<br />
c.kidner@rbge.ac.uk<br />
1 Royal Botanic Garden Edinburgh, UK; 2 University of Edinburgh, UK;<br />
3 University of Utah, USA<br />
The greatest diversity of tree species is found in tropical rain forests. It is notable that this diversity is<br />
found even at very local levels. For example, within a 50 ha plot on Barro Colorado Island in Panama<br />
303 tree species are found, including 16 species of a single genus – Inga. Inga species are found in<br />
high abundance across all neotropical rain forests. It is a genus of 300 legume tree species which<br />
radiated during the last 6 million years. We are investigating the role of herbivores in generating this<br />
species diversity and maintaining species coexistence in local communities. We have developed a<br />
hybrid capture protocol to resolve phylogenetic structure in the face of low sequence divergence<br />
shown in widely used phylogenetic markers. Our new phylogeny allows us to analyse evolutionary<br />
patterns in chemical diversity, herbivore load and gene expression as well as biogeographic patterns.<br />
Results support the hypothesis that a key factor in Inga diversity is herbivore pressure leading to<br />
divergence in secondary chemistry produced by variation in expression of biosynthetic enzymes.<br />
18
Comparative genomics of the quaking aspens<br />
Populus tremula and P. tremuloides<br />
S2.3<br />
YAO-CHENG LIN 1 , NICOLAS DELHOMME 2 , JING WANG 3 , 16:15–16:45<br />
BASTIAN SCHIFFTHALER 2 , MANFRED GRABHERR 4 , NEDA<br />
ZAMANI 4 , MARC P HÖPNNER 4 , CHANAKA<br />
MANNAPPERUMA 2 , NIKLAS MÄHLER 5 , DAVID SUNDELL 2 ,<br />
YVES VAN DE PEER 1,6 , TORGEIR R HVIDSTEN 5 , STEFAN<br />
JANSSON 2, PÄR K INGVARSSON 3 and NATHANIEL R<br />
STREET 1<br />
nathaniel.street@umu.se<br />
1 Department of Plant Systems Biology (VIB) and Department of Plant<br />
Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium;<br />
2 Umeå Plant Science Centre, Department of Plant Physiology, Umeå<br />
University, SE-907 81, Umeå, Sweden; 3 Umeå Plant Science Centre,<br />
Department of Ecology and Environmental Science, Umeå University, SE-<br />
901-97, Umeå, Sweden; 4 Department of Medical Biochemistry and<br />
Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;<br />
5 Department of Chemistry, Biotechnology and Food Science, Norwegian<br />
University of Life Sciences, 1432 Ås, Norway; 6 Genomics Research<br />
Institute, University of Pretoria, Hatfield Campus, 0028 Pretoria, South<br />
Africa<br />
European and North American aspens, Populus tremula and P. tremuloides, are keystone species in<br />
addition to being extensively used as model systems for forest tree research. To date, genomics<br />
analyses in these species required use of the P. trichocarpa reference genome sequence. However,<br />
this is often limiting due to poor sequence alignment rates. Given these limitations, we undertook<br />
sequencing and assembly of the two aspen genomes in addition to re-sequencing 24 P. tremula and<br />
22 P. tremuloides individuals and we are extending our sequencing to additional aspen species.<br />
Analysis of kmer content and alignment of sequence reads to the P. trichocarpa reference revealed<br />
rapid divergence of intergenic regions compared to the reference P. trichocarpa genome assembly in<br />
addition to high rates of heterozygosity. We subsequently produced next generation sequencing<br />
based de novo genome assemblies that were ab initio annotated. This resource allowed comparative<br />
analysis to the reference assembly as well as among aspen species. To complement these analyses,<br />
extensive RNA-Seq based transcript sequencing efforts were performed and used in combination<br />
with large-scale transcriptomics studies at the Umeå Plant Science Centre. Whole genome alignment<br />
and population level genotype data were used to identify regions of the aspen genome that have<br />
rapidly diverged from the reference P. trichocarpa genome as well as to identify novel, aspen<br />
specific features. We have focused on annotating and comparing both the protein coding and noncoding<br />
gene space.<br />
Assembling the aspen genome proved challenging as a result of extensive heterozygosity, driven by a<br />
combination of both SNPs and INDELs, leading to frequent haplotype splitting. However, the gene<br />
space is comprehensively represented, facilitating many comparative genomics analyses.<br />
The developed resources have been integrated within the PlantGenIE.org web platform to allow the<br />
wider community to benefit from and contribute to this genome project.<br />
19
Ginkgo: An evolutionary and cultural biography<br />
Keynote<br />
PETER CRANE 17:15–18:15<br />
peter.crane@yale.edu<br />
School of Forestry and Environmental Studies, Yale University, 195<br />
Prospect Street, New Haven, CT 06511, USA<br />
Perhaps the world’s most distinctive tree, Ginkgo is a botanical oddity that has remained little<br />
changed for more than two hundred million years. Once regarded as a conifer, Ginkgo was first<br />
recognized as distinct in plant classifications of the early nineteenth century, a conclusion underlined<br />
subsequent by the remarkable discovery in Ginkgo (and also in cycads) of motile sperm cells. Despite<br />
its long geologic record and former widespread distribution, Ginkgo barely survived the Pleistocene<br />
Ice Ages and today the only remaining putatively wild populations exist as relics in China.<br />
Nevertheless, Ginkgo began its remarkable contemporary renewal and resurgence when people first<br />
found it useful as a nut tree about a thousand years ago. Today Ginkgo is revered for its longevity,<br />
beloved for the elegance of its leaves, valued as medicinal herb, and widely cultivated as one of the<br />
world’s most popular street trees. It is also a source of artistic and religious inspiration. Scientifically<br />
Ginkgo is the most widely known of all botanical ‘living fossils’ and the last survivor of a lineage that<br />
was once much more diverse. Ginkgo may provide our best window into the genetics of the diverse<br />
ancient seed plants that flourished between about 200 and 100 million years ago, but became<br />
extinct during the later Mesozoic.<br />
20
Session 3: Molecular and computational approaches<br />
Chair: Carl Douglas<br />
Silver birch (Betula pendula): a novel model for<br />
forest tree genetics<br />
S3.1<br />
KAISA NIEMINEN 11:00–11:30<br />
kaisa.nieminen@helsinki.fi<br />
Natural Resources Institute Finland (Luke), Green Technology,<br />
Jokiniemenkuja 1, FI-01301 Vantaa, Finland<br />
The aim of our research is to understand molecular mechanisms controlling tree development. We<br />
will explore natural variation in forest trees to identify novel genetic regulators of cambial activity,<br />
wood formation and tree architecture. Our model is an important forestry tree, silver birch, whose<br />
small diploid genome is being sequenced. This tree is monoecious, and already young seedlings can<br />
be induced to flower. Birch brings the power of inbreeding and short generation times into tree<br />
genetics, enabling exploitation of advanced crossing schemes for genetic analyses. With birch as our<br />
model, our project represents a novel approach in tree genetics with potential for ground-breaking<br />
insights into tree development. Besides its fascinating basic science aspect (what makes a tree a<br />
tree?), this knowledge has immense applied value for forest tree breeding. Detailed knowledge<br />
about the regulatory mechanisms controlling tree traits will provide us tools for the domestication of<br />
forest trees. As wood represents a renewable source of lignocellulosic biomass, with potential for<br />
conversion into timber, pulp, fuels, energy, and value-added chemicals, boosting its efficient<br />
production in commercial forests is essential for sustainable management of natural resources.<br />
21
Transcriptional switches controlling wood cell fates<br />
S3.2<br />
MISATO OHTANI 1,2 , BO XU 2 , MASATOSHI YAMAGUCHI 3 , 11:30–12.00<br />
MINORU KUBO 2 , TAKU DEMURA 1,2<br />
demura@bs.naist.jp<br />
1 Graduate School of Biological Sciences, Nara Institute of Science and<br />
Technology, Ikoma, Nara, Japan; 2 RIKEN Center for Sustainable Resource<br />
Science, Yokohama, Kanagawa, Japan; 3 Institute for Environmental<br />
Science and Technology, Saitama University, Saitama, Japan; 4 Center for<br />
Frontier Science and Technology, Nara Institute of Science and<br />
Technology, Ikoma, Nara, Japan<br />
Wood has long been used for natural materials including pulp, timber, and wood products. Recently,<br />
in addition, wood is also expected to be utilized as a sustainable and carbon-neutral resource for<br />
bioenergy. Therefore, it is important to understand the process of wood formation for improving the<br />
quality and quantity of wood and wood product. Hard wood contains two major cell types, fiber and<br />
vessel, which have similar but distinct developmental processes. Recent considerable effort has<br />
identified the regulatory genes for the differentiation of each cell type. Using Arabidopsis, we<br />
showed that VASCULAR-RELATED NAC-DOMAIN6 (AtVND6) and AtVND7 are the transcriptional<br />
switches for metaxylem and protoxylem vessels, respectively: overexpression of AtVND6 and<br />
AtVND7 can induce the transdifferentiation of various types of cells into metaxylem and protoxylem<br />
vessels, respectively, not only in Arabidopsis but also heterologously in poplar. Further researches<br />
revealed that two genes (AtNST1 and AtNST3/SND1) belonging to the same gene family of AtVND6<br />
and AtVND7 are the key regulators of fiber differentiation in Arabidopsis. Based on the phylogenetic<br />
analysis, we also showed that 16 poplar genes (PtVNS1 to PtVNS16, of which 12 genes also called<br />
PtrWND1A to PtrWND6B) were homologous to the VND and NST/SND genes. Moreover, the<br />
functional analysis of these genes suggested that wood formation in poplar is regulated by the<br />
cooperative functions of the PtVNS/PtrWND genes.<br />
These transcriptional switches seem to be conserved in evolutionary history. We recently revealed<br />
that the differentiation of water-conducting and supporting cells in moss Physcomitrella patens,<br />
hydroid and stereid cells, respectively, is regulated by genes (PpVNS1 to PpVNS8) homologous to the<br />
VND/NST/SND genes. Concomitant loss of function of PpVNS1, 6, and 7 failed to form normal<br />
hydroid and stereid cells, suggesting conservation of the transcriptional between Arabidopsis and<br />
moss.<br />
22
Regulation of xylem cell specification and<br />
secondary cell wall synthesis in Arabidopsis<br />
thaliana<br />
MALLORIE TAYLOR-TEEPLES, MIGUEL DE LUCAS, GINA<br />
TURCO, ALLISON GAUDINIER, TED TOAL and SIOBHAN<br />
M. BRADY<br />
S3.3<br />
13:30–14.00<br />
sbrady@ucdavis.edu<br />
Plant Biology, University of California-Davis, Davis, CA 95616, USA;<br />
Arabidopsis root development provides a remarkably tractable system to delineate cell type-specific,<br />
developmental gene regulatory networks and to study their functionality in a complex multicellular<br />
model system over developmental time. We have mapped gene regulatory networks guiding two<br />
aspects of vascular cell type development, specifically xylem cell specification and differentiation<br />
and vascular proliferation. Together, these networks identify novel regulators of vascular<br />
development and provide considerable insight into the combinatorial nature of root development at<br />
cell type and temporal stage-resolution.<br />
23
Transcriptional networks regulating tension wood<br />
formation in Populus<br />
S3.4<br />
MATTHEW ZINKGRAF 1,2,4 , ANDREW GROOVER 2 , 14:00–14.30<br />
SUZANNE GERTTULA 2 , SHAWN D. MANSFIELD 3 and<br />
VLADIMIR FILKOV 4<br />
mszinkgraf@fs.fed.us<br />
1 Postdoctoral Research Fellow in Biology, National Science Foundation;<br />
2 Pacific Southwest Research Station, Forest Service, Davis CA USA;<br />
3 Department of Wood Science, University of British Columbia, Vancouver<br />
BC Canada; 4 Computer Science Department, University of California –<br />
Davis, Davis CA USA<br />
Angiosperm trees respond to gravitational and mechanical stresses by producing tension wood,<br />
which generates the tensile force necessary to reorient and reinforce woody stems. In this talk, we<br />
present results from Populus tension wood experiments that integrate data from genome-wide gene<br />
expression and transcription factor binding experiments with physiological and biochemical data.<br />
Treatments included perturbation of ARBORKNOX2 expression and treatment with gibberellic acid.<br />
Modules of genes were defined based on co-expression patterns across wood types, genotypes, and<br />
gibberellic acid treatments. Modules were then tested for correlations with wood types, genotypes,<br />
GA treatment, and various measures of wood chemistry attributes. Modules were identified that<br />
have significant correlations with phenotypes, and enrichment for ARK2 binding. Modules were also<br />
characterized by GO analysis, and modules were further annotated based on enrichment with key<br />
processes that contribute to cambium function, secondary cell wall biosynthesis and hormone<br />
regulation. We further show how these gene modules can be further dissected to identify candidate<br />
regulatory genes responsible for control of specific traits. Together, these results present an<br />
integrated view of the key changes in gene expression and transcription factor binding that influence<br />
tension wood development and generation of the forces underlying the reorientation of woody<br />
stems, and provide results and methods that can be applied for complex trait dissection in trees.<br />
24
Session 4: Comparative, functional and ecological genomics<br />
Chair: Catherine Kidner<br />
Ectomycorrhizal fungi are playing JAZs during<br />
symbiosis formation<br />
S4.1<br />
