PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE

www.global-engage.com/event/plant-genomics #GEPGC17

16-17 March 2017Amsterdam

PLANT GENOMICS & GENE EDITING

CONGRESS: EUROPE

GLOBAL ENGAGE’S 5TH

Developing Genome Editing, Next Generation Sequencing, and Omic Technologies to Progress Plant Research

WARM WELCOME

PLANT GENOMICS AND GENE EDITING 2017

Thank you for your interest in the 5TH Global Engage 2017 Plant Genomics and Gene Editing European Congress.

Global Engage are pleased to announce as part of their NGS and gene editing series of events the 5th Plant Genomics and Gene Editing Congress, which will be held on March 16-17 2017 in Amsterdam, Holland. The congress which frequently attracts over 250 attendees is the sister meeting to both the US and Asian Plant Genomics Congresses.

Attracting experts working in all areas of plant science, the event will examine the latest in gene editing methods as well as exploring developments in NGS and omic technologies being used for progressing plant based research in aspects such as crop trait development, epigenetics, phenotyping, plant microbiome, and disease resistance as well understanding tools to overcome bottlenecks and enable successful data analysis and management. Presentations concentrate on, but are not limited to plant, crop and forestry research ranging from wheat, barley, maize and rice to potato, tomato, Arabidopsis, biofuels and various fruits in order to attract delegates across Europe and beyond.

Plant research and its associated technologies have improved dramatically over the last 5 years as a result of the revolutionary breakthroughs including new gene editing technologies and reduction in the cost of sequencing. Many plants have now been successfully sequenced and a wide range of biological data sets made available. As a result, plant scientists are now more than ever making use of state of the art technology platforms to help explain biological principals, advance research and therefore enable benefits such as crop improvement / breeding etc. by harnessing the greater understanding of plant genomes.

Should you be either an expert already using gene editing, NGS, or other genomic technologies for plant analysis with a desire to extend your knowledge, or a researcher keen to invest in sequencing / omic technology and looking to learn which platform/technology best suits your requirements - the conference will provide an interactive networking forum to answer your queries through a vibrant exhibition room full of technology providers showcasing their technologies and other solutions, expert led case study presentations, interactive Q&A panel discussions, and two roundtable sessions examining various topics through six separate tracks.

NEAL GUTTERSONVice President of R&D, DuPont

Pioneer, USA

JANE PARKERProfessor, Department of Plant

Microbe Interactions, Max Planck Institute for Plant Breeding, Germany

ROGER BEACHYCSO, Indigo Agriculture,

USA

GERCO ANGENENTProfessor and Group Leader, Plant

Developmental Systems, Wageningen University, The Netherlands

EXPERT SPEAKERS Include:

CONFERENCE SYNOPSIS

DAY 1 TRACK 1

• Synthetic biology/Genome editing applications using techniques including TALENs, CRISPRs, and ZFNs

• Improving gene editing technology• Regulating Genome Editing• Metabolic Engineering

– Plant Metabolism/Pathway manipulation/System biology• Genome / DNA assembly• Case studies• Panel: The potential impact of genome editing on global food security

Plant Genome Engineering: Strategies and Developments

DAY 1 TRACK 2

• Molecular marker development / Marker assisted selection• Disease resistance• Stress resistance• Plant breeding• Evolution studies• Pathology

Plant Genomic Case Studies - CerealsApplications of NGS, omic, and gene editing technologies for:

DAY 2 TRACK 1

• Sample preparation technology • NGS platform comparison / Best practice guidelines / Future uses• Improving qPCR and digital PCR methods for plant genetic analysis• Phenomics and high throughput phenotyping technology• Metabolomics• Genotyping by sequencing• High resolution scanning• SNP discovery, QTL mapping, alternative splicing & marker-assisted

selection

Developments in NGS, RNA-seq, and Omic Technologies

DAY 2 TRACK 2

• Bioinformatics – analysis and challenges • Use of genomic data for candidate genes• Identifying novel functional genes /networks / knowledge from data• NGS data analysis• Application of bioinformatics software for DNA / RNA analysis • Sequencing pipelines and assembly• Cloud computing and storage solutions

A) Bioinformatics and Data Analysis

• Industry applications of the latest genomic technologies• Roundtable discussion: Collaborating with Industry Partners

B) Industry Showcase

DAY 1 TRACK 3

• Identifying microbes to enhance crop productivity & disease resistance

• Stress tolerance• Soil microbiome and root assembly• Host-pathogen interactions• Structure and specificity of plant microbiomes• Technologies and techniques for microbiome research• Disease resistance• Case studies• Panel: The potential of investing in the Plant Microbiome

Plant and Soil Microbiomes

DAY 2 TRACK 3

• Epigenetics• DNA methylation• miRNA / ncRNA analysis• Genomic evolution studies• Disease/stress resistance genomics• Plant breeding technologies• Pathogen analysis

Particularly focusing on the methodology and applications of:

• Gene Editing, Plant Microbiome, Data Analysis, Sequencing Workflow, and Genomic Selection

Roundtables on:

UNABLE TO MAKE THE EUROPEAN DATES? Why not sign up for either our Asia or US meeting

Asia: 10-11 April 2017 – Hong Kongwww.global-engage.com/event/plant-genomics-asia/

USA: 2-3 November 2017 – PhiladelphiaMore information coming soon on our website

BRIAN STASKAWICZProfessor, University of California Berkeley, USA

ANGELA SESSITSCHHead of Bioresources, Austrian Institute of Technology, Austria

JOACHIM SCHIEMANNProfessor and Former Head of the Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institut, Germany

JURIAAN TONProfessor of Plant Environmental Signalling, University of Sheffield, UK

CATHERINE FEUILLETSenior VP of Trait Research, Bayer CropScience, USA

SOFIE VANTHOURNOUTEU Director, Sense about Science, Belgium

MATTHEW ASHBYResearch Fellow, Trait Discovery and Optimisation, DuPont Pioneer

TOMASZ CALIKOWSKIResearch Programme Officer, European Commission

JANE PARKERProfessor, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding, Germany

VADIM BEILINSONVice President of Research, AgBiome, USA

JOHN BROWNProfessor, University of Dundee and James Hutton Institute, Scotland, UK

MICHIEL VAN LOOKEREN CAMPAGNEHead of Biology Research, Syngenta, Switzerland

PATRICK DESCOMBES(Roundtable Host)Head of Functional Genomics, Nestlé Institute of Health Sciences, Switzerland

ANA ATANASSOVA (Track Chair)Global Regulatory Manager, Seeds and Traits, Bayer Crop Science, Belgium

STIG ANDERSEN Assistant Professor, Plant Molecular Biology, University of Aarhus, Denmark

MOHAMED ZOUINEAssociate Professor and Project Leader, INRA/INP-ENSAT, France

YINPING JIAOResearcher, Cold Spring Harbor Laboratories, USA

BRANDE WULFFProject Leader, Crop Genetics, John Innes Centre, UK

GERCO ANGENENTProfessor and Group Leader, Plant Developmental Systems, Wageningen University, The Netherlands

CHIARA TONELLIProfessor of Genetics, University of Milan, Italy

KLAAS VANDEPOELEProfessor & Principal Investigator, Department of Plant Biotechnology and Bioinformatics, University of Ghent, Belgium

NICOLA PECCHIONIDirector, Cereal Research Centre, CREA, Italy

DAMIANO MARTIGNAGOGenome Editing Specialist, Rothamsted Research, UK

MATHILDE DANIAUPhD candidate, Wageningen UR, The Netherlands

FRANK JOHANNESAssistant Professor, Technical University of Munich, Germany

JAROSLAV DOLEZELProfessor and Head of the Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Republic

NEAL GUTTERSONVice President of R&D, DuPont Pioneer, USA

ROGER BEACHYChair, Scientific Advisory Board, Indigo Agriculture Inc, and Emeritus Professor of Biology, Washington University in St Louis, USA

DIEGO ORZAEZSenior Researcher, CSIC, and Co-Leader, Plant Genomics and Biotechnology Group, Institute for Molecular Plant Biology, Spain

IAN SANDERSProfessor, Department of Ecology and Evolution University of Lausanne, Switzerland

CHRISTA TESTERINKProfessor, University of Amsterdam, The Netherlands

ODD-ARNE OLSEN (Track Chair)Professor, Norwegian University of Life Science, Norway

ALIA RODRIGUEZ VILLATEAssociate Professor in Soil Microbiology, National University of Colombia, Colombia

JOHN ODIPIOVisiting Scientist at IICI, Donald Danforth Plant Science Center, USA

ESZTER KAPUSIAssistant Researcher, University of Natural Resources and Life Sciences (BOKU), Austria

KELLYE EVERSOLEExecutive Director, International Wheat Genome Sequencing Consortium and International Phytobiome Alliance, President of Eversole Associates, USA

