# Using crop-pathogen modeling to identify plant traits to control Zymoseptoria tritici epidemics on wheat

Christophe Gigot, David Claessen, Guillaume Garin, Christian Fournier, Christophe Pradal, Corinne Robert

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## To cite this version:

Christophe Gigot, David Claessen, Guillaume Garin, Christian Fournier, Christophe Pradal, et al. Using crop-pathogen modeling to identify plant traits to control Zymoseptoria tritici epidemics on wheat. EUCARPIA Cereal section Meeting "Breeeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France., 2018. hal-01800385

HAL Id: hal-01800385

https://hal.science/hal-01800385

Submitted on 2 Jun 2020

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EUCARPIA Cereal section meeting

&

2nd International Wheat Innovation workshop

March 19th - 22th, 2018
Polydôme, Clermont-Ferrand, France
Polydôme, Clermont-Ferrand, France

EUCARPIA Cereal section meeting - March 19-21 2018 -

2nd International Wheat Innovation Workshop - March 22 2018

**Congress Abstracts - Numeric Version**

Distributed into an USB key during the two seminars

**Copyright** © 2018 - INRA: https://symposium.inra.fr/eucarpia-cereal2018/ . All rights reserved
INRA, Institut National de la Recherche Agronomique (Établissement public à caractère scientifique et technologique)

**Editor** : Thierry LANGIN, Gilles CHARMET, Jacques LE GOUIS & Philippe LEROY
UMR INRA/UCA 1095 GDEC - 5 chemin de Beaulieu - 63000 CLERMONT-FERRAND - FRANCE

**Photos credits:** UMR INRA/UCA 1095 GDEC

While every precaution has been taken in the preparation of this numeric book, the editor assumes no responsibility for errors or ommissions.
Neither is any liability assumed for damages resulting from the use of the information contained herein.

ISBN: 978-2-9563873-0-5

EAN: 9782956387305

Le code de la propriété intellectuelle du 1er Juillet 1992 interdit la photocopie à usage collectif sans autorisation des ayants droit. Le non-respect de cette proposition met en danger l'édition, notamment scientifique. Toute reproduction, partielle ou totale, du présent ouvrage est interdite sans autorisation de l'éditeur ou du Centre Français d'exploitation du droit de copie (CFC), 20 rue des Grands-Augustins, 75006 Paris, France.
Eucarpia Edito

Small grain cereals are the most widely grown annual crops worldwide. Wheat and barley are the two major cereals with cultivated surfaces of 230 and 60 Mha, respectively. Cereal grains have a huge range of utilization and wheat represents ~19% of human calorie intake, up to 50% in some countries. It is processed in many different products (breads, biscuits, breakfast, beer...). It is also widely used for ruminant and monogastric feed, and by biofuel (ethanol) or biomaterial industry.

Cereal production dramatically increased after the green revolution (1960-1990), but the production rate is now decreasing (see http://www.wheatinitiative.org/about-wheat/factsheets-infographics). The reason is a slight decrease of the surface cultivated with cereals because of competition with other crops or non-agricultural uses. Another reason is a slower yield progression, partially attributed to climate change. To face the challenge of food security for an ever-growing world population, cereal yield must be pushed upward, but not at any cost. Indeed, intensive production systems using fertilizers and pesticides are increasingly questioned for their negative impacts on the environment or human health. For example, nitrates in fresh or marine water cause eutrophication and pesticide residues may have carcinogenic effect or act as endocrine disruptors. Consumers and citizen are also more and more demanding for sustainable farming systems and safe products.

Plant breeding is often presented as a sustainable way to produce more and better. Recent developments in genomics, genotyping, phenotyping and breeding methodologies open new perspectives to design future varieties, with higher performance or resilience, targeting more specific conditions and utilizations, and more environmentally friendly.