JONATHAN M PLETT 1,2 , YOHANN DAGUERRE 1 , IAN C 15:00–15.30<br />
ANDERSON 2 , CLAIRE VENEAULT-FOURREY 3 and FRANCIS<br />
MARTIN 1<br />
j.plett@uws.edu.au<br />
1 Labex ARBRE, Tree-Microbe Interactions’ department, INRA-Nancy,<br />
Champenoux, France; 2 Hawkesbury Institute for the Environment,<br />
University of Western Sydney, Richmond, NSW, Australia; 3 University of<br />
Lorraine, Nancy, 54000, France<br />
In forest ecosystems, ectomycorrhizal (ECM) fungi constitute a significant proportion of soil<br />
microbial biomass where they form symbioses with tree roots, providing growth limiting nutrients<br />
such as nitrogen and phosphorus to the tree in return for up to 20-30% of photosyntheticallyderived<br />
carbon from their hosts. While colonization of roots by ECM fungi is a very invasive process<br />
reminiscent of when pathogens take over plant tissues, in-growth of ECM fungal hyphae into roots is<br />
typically characterized by a relatively low defense response on the part of the tree host. Our ongoing<br />
research is beginning to uncover how the ECM fungus is able to avoid immune detection by<br />
the plant: through the use of small secreted effector proteins. I will focus on our current<br />
understanding of how one of these proteins, MiSSP7 encoded by the ECM fungus Laccaria bicolor,<br />
enters poplar tree root cells and interacts with JAZ proteins – the co-receptors to the plant defense<br />
hormone jasmonic acid (JA). Interaction between MiSSP7 and the JAZ proteins is essential for L.<br />
bicolor colonisation of poplar roots and leads to a repression of one part of the JA signaling pathway.<br />
I will cover our most recent findings concerning the role of JAZ proteins in poplar cellular biology as<br />
well as our preliminary work characterizing the role of these proteins during the interaction between<br />
Eucalyptus grandis and its ECM symbiont Pisolithus microcarpus.<br />
25
Computational tools and resources for comparative<br />
tree genomics<br />
S4.2<br />
JILL WEGRZYN 1,2 , EMILY GRAU 3 , HANS VASQUEZ- 15:30–16.00<br />
GROSS 3 , TAEIN LEE 4, JODI HUMANN 4 , STEPHEN FICKLIN 4 ,<br />
MARGARET STATON 5 , NATHAN HENRY 5 , DOREEN MAIN 4<br />
and DAVID NEALE 3<br />
jill.wegrzyn@uconn.edu<br />
1 Department of Ecology and Evolutionary Biology, University of<br />
Connecticut, Storrs, CT, USA; 2 Institute for Systems Genomics, University of<br />
Connecticut, Storrs, CT, USA; 3 Department of Plant Sciences, University of<br />
California at Davis, Davis, CA, USA; 4 Department of Horticulture,<br />
Washington State University, Pullman, WA, USA; 5 Department of<br />
Entomology and Plant Pathology, University of Tennessee, TN, USA<br />
Full genome sequences are being generated for the first time for several conifer and hardwood<br />
species. The recent influx of genomic resources from previously underserved tree species presents a<br />
wealth of information and scientific opportunities to the research community. Recipients of this data<br />
are often faced with navigating the complex landscape of online resources with conflicting genome<br />
versions, incomplete annotations, and various levels of resolution. As is often the case with early<br />
genome sequences and genomic sets that pre-date a full genome, the optimal data source and<br />
associated metadata are difficult to obtain. This problem is magnified by the size of genomic<br />
datasets which produce additional barriers once the user brings this information to a desktop<br />
machine for analysis. In addition to genomic data, we are increasingly interested in associating<br />
phenotypic and environmental metrics to geo-referenced trees. These datasets provide additional<br />
computational challenges and reside in repositories even more diverse than those holding genomic<br />
artefacts.<br />
Here, we will describe two clade organism databases – TreeGenes<br />
(http://dendrome.ucdavis.edu/treegenes) and the Hardwood Genomics Web<br />
(http://www.hardwoodgenomics.org/). Aside from direct access to curated genomic resources, we<br />
present two tools – GenSAS and CartograTree. GenSAS is a genome visualization tool that supports<br />
moderate to large genome assemblies and guides researchers through the process of repeat<br />
identification, gene prediction, structural annotation, and comparative genomics. CartograTree is an<br />
interactive workspace that allows for geographical visualization and engagement of high<br />
performance computing (HPC) resources. CartograTree merges genomic, phenotypic, and<br />
environmental data to facilitate association studies in a variety of forest trees.<br />
26
The how and Y of sex determination in<br />
persimmon<br />
S4.3<br />
ISABELLE M. HENRY 1 , TAKASHI AKAGI 2 , RYUTARO TAO 2<br />
and LUCA COMAI 1 16:30–17.00<br />
imhenry@ucdavis.edu<br />
1<br />
Department of Plant Biology and Genome Center, University of California<br />
Davis, Davis, USA; 2 Laboratory of Pomology, Graduate School of<br />
Agriculture, Kyoto University, Kyoto, Japan<br />
In approximately five percent of plant species, male and female flowers grow on separate trees. This<br />
sexual system, called dioecy, is often associated with sex chromosomes. Dioecy has evolved multiple<br />
times independently in different plant taxa, but the molecular mechanisms underlying sex<br />
determination remain poorly understood. We have tackled these questions in diploid Caucasian<br />
persimmon (Diospyros lotus). Using a combination of genomic and transcriptome sequencing, as well<br />
as evolutionary analyses, we were able to identify a potential master regulator of sex in this species,<br />
that we called OGI. Analyses of the genomic context surrounding OGI are consistent with those of Y-<br />
sequences from other species. Further small RNA and sequence analyses suggest that OGI produces<br />
small RNA that repress a homologous autosomal gene called MeGI. Heterologous transgenic<br />
experiments in Arabidopsis and Nicotiana confirmed the repressive role of OGI on MeGI and the<br />
feminizing role of MeGI, with transgenic plants exhibiting dosage-dependent phenotypes consistent<br />
with a repression of androecium development. Phenotypic comparison between the transgenic<br />
plants and male and female persimmon flowers provide clues about the potential mechanisms<br />
underlying sex-specific flower development in diploid persimmon. Further analyses suggest that<br />
MeGI promoter methylation, possibly triggered by the action of OGI smRNAs, might also play a role<br />
in MeGI regulation. A model summarizing our current understanding of the mechanisms underlying<br />
sex determination in diploid persimmon will be presented. The implications of this model to sex<br />
determination in hexaploid persimmon, in which trees either bear only female flowers or both male<br />
and female flowers, will be discussed as well.<br />
27
Amselem, Joelle<br />
Buggs, Richard<br />
Bullington, Lorinda<br />
Bultman, Hilary<br />
Casola, Claudio<br />
Chhatre, Vikram<br />
Cole, Christopher<br />
Cooke, Janice<br />
Daguerre, Yohann<br />
Daru, Barnabas<br />
De La Torre, Amanda<br />
El-Kassaby, Yousry<br />
Ensminger, Ingo<br />
Euring, Dejuan<br />
Fernando, Danilo<br />
Fetter, Karl<br />
Fitzek, Elisabeth<br />
Gerttula, Suzanne<br />
Gonzalez-Ibeas, Daniel<br />
Harada, Ko<br />
Khodwekar, Sudhir<br />
Lind, Brandon<br />
Lind-Riehl, Jennifer<br />
Lu, Meng-Zhu<br />
MacLachlan, Ian<br />
Menon, Mitra<br />
Michotey, Celia<br />
Pabon Mora, Natalia<br />
Parent, Geneviève<br />
Paul, Robin<br />
Polle, Andrea<br />
Potter, Ben<br />
Quintana Gonzalez, Julia<br />
Reza, Md Salim Hossain<br />
Sahli, Atef<br />
Schiffthaler, Bastian<br />
Scott, Alison Dawn<br />
Seguin, Armand<br />
Sharma, Prabha<br />
Showalter, David<br />
Supple, Megan<br />
28<br />
Poster Abstracts<br />
* P=poster <strong>abstract</strong>. Bold=presenting author<br />
P1<br />
P2<br />
P3<br />
P4<br />
P5<br />
P6, P16<br />
P7<br />
S1.3, P8<br />
S4.1, P9<br />
P10<br />
P11<br />
P12<br />
P13<br />
P14<br />
P15<br />
P16<br />
P17<br />
S3.4, P18<br />
P19, P30<br />
P20<br />
P21<br />
P22<br />
P23<br />
P24<br />
P25<br />
P26<br />
P1, P27<br />
P28<br />
P29<br />
P30<br />
P14, P31<br />
P32<br />
P33<br />
P34<br />
P35<br />
S2.3, P36<br />
P37<br />
S1.3, P38<br />
P39<br />
P40<br />
P41
Trippe, Elizabeth<br />
Uddenberg, Daniel<br />
Yakovlev, Igor<br />
Yeaman, Sam<br />
P42<br />
P43<br />
P44<br />
P45<br />
29
Poster Abstracts<br />
Poster <strong>abstract</strong>s are ordered alphabetically by presenting author (underlined).<br />
P1<br />
Oak genome sequencing project: genomic data and bioinformatic resources<br />
to study oak tree adaptation<br />
J. AMSELEM 1 , J.M. AURY 2 , N. FRANCILLONNE 1 , T. ALAEITABAR 1 , C. DA SILVA 2 , S. DUPLESSIS 3 ,<br />
F. EHRENMANN 4 , C. KLOPP 5 , K. LABADIE 2 , T. LEROY 4 , I. LESUR 4 , T. LETELLIER 1 , I. LUYTEN 1 ,<br />
C. MICHOTEY 1 , C. BODENES 4 , G. Le PROVOST 4 , F. MURAT 7 , P. FAIVRE RAMPANT 6 , A. KREMER 4 , F.<br />
MARTIN 3 , J. SALSE 7 , H. QUESNEVILLE 1 and C. PLOMION 4<br />
1 INRA, UR1164, URGI, Unité de Recherche Génomique Info, route de Saint-Cyr – RD 10, 78026<br />
Versailles, France; 2 CEA, Institut de Génomique (IG), Genoscope, 2 rue Gaston Crémieux, 91057 Evry,<br />
France; 3 INRA-Université́ de Lorraine, UMR1136, Interactions Arbres/Micro-organismes, 54280<br />
Champenoux, France; 4 INRA, UMR1202, BIOGECO, 69 route d’Arcachon, 33610 Cestas, France; 5 INRA,<br />
MIAT, Plateforme bioinformatique Toulouse Midi-Pyrénées, 24 chemin de Borde-Rouge, 31326<br />
Auzeville Castanet-Tolosan, France; 6 INRA, URGV, Plant Genomics Research, 2 rue Gaston Crémieux,<br />
91057 Evry, France; 7 INRA/UBP UMR1095, Laboratoire Génétique, Diversité́ et Ecophysiologie des<br />
Céréales, Site de Crouël 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France<br />
The large, complex and highly heterozygous genome of pedunculate oak (Quercus robur) was<br />
sequenced using a whole-genome shotgun approach. Roche 454 GS-FLX sequence reads were<br />
assembled into contigs and combined with Illumina reads from paired-end and mate-pair libraries to<br />
build a total of 17,910 scaffolds (> 2 kb; 1.34 Gb total size; N50=260 kb). Half of the genome was<br />
aligned to a high-density linkage map.<br />
We will present the results of the structural (Transposable Elements (TEs), genes) and functional<br />
annotations of automatically predicted genes. These data were obtained using robust pipelines (i)<br />
REPET to de novo detect, classify and annotate TEs (ii) Eugene to integrate ab initio and similarity<br />
gene finding softwares (iii) A functional annotation pipeline, based on Interproscan to search for<br />
patterns/motifs and Blast based comparative genomics. We also set up a dedicated integrated<br />
genome annotation system based on GMOD based web interfaces (WebApollo/JBrowse and<br />
Intermine) to make these data available under a user-friendly environment. This system allows<br />
experts of different gene families to curate/validate automatically predicted genes. All together<br />
these resources provide a framework to study the two key evolutionary processes that explain the<br />
remarkable diversity found within the Quercus genus: local adaptation and speciation.<br />
30
P2<br />
Genome sequencing of Fraxinus species to identify loci relevant to ash<br />
dieback and emerald ash borer<br />
E. SOLLARS 1,2 , L. J. KELLY 1 , B. CLAVIJO 3 , D. SWARBRECK 3 , J. ZOHREN 1 , D. BOSHIER 4 , J. CLARK 5 , S.<br />
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.<br />
JOECKER 2 , S. AYLING 3 , M. CACCAMO 3 and R. J. A. BUGGS 1<br />
1 School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road,<br />
London, E1 4NS, UK; 2 Qiagen Aarhus, Silkeborgvej 2, Prismet, 8000 Aarhus C., Denmark; 3 The<br />
Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK; 4 Department of Plant<br />
Sciences, University of Oxford, Oxford, OX1 3RB, UK; 5 The Earth Trust, Little Wittenham, Abingdon,<br />
Oxfordshire, OX14 4QZ, UK; 6 Forest Research, Northern Research Station, Roslin, Midlothian, EH25<br />
9SY, UK; 7 U.S.D.A. Forest Service, Northern Research Station, Delaware, OH 43015, USA; 8 Department<br />
of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802,<br />
USA; 9 Department of Geosciences and Natural Resource Management, University of Copenhagen,<br />
Rolighedsvej 23, 1958 Frederiksberg C, Denmark<br />
Fraxinus (ash) species are highly threatened by emerald ash borer (EAB) in North America and ash<br />
dieback (ADB) in Europe. Their future may depend on genomically assisted breeding for low<br />
susceptibility to these threats. We have produced a de novo reference genome from a lowheterozygosity<br />
British F. excelsior (European ash) tree (N50 = 99Kbp, Total length = 875Mbp; see<br />
www.ashgenome.org), and sequenced 38 further trees from this species across Europe, including a<br />
Danish tree with low susceptibility to ADB, which we are comparing. We are now sequencing the<br />
genomes of 35 other Fraxinus species from around the world. Genome size in Fraxinus varies from<br />
750Mbp to 4Gbp (1C-values), encompassing diploid, tetraploid and hexaploid taxa. Preliminary<br />
evidence suggests that Asiatic Fraxinus species have low susceptibility to EAB and ADB, which we are<br />
testing with genus-wide experimental EAB inoculation experiments in Ohio, and genus-wide field<br />
exposure to ADB in Britain. We aim to find loci relevant to low susceptibility to ADB and EAB by<br />
detecting genes in the genus Fraxinus that have phylogenies incongruent with the typical genus<br />
phylogeny, but congruent with patterns of low susceptibility among species. If successful, this<br />
method will be applicable to other tree pest/pathogen interactions.<br />
31
P3<br />
Using direct amplification and next-generation sequencing technology to<br />
explore foliar endophyte communities in experimentally inoculated western<br />
white pines<br />