GIL RONENFounder and CEO, NRGene

CONFIRMED SPEAKERS

PLANT GENOMICS AND GENE EDITING CONGRESS EUROPE 2017

CONFIRMED SPEAKERS

PATRICK SCHWEIZERGroup Leader, Pathogen-Stress Genomics, Leibniz-Insitut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Germany

MARIA KALYNAPrincipal Investigator, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Austria

JOE DON HEATHVP of Market Development, NuGEN

DAVID OWDirector, Plant Gene Engineering Center, South China Botanical Garden, CAS, China

DOROTHEE STAIGERProfessor and Head of Department of Molecular Cell Physiology, University of Bielefeld, Germany

MICHAEL PROEBSTINGPhD Student, Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Germany

JAMES PEARCEMicrobial Discovery Lead, Monsanto

KRISTINA GRUDENProfessor and Group Leader of Omics approaches, National Institute of Biology, Slovenia

SVEN TWARDZIOKResearcher, Helmholtz Zentrum Munchen, Germany

JOHNATHAN NAPIERProfessor and Associate Director for Research, Rothamsted Research, UK

JACK PEART(Track Chair)Senior Director of Sales and Support EMEA, BioNano Genomics

MITCH MCGRATHProfessor, Michigan State University and USDA, USA

HUA LUAssociate Professor, University of Maryland, USA

HENRIK BRINCH-PEDERSENAssociate Professor, University of Aarhus, Denmark

RY WAGNERCEO, Agrinos AS

ERIK ANDREASSONProfessor & Head, Division of Resistance Biology, Swedish University of Agricultural Sciences, Sweden

ALEXANDRE JOUSSETAssistant Professor, University of Utrecht, The Netherlands

AAKASH CHAWADE Assistant Professor, Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Sweden

RICCARDO VELASCOHead of Genomics Research, Fondazione Edmund Mach, Italy

JONATHAN JONESProfessor and Senior Scientist, The Sainsbury Laboratory, UK

ETIENNE BUCHERHead of the EpiCenter team of the Research Institute for Horticulture and Seeds (IRHS)

OFIR MEIRCrop Protection Biotechnology R&D Director, Evogene, Israel

CORNÉ PIETERSE(Roundtable Host)Professor of Plant-Microbe Interactions, University of Utrecht, The Netherlands

MARK BORODOVSKYRegents’ Professor at the Joint Georgia Tech and Emory University Department of Biomedical Engineering and the School of Computational Science and Engineering

FRED VAN EEUWIJK(Roundtable Host)Professor of Applied Statistics, Wageningen University, The Netherlands

HELENE BERGESDirector of the French Plant genomic Resource Center, INRA, France

PIOTR PUZIOHead of Crop Pipelines at BASF CropDesign, Belgium

LINDSAY MESURE(Track Chair)Senior Account Manager Belgium, Promega

TINGTING ZHOU(Track Chair)General Manager, Novogene

RUTGER PRINS(Track Chair)Regional Business Manager Benelux & Southern Europe, BioNano Genomics

DORA QUEST(Track Chair)Regional Marketing Manager for LGC Genomics

MAX VAN MINCo-Founder & CEO, Cergentis


2017 EVENT SPONSORS

SERIES SPONSOR


Gold Sponsors

Silver Sponsors

Exhibitors

Sponsors

POSTER PRESENTATIONS

MAKING A POSTER PRESENTATIONPoster presentation sessions will take place in breaks and alongside the other breakout sessions of the conference. Your presentation will be displayed in a dedicated area, with the other accepted posters from industry and academic presenters. We also issue a poster ebook to all attendees with all abstracts in full.

Whether looking for funding, employment opportunities or simply wanting to share your work with a like-minded and focused group, these are an excellent way to join the heart of this congress.

In order to present a poster at the forum you need to be registered as a delegate. Please note that there is limited space available and posters space is assigned on a first come first served basis (subject to checks and successful registration).


1Association mapping for fiber traits

and drought tolerance in elite cotton (Gossypium hirsutum L.) germplasm

Asena Akköse Baytar1, İbrahim Çelik1, Volkan Sezener3, Ceng Peynircioğlu2, Hüseyin Başal4, Kasım Külek Öz2, Anne Frary1, Sami Doğanlar1

POSTER TITLE PRINCIPAL AUTHOR(S) AFFILIATION

1Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla,

Izmir, Turkey 2Özaltın Tarım İşletmeleri Sanayi ve Ticaret A. Ş., Koçarlı, Aydın, Turkey 3Nazilli

Cotton Research Institute, Nazilli, Aydın, Turkey 4Department of Field Crops, Adnan Menderes

University, Koçarlı, Aydın, Turkey

2 PLAZA 3.0: an access point for comparative and regulatory genomics in plants Klaas Vandepoele Ghent University – VIB

POSTER PRESENTATION EXAMPLES

3The comparison of cotton cultivar under

salinity stress and salicylic acid: biochemical, cellular and genetic variations

Zahra Nourmohammadi, Elham Torabizadeh, Farah Farahani, Omran Alishah

Department of Biology, Science and Research Branch, Islamic Azad University,

Tehran, Iran

4Seeking the best de novo transcriptome

assembling in non-model plantsM. Espigares1, P. Seoane1, R. Bautista2, J.

Quintana3, L. Gómez3, M.G. Claros1,2

1Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Malaga,

Spain 2Plataforma Andaluza de Bioinformática, Universidad de Málaga, Malaga, Spain

3Departamento de Biotecnología, Universidad Politécnica de Madrid, Madrid, Spain

5

An overview of genes and transcripts corresponding to enzymes regulating

glutathione metabolism in the olive (Olea europaea L.) reproductive tissues.

García-Quirós E(1), Carmona R(1,2), Claros MG(2), Alché JD(1*)

(1)Department of Biochemistry, Cell and Molecular Biology of Plants.

Estación Experimental del Zaidín. CSIC.(2)Andalusian Bioinformatics Platform SCBI.

University of Málaga.

6Predictive S-nitrosylation and Tyr-nitration in the olive tree (Olea europaea L.) reproductive tissues transcriptomes: an in silico approach.

Carmona R(1,2), Jiménez-Quesada MJ(1), Zafra A(1), Castro AJ(1), Claros MG(2),

Juan de Dios Alché(1)*

(1)Department of Biochemistry, Cell and Molecular Biology of Plants.

Estación Experimental del Zaidín. CSIC.(2)Andalusian Bioinformatics Platform SCBI.

University of Málaga.

7Population genetics, molecular phylogeny

and biogeography of the genus Lallemantia Fisch. et Met. (Lamiaceae)

Fahimeh Koohdar , Masoud Sheidaei Shahid Beheshti University

8A Trait Stacking System in Plants via Intra Genomic Homologous Recombination and

Nuclease-Mediated Cassette Exchange

Sandeep Kumar, Andrew Worden, Stephen Novak, Ryan Lee, Joseph F. Petolino Dow AgroSciences LLC

9 Abiotic Stress Regulation of Root Development in Rice

Shuen-Fang Lo1, Yi-Shih Chen1, Chun-Hsien Lu1, Tuan-Hua David Ho2 and Su-May Yu1*

1Institute of Molecular Biology and 2Institute of Plant and Microbial Biology, Academia

Sinica, Nankang, Taipei 115, Taiwan

10 Mining microbe-induced metabolome reprograming in plants

Desalegn Etalo, Je-Seung Jeon, Natalia Carreno-Quintero, Ric C.H. de Vos, Henk

Gude, Jos M. RaaijmakersNetherlands Institute of Ecology, NIOO-KNAW

POSTER PRESENTATIONS

POSTER TITLE PRINCIPAL AUTHOR(S) AFFILIATION

11UNcleProt - Barley nuclear protein database:

the first of its kind discerning different cell cycle phases

Hana Jeřábková, Nicolas Blavet, Ivo Chamrád, Jan Vrána, René Lenobel, Jana Uřinovská, Jana Beinhauer, Marek Šebela, Jaroslav

Doležel & Beáta Petrovská

Institute of Experimental Botany, Centre of the Region Haná for Biotechnological

and Agricultural Research, Olomouc, Czech Republic

12 Is Banana streak virus able to infect Arabidopsis thaliana?

Nathalie LABOUREAU, Albin TEULET, Anne-Sophie MASSON, Marie-Line ISKRA-

CARUANA and Matthieu CHABANNESCIRAD

13 Modifying α-gliadin proteins in bread wheat to decrease the risk of Coeliac disease in humans

Aurélie Jouanin1,2, Fiona Leigh1, James Cockram1, Emma Wallington1, Jan Schaart2,

Marinus J.M. Smulders2

1NIAB, Genetics & Breeding, Cambridge, United Kingdom 2Wageningen UR, Plant Breeding, Wageningen, The Netherlands

14The identification of the molecular

background of the cell wall integrity signalling in flax

Marta Preisner, Wioleta Wojtasik , Aleksandra Boba, JanSzop and Anna Kulma

Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, PL Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and

Technology, Wroclaw University of Environmental and Plant Sciences, Wroclaw, PL

15

OSIRIS – Exploring the yield potential of novel spike architecture in hexaploid wheat by genome wide association mapping and targeted mutagenesis using RNA-guided

Cas endonuclease

Naser Poursarebani1, Christian Hertig1, Andreas Jacobi2, Jochen Kumlehn1,

Thorsten Schnurbusch1

1Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT

Gatersleben, 06466 Seeland, Germany2Strube Research GmbH & Co. KG, 38387

Söllingen, Germany

16 Nucleic Acid Purification From Plant Tissues for Viral Detection

Samantha Lewis1, Laurence Delaurière2, Becky Carroll1, Elisa Ruiz2, Ellyn Lepinski1,

Giuseppe Durante3, Caroline Chatillon4, Doug Wieczorek1, Céline Ménager2, Eric B. Vincent1

and Trista Schagat1

1Promega Corporation; 2Promega Europe Training and Applications Laboratory;

3International Plant Analysis and Diagnostics srl.; 4Qualiplante, Cap Alpha.