The cereal section congress of EUCARPIA (www.eucarpia.org) is the opportunity to learn about recent developments in genetics and cereal breeding, from basic research on quantitative genetics, breeding methodology, crop modelling, genome organization and evolution to applied research on genome editing, QTL detection for marker assisted selection, plant-micro-organism interaction, biotic and abiotic stresses.

The 2nd edition of the International Wheat Innovation Workshop (IWIW2) is the opportunity to present complementary results obtained in major wheat programmes and pave the way for future collaborations and funding opportunities.

Gilles CHARMET

February 25th, 2018, Clermont-Ferrand, France
Head of the Eucarpia Organizing Committee
IWIW Edito

In recent years, many scientific and technological advances have opened up huge opportunities to select more efficiently for complex traits and accelerate the pace of genetic progress. These include the long-awaited availability of the wheat genome reference sequence and its annotation, the development of genomic selection and high throughput phenotyping methods, and the fine-tuning of increasingly precise and specific genome editing techniques...

How can we use these fantastic opportunities to meet the challenge of global change? The issue is now to define optimal strategies to combine all these results and tools, all the multidisciplinary skills and all the academic, private and institutional partners to breed for better adapted cereals cultivars. We designed this day of exchange and reflexion to help generate these strategies.

The second edition of the International Wheat Innovation Workshop (IWIW2) is indeed the opportunity to exchange on topics of interest with the wheat community and pave the way for future collaborations and funding opportunities. It is built around topics which have known major evolutions recently and will probably continue change rapidly: Genetic resources, Phenotyping, Genome editing, Genomic selection and Bio-informatics.

This workshop is organized at the initiative of the BreedWheat project, and associates some of the major wheat programmes: Design Future Wheat program (UK BBSRC), proWeizen (German research and breeding alliance) and CRP Wheat (CGIAR challenge program) as well as the Wheat Initiative.

We thank in advance the speakers that accepted to describe the state of the art and speculate about the future in introductory and impulse talks that will feed the group sessions. We hope that this day and the World Café will be fruitful to all and lead to new networks of collaborations and relevant projects.

Jacques LE GOUIS

March 2nd, 2018, Clermont-Ferrand, France
Head of the IWIW Organizing Committee
## EUCARPIA Scientific Committee