L. S. BULLINGTON 1 and B. G. LARKIN 1<br />
1 MPG Operations, LLC, 1001 S Higgins Suite A3, Missoula, MT 59801, USA<br />
Fungal endophytes can influence survivability and disease severity of trees. Here we characterized<br />
the endophyte community in Pinus monticola (western white pine), an important species in the<br />
northwest USA, largely decimated by pathogenic fungi. We also assessed the ability to successfully<br />
inoculate seedlings with desirable endophytes, with the long-term goal of providing a protective<br />
microbiome and added defense from pathogens. We inoculated P. monticola seedlings in the field<br />
with potential pathogen antagonists and fungi isolated from healthy mature trees. Following<br />
inoculations we used direct amplification and next generation sequencing to characterize fungal<br />
endophyte communities, and explore interspecific competition, diversity, and co-occurrence<br />
patterns in needle tissues. Negative co-occurrence patterns between inoculated fungi and potential<br />
pathogens, as well as many other species, indicate early competitive interactions. Our results<br />
support the role of competitive interactions in early endophyte community assemblage and show<br />
that inoculations influence endophyte community development and tree health.<br />
P4<br />
Linking Populus genes to ecologically important traits and associated insect<br />
communities<br />
H. BULTMAN 1, 2 , L. HOLESKI 3 , P. INGVARSSON 4 and R. L. LINDROTH 1, 2<br />
1 ,2 Departments of Zoology and Entomology, University of Wisconsin-Madison, 1630 Linden Drive,<br />
Madison, WI 53706, USA; 3 Department of Biological Sciences, Northern Arizona University, 617 S.<br />
Beaver St., Flagstaff, AZ 86011, USA; 4 Department of Ecology and Environmental Sciences, Umeå<br />
University, Linnaeus väg 6, Umeå, SE-901 87, Sweden<br />
Community genetics aims to link intraspecific genetic variation in one organism to the diversity and<br />
composition of communities of interacting organisms. Populus genetics shape the community of<br />
insects that colonize the trees, although the particular genes involved have not been identified. To<br />
address this void, we have established a genetic mapping population (‘WisAsp’) of 515 aspen<br />
(Populus tremuloides) replicated genotypes to identify the genes associated with tree traits that<br />
influence communities of associated insects. Thus far, we have found substantial genotypic variation<br />
in both tree traits (e.g., growth, phytochemistry and phenology) and insect communities (e.g.,<br />
species richness) that colonize the trees. We have also found that insect communities vary across<br />
aspen genotypes at a nearby garden with a subset of nine genotypes from WisAsp (PerMANOVA F =<br />
2.02, P < 0.002). Phytochemical levels helped explain the variation in insect communities, indicating<br />
that tree traits can serve to shape insect communities. In the future we will use genome-wide<br />
association mapping to identify Populus genes underlying tree traits and insect communities. This<br />
work will advance community genetics by linking plant genes to tree traits that effect variation in<br />
dependent insect communities.<br />
32
P5<br />
An ancient trans-kingdom horizontal transfer of Penelope-like retroelements<br />
from insects to conifers<br />
X. LIN 1 , N. FARIDI 1, 2 , C. CASOLA 1<br />
1 Department of Ecosystem Science and Management, Texas A&M University, College Station, TX<br />
77843, USA; 2 USDA Forest Service Southern Research Station, Saucier, MS 77843, USA<br />
Penelope-like elements, or PLEs, represent a class of retroelements represented by two main types:<br />
EN(+)PLEs, which encode the unique combination of a reverse transcriptase (RT) domain and a GIY-<br />
YIG endonuclease (EN) domain; and EN(-)PLEs, encoding only a RT domain. While members of the<br />
second type occur in a variety of eukaryotes, EN(+)PLEs have thus far been detected only in animal<br />
genomes. In this work, we have investigated the evolutionary history of conifers EN(+)PLEs, which<br />
we have named Dryads, recently discovered in loblolly pine. In phylogenies of PLE sequences,<br />
Dryads form a monophyletic group placed within a major animal EN(+)PLE lineage. Furthermore,<br />
Dryads are closely related to a clade of EN(+)PLEs primarily found in insects. Bioinformatics surveys<br />
revealed no EN(+)PLEs in 625 fully sequenced non-metazoan and non-conifer genomes from twelve<br />
major eukaryotic lineages. Additionally, PCR assays indicate that Dryads are absent in non-conifer<br />
gymnosperms, including Ginkgo biloba and several cycads and gnetales. These findings indicate that<br />
Dryads emerged following an ancient horizontal transfer of Penelope-like elements from an insect<br />
group to a common ancestor of conifers in the late Paleozoic, and suggest that retroelements<br />
horizontal transfers might have played an important role in the expansion of the very large conifers<br />
genomes.<br />
P6<br />
Detecting local selection in spatially heterogeneous environments: clues from<br />
simulations and empirical data from a widespread boreal tree, Populus<br />
balsamifera<br />
V. E. CHHATRE 1 , M. C. FITZPATRICK 2 and S. R. KELLER 1<br />
1 Dept. of Plant Biology, University of Vermont, Burlington, VT 05405, USA; 2 Appalachian Laboratory,<br />
University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA<br />
Most widely distributed tree species inhabiting spatially heterogeneous environments experience<br />
varying strengths and types of ecological selection, often giving rise to strong local adaptation.<br />
Frequentist and Bayesian approaches to detect genomic responses to selection along environmental<br />
gradients typically assume linear responses, even though empirical allele frequencies often vary nonlinearly<br />
along environmental gradients. Here, we compare the power of several existing methods in<br />
SNP-environment association analysis (BayeScEnv, Bayenv2 and LFMM), as well as two more recent<br />
biodiversity modelling techniques – Generalized Dissimilarity Modeling (GDM) and Gradient Forests<br />
(GF), at detecting non-linear selection in population genomic datasets. We tested these methods<br />
using two approaches. First, we used spatially explicit simulations of 1000 loci in 30 populations<br />
arrayed in a linear stepping stone model with varying amounts of migration. Selection was applied to<br />
one locus in the form of differential mortality increasing either linearly or non-linearly along the<br />
gradient, and both false positive and false negative rates were calculated across replicate<br />
simulations of each scenario. Second, we compared the performance of the different methods on an<br />
empirical SNP data set from the widely distributed tree Populus balsamifera, consisting of ~1100<br />
trees from 90 populations genotyped at 297 candidate SNPs from the flowering time network<br />
controlling adaptive phenology.<br />
33
P7<br />
Distributed control constrains evolution of a major growth/defense pathway<br />
in Aspens<br />
C. T. COLE 1 , V. H. GUO DECKER 2 , B. R. ALBRECTSEN 2,3 and P. INGVARSSON 2<br />
1 Division of Science & Mathematics, University of Minnesota, Morris, MN 56267, USA; 2 Plant Science<br />
Center, Umeå University, 6 Linnaeus Vag, Umeå, 90187, Sweden; 3 University of Copenhagen,<br />
Thorvaldsenvej 40, DK 1871 Frederiksberg C, Denmark<br />
Aspens and their relatives (Populus spp.) are classical foundation species for major biomes across the<br />
northern hemisphere. Trade-offs between aspen growth and defense, as well as interactions with<br />
fungi, insects, mammals, and birds, are strongly influenced by products of the phenylpropanoid<br />
pathway (PPP), which produces lignin as well as condensed tannins (CTs) and salicinoids. In Populus,<br />
the PPP is a pleiotropic, highly branching pathway of enzymes from multi-gene families.<br />
We investigated whether regulation of the PPP is focused on a single step or distributed throughout<br />
the pathway, and assessed how that pattern of control has affected the pattern of selection on the<br />
pathway.<br />
Both intrinsic (genotype) and extrinsic (nutrient) factors altered expression levels of 8 enzyme genes<br />
throughout the CT pathway, rather than at a single control point; this ‘distributed control’ was<br />
evident as highly correlated expression levels throughout the pathway. Comparing the sequences<br />
for 10 PPP enzymes (25 genes from 12 individuals) with P. trichocarpa showed that selection<br />
constrains divergence of genes throughout the pathway, acting most strongly on upstream genes.<br />
This signature of negative selection appeared despite the presence of multiple genes in most<br />
families.<br />
P8<br />
Could host species and environmental factors affect mountain pine beetle<br />
dynamics?<br />
J. E. K. COOKE 1 , A. ARANGO-VELEZ 1 , C. I. CULLINGHAM 1 , E. MAHON 1 , M. MEENTS 1 , B. J. COOKE 2<br />
and D. W. COLTMAN 1<br />
1 University of Alberta, Department of Biological Sciences, Edmonton, AB, T6G 2E9, Canada; 2 Natural<br />
Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, AB, T6H 3S5,<br />
Canada<br />
The current outbreak of mountain pine beetle (MPB) in western North America has impacted more<br />
than 28 million hectares of pine forests. Lodgepole pine is the primary species that has been<br />
impacted. In recent years, MPB has undergone range expansion from central British Columbia<br />
across northern Alberta, where lodgepole pine hybridizes with a new host, jack pine. We used<br />
population genetics to refine this hybrid zone, and demonstrate that population structures of<br />
lodgepole and jack pine are influenced by introgression. We are testing the hypotheses that<br />
lodgepole and jack pine exhibit differing responses to MPB and pathogenic fungal associates such as<br />
Grosmannia clavigera, and that water limitation compromises these responses. G. clavigerainduced<br />
lesion development was slower in jack pine than lodgepole pine, and lesion development in<br />
both species was delayed by water deficit. Microarray analyses identified thousands of pine genes<br />
responding to G. clavigera infection. There are substantial differences in lodgepole and jack pine<br />
transcriptomic responses to G. clavigera, and water limitation alters these transcriptomic responses.<br />
Some differentially expressed genes also showed signatures of selection in population genomic<br />
analyses. Collaborations with modellers are enabling us to connect insights from these genomic<br />
analyses to models of MPB population dynamics.<br />
34
P9<br />
PtJAZ5 and PtJAZ5 complexes in Populus trichocarpa and their roles in the<br />
ectomycorrhizal development<br />
Y. DAGUERRE, S. WITTULSKY, J. PLETT, R. SCHELLENBERGER, A. VAYSSIERES, A. KOHLER, C.<br />
VENEAULT-FOURREY and F. MARTIN<br />
Labex ARBRE, Tree-Microbe Interactions’ Department, INRA-Nancy, 54280 Champenoux, France<br />
Roots of most trees form symbiosis with mutualistic soil-borne fungi. The crosstalk between the two<br />
partners is fundamental for the establishment and maintenance of beneficial relationships.<br />
However, little is known about how symbiosis is initiated. We showed that the ectomycorrhizal<br />
basidiomycete Laccaria bicolor relies on Mycorrhizal-induced Small Secreted Proteins (MiSSP) to<br />
establish the interaction. In particular MiSSP7 interacts with the jasmonic acid (JA) co-receptors<br />
PtJAZ5 and PtJAZ6 of P. trichocarpa, blocking JA signaling and promoting mutualism. JAZ proteins are<br />
known to interact with NINJA and TOPLESS proteins as well as bHLH transcriptional factor in<br />
Arabidopsis leaves. Using Y2H and BiFC assays, we aim identifying the proteins interacting with<br />
PtJAZ6 and PtJAZ5 in P. trichocarpa roots. First results show that PtJAZ5 and PtJAZ6 form homo- and<br />
heterodimers and interact with at last one bHLH transcriptional factor. Next step will be the<br />
identification of genes targeted by this transcription factor, using ChipSeq assay in order to fully<br />
understand mechanism underlying ectomycorrhizal ontogenesis.<br />
P10<br />
A molecular phylogenetic analysis of tree diversity hotspots in southern<br />
Africa<br />
B. H. DARU, M. VAN DER BANK and T. J. DAVIES<br />
Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa<br />
Biodiversity hotspots have important roles in conservation prioritisation, but efficient methods for<br />
selecting among them remain debated. In this study, we assembled the most comprehensive dated<br />
molecular phylogeny for the southern Africa’s tree flora along with their geographical distribution to<br />
map and contrast regional hotspots of species richness and phylogenetic diversity. In addition, we<br />
evaluated the efficiency of hotspots in capturing complementary areas of species richness and<br />
phylogenetic diversity. We then explored the environmental factors influencing the distribution of<br />
these diversity metrics in southern Africa. We showed that the different hotspots did not overlap,<br />
but captured different conservation currencies. Areas selected using complementarity are even<br />
more dispersed, but capture rare diversity that is overlooked by the hotspot approach. An<br />
integrative approach that considers multiple facets of biodiversity is needed if we are to maximise<br />
the conservation of tree diversity in southern Africa.<br />
35
P11<br />
Gene expression and natural selection shape the evolution of protein-coding<br />
genes in Picea<br />
A. R. DE LA TORRE 1, 2 , Y-C. LIN 3 , .Y. VAN DE PEER 3, 4 and P. INGVARSSON 1, 2<br />
1 Department of Ecology and Environmental Science, Umeå University, Linneaus väg 6, SE-901 87<br />
Umeå, Sweden; 2 Umeå Plant Science Centre, Umeå, Sweden; 3 Department of Plant Systems Biology,<br />
VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark<br />
927, 9052 Ghent, Belgium; 4 Genomics Research Institute, University of Pretoria, Hatfield Campus,<br />