17 Identification of VOCs from guava to repel a citrus pest Berta Alquezar, Leandro Peña Fundecitrus-IBMCP (UPV-CSIC)

18 Deciphering the pathways for IAA metabolism and homeostasis

Rubén Casanova-Sáez, Aleš Pěnčík, Afaf Rashed, Ute Voß, Silvana Porco, Nathan

Mellor, John R. King, Rui Pinto, Ondřej Novák, Paul E. Staswick, Markus Owen, Malcolm J.

Bennett and Karin Ljung

SLU

19 Low temperature storage effect on anthocyanin biosynthesis in blood orange fruit

Carmona, L., Alquézar, B., Marques, V.V. and Pena, L. Fundo de Defesa da Citricultura (Fundecitrus)

20Genetic interventions to reduce the

acrylamide-forming potential of wheat

Sarah Raffan1, Tanya Y. Curtis1, Damiano Martignago1, Caroline Sparks1,

Alison Huttly1, Andy Phillips1, Keith J. Edwards2 and Nigel G. Halford1

1Rothamsted Research and 2University of Bristol, UK

21

Expanding the genetic toolbox for Brachypodium distachyon

Transforming winter accessions and implementing CRISPR-Cas9

Niklas Dochy, Fuchao Jiao, Koen Geuten KU Leuven

22

Genome Wide Association analysis of biomass yield and stem composition in a sorghum Backcross Nested Association

Mapping design.

Korotimi Théra1, Niaba Témé1, Mohamed Doumbia1, Mohamed Lamine Tékété1, Michel Vaksmann2, Mamoutou Kouressy1, Aliou Sissoko1, Sekouba Sanogo1, Yaya Bouaré1, Issa Sogoba1, Baptiste

Guitton2, Jean-François Rami2, Sidi B. Coulibaly1, Laurent Bonnal3, Denis Bastineli3, David Pot2

CIRAD

23 Hormone signaling to induce hypocotyl adventitious roots in Arabidopsis

Hoang Khai Trinh1, Inge Verstraeten1,2, Sebastien Schotte1, Damilola Olatunji1, Christopher

Sheridan1, Tim De Meyer1 and Danny Geelen1

1Ghent University, Gent, Belgium; 2University of California, Riverside, USA

24 Characterization of FDP and its interaction with floral regulators

Om Narayan, Nina Jaspert and Claudia Oecking

Center for Plant Molecular Biology, Uni Tuebingen

CONGRESS SCHEDULE DAY 1 THURSDAY 16TH MARCH 2017

Registration & Refreshments08:00-08:50

08:50-09:00 Global Engage Welcome Address and Track Chair’s Opening Remarks: Anna Atanassova, Global Regulatory Manager, Seeds and Traits, Bayer Crop Science, Belgium


09:0

0-09

:40

KEYNOTE ADDRESS:JONATHAN JONESProfessor and Senior Scientist, The Sainsbury Laboratory, UKResistance (R) gene enrichment sequencing (Renseq) to investigate and exploit R gene diversity• Sequence capture allows us to define more reliable R gene repertoires• Combining Renseq with long read sequencing enables unambiguous full length R gene definition in multigene families• This enables accelerated cloning of new R genes, and new insights into R gene evolution

PLANT GENOME ENGINEERING: STRATEGIES AND DEVELOPMENTSTrack Chair: Anna Atanassova, Global Regulatory Manager,

Seeds and Traits, Bayer Crop Science, Belgium

10:10

-10:

35

BRIAN STASKAWICZProfessor, University of California Berkeley, USAGenome Editing Strategies for the Control of Plant DiseasesIn our laboratory, we are developing genomic strategies are part of a multi-pronged approach

to develop durable resistance in agricultural crops such as tomato. I will discuss our current data on the identification of host susceptibility genes in tomato. Furthermore, I will present our recent results on the use of genome editing tools to create mutations in host susceptibility genes that result in disease resistance.

10:10

-10:

35

PATRICK SCHWEIZERGroup Leader, Pathogen-Stress Genomics, Leibniz-Insitut für Pflanzengenetik und Kulturpflanzenforschung (IPK), GermanyGenes and alleles for durable resistance of barley to powdery mildew

• Genes for polygenically inherited, durable resistance in barley are being discovered by high-throuhgput RNAi

• Of special interest are factors of susceptibility because they have not been widely studied until present

• Mutants and superior alleles of such susceptibility-related factors bear the promise to enhance disease resistance in a durable manner

Track Chair: Odd-Arne Olsen, Professor, Norwegian University of life Science, Norway

10:10

-10:

35

ANGELA SESSITSCHHead of Bioresources, Austrian Institute of Technology, AustriaThe hidden world within plants: ecological considerations and functioning of microbial endophytes

Plants are colonized by complex microbial microbial communities. Endophytes are found in most plant tissues and have multiple beneficial effects on plants by providing nutrients, antagonizing pathogens and reducing plant stress symptoms. Microbiome analyses have shown that the plant genotype, tissue, the vegetation stage as well as stress factors influence the structure and possibly functioning of endophyte communities. Metagenome analysis as well as genome, transcriptome and functional analysis of individual strains have provided important functional insight how microbial endophytes colonize plants and improve stress tolerance of their host. Based on this knowledge we have developed approaches to apply microorganisms for crop improvement.

PLANT GENOMICS CASE STUDIES: CEREALS PLANT AND SOIL MICROBIOMES

Morning Refreshments / Even Numbered Poster Presentations10:35-11:45

09:4

0-10

:10

SOLUTION PROVIDER PRESENTATION:GIL RONENFounder and CEO, NRGene2017, the year of the PanGenomesThe genetic diversity currently exploited and employed in breeding is only partially represented by one reference genome, due to interspecies variability such as INdels translocations and inversions, which are abundant in plants. To capture the genomic diversity of a given plant species, one needs to create and compare multiple de-novo full genomes representing genetically distinguished lines, ultimately creating a pan-genomic view. Here we present the successful de novo assembly and all-to-all comparison of several maize and bread-wheat genomes, revealing significant genomic and intragenic sequence additions to the first available reference genome. In addition, we announce a global effort to create a pan-genome of virtually every major crop plant within 2017.

Room: Grote Zaal

Room: Grote Zaal Room: Berlage Zaal Room: Administratiezaal



11:4

5-12

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11:4

5-12

:10

11:4

5-12

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12:10

-12:

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EARLY CAREER RESEARCHER PRESENTATION:DAMIANO MARTIGNAGOGenome Editing Specialist, Rothamsted Research, UKCRISPR is on the move: genome editing from rice to wheat

My experience with CRISPR/Cas9 begun in the lab of Prof. Fabio Fornara (University of Milan), where photoperiodic rice adaptation to Europe was studied. We used CRISPR/Cas9 to target genes of interest, in particular the two rice florigens, HD3A and HD3B (formerly RFT1). Success in rice is not equalled in wheat: CRISPR/Cas9 efficiency is around 5% and requires a time-consuming downstream identification of the genome edited plants. At Rothamsted Research, this problem is being tackled producing wheat lines that constitutively express a wheat-optimised Cas9, testing the guide RNAs in vitro and targeting target genes with easily recognisable phenotypes. Results of the successful rice CRISPR/Cas9 editing of florigen genes will be presented plus progress with transfer of the technology to wheat.