**Alison Bentley**, NIAB, UK

**François Balfourier**, INRA, France

**Bernard Béjar**, Céréales vallée, France

**Andreas Borner**, chair EUCARPIA cereal, IPK Germany section

**Luigi Cattivelli**, CREA, Italy

**Gilles Charmet**, INRA, France

**Fiona Doohan**, University of Dublin, Ireland

**Catherine Feuillet**, Bayer, USA

**Simon Griffiths**, John Innes Centre, UK

**Beat Keller**, University of Zürich, Switzerland

**Elena Khlestkina**, University of Novossibirsk, Russia

**Thierry Langin**, CNRS, France

**Valérie Mazza**, Limagrain, France

**Frank Ordon**, JKI, Germany

**Etienne Paux**, INRA, France

**Catherine Ravel**, INRA, France

**Laura Rossini**, University of Milano, Italy

**Jérôme Salse**, INRA, France

**Pierre Sourdille**, INRA, France

**Nils Stein**, IPK, Germany

## IWIW2 Organizing Committee

**Jacques Le Gouis**, INRA, France

**Graham Moore**, John Innes Centre, UK

**Victor Kommerell**, CIMMYT, Germany

**Tanja Gerjets**, proWeizen, Germany

**Emmanuelle Lagendijk**, INRA Transfert, France

**Claire-Marie Sonnier**, Céréales Vallée, France

**Bernard Bejar**, Céréales Vallée, France
Logistics Committee

UMR INRA/UCA 1095 GDEC, France

François Balfourier

Gilles Charmet

Nicolas Guilhot

Emmanuelle Lagendijk

Thierry Langin

Jacques Le Gouis

Philippe Leroy

Isabelle Lhommet

Christine Mauny

Valérie Martignac

Etienne Paux

Catherine Ravel

Karine Ribeyre

Annie Rigaud

Jérôme Salse

Pierre Sourdille

Patricia Tixier-Leyre
Sponsors

EUCARPIA

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EUCARPIA

Wageningen, The Netherlands

http://www.ecpgr.cgiar.org/

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Science For A Better Life

<figure><img src="image_7.png" /></figure>

Bayer CropScience

35000 Paramount Parkway, Morrisville, NC 27 560, USA

http://www.cropscience.bayer.com/

<figure><img src="image_8.png" /></figure>

Biovitis

Biovitis

Le Bourg, 15 400 Saint Etienne de Chomeil, France

http://www.greentech.fr/biovitis-les-micro-organismes/

<figure><img src="image_9.png" /></figure>

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Limagrain
from earth to life

Limagrain

Biopôle Clermont-Limagne, Rue Henri Mondor, 63 360, Saint Beauzire,
France

http://www.limagrain.com/

<figure><img src="image_11.png" /></figure>

KWS

<figure><img src="image_12.png" /></figure>

KWS UK LTD

56 Church Street, Thriplow, Royston, Hertfordshire, SG8 7RE, UK

http://www.kws-uk.com/

<figure><img src="image_13.png" /></figure>

ao

Agri Obtentions

Semencier de l'agriculture durable

Agri Obtentions

Chemin de la petite Minière, 78 280 Guyancourt, France

http://www.agriobtentions.fr/

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## Partners

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**Breedwheat**
Clermont-Ferrand, France
http://breedwheat.fr

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Inventing
tomorrow's
cereals

**Céréales Vallée**
Biopôle Clermont-Limagne, 63 360 Saint-Beauzire, France
http://www.cereales-vallee.org

<figure><img src="image_17.png" /></figure>

**Biogemma**
Route d'Ennezat, 63 720 Chappes, France
http://www.biogemma.com

<figure><img src="image_18.png" /></figure>

**Optomachines**
8 rue Richard Wagner, 63 200 Riom, France
http://www.optomachines.fr

<figure><img src="image_19.png" /></figure>

**Burleigh Dodds Science Publishers**
82 Hihg Street, Sawston, Cambridge CB22 3HJ, UK
http://www.bdspublishing.com

<figure><img src="image_20.png" /></figure>

**Volvic**
Société des eaux de Volvic, ZI du Chancet, CS 700 35, 63 530 Volvic, France
http://www.volvic.fr

<figure><img src="image_21.png" /></figure>

**Ville de Clermont-Ferrand**
Hôtel de Ville, 10 rue Philippe-Marcombes, BP 60, 63 033 Clermont-Ferrand Cedex 1, France
https://clermont-ferrand.fr/

<figure><img src="image_22.png" /></figure>

**Région Auvergne-Rhône-Alpes**
59 Boulevard Léon Jouhaux, 63 000, Clermont-Ferrand, France
https://www.auvergnerhonealpes.fr/

+
clermont
auvergne
métropole

**Clermont Auvergne Métropole**
64-66 avenue de l'Union Soviétique, BP 231, 63 007, Clermont-Ferrand, France
https://www.clermontmetropole.eu/
Institutions

<figure><img src="image_23.png" /></figure>

INRA
SCIENCE & IMPACT

**INRA**
147 rue de l'Université, 75 338 Paris Cedex, France
http://www.inra.fr

<figure><img src="image_24.png" /></figure>

INRA
Transfert

**INRA Transfert**
28 rue du Docteur Finlay, 75 015 Paris, France
http://www.inra-transfert.fr/fr/

<figure><img src="image_25.png" /></figure>

UNIVERSITÉ
Clermont
Auvergne

**Université Clermont-Auvergne**
9 boulevard François-Mitterrand, CS 60032, 63 001 Clermont-Ferrand cedex 1, France
http://www.uca.fr
<figure><img src="image_26.png" /></figure>

We are on a journey of discovery

The Bayer Hybrid Wheat Project will deliver improved, more stable, predictable yields with quality parameters and a more prosperous future for wheat growers wherever they are in the world.