Pretoria 0028, South Africa<br />
The role of natural selection on the evolution of gene expression levels remains largely unknown in<br />
non-model species. In this study, we use the first two fully sequenced representatives of the<br />
gymnosperm plant clade (Picea abies and Picea glauca) to test for the evidence of expressionmediated<br />
selection. We used whole-genome gene expression data (>50,000 genes) to study the<br />
relationship between gene expression, codon bias, rates of sequence divergence, protein length,<br />
pathway position and gene duplication. We found that gene expression correlates with rates of<br />
sequence divergence and codon bias for translational efficiency. A strong correlation between gene<br />
expression and gene duplication was found, with genes in large multi-copy gene families having, on<br />
average, a lower expression level and breadth, lower codon bias, and higher rates of sequence<br />
divergence than single-copy gene families. A correlation between pathway position and gene<br />
duplication was also found. Single-copy genes encoded essential biological functions and were under<br />
strong selective pressures to maintain their copy number in Picea. In contrast, large paralogous gene<br />
families had great expression divergence and higher levels of tissue-specific genes. Our study<br />
highlights the importance of gene expression and natural selection in shaping the evolution of<br />
protein-coding genes in Picea species.<br />
P12<br />
Forest tree improvement: the shift from quantitative genetics to quantitative<br />
genomics<br />
Y. A. EL-KASSABY and J. KLÁPŠTĚ<br />
Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British<br />
Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada<br />
Traditional and Next Generation Sequencing technologies increased the availability of sequence data<br />
for model and non-model forest tree species. This in turn transformed quantitative genetics from<br />
the pedigree-based founded on the utilization of Sewell Wright’s coefficient of relationship between<br />
individuals (Wright S. 1922; Amr Nat 56:330-338) to a genomic-based realized kinship method for<br />
estimating individuals’ breeding values and traits’ heritability and genetic correlation. This<br />
substantial shift literally changed quantitative genetics to quantitative genomics and led to the<br />
development of innovative methods such as the pedigree-free and the unified single-step (a<br />
combination of pedigree and genomic realized kinship) evaluation approaches where the classical<br />
Best Linear Unbiased Predictor (BLUP) is replaced by the Genomic Best Linear Unbiased Predictor<br />
(GBLUP). The advantages of quantitative genomics offered opportunities for obtaining more precise<br />
genetic parameters, better partition of the genetic variance, and even breeding without structured<br />
pedigree. Examples from unstructured black cottonwood and white spruce open-pollinated<br />
populations will be presented to demonstrate the unsurpassed potential of incorporating sequence<br />
data in classical breeding.<br />
36
P13<br />
A catalogue of putative unique transcripts reveals tissue specific<br />
transcriptome responses during the winter-spring transition in Eastern white<br />
pine (Pinus strobus)<br />
I. ENSMINGER and C. RASHEED-DEPARDIEU<br />
Department of Biology, University of Toronto Mississauga, Mississauga Road, Mississauga, ON L5L<br />
1C6, Canada<br />
In the present study we report a catalog of putative unique transcripts enriched for genes associated<br />
with freezing tolerance from Eastern white pine (EWP), a conifer native to Northern America. EWP<br />
seedlings were exposed to a simulated transition from winter to spring and summer in controlled<br />
environments in order to generate a catalogue of unique transcripts representing the EWP<br />
transcriptome during various seasons and in different tissues. 44 libraries were generated including<br />
needle, bud, stem and root tissues of pine seedlings. 1,118,287,330 raw reads were obtained using<br />
the Illumina HiSeq 2000 sequencing platform. The EWP transcriptome was sequentially assembled<br />
using a de-Bruijn graph and overlap-layout-consensus assemblers. This de novo assembly generated<br />
a set of 339,371 putative unique transcripts. Functional characterization of transcripts included<br />
BLAST searches against NR, PLAZA 2.5 and UNIPROT databases and mapping against GO, KEGG and<br />
InterPro databases. We discuss the quality of the reference transcriptome using assembly statistics<br />
as well as functional and comparative analysis with assembled transcriptomes of five other conifer<br />
species. The present draft assembly and annotation of the EWP transcriptome provides a resource<br />
for further gene expression analysis, comparative genomic studies and will further improve the<br />
molecular understanding of frost tolerance in conifers.<br />
P14<br />
N-responsive gene expression of cell wall modification and dynamic changes<br />
in wood anatomy in the elongation zone of poplar<br />
D. J. EURING and A. POLLE<br />
Department of Forst Botany and Tree Physiology, Georg-August Universität, Büsgenweg 2,<br />
Göttingen, 37077, Germany<br />
Nitrogen (N) is an important nutrient, often limiting plant productivity and yield. Fast growing trees,<br />
such as poplars are increasingly used as a feedstock for wood production and biofuel generation. It<br />
is therefore critical to understand how N availability affects growth and wood formation of poplar. In<br />
this study, we characterized N-responsive dynamic changes in wood anatomy along the elongation<br />
zone of poplar and identified an N-responsive cell wall modification gene expression network in the<br />
elongation zone (first two internodes). Anatomical and biochemical analysis revealed increased cell<br />
wall thickness and secondary metabolites in the elongation zone. The finding of an N-responsive cell<br />
wall hub may have wider implications for the improvement of tree N use efficiency and opens new<br />
perspectives on the enhancement of wood composition as a feedstock for biofuels.<br />
37
P15<br />
How has our understanding of the conifer sexual reproductive process<br />
advanced in the age of genomics?<br />
D.D. FERNANDO<br />
Department of Environmental and Forest Biology, State University of New York College of<br />
Environmental Science and Forestry, One Forestry Drive, Syracuse, NY 13210, USA<br />
The long generation time and lengthy reproductive process in conifers are major barriers to<br />
functional genomics and genetic improvement. Therefore, our understanding of conifer sexual<br />
reproduction has also been mostly confined to comparative evolutionary genomics. This approach<br />
has provided insights on the divergence of sequences related to angiosperm genes involved in<br />
flowering time and floral organ identities, embryo formation, and other genes expressed in the<br />
sporophyte phase of the reproductive stage. My lab is focused on the analysis of genes expressed in<br />
the haploid phase of the reproductive stage, particularly male gametophyte development. We have<br />
identified and characterized genes using various genomic and proteomic approaches including<br />
microRNA analysis. We have described several conserved miRNAs in mature and germinated loblolly<br />
pine pollen and many of these are differentially expressed indicating that male gametophyte<br />
development is regulated at the miRNA level. This presentation/poster will focus on some of our<br />
unpublished results on the correlation between conserved miRNA genes and their respective target<br />
sequences. We have also introduced novel miRNA genes into pollen tubes through Agrobacterium<br />
transformation and interesting phenotypes were obtained. We are developing a microgenomic<br />
approach to validate transformed pollen tubes. The main goal of my lab is to understand the<br />
molecular mechanism underlying conifer pollen germination which is necessary to be able to<br />
facilitate germination and tube growth so as we may be able to bypass incompatibility barriers and<br />
thus create novel hybrids or prevent germination as a gene containment strategy.<br />
38
P16<br />
Local adaptation to environment is observed from genome-wide SNP data in<br />
Populus balsamifera (L.)<br />
K. C. FETTER, V. E. CHHATRE and S. R. KELLER<br />
Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Dr., Burlington, VT<br />
05401, USA<br />
Populus balsamifera has a large geographic range and local populations occupy distinct locations<br />
along strong environmental gradients of climate and photoperiod. Range-edge populations,<br />
particularly southern populations, may contain high levels of standing genetic diversity and harbor<br />
unique alleles adapted to longer, warmer, and drier growing seasons, environments that may<br />
become more widespread in the future. At the same time, southern populations are likely to be at<br />
greater risk of extirpation from climate change. In this study, we characterize the population<br />
structure and diversity of southern range-edge versus range-core populations, and identify genomic<br />
regions associated with local adaptation. We analyzed 534 individuals collected from 63 core and<br />
range-edge populations, and obtained genome-wide SNP data from >150K loci using genotype-bysequencing<br />
at 48-plex. Population structure was estimated using Bayesian clustering<br />
(fastSTRUCTURE) and discriminant analysis of principal components (DAPC). Tests for local<br />
adaptation manifest as F ST outliers and SNP-environmental associations were estimated with<br />
Bayescan, BAYENV, and LFMM. We find genomic regions suggesting novel, locally adapted loci in<br />
range-edge populations that likely contribute to their fitness in warmer, drier environments. Loci<br />
adapted to longer growing seasons and warm, dry environments may be useful for integrating into<br />
poplar breeding programs under future climates.<br />
P17<br />
Oakcoding: a nuclear DNA barcode for evolutionary studies in oaks<br />
E. FITZEK 1 , E. GUICHOUX 2 , R. PETIT 2 and A. HIPP 1<br />
1 The Morton Arboretum, Herbarium, 4100 Illinois Route 53, Lisle, IL 60532, USA; 2 Platforme Genome<br />
Transcriptome, 69 Route d’Arcachon INRA, Site de Pierroton/Btmt ARTIGA CESTAS, 33610 France<br />
Oaks (Quercus, Fagaceae) are keystone species in forests and savannas across the northern<br />
hemisphere. They are a model genus for studying tempo and rate of hybridization. Single-nucleotide<br />
polymorphisms (SNP) genotyping is increasingly used to study population structure and hybridization<br />
rates within a population. The goal of OAKCODING is to develop a single-multiplex (40 SNPs) as an<br />
easy-to-use genotyping tool to distinguish a set of the most common North American white oaks.<br />
Secondly, these SNPs will help to distinguish them from the Eurasian white oaks with which they can<br />
hybridize in cultivation. An existing RADseq dataset for 69 samples representing the eastern North<br />
American and Eurasian white oaks was utilized to identify species-specific SNPs. RADami, pyRAD,<br />
STACKS and custom scripts were used to generate a list of potential SNPs and screen 10-plex (total of<br />
344 SNPs) on ca. 200 DNA extractions to evaluate barcoding success rate using the SEQUENOM<br />
(INRA, Pierroton). Currently, we have 26 verified SNPs that will count towards OAKCODING and are<br />
specific to Quercus michauxi, Q. lyrata and Q. bicolor. We then propose to utilize this toolkit to study<br />
hybridization patterns in a unique and old (> 90 years old) oak taxonomic collection at The Morton<br />
Arboretum.<br />
39
P18<br />
Visualizing molecular changes associated with gravitropism and tension wood<br />
formation in Populus<br />
S. GERTTULA, H. BRUMER 2 , S. MANSFIELD 2 , M. ZINKGRAF 1 and A. GROOVER 1,3<br />
1 US Forest Service, Pacific Southwest Research Station, Davis CA, USA; 2 University of British Columbia,<br />
Vancouver BC, Canada; 3 Department of Plant Biology, University of California Davis, USA<br />
Woody species have evolved specialized mechanisms for responding to gravity. In angiosperms, the<br />
upper surface of a leaning stem develops tension wood in which a strong tensile force is generated<br />
and used to counteract the force of gravity. Here, confocal imaging was used to visualize molecular<br />
events occurring during graviperception and tension wood development in wild type and trees<br />
transformed with ARBORKNOX2 (ARK2), a Class I Homeobox transcription factor. When ARK2<br />
transcript levels are lowered, gravibending is compromised, while elevated ARK2 transcript levels<br />
enhance gravibending. Immunolocalization against the poplar ptPIN3 auxin transport protein shows<br />
that ptPIN3 undergoes dynamic polar relocalization events in response to gravity perception with<br />
differences among the genotypes. Arabinogalactan proteins (AGPs), key markers of tension wood,<br />
were visualized using an AGP specific antibody (JIM14) and showed strong labelling in developing<br />
tension wood fibers. JIM14 labelling appeared in fibers closer to or further from the cambium<br />
depending on the genotype. Xyloglucan endotransglycosylase (XET) activity has been proposed to<br />
play an important role in force generation of tension wood fibers. XET activity was visualized after<br />
incubation of wood tissue sections with a rhodamine-labelled XXXG oligomer. XET activity was strong<br />
in developing tension wood fibers. Similar to JIM14 labelling, XET labelling occurred in fibers closer<br />
to the cambium in ARK2 overexpressing plants. Together, these imaging techniques provide new<br />
insights and tools for the study of graviperception, gravitropism, and wood development in<br />
angiosperm trees.<br />
40
P19<br />
Survey of the sugar pine (Pinus lambertiana) transcriptome by deep<br />
sequencing<br />