EARLY CAREER RESEARCHER PRESENTATION:JOHN ODIPIOVisiting Scientist at IICI, Donald Danforth Plant Science Center, USAInduction of flowering in cassava by CRISPCR/CAS9 mediated knockout of floral repressor-like genes

Cassava supports over 6 billion lives in tropics. There is urgent need for improved cultivars to feed ever-increasing global human population and cassava dependent agro-industries. Irregular flowering habit has led to underutilization of shy flowering genotypes in conventional breeding programs. Genes promoting flowering have been identified in Arabidopsis but poor flowering in related species is also result of floral inhibitors like Terminal Flower 1 (TFL1). The role of TFL1 in regulation of flowering and or storage root development in cassava is unknown This study has optimized CRISPR/CAS9 genome editing system for targeted and down regulation of TFL1-like genes in a poorly flowering Ugandan farmer preferred cultivar. This is projected to boost transcript abundance of flower promoting FT-like genes thus inducing flowering in cassava.

12:10

-12:

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12:10

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IAN SANDERSProfessor, Department of Ecology and Evolution, University of Lausanne, Switzerland

ALIA RODRIGUEZ VILLATEAssociate Professor in Soil Microbiology, National University of Colombia, Colombia

A Microbial-Driven Green Revolution? The Power of Fungal Genomics for Feeding the PlanetMycorrhizal fungi have an enormous potential to increase crop yields on a global scale because all globally important plants form the mycorrhizal symbiosis. In this presentation, we will demonstrate how information on the genomes of mycorrhizal fungi is crucial to understanding plant growth responses to mycorrhizal fungi. We will show our approach to finding which parts of the mycorrhizal fungal genome make plants grow bigger. We will demonstrate how this can then be used to develop fungal strains that increase crop yields of a globally important plant in a real farming situation in Colombia. Finally, we will discuss why it is so important to consider the interactions between the fungal genomes and plant genomes in order to understand what makes the interaction function in a way that is beneficial for humans.

HENRIK BRINCH-PEDERSENAssociate Professor, University of Aarhus, DenmarkPotentials of the New Breeding Techniques Cis-Genesis, TALEN and CRISPR/Cas for specific trait targeting in barley

• The new breeding techniques (NBTs) cis-genesis, TALEN and CRISPR/Cas were evaluated for targeting a specific trait in the crop plant barley.

• TALEN and CRISPR/Cas generated significantly different patterns of mutations.

• Stable inheritance of mutations in barley was achieved only after using a double promoter strategy.

ESZTER KAPUSIAssistant Researcher, University of Natural Resources and Life Sciences (BOKU), AustriaHeritable chromosomal fragment deletions and small in-dels in the putative ENGase gene induced by CRISPR/Cas9 in barley

Targeted genome editing with the CRISPR/Cas9 system has been used extensively for the selective mutation of plant genes. We used CRISPR/Cas9 to disrupt the putative barley (Hordeum vulgare cv. Golden Promise) endo-N-acetyl-β-D-glucosaminidase (ENGase) gene. Defined fragment deletions were induced by five single guide RNAs (sgRNAs) designed for different target sites in the upstream part of the ENGase coding region. Genotype screening was carried out in the primary transformants (T0) and their T1 progeny to confirm the presence of site-specific small deletions, insertions (indels) and genomic fragment deletions between pairs of selected targets. Cas9-induced mutations were observed in 78% of the plants, a much higher efficiency than previously reported in various crop species. Notably, there were differences in performance among the five sgRNAs. The induced indels and fragment deletions were transmitted to the T1 generation, and transgene free (sgRNA:Cas9 negative) genome-edited homozygous ENGase knockouts were identified among the T1 progeny.

ALEXANDRE JOUSSET Assistant Professor, University of Utrecht, The NetherlandsEngineering of the rhizosphere microbiome with probiotic consortia• Plants feed microbial communities that in

return provide the plant with growth hormones and antibiotics• Application of probiotics microbes can restore disturbed

functions, yet the most promising microbes often fail to establish• Here I present how customised probiotics consortia can be

selected to form together a strong team that will form a shield around plant roots and eliminate the pathogen Ralstonia solanacearum, a major threat to crops worldwide

RICCARDO VELASCO Head of Genomics Research, Fondazione Edmund Mach, ItalyFrom Genome to Genes: Cis-genesis and Genome Editing in Fruit TreesDuring the last ten years, fruit-trees genomics

has developed so much that today we have several high quality draft of genomes available. Identify gene functions, via appropriate gene prediction and association of genes with phenotypes is the real challenge of the next decade. Once gene function is well defined, the successful use in fruit breeding is the next trouble. In fact, in fruit trees, long-span life cycle and plant size are the major limitations. Additionally in fruit trees, with respect to cereals and other annual crops, high quality products are maintained via clonal reproduction of highly heterozygous accessions. Cis-genesis and genome editing approaches may represent straight forward alternatives in order to speed up solutions.



12:4

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Lunch13:10-14:10

SOLUTION PROVIDER PRESENTATION:MAX VAN MINCo-Founder & CEO, CergentisTLA Technology for targeted complete Next Generation Sequencing and haplotypingCergentis’ Targeted Locus Amplification (TLA) Technology (published in Nature

Biotechnology in 2014) is a strategy to selectively amplify and sequence entire genes on the basis of the crosslinking of physically proximal sequences. Unlike other targeted re-sequencing methods, TLA works without detailed prior locus information, as one or a few primer pairs are sufficient for sequencing tens to hundreds of kilobases of surrounding DNA. TLA enables robust detection of single nucleotide variants, structural variants as well as haplotyping. Key applications of TLA include the targeted resequencing of genes of interest, gene-editing events and complete transgene & integration site sequencing.

PLANT GENOME ENGINEERING: STRATEGIES AND DEVELOPMENTS

Track Chair: Gil Ronen, Founder and CEO, NRGene

PLANT GENOMICS CASE STUDIES: CEREALS PLANT AND SOIL MICROBIOMES

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JOACHIM SCHIEMANNProfessor and Former Head of the institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, GermanyPlant genome editing: application, risk assessment and regulation

The genome editing and modification techniques are tools for sequence-specific changes in the plant genome. These techniques enable breeders to introduce a single point mutation or a new DNA sequence at a specific location in the plant genome, thereby circumventing the negative side effects of conventional mutagenesis. The potential risks of exploring these new genome editing techniques are comparable to conventional mutagenesis or genetic engineering. Considering these techniques and emerging new breeding techniques, the GMO-legislation framework in the EU, which is mainly interpreted and executed as being based on the technique which is used to produce a new plant, is not reflecting the progress made in recent development of genome editing.

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MATTHEW ASHBYResearch Fellow, Trait Discovery and Optimisation, DuPont PioneerFinding plant beneficial microbes with commercial value using a novel genomics/computational biology platform

Plants display myriad interactions with microbes, many of which are beneficial to plant health and yield performance. The challenge remains how to identify the most beneficial microbes in a background of thousands to tens of thousands of distinct microbial species. The task is further complicated by the organization of these communities into functional consortia which precludes their characterization through traditional screens of individual microbes. 16S rRNA gene profiling of rhizosphere microbial communities can produce large data sets that reflect the vibrant species diversity/richness and species interactions present in these environments. A description of the microbial genomics/bioinformatics platform we developed that enables teasing out microbes and microbial consortia with commercial potential for enhancing productivity and sustainability of large acre row crops will be presented.

NICOLA PECCHIONIDirector, Cereal Research Center, CREA, ItalyGenomic approaches to improve disease resistance in durum wheat• GWAS identification of SNP loci associated to quantitative resistance to stem rust of wheat in a tetraploid wheat genetic panel

• Common and specific QTLs of resistance to different foliar diseases in tetraploid wheat

• Search for candidate genes underlining disease resistance QTLs is helped by the newly assembled genome sequence of durum wheat

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SOLUTION PROVIDER PRESENTATION:OFIR MEIRCrop Protection Biotechnology R&D Director, Evogene, Israel Discovery of novel toxin families as solutions to BT resistanceEvogene has a long and successful strategy of identifying valuable genes for improving a variety of key plant traits; from resistance to nematode infestation

and fungal diseases to yield and abiotic stresses. Over the last two years, Evogene has established a new discovery program focused on insect control traits aimed at identifying toxins conferring novel mode of actions. Evogene’s strategy is based on innovative experimental designs generating unique genomic data for both cultured and uncultured bacteria, integrating that data into comprehensive databases, and world class dedicated computational platform (BiomeMinerTM) which is used to prioritize the best toxin candidates. All potential toxin genes are then expressed, purified and examined in a diet validation assay, based on industry standards, at Evogene’s US site in St. Louis. This talk will outline the general approaches, challenges, early proof of concept and future plans for this program.