<figure><img src="image_27.png" /></figure>

A more **prosperous**
**future** for farmers

<figure><img src="image_28.png" /></figure>

A wheat **tailored to local needs and environments**, delivering improved, **more predictable yields**

<figure><img src="image_29.png" /></figure>

A wheat supply able to **feed a**
**growing world population**

Enabling Bayer to successfully
 unlock the performance potential of wheat

<figure><img src="image_30.png" /></figure>

www.bayer.com
Biovitis

**BIOVITIS** is a SME producing biomass and natural active ingredients, located in Saint-Etienne-de-Chomeil, Cantal.

We rely on our Industrial Fermentation Tools (Liquid and Solid States), R&D and commercial teams to develop products for different fields:

<figure><img src="image_31.png" /></figure>

**Food and Feed Industries**

<figure><img src="image_32.png" /></figure>

**Health and Wellness**

<figure><img src="image_33.png" /></figure>

**Environment**

<figure><img src="image_34.png" /></figure>

**Agronomy**

We are part of Greentech Group, alongside Greentech (plant bioactives) and Greensea (biomarine actives)

**Meet us at our booth**

<figure><img src="image_35.png" /></figure>

BIOVITIS S.A. - Le Bourg - 15400 SAINT-ETIENNE-DE-CHOMEIL

(33) 04 71 78 37 00 -

<figure><img src="image_36.png" /></figure>

biovitis@sabiovitis.fr -

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www.laboratoires-biovitis.fr
Advertising

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# EUCARPIA
## SCIENTIFIC PROGRAMME

Monday March 19th, 2018

<table><thead><tr><th></th><th></th></tr></thead><tbody><tr><td>7h30 am - 9h30 am</td><td>Registration & Welcome coffee (poster hanging)</td></tr><tr><td>9h30 am - 10h10 am</td><td>Welcome talks by Andreas BORNER EUCARPIA cereal section chairman and organizers</td></tr><tr><td>10h10 am - 10h50 am</td><td>Introductory talk: Raphaël DUMAIN (Bayer - Germany): Global context for wheat, Innovation & Bayer Activities</td></tr><tr><td colspan="2"><strong>Session I. Characterization and use of genetic resources</strong></td></tr><tr><td colspan="2">Chair: François Balfourier, INRA, France</td></tr><tr><td>10h50 am - 11h30 am</td><td>Keynote speaker: Andreas GRANER (IPK - Germany): Ex situ collections: getting dressed up for another green revolution</td></tr><tr><td>11h30 am - 11h55 am</td><td>Davide GUERRA (CREA - Italy): Studying the genetic basis of barley adaptation to contrasting environments in the WHEALBI collection</td></tr><tr><td>11h55 am - 12h30 am</td><td>Ernesto IGARTUA (EEAD-CSIC - Spain): Association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula</td></tr><tr><td>12h30 pm - 2h00 pm</td><td>Lunch break</td></tr><tr><td>2h00 pm - 2h25 pm</td><td>Marco MACCAFERRI (U Bologna - Italy): SNP-based characterization of a wide collection of tetraploid wheat reveals extensive domestication sweeps and haplotypes associated to traits of breeding interest</td></tr><tr><td>2h25 pm - 2h40 pm</td><td>Helmy M YOUSSEF (IPK - Germany): Natural Diversity of Inflorescence Architecture Traces Cryptic Domestication Genes in Barley (Hordeum vulgare L.)</td></tr><tr><td>2h40 pm - 2h55 pm</td><td>Constance LAVERGNE (U Nottingham - UK): Introduction of Aegilops sharonensis cytoplasm into common wheat and production of addition / wheat - Ae. sharonensis lines translocation lines</td></tr><tr><td colspan="2"><strong>Session II. Genomics and epigenomics in the post sequence era</strong></td></tr><tr><td colspan="2">Chair: Laura Rossini, University of Milano, Italy</td></tr><tr><td>2h55 pm - 3h35 pm</td><td>Keynote speaker: Scott Allen JACKSON (U Georgia - USA): Sources of variation in crop legumes—genetic, epigenetic and structural</td></tr><tr><td>3h35 pm - 4h00 pm</td><td>Luigi CATTIVELLI (CREA - Italy): Durum wheat genome reveals the signature of 10,000 years of selection</td></tr><tr><td>4h00 pm - 4h30 pm</td><td>Coffee break & poster session</td></tr><tr><td>4h30 pm - 4h55 pm</td><td>Caroline JUERY (INRA GDEC - France): Linking genomic and epigenomic features in hexaploid wheat genome</td></tr><tr><td>4h55 pm - 5h20 pm</td><td>Cécile MONAT (IPK - Germany): Hi-C and chromosome-scale assembly to detect large chromosomal rearrangements in wheat genomes</td></tr><tr><td>5h20 pm - 5h35 pm</td><td>Maria BUERSTMAYR (BOKU - Austria): High-resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harboring the Fusarium head blight resistance QTL Qfhs.ifa-5A</td></tr><tr><td>5h35 pm - 6h30 pm</td><td>Romain DE OLIVEIRA (INRA GDEC - France): Deciphering Structural Variations in the Wheat Genome Using Resequencing Data</td></tr><tr><td>6h30 pm - 8h00 pm</td><td>Cocktail at the Clermont-Ferrand city hall</td></tr></tbody></table>
## Session III. Yield potential and resource efficiency