D. GONZALEZ-IBEAS 1 , P. J. MARTINEZ-GARCIA 2 , R. FAMULA 2 , C. A. LOOPSTRA 3 , J. PURYEAR 3 , D.<br />
NEALE 2 and J. L. WEGRZYN 1<br />
1 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA:<br />
2 Department of Plant Sciences, University of California Davis, Davis, CA, USA: 3 Department of<br />
Ecosystem Science and Management, Texas A&M University, College Station, TX, USA<br />
While rapid progress has been made in characterizing the genomes of angiosperms, the same is not<br />
true for gymnosperms, in part due to their size and complexity. The advent of high-throughput<br />
sequencing technologies has enabled complete genomes in a few economically important conifer<br />
species. In this study, we present a comprehensive transcriptome of one of the largest conifer<br />
genomes, sugar pine. Thirty-one tissue-specific RNA libraries have been constructed, including<br />
needle, root, stem, pollen, cone, strobili, and embryonic tissues. Short read technologies (Illumina<br />
MiSeq and HiSeq) and the Pacific Biosciences Iso-Seq reads which result from size-selected libraries<br />
ranging from 1,000 to over 6,000 bp, have been included to combat many of the existing challenges<br />
in transcriptome assembly. A description of the contribution of each technology is presented, in<br />
terms of transcript length and coverage, mapping rate on the genome, and transcriptome<br />
completeness. Two different approaches for protein coding region identification have been<br />
compared to deal with the different type of technologies, and transcriptome composition has been<br />
analysed per library. The assembly, which has been used to scaffolding and annotate the full genome<br />
assembly, represents the first comprehensive survey of the sugar pine transcriptome.<br />
P20<br />
Phylogeography and genetic structure of two closely related species,<br />
Dryobalanops aromatica and D. beccarii (Dipterocarpaceae) in Sundaland<br />
K. HARADA, F. G. DWIYANTI, L. CHONG, B. DIWAY, Y. F. LEE, I. Z. SIREGAR, A. SBIAKTO, I.<br />
NINOMIYA, K. KAMIYA<br />
Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan<br />
Dipterocarps predominate the lowland evergreen forest in Sundaland and characterize the east<br />
Malaysian tropical rain forest. Two congenic dipterocarp species, Dryobalanops aromatica Gaertn. F.<br />
and D. beccarii Dyer were examined for their phylogeographic history and genetic structure by using<br />
nuclear microsatellite markers. Bayesian model-based clustering analysis showed that the species<br />
were clearly differentiated although hybridization probably occurred in two sympatric populations.<br />
D. aromatica could be divided into two genetically distinct groups: Malay-Sumatra and Borneo. An<br />
isolation with migration analysis using IMa program estimated the time of divergence of the two<br />
population groups to be 7,300–3,600 years ago, i.e. after the last glacial maximum. This analysis also<br />
suggested that the ancestral population was much larger than today’s populations. This supports the<br />
idea that the present tropical rainforest is in a refugial state, and also suggests that the savanna<br />
corridor that is hypothesized to have covered the central part of the exposed Sundaland during the<br />
last glacial period, if it existed, was not contiguous but rather permeated by forest in some places.<br />
41
P21<br />
Nuclear microsatellite markers for population studies in sugar maple (Acer<br />
saccharum Marsh.)<br />
S. KHODWEKAR and O. GAILING<br />
School of Forest and Environmental Sciences, Michigan Technological University, 1400 Townsend<br />
Drive, Houghton, MI 49931, USA<br />
A set of seven new nuclear microsatellite markers (nSSRs) was developed for sugar maple (Acer<br />
saccharum Marsh.) using paired-end Illumina sequencing. Out of 96 primers screened in a panel of<br />
six unrelated individuals, seven markers amplified polymorphic products. The utility of these<br />
markers, in addition to six already published microsatellites, for genetic variation and gene flow<br />
studies is assessed. Out of the seven newly developed markers three amplified multiple fragments<br />
and were interpreted as dominant (absence/presence) markers, while four markers amplified a<br />
maximum of two amplification products per sample. The six published microsatellites and three of<br />
the four newly developed markers showed regular segregation in an open-pollinated single tree<br />
progeny. Observed heterozygosity (H o ) and expected heterozygosity (H e ) in 48 individuals from one<br />
population ranged from 0.436 to 0.917 and from 0.726 to 0.894, respectively. Paternity analyses in<br />
the program CERVUS at co-dominant markers showed effective dispersal of pollen in the sugar<br />
maple population. The absence of fine-scale Spatial Genetic Structure (SGS) suggested effective<br />
dispersal of both seeds and pollen.<br />
P22<br />
The genetic architecture of fitness-related traits within whitebark pine (Pinus<br />
albicaulis)<br />
B. M. LIND 1 , P. E. MALONEY 2 , D. R. VOGLER 3 , D. B. NEALE 4 and A. J. ECKERT 5<br />
1 Integrative Life Sciences or 5 Department of Biology, Virginia Commonwealth University, Life<br />
Science Building 126, 1000 West Cary Street, Richmond, VA 23284, USA; 2 Department of Plant<br />
Pathology and Tahoe Environmental Research Center or 4 Department of Plant Sciences, University of<br />
California, One Shields Avenue, Davis, CA 95616, USA; 3 USDA, Forest Service, Pacific Southwest<br />
Research Station, Institute of Forest Genetics, 2480 Carson Road, Placerville, CA 95667, USA<br />
For populations of forest trees, fitness-related traits associated with survival, especially during<br />
seedling and juvenile stages, are indicative of total lifetime fitness and are composed of phenotypic<br />
traits related to growth, phenology, resource allocation patterns, water-use efficiency, and disease<br />
resistance. As expected of traits having strong influence on fitness, these traits are often correlated<br />
with environmental conditions. Yet, climate models predict redistribution of environmental variables<br />
currently structuring standing genetic variation of such phenotypic traits, which could lead to<br />
discordance between the environmental optima of tree populations and concurrent environmental<br />
conditions. Temperature and precipitation gradients within the southern range of whitebark pine<br />
(Pinus albicaulis, WbP) are predicted to be acutely impacted by climate change, thus necessitating<br />
the preservation of heritable genetic variation for continued adaptation. Recently we have shown<br />
WbP populations from Lake Tahoe Basin, California (LTB) to have heritable genetic variation<br />
(h2=0.0608–0.7787) for fitness-related traits associated with survival. Here, we describe the genetic<br />
architecture of local adaptation within WbP through results from genomic interrogation of these<br />
traits using ddRADseq. Specifically, using tens-of-thousands of SNPs, we will discuss population<br />
structure among 6 WbP populations within the LTB, and the links between genotype and phenotype<br />
and those of genotype and environment.<br />
42
P23<br />
Sequence characterization of a CONSTANS-like gene in North American red<br />
oaks<br />
J. F. LIND-RIEHL and O. GAILING<br />
Forest Resources and Environmental Sciences, Michigan Technological University, 1400 Townsend Dr,<br />
Houghton, MI 49931, USA<br />
Oaks (Quercus spp.) provide a model system to study local adaptation since they maintain species<br />
identity despite frequent interfertile hybridization. Genome scans between two European white oak<br />
species have found a largely homogenized genome resulting from interspecific gene flow. However,<br />
a few genomic areas showed high interspecific differentiation thought to be involved in the<br />
maintenance of species identity through divergent selection. Quercus rubra and Q. ellipsoidalis, two<br />
interfertile North American oak species, show differences in flowering time and adaptations to<br />
drought. Previously, we discovered a genic microsatellite nearly fixed on alternative alleles in each<br />
species. This locus has a putative function as CONSTANS-like gene, which is thought to be involved in<br />
flowering time and growth. To further elucidate the basis of this differentiation we have begun<br />
sequencing the coding region of this gene in individuals from both species. Our initial findings<br />
indicate that the differences in allele frequencies are the result of sequence variability in the<br />
microsatellite motif that encodes a poly-Q repeat potentially involved in transcription regulation or<br />
protein stabilization. We plan to continue this work by sequencing additional areas around the<br />
microsatellite to determine whether or not surrounding areas display variations associated with<br />
species differences.<br />
P24<br />
Identifying microRNAs involved in Regeneration of Secondary Vascular<br />
System in 4 Populus tomentosa Carr.<br />
F. TANG 1 , H. WEI 2 and M-Z LU 1<br />
1 State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091,<br />
China; 2 School of Forestry Resources and Environment Science, MTU, USA<br />
Wood formation is a complex developmental process governed primarily by a regulatory<br />
transcription network. MicroRNAs can exert regulatory roles over transcription of their target genes<br />
involved in plant growth and development. We used the regeneration of the secondary vascular<br />
system established in Populus tomentosa to harvest tissues generated from differentiating xylem in<br />
a time series for small RNA high-throughput sequencing. 209 known and 189 novel miRNAs were<br />
identified and Degradome sequencing analysis was then performed and 223 and 126 genes were<br />
obtained. GO enrichment of these target genes revealed that the targets of 15 miRNAs were<br />
enriched in the auxin signaling pathway, cell differentiation, meristem development and pattern<br />
specification process, which were main biological events during the regeneration of secondary<br />
vascular system. This study provides the basis for further analysis of these miRNAs to gain insight<br />
into their regulatory roles in wood development in trees.<br />
43
P25<br />
The effects of selective breeding on adaptive phenotypic traits in the interior<br />
spruce (Picea engelmannii x P. glauca) of western Canada<br />
I. R. MACLACHLAN 1 , T. WANG 1 , A. HAMANN 2 , P. SMETS 1 , J. TUTYEL 1 and S. N. AITKEN 1<br />
1 Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main<br />
Mall, Vancouver, BC, V6T 1Z4, Canada; 2 Department of Renewable Resources, University of Alberta,<br />
751 General Services Building, Edmonton, AB, T6G 2H1, Canada<br />
The AdapTree project is quantifying phenotypic and genomic architectures of local adaptation to<br />
climate in interior spruce (Picea glauca (Moench) Voss x P. engelmannii Parry ex Engelm.) to inform<br />
future provincial climate-based seed transfer policies. In Western Canada, reforestation using<br />
seedlots from selective breeding programs is increasing rapidly, but the impacts of selective<br />
breeding on climate-relevant phenotypic traits in current and future climates remain unclear. To<br />
address this knowledge gap, we established a large seedling common garden (n = 2880 individuals)<br />
representing 254 natural seedlots and 18 selectively bred seedlots from provenances across British<br />
Columbia and Alberta. We have made detailed assessments of growth, phenology and cold<br />
hardiness traits. Our analyses compare trait means, climatic clines and trait-trait correlations<br />
between natural and corresponding selectively bred seedlots. All seedlings are currently being<br />
genotyped using the AdapTree 50K interior spruce SNP array.<br />
Growth traits show large differences between seedlot types within breeding zones resulting from<br />
selective breeding. Clines in growth traits along provenance climate gradients are steeper in<br />
selectively bred material than natural populations, indicating that selection for timber volume has<br />
increased the strength of local adaptation. However, trade-offs between gains in growth from<br />
selection and phenology or cold hardiness traits are weak enough to suggest that the same assisted<br />
gene flow prescriptions can be used for selectively bred and natural reforestation seedlots to preadapt<br />
planted forests to new climates.<br />
P26<br />
Population genetics of freeze tolerance in Populus balsamifera across the<br />
growing season and its implications for future climate adaptation<br />
M. MENON, W. BARNES and M. OLSON<br />
Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Biological<br />
Sciences, Texas Tech University, Lubbock, TX, USA<br />
Protection against freeze damage during the growing season influences the northern range limits of<br />
many plant species. Winter survival strategies have been extensively studied in perennials, but few<br />
have addressed them and their genetic basis during the growing season. We examined intraspecific<br />
phenotypic variation in growing season freeze resistance across latitude and its molecular basis in<br />
Populus balsamifera. Foliar tissues exhibited latitudinal and seasonal cline in freeze tolerance but<br />
not freeze avoidance. The timing and rate of initiating freeze tolerance rather than the depth of<br />
freeze tolerance is likely to be a trait under strong selection in P. balsamifera. Of the 46 SNPs<br />
surveyed across the 6 CBF homologs, only CBF2_619 exhibited latitudinal differences consistent with<br />
increased freeze tolerance in the north and also caused a conformational change in the predicted<br />
protein structure. All 6 CBF genes were cold inducible, but showed varying patterns of expression<br />
across the growing season. CBF genes only contributed to some amount of variation in freeze<br />
tolerance indicating the role of other regulatory pathways and genes in nature. Overall, our study<br />