Room: Grote Zaal



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:15PANEL DISCUSSION:The potential impact of gene editing on global food securityCovering topics including:• Current challenges in global food secturity• The impact of public perception on advances in gene editing

research and ways to overcome this• How regulation and politics impacts gene editing progression• The future of gene editing technologies• Current applications of gene editing and how these relate to

global food security issues• Hurdles to be overcome in pursuit of food security

CHAIR:BRIAN STASKAWICZ Professor, University of California Berkeley, USA

PANELLISTS:SOFIE VANTHOURNOUTDirector, Sense about Science EU, Belgium

NEAL GUTTERSONVice President of R&D, DuPont Pioneer, USA

JOACHIM SCHIEMANNProfessor and Former Head of the institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Federal

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PANEL DISCUSSION:The potential of investing in the plant microbiomeCovering topics including:• Investment opportunities and the current status of the plant

microbiome industry in Europe• Commercial applications of plant microbiome research• The future of the plant microbiome market• How businesses and academia can collaborate to advance plant

microbiome research

CHAIR:ROGER BEACHYChair, Scientific Advisory Board, Indigo Agriculture Inc, and Emeritus Professor of Biology, Washington University in St Louis, USA

PANELLISTS:RY WAGNERCTO, Agrinos, USA

TOMASZ CALIKOWSKIResearch Programme Officer, European Commission

ANGELA SESSITSCHHead of Bioresources, Austrian Institute of Technology, Austria


KELLYE EVERSOLEExecutive Director, International Wheat Genome Sequencing Consortium and International Phytobiome Alliance, President of Eversole Associates, USAOdyssey of the IWGSC Reference Genome Sequence: 12 years 1 month 28

days 11 hours 10 minutes and 14 secondsThe International Wheat Genome Sequencing Consortium (IWGSC) is an international, collaborative consortium, established in 2005 by a group of wheat growers, plant scientists, and public and private breeders with the goal of producing a high quality, annotated reference genome sequence for bread wheat. To meet the challenges of sequencing the large, hexaploid genome, the IWGSC focused initially on developing a solid foundation for sequencing that would accommodate any future advancements in sequencing technologies: i.e., producing physical maps for all 21 individual bread wheat chromosomes. Subsequent sequencing projects included sequencing of minimal tiling paths of mapped BACs, a chromosome-based survey sequence of the genome, and a whole genome assembly using the NRGene DeNovoMAGICTM software. By integrating whole genome and chromosome data with the BAC-based resources (sequences, physical maps, WGPTM tags), the IWGSC will release an annotated reference sequence of bread wheat cv. Chinese Spring this year while continuing manual annotation and sequencing other varieties that represent the breadth of the wheat gene pool.

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EARLY CAREER RESEARCHER PRESENTATION:SVEN TWARDZIOKResearcher, Helmholtz Zentrum Muenchen, GermanyAnnotation and analysis of the wild emmer wheat genome

• Introduction to the gene annotation of the wild emmer wheat genome assembly

• Functional annotation for gene candidates, including gene onthology (GO) terms and protein domains (PFAM/INTERPRO)

• Genome wide analysis of gene content and comparison of A and B subgenomes

• Gene expression analysis with diverse samples representing different tissues and developmental stages using RNA sequencing



Afternoon Refreshments / Poster Presentation Sessions15:45-16:35

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45SOLUTION PROVIDER PRESENTATION:JOE DON HEATHVP of Market Development, NuGENTrait to Table: NSG Solutions for Targeted Genotyping and TranscriptomicsNext-generation sequencing (NGS) technology is being widely adopted as an essential research and development tool in plant genomics. As accessibility and affordability of NGS technologies continue to improve, the tool is being applied to marker-assisted selection to accelerate plant breeding and selection, as well as in transcriptomics,

plant-pathogen interactions and epigenetics. We will present NuGEN’s novel and flexible transcript depletion strategy for enabling whole transcriptome and mRNA studies on any species. In addition, we will highlight our recently introduced targeted genotyping solution based on our novel SPET (Single Primer Enrichment Technology). Our complete sequencing library systems feature simple workflows that are cost-effective, flexible and easy to automate.

DIEGO ORZAEZSenior Researcher, CSIC, and Co-Leader, Plant Genomics and Biotechnology Group, Institute for Molecular Plant Biology, SpainA toolbox of programmable DNA-binding proteins for plant genome engineering

GoldenBraid (GB) is a modular DNA assembly tool for multigene engineering and Synthetic Biology in plants. GB2.0 now incorporates tools for CRISPR/Cas9 genome engineering. We have created a toolbox of elements dedicated to genome engineering on top of the GB2.0 collection of plant genetic elements. We will show how the combination of multigene engineering with the multiplexing capacity of CRISPR/Cas9 opens new possibilities for plant breeding. We will also show how modular cloning facilitates de design of artificial transcriptional regulators based on CRISPR/Cas9 architecture.

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VADIM BEILINSONVP of Research, AgBiomeAgBiome Inc. – microbial diversity and development of new agricultural productsAgBiome is a 4 year old innovative Agricultural Biotech company that discovers and develops

new products for the biologicals and traits markets. Our proprietary collection of fully sequenced microbial strains serves as the starting platform for all the discoveries. Over 36,000 bacterial strains represent the diversity of the microorganisms collected from a broad variety of environmental samples over 46 states in the US. AgBiome has discovered more than 2500 putative insecticidal genes in these bacterial genomes; several of these genes have shown activity against important agricultural pests and have a potential to be trait products. In addition, several microbial strains show activity against fungal and insect targets and are in development as biological products. Our first biological, a fungicide branded as Howler™ is on the market now.

HELENE BERGESDirector of the French Plant genomic Resource Center, INRA, FranceToward a better understanding of plant genomes structure: Combining NGS, optical mapping technology and CRISPR-CATCH approach

In a context of climate change and limited energy resources, better understanding how plants evolve and adapt is a major goal. However, despite the revolution of the Next Generation Sequencing technologies, the study of plant genomes remains challenging due to their size, polyploidy and high percentage of repetitive elements. The French Plant Genomic Center (CNRGV) is actively involved in providing innovative solutions. In order to help deciphering the complexity of plant genomes, the CNRGV has developed various approaches combining NGS, optical map and CRISPR-CATCH targeting strategy. We’ll present the improvement of a whole genome assembly using hybrid scaffolding combining PacBio sequencing and Bionano Genomics mapping data. We’ll also illustrate a new sequence capture approach for large DNA fragments, using the CATCH method (Cas9-Assisted Targeting of CHromosomal segments).

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Room: Grote Zaal

ROUNDTABLE DISCUSSIONS:

1) Gene EditingRICCARDO VELASCO (Host)Head of Genomics Research, Fondazione Edmund Mach, Italy

2) Plant MicrobiomeCORNÉ PIETERSE (Host)Professor of Plant-Microbe Interactions, University of Utrecht, The Netherlands

3) Data AnalysisFRED VAN EEUWIJK (Host)Professor of Applied Statistics, Wageningen University, The Netherlands

4) Ethics in Science – Plagiarism and data BRANDE WULFF (Host)Project Leader, Crop Genetics, John Innes Centre, UK

*more roundtable discussion information can be found at the end of the agenda



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JOHNATHAN NAPIERProfessor and Associate Director for Research, Rothamsted Research, UKMetabolic engineering of transgenic Camelina for the sustainable production of omega-3 fish oils

• Higher plants completely lack the biosynthetic capacity to synthesise omega-3 long chain polyunsaturated fatty acids (fish oils)

• Systematic and iterative metabolic engineering have allowed for the generation of this trait in transgenic Camelina

• Further enhancement can be envisaged via genome editing approaches, coupled with a better understanding of endogenous lipid metabolism

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RY WAGNERCEO, Agrinos ASDiscovering and Commercializing the Soil Microbiome to improve Crop Productivity • The role of the soil microbiome in plant growth and development

• Discovering and commercializing the soil microbiome for improved crop production

• Microbial products as an integral part of future agricultural solutions

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JAMES PEARCEMicrobial Discovery Lead, Monsanto From comparative metagenomics to sustainable agriculture: How an analysis of the corn and soy metagenomes can lead to microbial solutions.

It is well established that the endosphere and rhizosphere microbiomes are key influencers of plant health and that microbials introduced as seed treatments can positively affect the plant microbiome. The BioAg Alliance, a partnership between Monsanto and Novozymes to develop microbial solutions for agriculture, is in its fourth year of field testing. Critical to our success is an understanding of why, when and where a microbe works. To this end Monsanto sequenced the functional metagenomes of corn and soy endospheres and rhizospheres across their field testing locations. This represents the first in-depth characterization of these microbiomes on a broad geographic scale. Our results point to important differences between crops that inform our seed inoculation strategies to reduce nutrient-limitation on crops and belowground communities. This seminar will demonstrate how Monsanto is leveraging these data sets to discover microbials with predictive and consistent performance.