Chair: Frank Ordon, JKl, Germany

8h30 am - 9h10 am

**Keynote speaker: John FOULKES** (U Nottingham - UK): Exploiting Genetic Diversity for Enhancing Yield Potential and Resource Efficiency in Wheat

9h10 am - 9h35 am

**Bruno CONTRERAS-MOREIRA** (ADES-CSIC - Spain): Agronomic advantage of presence of PpdH2 in winter barleys proven through a natural selection approach using GBS in pools of field-grown populations

9h35 am - 10h00 am

**Gaëtan TOUZY** (Arvalis - France): Improving Water Use Efficiency in Bread Wheat by Multi-trait multi-Environment Genome-Wide Association Studies

10h00 am - 10h30 am

**Eric OBER** (NIAB - UK): Implementing large-scale field phenotyping in genomic selection to accelerate wheat breeding

10h30 am - 11h00 am

**Coffee break & poster session**

11h00 am - 11h15 am

**Kerstin NEUMANN** (IPK - Germany): Non-invasive phenotyping reveals stress adaptive and constitutive biomass QTL in cereals

11h15 am - 11h30 am

**Ulrike LOHWASSER** (IPK - Germany): Searching for Frost Tolerance in Wheat (Triticum aestivum L.) – A genome wide association study

## Session IV. Improving tolerance to biotic and abiotic stress

Chair: Fiona Doohan, University of Dublin, Ireland

11h30 am - 12h10 pm

**Keynote speaker: Heribert HIRT** (KAUST - Saudia Arabia): Using beneficial endophytes to enhance abiotic stress tolerance and yield of plants

12h10 pm - 12h30 pm

**Ewen MULLINS** (Teagasc - Ireland): Intensive field phenotyping to support breeding initiatives against septoria tritici blotch (STB) disease of wheat

12h30 pm - 2h00 pm

**Lunch break**

2h00 pm - 2h25 pm

**Yvan MOËNNE-LOCCOZ** (U Lyon - France): Interactions of plant-beneficial rhizosphere bacteria according to cereal genotype

2h25 pm - 2h50 pm

**Laetitia WILLOCQUET** (INRA - France): Developing phenotyping methods for quantitative host plant resistance using simulation modelling and ROC curves