suggests the role of both coding and regulatory variations as important contributors to clinal<br />
adaptation and migration responses to historical climate shifts.<br />
44
P27<br />
Forest tree GnpIS: an information system dedicated to forest tree genetics,<br />
genomics and phenomics<br />
C. MICHOTEY 1 , C.ANGER 2 , F. EHRENMANN 4 , O. ROGIER 3 , V. JORGE 3 , C. POMMIER 1 , C. BASTIEN 3 , C.<br />
PLOMION 4 , C. PICHOT 5 , H. QUESNEVILLE 1 and D. STEINBACH 1<br />
1 INRA, UR1164 - URGI (Unité de Recherche en Génomique-Info), route de Saint-Cyr – RD 10, 78026<br />
Versailles cedex, France ; 2 INRA, UE0995 - GBFOR (Génétique et Biomasse Forestière ORléans), 2163<br />
avenue de la Pomme de Pin, CS 40001 Ardon, 45075 Orléans cedex, France; 3 INRA, UR0588 - AGPF<br />
(Amélioration, Génétique et Physiologie Forestières), 2163 avenue de la Pomme de Pin, CS 40001<br />
Ardon, 45075 Orléans cedex, France ; 4 INRA, UMR1202 - BIOGECO (BIOdiversité, GEnes et<br />
COmmunautés), 69 route d’Arcachon, 33612 Cestas cedex, France; 5 INRA, UR0629 - URFM (Ecologie<br />
des Forêts Méditerranéennes), 228 route de l’Aérodrome, 84914 Avignon, France<br />
GnpIS is a multispecies integrative information system dedicated to plants and fungi pests. It<br />
integrates and links genetic, genomic, phenomic and environmental data into a single environment,<br />
allowing researchers to store, query and explore information from different angles. The Ecology<br />
division of the French National Institute for Agricultural Research (INRA) uses GnpIS as its referential<br />
information system to manage forest tree genetic, genomic and phenomic data.<br />
The forest tree resources are accessible through the GnpIS web portal<br />
(https://urgi.versailles.inra.fr/gnpis/). Its main entry point is a google-like search for data discovery.<br />
This bird’s eye view allows navigation through the data with specific querying tools. It is regularly<br />
improved with new functionalities answering specific needs raised by scientists and is released<br />
several times a year. Data are supplied by local sources (files, databases …) produced and managed<br />
by research teams working on forest trees.<br />
Pine, spruce and oak data have been already integrated into this forest information system and we<br />
are giving access to poplar genetic, phenomic and genomic data<br />
(https://urgi.versailles.inra.fr/Species/Forest-trees/Database-overview). Integration of the data<br />
produced within the common garden network (over 1,000 trials with genotypes gathered from ~15<br />
species) is in progress.<br />
45
P28<br />
A developmental and genetic study of petal-less neotropical poppy trees<br />
N. PABÓN-MORA 1* , C. ARANGO OCAMPO 1 , J. F. ALZATE 2 and F. GONZÁLEZ 3<br />
1 Instituto de Biología, Universidad de Antioquia, AA 1226; 2 Centro de Secuenciación Genómico<br />
Nacional, Universidad de Antioquia, AA 1226; 3 Instituto de Ciencias Naturales, Universidad Nacional<br />
de Colombia, AA 7495<br />
Flowers of most Papaveraceae (760 spp.) exhibit a dimerous groundplan with 2 deciduous sepals, 4<br />
petals, many stamens and 2-8 carpels. The genera Bocconia (9 spp.) and Macleaya (2 spp.) are<br />
atypical in their tree- or shrubby habit, and in having perianth-less flowers. By comparing flower<br />
development in B. frutescens, M. cordata and its closely related species Stylophorum diphyllum, we<br />
show that petal-to-stamen homeosis occurs early in development, but different ontogenetic<br />
pathways underlie petal-loss in Bocconia and Macleaya. In order to explore the genetic basis of<br />
apetaly, we generated a floral transcriptome of B. frutescens and identified all MADS-box<br />
transcription factors that are part of the ABCE genetic model of floral development. We present data<br />
on the evolution of these genes in the Ranunculales and their expression in dissected floral organs,<br />
leaves and fruits in B. frutescens We also propose that the lack of expression of an AP3-3 ortholog is<br />
responsible for such apetaly, as it occurs in species of Ranunculaceae. We identified local<br />
duplications in FUL-like and PI genes likely resulting in pseudogenization and neofunctionalization,<br />
respectively. Based on the number of copies and patterns of expression, we propose a modified<br />
ABCE model for the petal-less poppy trees.<br />
P29<br />
Microevolutionary patterns of a resistance mechanism in white spruce<br />
G.J. PARENT 1 , I. GIGUÈRE 1 and J.J. MACKAY 1, 2<br />
1 Centre d’étude de la Forêt, Département des Sciences du Bois et de la Forêt, Université Laval, G1A<br />
1V6, Québec, Canada; 2 Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK<br />
The accumulation of two foliar acetophenone compounds (piceol and pungenol) plays a key role in<br />
the defense of white spruce (Picea glauca) against spruce budworm (SBW, Choristoneura<br />
fumiferana). Variability in the expression of a beta-glucosidase, PGβGLU-1, responsible for their<br />
release was linked to SBW resistance. This novel resistance mechanism is constitutive, genetically<br />
transmissible and variable in the natural white spruce population. We were interested in<br />
characterizing its microevolutionary patterns to better understand its importance. Levels of Pgβglu-1<br />
transcripts and toxic acetophenones were measured in white spruce from multiple provenances and<br />
preliminary results indicated a clear geographic pattern. Foliage expression of Pgβglu-1 was lower in<br />
provenances south of the 48th parallel. This result may be accounted for by lower selection pressure<br />
exerted by SBW associated with a reduced survival rate at the southern limit of its distribution.<br />
However, concentrations of piceol and pungenol in white spruce foliage did not follow the<br />
geographic pattern found for gene expression. This suggests that control of these specific<br />
acetophenone compounds may also be affected by other factors than the expression of Pgβglu-1.<br />
We are currently working to find other members of the biochemical pathway and regulatory<br />
network through association testing and other genome analysis methods.<br />
46
P30<br />
Strategies for classifying repeats in conifer genomes<br />
R. PAUL 1 , K. PRATT 1 , K. STEVENS 2 , D. GONZALEZ-IBEAS 1 , C. A. LOOPSTRA 3 , A. V. ZIMIN 4 , A. HOLTZ-<br />
MORRIS 6 , M. KORIABINE 6 , J. A. YORKE 4, 5 , M. W. CREPEAU 2 , D. PUIU 7 , S. L. SALZBERG 7 , P. J. DE<br />
JONG 6 , C. H. LANGLEY 2 , D.B. NEALE 3 and J. L. WEGRZYN 1<br />
1 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA;<br />
2 Department of Evolution and Ecology, University of California, Davis, CA, USA; 3 Department of<br />
Ecosystem Science and Management, Texas A&M University, College Station, TX, USA; 4 Institute for<br />
Physical Sciences and Technology, and 5 Departments of Mathematics and Physics, University of<br />
Maryland, College Park, MD, USA; 6 Children’s Hospital Oakland Research Institute, Oakland, CA,<br />
USA; 7 Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns<br />
Hopkins University, Baltimore, MD, USA<br />
Conifers are dominant life forms in temperate and boreal forests with important applications<br />
towards wood production, carbon sequesterization, and renewal energy. Interspersed repeats<br />
constitute up to 85% of these large, complex conifer genomes (20-40 gigabases). Characterizing<br />
these repeats is a challenge due to extensive retrotransposon proliferation and the highly diverged<br />
nature of the sequences. We have developed a pipeline that both identifies and characterizes the<br />
repeat content through a combination of de novo and library based strategies. The homology-based<br />
strategy provides comparisons against the plant component of Repbase while de novo identification<br />
combined structural and alignment methods via RepeatModeler. The final resolution considers<br />
alignment quality as well as manual and semi-automated repeat family classifications. This pipeline<br />
was used to evaluate the repetitive content of the Pinus lambertiana (sugar pine) genome which is<br />
estimated to be 79%. Over 1570 families were uniquely identified de novo and 1693 were previously<br />
characterized in other plants. Future work includes identifying unclassified repeats via conserved<br />
domains and machine learning strategies. Analysis of these diverged retrotransposon families in<br />
sugar pine and the other sequenced conifers (Pinus taeda and Pseudotsuga menziesii) will help<br />
explain evolutionary patterns as well as gene-duplication events.<br />
47
P31<br />
Wood formation in the real world<br />
N. Q. NGUYEN 1 , D. JANZ 1 , C. CARSJENS 1 , G. LOHAUS 1 , T. IVEN 2 , I. FEUSSNER 2 and A. POLLE 1<br />
1 Dept. for Forest Botany and Tree Physiology, Georg-August Universität Göttingen, Büsgenweg 2,<br />
37077 Göttingen, Germany; 2 Dept. for Plant Biochemistry, Georg-August Universität Göttingen,<br />
Justus von Liebig Weg 11, 37077 Göttingen, Germany<br />
In temperate ecosystems, wood formation of deciduous tree species undergoes seasonal<br />
fluctuations, usually with the production of larger vessels early and the formation of smaller vessel<br />
lumina, more fibers and thicker cell walls towards the end of the growth phase. The transcriptional<br />
networks and hormonal regulation underlying wood formation of non-model trees has barely been<br />
studied. Here, we investigated the formation of beech wood (Fagus sylvatica L.). Although beech is a<br />
key stone species in temperate European forests, genomic information is lacking. To increase our<br />
knowledge on wood formation of beech, we used RNA sequencing of the developing xylem of<br />
mature field grown trees located at two field sites. The transcriptomic data were related to the<br />
hormonal status and wood anatomy employing weighted gene correlation network analysis.<br />
Thereby, co-regulated genes and hormones were assigned to the formation of specific cell types.<br />
Our analysis suggests that ABA (abscisic acid) is a main player in seasonal acclimation of the wood<br />
structure balancing vessel lumina and fibre numbers.<br />
P32<br />
What are the drivers of non-coding plastome variation in the New Zealand<br />
tree flora?<br />
B. C. M. POTTER, A. J. DRUMMOND, R. D. NEWCOMB and W. G. LEE<br />
School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1010, New<br />
Zealand<br />
The native tree flora of New Zealand is diverse (ca. 320 species), highly endemic (over 90%), and<br />
situated on a landmass with a deep history of geographic isolation in the southern Pacific (ca. 80<br />
Ma.). As a result this region provides an excellent system for the study of forest tree genetics, as the<br />
lineages have estimable island colonisation ages, display a range of generation times and seed<br />
dispersal strategies, and encompass a broad array of phylogenetic diversity – from tree ferns to tree<br />
daisies. To better understand the drivers of non-coding chloroplast variation in forest trees, targeted<br />
sequencing was performed (e.g. trnQ-rps16, rpL32-trnL, psbA-trnH, rpoB-trnC, and trnL-trnF) on<br />
numerous accessions of a broad selection of 20 widespread species. The results show a direct<br />
correlation between lineage age and genetic variation in some taxa (e.g. Nothofagus spp., Nestegis<br />
spp., Rhopalostylis sapida), highlighting the importance of the temporal driver. However, in other<br />
species the opposite pattern was recovered, with a recently colonised tree (Geniostoma<br />
ligustrifolium) representing the most genetically variable species – potentially owing to its rapid<br />
generation time. While one of the most ancient species in the flora (Agathis australis) was found to<br />
be one of the least variable – possibly owing to a slow-down in the evolutionary rate of the<br />
araucarian plastome. These findings are discussed along with directions for further research.<br />
48
P33<br />
Transcriptome sequencing reveals new insights into the interaction of<br />
European chestnut with the causal agent of chestnut blight<br />
J. QUINTANA 1, 2 , I. MERINO 1 , A. CONTRERAS 1 , G. OROZCO 1 , A. VINUESA 1 , F.O. ASIEGBU 2 and L.<br />
GÓMEZ 1<br />
1 Center for Plant Biotechnology and Genomics, Polytechnic University, 28223 Pozuelo de Alarcón,<br />
Spain; 2 Department of Forest Sciences, Helsinki University, Latokartanonkaari 7, FIN- 00014, Finland<br />
European chestnut is a multipurpose tree with a diversification history tightly linked to human<br />
management. Nonetheless, several diseases have diminished its natural range and economic impact.<br />
Chestnut blight, caused by the ascomycete Cryphonectria parasitica, is a prominent example. Here<br />
we present the first transcriptome reconstruction of European chestnut after challenge with this<br />
pathogen. Four libraries were constructed and an Illumina HiSeq2000 platform was used to generate<br />
over 90 million reads. De novo assembly produced 104,310 contigs. Extensive analysis on the<br />
functional annotation of Differentially Expressed Transcripts (DEGs) revealed that JA/ET-mediated<br />
signalling pathways are crucial to fine-tune defense response. The large number of DEGs encoding<br />
transcription factors evidences a deep transcriptional reprograming, which leads to the upregulation<br />
of several genes encoding for proteins with potential antimicrobial activity. Our results represent a<br />
valuable source of information to be used in programs aimed to develop resistant cultivars.<br />
P34<br />
Functional genomics of developmental programmed cell death in the Norway<br />
spruce embryo-suspensor<br />
S. H. REZA 1 , N. DELHOMME 2 , N. R. STREET 2 , O. NILSSON 3 , H. TUOMINEN 2 , E. A. MININA 1 and P. V.<br />
BOZHKOV 1<br />
1 Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and<br />
Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden; 2 Umeå Plant Science Centre,<br />
Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden; 3 Umeå Plant Science<br />
Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural<br />
Sciences, 901 83 Umeå, Sweden<br />
In Norway spruce (Picea abies) the embryo-suspensor is composed of several layers of terminally<br />
differentiated cells, originating from asymmetric cell divisions in the embryonal mass. While the cells<br />
in the upper layer of the suspensor (i.e. adjacent to the embryonal mass) are in the commitment<br />
phase of PCD, the cells in the lower layers exhibit a gradient of successive stages of vacuolar cell<br />
death towards the basal end of the suspensor where hollow walled cell corpses are located. The goal<br />
of this study is to find out a critical subset of genes, required for vacuolar cell death in the Norway<br />
spruce embryo-suspensor. We performed deep sequencing of RNA isolated from the suspensors and<br />
the embryonal masses of embryogenic cell line 88:22 and identified 136 up- and 31 down-regulated<br />
transcripts in the suspensors. Up-regulated transcripts were enriched with cell death-related genes<br />
and genes encoding proteins involved in catabolic processes. Our next goal is to investigate the role<br />
of these genes in the cell death and embryo development using reverse genetics.<br />
49
P35<br />
Population-scale characterisation of copy number variations in the gene<br />
space of Picea glauca<br />
A. SAHLI 1 , I. GIGUÈRE 1 , J. PRUNIER 1 , N. ISABEL 2 , J. BEAULIEU 1 , J. BOUSQUET 1 and J. MACKAY 1, 3<br />
1 Center for Forest Research and Institute for Systems and Integrative Biology, Université Laval, 1030,<br />
avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada; 2 Natural Resources Canada, Canadian<br />
Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., Stn. Sainte-Foy, Quebec City, QC, G1V<br />
4C7, Canada; 3 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1<br />
3RB, UK<br />
Copy number variations (CNVs) are large genetic variations present in the genome of every<br />
multicellular organism examined so far. They are believed to play an important role in the evolution<br />
and adaptation of species. In plants, little is known about the characteristics of CNVs. Here, we used<br />
SNP-array intensity data for pedigrees and trees sampled from natural populations to scan the gene<br />
space of Picea glauca for CNVs. We were particularly interested in the characterisation of CNVs<br />
abundance, inheritance modalities, frequency spectrum and functional impact. Our findings<br />
indicated that CNVs affect a small proportion of the gene space (less than 5%) and are<br />
predominantly bi-allelic copy number losses. CNVs were found to follow the Mendelian inheritance<br />
and many resulted from spontaneous mutations. The CNV frequency spectrum suggests that they<br />
are mostly under purifying selection and that few genes may be under positive or balancing<br />
selection. The functional annotation of CNV genes shows enrichment in genes involved in response<br />
to environment, growth and development regulation processes. This study represents a first report<br />
on CNVs in conifer trees at the genome and population scale and contributes to our understanding<br />
of the genomic basis of evolution and population diversity in forest trees.<br />
P36<br />
Assembly challenges of the highly heterogeneous and repetitive genomes of<br />
Populus tremula and Populus tremuloides<br />
Y.-C. LIN, J. WANG, N. DELHOMME, B. SCHIFFTHALER, N. MÄHLER, D. SUNDELL, C.<br />
MANNAPERUMA, K.M. ROBINSON, Y. VAN DE PEER, P. INGVERSSON, T.R. HVIDSTEN, S. JANSSON<br />
and N.R. STREET<br />
Department of Plant Physiology, Umeå University, Artedigränd 7, 90736 Umeå, Sweden; Department<br />
of Biostatistics, Norwegian University of Life Sciences, Universitetstunet 3, 1432 Ås, Norway;<br />
Department of Bioinformatics and Systems Biology, University of Ghent, Technologiepark 927, 9052<br />
Ghent, Belgium<br />
The European and American aspens, Populus tremula and Populus tremuloides, are ecological keystone and<br />
scientific model forest tree species. Currently, most of the sequencing-based analyses of these species are<br />
based on the genome assembly of the black cottonwood P. trichocarpa, a distant relative. This affects<br />
alignment rates, especially for nongenic analyses. The aspen science community in particular, but also the<br />
plant science community as a whole, would therefore benefit from genome assemblies of these two aspens.<br />
These, currently undergoing, are challenging, as their genomes are highly heterozygous and repetitive, causing<br />
extensive assembly fragmentation. Here, we first demonstrate the need for assemblies of P. tremula and P.<br />
tremuloides by evaluating sequence alignment to the existing P. trichocarpa reference. We further present our<br />
refined genome assembly strategies, leading to better assemblies of these two genomes. In parallel to this<br />
genomic effort, we also present our de-novo transcriptome assembly of P. tremula, based on a comprehensive<br />
RNA-Seq tissue catalog. Integrating these together, we assess the completeness of the genomes and their gene<br />
spaces in our assemblies. This, ultimately, allows us to conduct a comparative genomics analysis that gives<br />
insight into three members of the genus Populus, discussing their biological key differences and similarities.<br />
50
P37<br />
Unraveling the polyploid origin of coast redwood (Sequoia sempervirens)<br />
with Bayesian concordance analysis<br />
A. D. SCOTT, N. STENZ and D. A. BAUM<br />
Department of Botany, University of Wisconsin - Madison, 430 Lincoln Drive, Madison, WI 53706,<br />
USA<br />
Coast redwood (Sequoia sempervirens) stands out as not only one of the tallest, longest-lived trees,<br />
but as the only hexaploid conifer. As whole genome duplication is rare in gymnosperms, a better<br />
understanding of the causes of polyploidy in Sequoia may clarify why polyploidy has played a<br />
relatively minimal role in gymnosperm evolution. We sequenced transcriptomes from Sequoia,<br />
Sequoiadendron, and Metasequoia, and estimated phylogenetic trees for 3,605 genes. Bayesian<br />
concordance analysis of 3,045 low-copy genes suggests Sequoiadendron is the closest relative of<br />
Sequoia for ~80% of the genome. Gene trees with multiple homeologs in coast redwood consistently<br />
show monophyly of those homeologs. This suggests that hexaploidy is a result of autopolyploidy or,<br />
that if hybridization did occur, it involved only species that are more closely related to Sequoia than<br />
either Sequoiadendron or Metasequoia. Our analyses suggest a polyploid origin for Sequoia ~24 mya<br />
(homeolog divergence at K s ~ 0.0168), in apparent contradiction to the fossil record.<br />
P38<br />
Who’s who? Finding the CESA genes in White Spruce encoding the secondary<br />
wall specific cellulose synthase<br />
I. DUVAL 1 , D. LACHANCE 1 , I. GIGUÈRE 2 , M-J. MORENCY 1 , G. PELLETIER 1 , J. J. MACKAY 2, 3 and A.<br />
SÉGUIN 1*<br />
1 Natural Resources Canada, Laurentian Forestry Centre, Québec QC G1V 4C7, Canada; 2 Centre<br />
d’Étude de la Forêt, Université Laval, Québec (QC), G1V A06, Canada; 3 Department of Plant Sciences,<br />
University of Oxford, Oxford, OX1 2RB, UK<br />
Phylogenetic analyses of CESA genes have shown specific divergence within the gene family for<br />
either primary or secondary wall development. In Picea glauca (white spruce) the PgCESA3 gene has<br />
been principally associated to developing xylem. Tissue specific gene expression analyses using a<br />
PgCESA3 promoter-GUS reporter construct revealed localised expression associated to secondary<br />
wall formation. We also obtained evidences that specific spruce MYB transcription factors are<br />
implicated in the regulation of PgCESA3 gene promoter by using a tissue culture based system and a<br />
transactivation approach. Furthermore, using electrophoretic mobility shift assay (EMSA) we<br />
confirmed that PgMYB12 directly binds in vitro to the PgCESA3 promoter. Overall, functional<br />
genomic tools and global expression data for white spruce is a powerful assets for delineating the<br />
evolution and dynamics of complex gene families such as CESA.<br />
51
P39<br />
Conifer’s comparative genomics – a novel topic for global collaborative, open<br />
access, policy adoption<br />
P. SHARMA and P. L. UNIYAL<br />
Department of Botany, University of Delhi, Delhi 110007, India<br />
Gymnosperms comprise 83 genera, and about 1000 species worldwide and 47 species in 14 genera<br />
occur in India. Conifers form dominant component of vegetation in Western Himalaya. The data on<br />
phenological studies in conifers reflects that the phenotype and thus the genotype have strong<br />
affinities with the existing environment. However, the research data on the phenologiy of conifers in<br />
India relating the concept of speciation and evolution is very meager. The importance of<br />
comparative-genomic approaches for understanding functions in an evolutionary framework should<br />
be highlighted, which may expose much novel information. There is an enormous variation in the<br />
morphology in the populations of Taxus in Himachal Pradesh. I invite people for a comparative<br />
genomics approach by pooling the data for research. I wish to put forward my step in this direction<br />
for the collaborative work in comparative genomic approaches for this study with the forest tree<br />
genomics.<br />
P40<br />
Transcriptional responses of resistant and susceptible ash species under<br />
attack by emerald ash borer<br />
D.N. SHOWALTER, R.C. HANSEN, D.A. HERMS, S. WIJERATNE, A. WIJERATNE and P. BONELLO<br />
Department of Plant Pathology, The Ohio State University, 201 Kottman Hall, 2021 Coffey Road,<br />
Columbus, OH 43210, USA; Department of Food, Agricultural, and Biological Engineering,<br />
Department of Entomology, and Molecular and Cellular Imaging Center, Ohio Agricultural Research<br />
and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691, USA<br />
The alien, invasive wood boring beetle known as emerald ash borer (EAB, Agrilus planipennis<br />
Fairmaire) is devastating North American ash (Fraxinus spp.) populations in urban and natural forest<br />
settings. A critical part of landscape-scale, long-term management will be deployment of host<br />
resistance traits, which are present in coevolved Asian ash species, but have not yet been<br />
characterized. In an effort to understand ash defense responses against EAB, we are comparing<br />
transcription, hormone signaling, and phenolic secondary metabolism in phloem and cambial tissue<br />
from resistant Asian and susceptible North American ash before and immediately after EAB attack.<br />
Qualitative comparisons of species-specific transcriptomes are revealing sequences in resistant or<br />
susceptible species for which no orthologous transcription is detected in the other species.<br />
Quantitative comparisons are identifying orthologous transcripts differentially expressed between<br />
species, either constitutively or following EAB-attack. Genes of interest with support from signaling<br />
and defense metabolite analysis may be useful targets for ash resistance breeding programs and<br />
improve understanding of the genetic basis of angiosperm defenses against wood boring insects.<br />
Species-specific transcriptome data will assist ongoing assembly and annotation of Fraxinus<br />
genomes.<br />
52
P41<br />
Landscape genomics for climate adaptation in Eucalyptus trees<br />
M. A. SUPPLE, J. BRAGG, R. ANDREW, A. NICOTRA, M. BYRNE, L. BROADHURST and J. O. BOREVITZ<br />
The Australian National University, Canberra, ACT 2601, Australia<br />
The rapid pace of climate change is threatening the survival of many species. Especially vulnerable<br />
are long lived species with slow migration rates, which have limited ability to move with favorable<br />
climatic conditions. Extensive reforestation projects are ongoing across Australia, providing the<br />
opportunity to assist migration of potentially adaptive alleles. Eucalyptuses, which are foundation<br />
species in forests and woodlands across Australia, are focal species of the reforestation effort. We<br />
are using landscape genomic techniques to identify alleles associated with various climate conditions<br />
in two Eucalyptus species. Using genotype by sequencing methods, we have genotyped hundreds of<br />
samples across the distributions of each species. Each sampling location is associated with numerous<br />
climate variables, enabling us to identify specific alleles associated with specific climatic conditions.<br />
This association is suggestive of adaptation, which we can test experimentally in climate controlled<br />
growth chambers. Populations harboring alleles that are potentially adaptive to predicted future<br />
climates can be used as sources of seeds for reforestation, thereby assisting migration of the<br />
adaptive alleles.<br />
P42<br />
Comparative analysis of pollen transcriptomes reveals distinct sucrose<br />
utilization mechanisms in angiosperm trees<br />
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.<br />
HARDING 2, 3 1, 2, 3<br />
and C. J. TSAI<br />
1 Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 2 Warnell School of<br />
Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA; 3 Department of<br />
Genetics, University of Georgia, Athens, GA 30602, USA<br />
Carbohydrate allocation is an important fundamental process during reproduction, and is best<br />
understood in herbaceous annuals. Woody perennials exhibit distinct flowering phenology<br />
(precocious versus serotinous flowering), but the genetic underpinning is poorly understood. We<br />
found that flowering phenology is linked to pollen expression of distinct sucrose transporter (SUT)<br />
family members. Plasma membrane SUTs are dominant in the pollen of herbaceous annuals, as well<br />
as woody perennials with serotinous flowering, such as grapevine and Eucalyptus. In contrast, early<br />