Chair’s Closing Remarks and End of Day 1 / Networking Drinks Reception17:50-18:50

DAVID OWDirector of Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, China Gene stacking in rice starting with a low Cd trait

Transgenes introduced into transformable varieties need to be introgressed to field cultivars. As new traits are added, clustering them at a transgenic locus minimizes the number of segregating units that must be reassembled back into a breeding line. The open source system we developed for site-specific recombinase-mediated gene stacking has freedom to operate, providing an alternative for crop improvement by less developed countries where food security is most at risk. We are using our target sites in the rice genome to host transgenes for crop improvement. Due to soil pollution problems in China, rice with high cadmium content has been reported in recent years. Since this problem cannot be solved easily through soil remediation, we have engineered rice to take up less Cd.

Room: Grote Zaal

CONGRESS SCHEDULE DAY 2 FRIDAY 17TH MARCH 2017

Refreshments08:10-08:40

Welcome Address and Track Chair: Rutger Prins, Regional Business Manager Benelux & Southern Europe, BioNano Genomics


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KEYNOTE ADDRESS:ROGER BEACHYChair, Scientific Advisory Board, Indigo Agriculture Inc, and Emeritus Professor of Biology, Washington University in St Louis, USAPlant Microbiomes and Sustainability in AgricultureFarmers face many challenges, including changing weather patterns and selection of costly inputs. When market prices are low, they seek ways to reduce costs; for example by reducing use of agrichemicals or improved seed varieties. While the ag chemical industry predicts increased use of products to counter increasing pressure from diseases and pests, consumers urge farmers to reduce chemical use. There is growing interest in using naturally occurring, living microbes and microbial products to reduce reliance on agrichemicals, as advances in genomic sciences improve the efficiency of discovering biological solutions. Indigo (www.indigoag.com) is focused on improving crop endobiomes to enhance the performance and productivity of crops. While additional research of factors which govern the success of microbes is required, the future of this field is bright.

DEVELOPMENTS IN NGS, RNA-SEQ, AND OMIC TECHNOLOGIES BIOINFORMATICS AND DATA ANALYSIS PLANT GENOMICS CASE STUDIES

Track Chair: Tingting Zhou, General Manager, Novogene

Track Chair: Rutger Prins, Regional Business Manager Benelux & Southern Europe, BioNano Genomics

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SOLUTION PROVIDER PRESENTATION:ETIENNE BUCHERHead of the EpiCenter team of the Research Institute for Horticulture and Seeds (IRHS) The apple genome: Its evolution and epigenetic regulation of fruit developmentUsing the latest sequencing and BioNano optical mapping technologies we have produced a high-quality de novo assembly of the apple genome. Repeat sequences, representing over half of the assembly, provided an unprecedented opportunity to investigate the ‘dark matter’ of a tree genome: we identified a new hyper-repetitive retrotransposon sequence which is over-represented in

heterochromatic regions. It is arranged in tandem repeat arrays that were detectable thanks to the BioNano optical maps. We estimate that a major transposable element (TE) burst occurred 21 My ago which seems to coincide with the uplift of the Tian Shan mountains, the center of origin of apple, suggesting that TEs may have contributed to its divergence from pear. Finally, I’ll report on epigenetic phenomena that contribute to apple fruit development.

Track Chair: Dora Quest, Regional Marketing Manager for LGC Genomics

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DOROTHEE STAIGERProfessor and Head of Department of Molecular Cell Physiology, University of Bielefeld, GermanyRibonomics approaches to decipher posttranscriptional regulation in Arabidopsis

• Genome-wide identification of in vivo substrates of RNA-binding proteins by RNA immunoprecipitation (RIP)-seq and CLIP-seq

• Transcript profiling of RBP mutants to determine how RBPs impact the fate of their binding substrates

• Analysis of alternative splicing by Next generation sequencing

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MOHAMED ZOUINEAssociate Professor and Project Leader, INRA/INP-ENSAT, FranceTomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks

TomExpress platform was developed to provide the tomato community with a browser and integrated web-tools for public RNA-Seq data visualization and data mining. RNA-Seq raw sequence data available in public databases were mapped de novo on a unique tomato reference genome sequence, and post-processed using the same pipeline with accurate parameters. A commune global normalization method was applied to all expression values. This unifies the whole set of expression data and makes them comparable. A friendly web interface has been developed which provides versatile data mining web-tools via on-the-fly generation of output graphics like expression bar plots, comprehensive in planta representations and heatmaps of hierarchically clustered expression data and correlation networks of co-regulated gene groups.

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FRANK JOHANNESAssistant Professor, Technical University of Munich, GermanyMethylome evolution in plantsCytosine methylation is a pervasive feature of most plant genomes. Despite major progress

in dissecting the molecular pathways that establish and maintain DNA methylation patterns, little is known about the mechanisms that shape methylomes over evolutionary time. Emerging inter- and intraspecific epigenomic data indicate that methylome evolution over long time scales is mainly a byproduct of genomic changes. By contrast, methylome evolution over short time scales is dominated by spontaneous epimutational events that arise at rates far exceeding those of DNA sequence mutations. We argue that deeper insights into plant methylome evolution requires knowledge of how these time scales are integrated, and show that inference methods based on the methylation site frequency spectrum (mSFS) of natural plant populations provide a first step in this direction.

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:15MITCH MCGRATHProfessor, USDA and Michigan State University, USAA nine-scaffold genome assembly of the nine chromosome sugar beetOver the course of 20 months, we assembled a sugar beet genome (700 - 800 Mb) into a

close representation of the nine haploid chromosomes of beet. This result was obtained by sequentially assembling sequences >40 kb in length, orienting these assemblies via optical mapping, and scaffolding with in vivo cross-linked, paired-end reads. Accurate and highly contiguous assemblies likely afford opportunities over their highly fragmented counterparts, in part because they may better capture the organization of tandem-duplicated gene families. In this talk, we will walk through the steps used to achieve this reference assembly, relatively simply and inexpensively, and look towards some of the applications allowing facile discovery of trait genes.

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MARK BORODOVSKYRegents’ Professor at the Joint Georgia Tech and Emory University Department of Biomedical Engineering and the School of Computational Science and EngineeringMachine Learning for Plant Genome Annotation Algorithms

Plant genomes, from Arabidopsis to recently sequenced Kiwi, present a challenge for annotation due to sequence length, number of genes, short range inhomogeneity of sequence composition and expanded in evolution non-coding regions. Inference of gene structures from the complex genomic data is supposed to be simplified by addition of RNA-Seq and protein level data. However, additional data that may carry inherent noise may bring new sources of errors. The task of gene finding that plays fundamental role in the ‘food chain’ of bioinformatics remains non-trivial. In the talk I will focus on original machine learning methods developed in my lab for ab initio as well as evidence based (e.g. transcript, protein data based) gene finding in novel eukaryotic and particularly plant genomes. These methods do not require painstaking construction of training sets of reliably annotated sequences or even an assembly of RNA-Seq reads into full length transcripts. Gene finding and annotation in tomato, cucumber, peach, sweet orange, strawberry and other plant genomes was done with help of such methods.

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STIG ANDERSENAssistant Professor of Plant Molecular Biology, University of Aarhus, DenmarkSpecialist progenitor genomes persist in globally adapted allopolyploid white clover• Sequencing the genomes of white clover and

its diploid progenitors indicated that the specialist progenitor genomes had retained their integrity following the hybridisation event 20-60,000 years ago

• Subgenome-specific expression analysis across multiple tissues provided novel insights into the genome-wide transcriptional consequences of genomic hybridisation

Morning Refreshments / Odd and Even Numbered Poster Presentations10:15-11:25 Room: Grote Zaal



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MARIA KALYNAPrincipal Investigator, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Austria Exitron splicing: discovery, characterization, evolutionary origin, and its role in proteome plasticity

Alternative splicing generates multiple transcript and protein variants from a single gene. We identified unusual alternative splicing inside protein-coding exons that we termed exitron (exonic intron) splicing. Based on RNA-Seq data, exitron splicing occurs in ~3.3% and 3.7% of Arabidopsis and human protein-coding genes. About half of the exitrons have sizes of multiples of three nucleotides. Their splicing results in internally deleted protein isoforms often affecting protein domains, disordered regions and post-translational modification sites, thus broadly impacting protein function. Exitron splicing is regulated across tissues, in response to stress and in carcinogenesis. We found that some exitrons originate from ancestral protein-coding exons and their evolution involved intron loss. Exitron splicing is a conserved strategy for increasing proteome plasticity complementing the repertoire of alternative splicing events.