2h50 pm - 2h15 pm

**Hermann BUERSTMAYR** (BOKU - Austria): Genomics assisted improvement of Fusarium head blight resistance in bread wheat, durum wheat and triticale

3h15 pm - 3h30 pm

**Javier SANCHEZ-MARTIN** (U Zürich - Switzerland): GWAS Reveals New Race-Specific Resistance Genes to Powdery Mildew in Wheat

3h30 pm - 3h45 pm

**Ali NIAZ** (U Leicester - UK): Novel rye-wheat translocations in Thinopyrum intermedium wheat introgression lines enhancing Wheat streak mosaic virus resistance

3h45 pm - 4h00 pm

**Pierre-Antoine PRECIGOUT** (U Paris-Saclay- France): Questioning the sustainability of quantitative physiological resistance: epidemiological and evolutionary responses of foliar fungal pathogens to changes in wheat plant traits

4h00 pm - 4h30 pm

**Coffee break & poster session**

4h30 pm - 11h00 pm

**Excursion & Gala Dinner**
Session V. High quality and safe cereals for food, feed and industry

Chair: Dario Fossati, Agroscope Switzerland

8h30 am - 9h10 am

Keynote speaker: Tatsuya IKEDA (NARO - Japan): Importance of international collaboration on wheat quality and safety

9h10 am - 9h35 am

Sebastian MICHEL (U Vienna - Austria): Multiple to conquer: Simultaneous selection for grain yield and baking quality in genomics-assisted wheat breeding

9h35 am - 10h00 am

Suong CU (Flinders U - Australia): Genome-wide association studies of zinc, iron, copper, manganese and phosphorus in wheat (Triticum aestivum L.) grain and rachis at two developmental stages

10h00 am - 10h30 am

Simon GRIFFITHS (JIC - UK): Biochemical and genetic analysis of arabinoxylan fibre in wheat grain

10h30 am - 11h00 am

Coffee break & poster session

Session VI. Future challenges and innovations

Chair: Roberto Tuberosa, University of Bologna, Italy

11h00 am - 11h40 am

Keynote speaker: Peter ROGOWSKY (INRA Lyon - France): CRISPR-Cas9 technology in plant science

11h40 am - 12h05 pm

Fred VAN EEUWIJK (Wageningen U - The Netherlands): Statistical methodology for modelling genotype by environment interactions in QTL mapping and genomic prediction, with applications to barley and wheat

12h05 pm - 12h30 pm

Andreas HUND (ETH Zürich - Switzerland): Zooming into GxE by means of modern field phenotyping techniques

12h30 pm - 2h00 pm

Lunch break

2h00 pm - 2h25 pm

Friedrich LONGIN (U Hohenheim - Germany): Optimum breeding schemes for line breeding in wheat

2h25 pm - 2h40 pm

Daniela BUSTOS-KORTS (Wageningen U - The Netherlands): A synthesis of crop growth and statistical genetic modelling to evaluate phenotyping strategies in wheat

2h40 pm - 2h55 pm

Renaud RINCENT (INRA GDEC - France): Genomic prediction of genotype by environment interactions by coupling genetic and physiological modelling

2h55 pm - 3h10 pm

Philipp BOEVEN (Limagrain - France): Rare and wanted! How to breed for favorable male floral traits required for hybrid wheat?

3h10 pm - 3h30 pm

Funmi LADEJOBI (NIAB - UK): Differentially penalized regression improves genomic prediction of wheat flowering time