flowering Populus, willow and oak pollen show high transcript levels of tonoplast-localized SUT.<br />
Additionally, our analysis reveals differential expression of vacuolar and cell wall invertases between<br />
pollen of early- and late-flowering trees. The observation of differential compartmentalization of<br />
sucrose transport and processing enzymes suggests alternative carbohydrate utilization mechanisms<br />
in pollen during angiosperm evolution. Comparative gene co-expression analysis is underway to<br />
identify other molecular candidates that are involved in different carbohydrate allocation pathways<br />
during reproduction.<br />
53
P43<br />
Molecular control of vasculature development in Norway spruce<br />
D. UDDENBERG, P. RAMACHANDRAN and A. CARLSBECKER<br />
Department of Organismal Biology, Physiological Botany, Uppsala University and the Linnean Centre<br />
for Plant Biology, PO Box 7080, SE 75007 Uppsala, Sweden<br />
The wood forming vascular tissues are vital for water and nutrient transport, as well as mechanical<br />
support thus enabling plants to stand upright and to grow large. Tissue-specific transcriptomics of<br />
the seedling root of the model plant Arabidopsis thaliana has been instrumental in identifying<br />
genetic control mechanisms for vascular patterning and xylem differentiation. Moreover, class III<br />
HD-ZIP transcription factors and their interactome have emerged as key regulators of xylem<br />
formation and cambium activity in angiosperms. While the molecular control of angiosperm vascular<br />
development is well understood, at least for certain model plants, we know little about this in<br />
woody perennials such as the conifers.<br />
We aim at developing the Norway spruce seedling root as a model system to elucidate the molecular<br />
regulation of conifer vasculature development. To do so, we will generate tissue-specific expression<br />
profiles using high throughput RNA sequencing following micro-dissection. We have also identified a<br />
set of Norway spruce HD-ZIP III genes together with their regulatory miRNAs and precursors. To<br />
elucidate their role in conifer vasculature development we will in depth characterize their<br />
endogenous expression patterns and transgenic assays will reveal their function.<br />
P44<br />
Genome-wide identification and profiling of novel and conserved miRNAs in<br />
somatic embryos of Norway spruce during formation of an epigenetic<br />
memory<br />
I. A. YAKOVLEV and C. G. FOSSDAL<br />
Norwegian Forest and Landscape Institute, PO Box 115, 1431, Ås, Norway<br />
Epigenetic memory in Norway spruce permanently affect the timing of bud burst and bud set, vitally<br />
important adaptive traits, in this long-lived forest species. MicroRNAs (miRNAs), a class of small noncoding<br />
RNA molecules have recently drawn attention for their prominent role in development and<br />
epigenetic regulations.<br />
We prepared 18 small RNA libraries from embryogenic tissues of two individuals at three stages of<br />
maturation grown up in vitro at three culturing temperatures (18, 23 and 28°C). Obtained libraries<br />
were sequenced in duplicate on PGM (Ion Torrent) system and analyzed using CLC genomic<br />
workbench.<br />
In this study, we report the identification of more than 1600 novel and conserved miRNAs in Norway<br />
spruce derived from 1050 precursors. Precursors could be transcribed from around 3400 miRNA<br />
genes. We found high amount of isomiRs and high redundancy of putative miRNA genes in released<br />
Norway spruce genome v1. Based on identified miRNAs we studied their expression patterns in<br />
dependence on the temperature prevailing during SE growth and leading to establishing of<br />
epigenetic marks. Distinct temperature dependent expression patterns were determined for most of<br />
analyzed miRNAs. miRNAs are targeting the large amounts of spruce genes with a wide range of<br />
functions, including genes involved in epigenetic regulation.<br />
54
P45<br />
Contrasting genomic signatures of local adaptation in lodgepole pine (Pinus<br />
contorta) and interior spruce (Picea glauca x Picea engelmannii)<br />
S. YEAMAN, K. A. HODGINS, K. LOTTERHOS, H. SUREN, T. WANG, P. SMETS, K. NURKOWSKI, J. A.<br />
HOLLIDAY, L. H. RIESEBERG, M. C. WHITLOCK and S. N. AITKEN<br />
Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall,<br />
Vancouver, BC, V6T 1Z4, Canada<br />
Understanding the genomic basis of local adaptation is a central question in evolutionary biology,<br />
with important applications to forestry management. Common garden studies in both lodgepole<br />
pine (Pinus contorta) and interior spruce (Picea glauca x Picea engelmannii) have shown<br />
considerable local adaptation, yet the genomic basis of this adaptation is poorly understood. Here,<br />
we use targeted resequencing of a large fraction of the exome to characterize the genomic basis of<br />
adaptation in hundreds of individuals of each species, sampled along wide geographical and climatic<br />
gradients. We use a combination of GWAS and environment association analyses to identify regions<br />
of the genome with signatures that are strongly consistent with local adaptation. By examining<br />
comparing these signatures among species for thousands of SNPs within 11,833 orthologous genes,<br />
we explore the extent of parallelism and gene re-use in local adaptation.<br />
55
Participants<br />
Amselem, Joelle INRA joelle.amselem@versailles.inra.fr<br />
Blumstein, Meghan Harvard University blumstein@fas.harvard.edu<br />
Borevitz, Justin<br />
The Australian National justin.borevitz@anu.edu.au<br />
University<br />
Brady, Siobhan<br />
University of California, sbrady@ucdavis.edu<br />
Davis<br />
Buggs, Richard<br />
Queen Mary University r.buggs@qmul.ac.uk<br />
of London<br />
Bullington, Lorinda MPG Operations LLC lbullington@mpgranch.com<br />
Bultman, Hilary<br />
University of Wisconsin, hlbultman@wisc.edu<br />
Madison<br />
Casola, Claudio Texas A&M University ccasola@tamu.edu<br />
Chhatre, Vikram University of Vermont vchhatre@uvm.edu<br />
Cole, Christopher<br />
Cook, Bob<br />
University of Minnesota,<br />
Morris<br />
colect@morris.umn.edu<br />
4cooki4@gmail.com<br />
Cooke, Janice University of Alberta janice.cooke@ualberta.ca<br />
Crane, Peter Yale University peter.crane@yale.edu<br />
Daguerre, Yohann INRA de Nancy yohann.daguerre@nancy.inra.fr<br />
Dardick, Chris<br />
USDA ARS Appalachian chris.dardick@ars.usda.gov<br />
Fruit Research Station<br />
Daru, Barnabas University of Pretoria darunabas@gmail.com<br />
De La Torre, Amanda Umea Plant Science amandarodltc@gmail.com<br />
Centre<br />
Delph, Lynda Indiana University ldelph@indiana.edu<br />
Demura, Taku<br />
Nara Institute of Science demura@bs.naist.jp<br />
and Technology<br />
DiFazio, Stephen West Virginia University spdifazio@mail.wvu.edu<br />
Diggle, Pamela University of Connecticut pamela.diggle@uconn.edu<br />
Douglas, Carl<br />
El-Kassaby, Yousry<br />
University of British<br />
Columbia<br />
University of British<br />
Columbia<br />
carl.douglas@ubc.ca<br />
y.el-kassaby@ubc.ca<br />
56
Ensminger, Ingo University of Toronto ingo.ensminger@utoronto.ca<br />
Euring, Dejuan Büsgen-Institut dning@gwdg.de<br />
Fernando, Danilo State University of New fernando@esf.edu<br />
York<br />
Fetter, Karl University of Vermont kfetter@uvm.edu<br />
Fitzek, Elisabeth The Morton Arboretum elisha.fitzek@gmail.com<br />
Friedman, William Harvard University ned@oeb.harvard.edu<br />
Gerttula, Suzanne USDA Forest Service 35sgerttula@gmail.com<br />
Gonzalez-Ibeas, Daniel University of Connecticut gonzalez.ibeas@gmail.com<br />
Groover, Andrew US Forest Service agroover@fs.fed.us<br />
Guseman, Jessica USDA Jessica.Guseman@ars.usda.gov<br />
Harada, Ko Ehime University kharada@agr.ehime-u.ac.jp<br />
Henry, Isabelle<br />
University of California, imhenry@ucdavis.edu<br />
Davis<br />
Hetherington, Alistair University of Bristol alistair.hetherington@bristol.ac.uk<br />
Hollender, Courtney USDA Courtney.Hollender@ars.usda.gov<br />
Isabel, Nathalie<br />
Natural Resources nisabel@rncan-nrcan.gc.ca<br />
Canada<br />
Khodwekar, Sudhir Michigan Technological sdkhodwe@mtu.edu<br />
University<br />
Kidner, Catherine University of Edinburgh c.kidner@rbge.ac.uk<br />
Kramer, Elena Harvard University ekramer@oeb.harvard.edu<br />
Leslie, Andrew Brown University Andrew_Leslie@brown.edu<br />
Lind, Brandon<br />
Virginia Commonwealth lindb@vcu.edu<br />
University<br />
Lind-Riehl, Jennifer Michigan Technological jflind@mtu.edu<br />
University<br />
Lindroth, Richard University of Wisconsin, richard.lindroth@wisc.edu<br />
Madison<br />
Lindsey, Keith University of Durham keith.lindsey@durham.ac.uk<br />
Lu, Meng-Zhu<br />
MacLachlan, Ian<br />
Chinese Academy of<br />
Forestry<br />
University of British<br />
Columbia<br />
lumz@caf.ac.cn<br />
ian.maclachlan@forestry.ubc.ca<br />
57
Menon, Mitra University of Virginia mm4kx@virginia.edu<br />
Michotey, Celia INRA celia.michotey@versailles.inra.fr<br />
Neale, David<br />
University of California, dbneale@ucdavis.edu<br />
Davis<br />
Nieminen, Kaisa<br />
Natural Resources kaisa.nieminen@helsinki.fi<br />
Institute Finland<br />
Pabon Mora, Natalia Universidad de Antioquia lucia.pabon@udea.edu.co<br />
Parent, Geneviève Université Laval genevieve.parent.5@ulaval.ca<br />
Paul, Robin University of Connecticut robin.paul@uconn.edu<br />
Pinfield-Wells, Helen New Phytologist h.pinfield-wells@lancaster.ac.uk<br />
Plett, Jonathan<br />
University of Western j.plett@uws.edu.au<br />
Sydney<br />
Polle, Andrea University of Göttingen apolle@gwdg.de<br />
Potter, Ben University of Auckland bmyl026@aucklanduni.ac.nz<br />
Quintana Gonzalez, Julia Helsinki University julia.quintana@helsinki.fi<br />
Reza, Md Salim Hossain Swedish University of salim.hossain.reza@slu.se<br />
Agricultural Sciences<br />
Romero-Severson, University of Notre Dame jromeros@nd.edu<br />
Jeanne<br />
Sahli, Atef Université Laval atef.sahli.1@ulaval.ca<br />
Schiffthaler, Bastian Umeå Plant Science bastian.schiffthaler@umu.se<br />
Center<br />
Scott, Alison Dawn University of Wisconsin, adscott4@wisc.edu<br />
Madison<br />
Seguin, Armand<br />
Natural Resources armand.seguin@nrcan.gc.ca<br />
Canada<br />
Sezen, Uzay University of Connecticut uzay@uga.edu<br />
Sharma, Prabha University Of Delhi sharmaprabha3@gmail.com<br />
Showalter, David The Ohio State University showalter.53@osu.edu<br />
Strauss, Steven Oregon State University steve.strauss@oregonstate.edu<br />
Street, Nathaniel Umeå University nathaniel.street@umu.se<br />
Supple, Megan<br />
The Australian National megan.supple@anu.edu.au<br />
University<br />
Trippe, Elizabeth University of Georgia elizabeth.trippe25@uga.edu<br />
58
Uddenberg, Daniel Uppsala University daniel.uddenberg@ebc.uu.se<br />
Wan, Tao<br />
Fairylake Botanical wantao1983@gmail.com<br />
Garden<br />
Wegrzyn, Jill University of Connecticut jill.wegrzyn@uconn.edu<br />
Yakovlev, Igor<br />
Norwegian Forest and yai@skogoglandskap.no<br />
Landscape Institute<br />
Yeaman, Sam<br />
University of British yeaman@zoology.ubc.ca<br />
Columbia<br />
Zinkgraf, Matthew USDA Forest Service mszinkgraf@fs.fed.us<br />
59
HUNNEWELL<br />
VISITOR CENTER<br />
A RBORWAY<br />
G ATE<br />
Magnolias<br />
Dawn<br />
Redwoods<br />
Tulip Trees<br />
Lindens<br />
L ARZ A NDERSON<br />
B ONSAI C OLLECTION<br />
Dana Greenhouses<br />
(No Public Access)<br />
Linden Path<br />
L EVENTRITT<br />
S HRUB & V INE<br />
G ARDEN<br />
Cork Trees<br />
Meadow Road<br />
Willow Path<br />
Willows<br />
Horsechestnuts<br />
Maples<br />
Arborway/Route 203<br />
F OREST H ILLS<br />
G ATE<br />
Faulkner<br />
Hospital<br />
C ENTRE S TREET<br />
G ATE<br />
Centre Street<br />
Hickories<br />
Walnuts<br />
Elms<br />
Birches<br />
Bussey Hill Road<br />
Lilacs<br />
B USSEY H ILL<br />
Ashes<br />
B RADLEY<br />
R OSACEOUS<br />
Faxon<br />
Pond C OLLECTION<br />
Rehder<br />
Pond<br />
Dawson<br />
Pond<br />
Cherries<br />
Forest Hills Road<br />
VFW Parkway<br />
Weld Hill Research<br />
& Administration Building<br />
(No Public Access)<br />
Centre Street<br />
W ELD H ILL<br />
Weld Street<br />
Hebrew<br />
Rehabilitation<br />
Center<br />
Walter Street<br />
Conifer Path<br />
Firs<br />
Larches<br />
Honey Locusts<br />
Spruces<br />
Conifer Path<br />
W ALTER S TREET<br />
G ATE<br />
B USSEY S TREET<br />
G ATE<br />
P ETERS H ILL<br />
G ATE<br />
Pines<br />
P ETERS H ILL<br />
Hemlock Hill Road<br />
Bussey Street<br />
Valley Road<br />
Peters Hill Road<br />
Yews<br />
Crabapples<br />
Oaks<br />
Oak Path<br />
Junipers<br />
Mountain Laurels<br />
Pears<br />
Azaleas<br />
Chinese Path<br />
Rhododendron Path<br />
South Street<br />
E XPLORERS<br />
G ARDEN<br />
Dove Tree<br />
Stewartias<br />
Beech Path<br />
Rhododendrons<br />
Beech Path<br />
S OUTH S TREET<br />
Beeches G ATE<br />
H EMLOCK H ILL<br />
P OPLAR<br />
G ATE<br />
South Street<br />
Blackwell Footpath<br />
B U S<br />
N<br />
S E Y<br />
B R O O<br />
K M E A<br />
D O W<br />
M AP K EY<br />
Valley Road<br />
W ASHINGTON<br />
S TREET<br />
G ATE<br />
Walnuts<br />
Oak Path<br />
Oaks<br />
Public Restrooms<br />
Visitor Information<br />
Washington Street<br />
City Street (traffic)<br />
Entrance Gate<br />
Access Road (paved)<br />
Plant Collection<br />
Walking Path (unpaved)<br />
Main Road (paved)<br />
Forest Hills<br />
MBTA Station<br />
Orange Line<br />
Peters Hill Road<br />
Drinking Fountain<br />
WALTER S TREET<br />
B URYING G ROUND<br />
M ENDUM S TREET<br />
G ATE<br />
Oaks<br />
Hawthorns<br />
Hunnewell Building Hours<br />
April–October<br />
Weekdays: 9:00am–5:00pm<br />
Weekends: 10:00am–5:00pm<br />
November–March<br />
Weekdays: 9:00am–4:00pm<br />
Weekends: noon–4:00pm<br />
Visitor Center Hours<br />
April–October, 10:00am–5:00pm<br />
November–March, noon–4:00pm<br />
Closed Wednesdays<br />
Closed holidays<br />
www.arboretum.harvard.edu<br />
617-524-1718<br />
mi.<br />
mi. mi. mi.<br />
.25 km. .50 km. .75 km.
Change language