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HUA LUAssociate Professor, University of Maryland, USAHow the circadian clock genes regulate Arabidopsis defense through salicylic acidLUX ARRHYTHMO is a core clock component in Arabidopsis. We found that the lux-1 mutant was

compromised to both basal and resistance-gene mediated defense against Pseudomonas syringae. lux-1 had reduced SA accumulation upon P. syringae infection and suppressed high SA levels in the constitutive defense mutant acd6-1. RNAseq analysis revealed both defense- and development-related genes are regulated by LUX. ChIP experiments further identified several defense and clock genes being direct transcriptional targets of LUX.

LUX regulates Arabidopsis defense at least partly through affecting SA signaling and LUX is tightly linked to other clock proteins. Thus LUX represents a pivotal crosstalk point between the circadian clock and plant defense.

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GERCO ANGENENTProfessor and Group Leader, Plant Developmental Systems, Wageningen University, The NetherlandsHistone modifications control temperature-induced alternative splicing and flowering in Arabidopsis

Alternative splicing of pre-mRNA generates protein diversity and is a key mechanism underlying adaptation to changing ambient temperatures in plants. We discovered a direct role for histone modifications in alternative splicing regulation and flowering induction by temperature. We found distinctive histone methylation signatures in temperature-induced differentially spliced Arabidopsis genes. Modulation of these histone H3 lysine 36 methylation patterns in various mutants causes alteration in temperature-induced alternative splicing. Our data support the model that specific histone marks recruit splicing regulators via a chromatin-binding protein and as such affects the splicing outcome. In plants with reduced H3K36me3 modification, induction of flowering by temperature is abolished, highlighting the role of this histone mark in plant plasticity to environmental changes.

Lunch12:40-13:40

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:15JOHN BROWNProfessor, University of Dundee and James Hutton Institute, Scotland, UKAn ultra-deep RNA-seq time-course defines alternative splicing in the cold temperature response of Arabidopsis

To analyse dynamic reprogramming of the transcriptome of Arabidopsis plants transferred to the cold, we have an ultra-deep RNA-seq time-course. We use Salmon and a comprehensive, non-redundant Reference Transcript Dataset (AtRTD2 – bioRxiv May 2016) to quantify expression at the transcript level. Differential expression at the gene and transcript level as well as differential alternative splicing identifies around a third of genes which are differentially expressed and undergo AS. We identify genes regulated only by transcription, only by AS and by both transcription and AS including isoform switches and changes in rhythmic expression.

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KLAAS VANDEPOELEProfessor & Principal Investigator, Department of Plant Biotechnology and Bioinformatics, University of Ghent, BelgiumComparative genomics to the rescue: using available sequence data to better understand new plant genomes

Genome sequencing is becoming cheaper and faster thanks to next-generation sequencing. Obviously, the complexity of a plant genome poses major challenges to obtain a contiguous and complete genome sequence where all genes are correctly identified. Recently, we performed a systematic analysis on how to reliably estimate the completeness of a genome assembly and annotated gene space. Different measures of completeness were compared in twelve recently published plant genomes. I will highlight several cases where dissimilar completeness scores are the consequence of technical issues of assembly or annotation, or due to strong biases in the expected gene space. Furthermore, based on our PLAZA comparative genomics, I will demonstrate how integrative sequence repositories can facilitate new discoveries both in model and non-model species.

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CHRISTA TESTERINKProfessor of Plant Cell Biology, University of Amsterdam, The NetherlandsNatural variation in root architecture responses to salinity stress reveals novel regulators of root developmental plasticity

Salt stress is one of the major threats for modern agriculture, and exposure to salt alters root architecture. Yet genes underlying salinity-induced changes in Root System Architecture (RSA) remain to be identified. We examined natural variation among 347 Arabidopsis accessions in root development under salt stress and identified different root plasticity ideotypes. Furthermore, salt induced changes in RSA were associated with 100 genetic loci using genome-wide association study (GWAS). Validation of selected novel genetic loci show a role for regulation of ion transport in early stages of root development, which affects plant performance in saline soils.

Room: Grote Zaal



BRANDE WULFFProject Leader, Crop Genetics, John Innes Centre, UKRapid gene cloning in plants• Molecular cloning of genes underpinning genetic variation in the wild ancestors of our domesticated crops opens up novel precision-deployment possibilities in elite cultivars via gene editing and transgenesis.

• However, large genomes, extensive regions of suppressed recombination, and long generation times, often impose significant barriers to gene cloning in crops and crop wild relatives.

• Using a series of case-studies in small-grain cereals, I will present a suite of enabling technologies that can overcome these obstacles and speed up gene cloning.

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COLLABORATION ROUNDTABLE DISCUSSIONS:This session offers an opportunity for academics and industry representatives to come together and discuss their experiences working on collaborative projects, examining both the challenges and the benefits of such arrangements. There will also be a chance to network and consider partnering opportunities with each table being hosted by a leading expert from some of the top plant science companies in the world. The focus of the roundtable discussion groups is predominantly to provide a platform for debate and discussion between academia and industry to help progress plant genomic and gene editing research and provide a better future for the field through collaboration.

1) PATRICK DESCOMBESHead of Functional Genomics, Nestlé Institute of Health Sciences, Switzerland

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JANE PARKERProfessor, Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, GermanyPlant intracellular immunity networks Plants have evolved a multi-layered innate immune

system to respond to pathogenic microbes. At the heart of this resistance network is a large family of intracellular nucleotide-binding/leucine rich repeat (NLR) receptors which guard against microbial interference. In the absence of an attacking pathogen NLRs need to be tightly controlled because, once activated, they disturb normal growth and fitness. We’re using Arabidopsis interactions with biotrophic pathogens to understand intracellular immunity signaling. I’ll describe our dissection of resistance pathways and how they steer the plant stress network to respond appropriately to environmental perturbations. I’ll also describe an exploration we’ve started of how certain NLR allelic forms or ‘haplotypes’ behave in a natural Arabidopsis population at the level of plant fitness, stress pathway homeostasis and interactions with microbes.

DEVELOPMENTS IN NGS, RNA-SEQ, AND OMIC TECHNOLOGIES INDUSTRY SHOWCASE PLANT GENOMICS CASE STUDIES

Track Chair: Lindsay Mesure, Senior Account Manager Belgium, Promega

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NEAL GUTTERSONVice President of R&D, DuPont Pioneer, USATargeted breeding applications of CRISPR-Cas technology for European marketsCRISPR-Cas as an advanced plant breeding tool is a more efficient way to improve plants and help

farmers produce more and better food, with fewer resources. The superior properties of CRISPR-Cas allows DuPont Pioneer scientists to develop innovative and sustainable seed products for growers similar to those realized through conventional plant breeding, but with even greater efficiency, accuracy and quality. Pioneer is leading the application of this tool to develop customized agriculture solutions.

In this talk, potential product targets of this promising technology will be discussed, including wheat improvement based on a rich understanding of the wheat genome. Approaches to fostering social license and developing an open innovation model for CRISPR-Cas will also be reviewed.

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JURRIAAN TONProfessor and Co-Director of the P3 Institute, University of Sheffield, UKThe epigenetic basis of plant immunityWe previously discovered that progeny from diseased Arabidopsis are epigenetically

primed for salicylic acid (SA)-dependent defence. Currently, we are addressing 3 questions to explore the epigenetic basis of Arabidopsis immunity:• How does DNA (de)methylation influence SA-dependent immune

responsiveness? Analysis of DNA (de)methylation mutants revealed that half of the defence-related transcriptome is under control by DNA (de)methylation. The majority of these epigenetically controlled defence genes are regulated in trans by DNA (de)methylation.

• What is the transgenerational impact of disease on global DNA methylation? We are comparing methylomes of progenies from diseased/healthy plants at different generations. Preliminary results suggest that disease augments spontaneously occurring variation in DNA methylation.

• What are the epi-alleles of transgenerational resistance? Using a population of epigenetic recombinant inbred lines (epiRILs), we identified four epi-QTLs controlling transgenerational immune priming. To identify the underpinning epi-alleles, we are comparing the transcriptomes and methylomes of highly resistant epiRILs.

JAROSLAV DOLEZELProfessor of Molecular Biology and Genetics and Head of Centre of Plant Structural and Functional Genomics, Palacky University, Czech RepublicChromosome-centric approaches in plant genome assembly and gene cloning

• Dissection of genomes to chromosomes by flow-sorting provides a lossless and sequence-unbiased approach to genome complexity reduction

• The ability to isolate individual chromosomes combined with next generation sequencing permits the validation of whole genome shotgun assemblies

• Sequencing of chromosomes from particular genotypes enables rapid identification of candidate genes

Track Chair: Jack Peart, Senior Director of Sales and Support EMEA, BioNano Genomics




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EARLY CAREER RESEARCHER PRESENTATION:MICHAEL PROEBSTINGPhD Student, Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Germany

Application of CRISPR-Cas9 genome editing systems for improving oilseed rape disease resistance• A new strategy for increase in resistance of oilseed rape against

the fungal pathogen by interrupting the compatible plant-pathogen interaction.

• A CRISPR/Cas9-based tool to specifically knock-out genes coding for host susceptibility factors.

• A novel approach for modification of candidate target sequences via homology directed repair (HDR).

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EARLY CAREER RESEARCHER PRESENTATION:YINPING JIAOResearch Associate, Cold Spring Harbor Laboratory and USDA-ARS, USAThe complex sequence landscape of maize revealed by single molecule technologies

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. Here, we report the assembly and annotation of maize, a genetic and agricultural model organism using single molecule technologies. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and significant improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed over 130,000 intact transposable elements, allowing us to identify TE lineage expansions unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by SMRT sequencing. In addition, comparative optical mapping of two other inbreds revealed a prevalence of deletions in the region of low gene density and maize lineage-specific genes.

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2) MICHIEL VAN LOOKEREN CAMPAGNEHead of Biology Research, Syngenta, Switzerland

3) NEAL GUTTERSONVice President of R&D, DuPont Pioneer, USA

4) JAMES PEARCEMicrobial Discovery Lead, Monsanto

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ERIK ANDREASSONProfessor & Head, Division of Resistance Biology, Swedish University of Agricultural Sciences, SwedenDisease resistance and stress physiology in potato

• Early senescence in field grown RNAi-silenced coi1 potato• Alternaria solani, citrate binding protein and citrate in potato• Proteomics field data from potato leaves

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CATHERINE FEUILLETSenior VP of Trait Research, Bayer CropScienceWhat do we need to hold the promises of genome editing in crops?• The first successes in editing crops through different technologies have paved the way to deploy

targeted genome optimization for achieving precision breeding• Several systems enable already precise DNA targeting and break

induction, and gene Knock outs have been achieved through the most efficient DNA repair pathway.

• Consequently, most crop editing examples are gene knock outs but precision breeding requires also precise gene editing and gene stacking

• Additional technology advances are needed to achieve efficient gene editing and gene stacking in all crops

• Beyond the technology, we need targets and therefore a better understanding of the molecular basis of traits underlying crop performance

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EARLY CAREER RESEARCHER PRESENTATION:MATHILDE DANIAUPhD candidate, Wageningen UR, The NetherlandsNew strategy to get durable disease resistance in wheat

Nonhost resistance (NHR) is the immunity displayed by all genotypes of a plant species towards all pathotypes of a potential pathogenic species. NHR is the most common form of disease resistance in plants; and this resistance is durable. From previous research at IPK (Dr. Patrick Schweizer, Gatersleben, DE) using transient expression system, two barley Receptor-Like Kinases (RLKs) genes have been shown to play a role in NHR to the wheat powdery mildew pathogen, Blumeria graminis tritici (Bgt). The current research aims to validate this through stable over-expression studies in wheat. Assessment of these barley genes in wheat transgenic lines for response to Bgt inoculation will determine whether genes involved in NHR in barley could confer host resistance when expressed in wheat.

Afternoon Refreshments15:10-15:30 Room: Grote Zaal


Conference Close16:20

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AAKASH CHAWADEAssistant Professor, Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), SwedenPrecision plant breeding with omicsRecent and continuous development of the -omics methods and techniques has allowed high-throughput and precision measurements of the transcriptome, proteome, metabolome and the phenome of a plant. This has led to the application of these

techniques for generation of high-throughput data for precision plant breeding. We have shown that targeted proteomics is a promising technique for developing protein based markers for late blight resistance breeding in potato. By integrating QTL and transcriptomics, we identified candidate gene specific markers for yellow rust resistance in wheat and with high-throughput phenotyping and machine learning we developed prediction models for yellow rust resistance in wheat. These results will be presented.

ROUNDTABLE DISCUSSION DAY 1, TRACK 2 (17:25-18:15)Each roundtable discussion will last for 50 minutes and be led by a roundtable host who will supply some initial points to consider within the scope of the general topic which the participants can discuss. The tables will be running alongside each other at delegates will have the opportunity to choose which table they would like to join before the meeting. This is the perfect opportunity to troubleshoot and interact with other experts in these fields and learn from other people’s experience to improve your own work in plant genomics and gene editing research. The 5 tables will cover:

1) Gene EditingConfirmed Host: Riccardo Velasco, , Head of Genomics Research, Fondazione Edmund Mach, Italy • Improved process and workflow systems• Future applications of the technology• Troubleshooting and problem solving

4) Ethics in Science – Plagiarism and data manipulation

Confirmed Host: Brande Wulff, Project Leader, Crop Genetics, John Innes Centre, UK

2) Plant MicrobiomeConfirmed Host: Corné Pieterse, Professor of Plant-Microbe Interactions, University of Utrecht, The Netherlands• Urgent scientific questions in modern-day plant

microbiomics – towards a deep mechanistic understanding of interactions between plants, microbiomes, and their (soil) environment.

• Technical challenges in plant microbiomics – towards a standardized multi model system?

• Applying plant microbiomics: learning from nature – towards sustainable innovations in microbial agriculture.

3) Data AnalysisConfirmed Host: Fred Van Eeuwijk, Professor of Applied Statistics, Wageningen University, The NetherlandsMethods to analyse large amounts of data• Do we have adequate quantitative tools in plant

breeding and genetics to take full benefit of the increased volumes of genotypic, phenotypic and environmental volumes of data?

• Does the design and analysis of field and platform experiments receive enough attention in the era of machine learning and data science?

• Does the university education in quantitative methods of plant breeders and geneticists prepare them well for their future work?


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PIOTR PUZIO Head of Crop Pipelines at BASF CropDesign, BelgiumTraitMill™: The crop phenotyping platform for functional genomics and beyond With the TraitMill™ technology platform, CropDesign has created one of the largest corporate programs for high-throughput identification of agronomic traits in cereals. TraitMill™ closes the gap between genomics and the phenome. The heart of TraitMill™is the automated phenotyping platform which allows analysis of over 100 different

phenotypic parameters of leaves, root and yield components at different environmental conditions. The phenotyping approaches used for the evaluation of all the parameters will be outlined in the presentation.

Further potential for TraitMill™ lies in assessing the effect of applied active ingredients, or functional crop care solutions, on the stimulation of plant growth and plant productivity. Thus TraitMill™ platform has a high potential for a broad range of applications in omics research and beyound.

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KRISTINA GRUDENProfessor and Group Leader, Omics Approaches, National Institute of Biology, SloveniaTolerance to virus infection in plants resembles mutualism and is conditioned by changes in plant small RNA and hormonal signalling pathways

Potato virus Y (PVY) is the most economically important potato viral pathogen worldwide. We unravelled the roles of miRNAs in the complex immune signalling network controlling defence responses that can render plants tolerant to viral infection. We show that sRNA regulatory network is linking immune and developmental signalling in potato. Tolerant interaction of potato with the virus perturbs sRNAs network resulting in the downregulation of GA signalling as well as modulation of R-gene transcript levels, leading to minimalisation of disease symptoms. Supporting this, the responses observed for individual miRNAs, R-genes and GA signalling bear striking similarity to mutualistic symbiosis. It is thus plausible that a similar modulation of plant responses occurs in both mutualistic symbiosis and tolerance.

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MICHIEL VAN LOOKEREN CAMPAGNEHead of Biology Research, Syngenta, SwitzerlandConverging science driving innovation at Syngenta• Convergence between biotechnology and

breeding is driving innovation in the seeds industry, and we now are entering the age of predictive breeding at scale. Next is the convergence between chemistry and biology, with RNA-based Biocontrols and synthetic biology at the horizon.

• Both product innovation and cost innovation will have equally important parts to play in creating value to the growers.

• Our ability to explain the societal benefits of these innovations will be pivotal in determining the role of technology in accelerating the sustainable intensification of agriculture that society will need.

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CHIARA TONELLIProfessor of Genetics, University of Milan, ItalyModulating Stomatal Activity for Water Use Efficiency and Stress ToleranceDrought is a major threat to agriculture and food production. Considering that over 70% of the

globally available fresh water is used in agriculture to sustain crop production, it will be imperative to develop new crops with higher performance under water scarcity and able to consume less water and to maintain high efficiency. Functional genomics studies allowed a precise understanding of some of the physiological mechanisms governing plant adaptations to drought. Examples will be presented of how to improve crop yields under water scarcity through target-specific genetic engineering for modulation of stomata closure.

Room: Grote Zaal

VENUE INFORMATION

Beurs van Berlage, Conference Centre, Damrak 243,1012 ZJ, Amsterdam, The Netherlands

Located in the heart of Amsterdam, the historic Beurs van Berlage is a nationally listed building and former stock exchange offering a one-of-a-kind conference experience. A range of accommodation to suit all budgets can be sourced locally. For more information, please contact Scott Taylor at [email protected]


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PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE

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