3h30 pm - 4h00 pm

Concluding remarks and prizes for the three best posters

4h00 pm - 4h30 pm

Coffee break
# IWIW2
## SCIENTIFIC PROGRAMME

Thursday March 22th, 2018

<table><tr><td>7h45 am - 8h30 am</td><td>Registration & Welcome coffee</td></tr><tr><td colspan="2">Introduction</td></tr><tr><td>8h30 am - 9h00 am</td><td>Frank Ordon, Julius Kühn-Institut (JKI) - Wheat Initiative Research Committee<br/>Achievements of the Wheat Initiative</td></tr><tr><td>9h00 am - 9h30 am</td><td>Victor Kommerell, International Maize and Wheat Improvement Center (CIMMYT)<br/>Progress update on major multi-country/institutions wheat research programs</td></tr><tr><td>9h30 am - 10h00 am</td><td>Laurène Coral, Institut National de la Recherche Agronomique (INRA); Directorate for regional policy, higher education and Europe - management (DARESE)<br/>European Commission funding opportunities</td></tr><tr><td>10h00 am - 10h30 am</td><td>Viktor Korzun, KWS Cereals Breeding Technologies<br/>Future important breeding targets</td></tr><tr><td>10h30 am - 11h00 am</td><td>Coffee break</td></tr><tr><td colspan="2">Impulse talks</td></tr><tr><td>11h00 am - 11h20 am</td><td>SESSION I - Genetic resources: Simon Griffiths, John Innes Centre (JIC)</td></tr><tr><td>11h20 am - 11h40 am</td><td>SESSION II - Phenotyping: Jérémy Derory, Limagrain Europe</td></tr><tr><td>11h40 am - 12h00 am</td><td>SESSION III - Genome editing: Pierre Barret, Institut National de la Recherche Agronomique (INRA)</td></tr><tr><td>12h00 am - 12h20 pm</td><td>SESSION IV - Genomic selection: Friedrich Longin, University of Hohenheim</td></tr><tr><td>12h20 pm - 12h40 pm</td><td>SESSION V - Bio Informatics: Hillary Sullivan, DuPont Pioneer</td></tr><tr><td colspan="2">World café</td></tr><tr><td>12h40 pm - 12h50 pm</td><td>Introduction</td></tr><tr><td>12h50 pm - 2h00 pm</td><td>Lunch break</td></tr><tr><td>2h00 pm - 2h45 pm</td><td>Phase 1: exchange on the 5 topics (10 groups)</td></tr><tr><td>3h00 pm - 3h45 pm</td><td>Phase 2: exchange on the 5 topics (10 groups)</td></tr><tr><td>4h00 am - 4h30 am</td><td>Coffee break</td></tr><tr><td>4h30 pm - 5h30 pm</td><td>Conclusion for each of the 5 topics discussed during the world café</td></tr></table>
TABLE OF CONTENTS

<table><tr><td>Eucarpia Edito - Gilles Charmet</td><td>i</td></tr><tr><td>IWIW Edito - Jacques Le Gouis</td><td>ii</td></tr><tr><td>Eucarpia Scientific committee</td><td>iii</td></tr><tr><td>IWIW2 organizing committee</td><td>iii</td></tr><tr><td>Logistics committee</td><td>iv</td></tr><tr><td>Sponsors</td><td>v</td></tr><tr><td>Partners</td><td>vi</td></tr><tr><td>Institutions</td><td>vii</td></tr><tr><td>Advertisations</td><td>viii</td></tr><tr><td>EUCARPIA scientific programme</td><td>xi</td></tr><tr><td>IWIW2 scientific programme</td><td>xiv</td></tr><tr><td>Table of Content</td><td>xv</td></tr><tr><td>Introduction Talk</td><td>xvi</td></tr><tr><td>Session I – Characterization and use of genetic resources</td><td>1</td></tr><tr><td>Session II – Genomics and epigenomics in the post sequence era</td><td>9</td></tr><tr><td>Session III – Yield potential and resource efficiency</td><td>17</td></tr><tr><td>Session IV – Improving tolerance to biotic and abiotic stress</td><td>24</td></tr><tr><td>Session V – High quality and safe cereals for food, feed and industry</td><td>33</td></tr><tr><td>Session VI – Future challenges and innovations</td><td>38</td></tr><tr><td>Posters</td><td>47</td></tr><tr><td>Characterization and use of genetic resources</td><td>48</td></tr><tr><td>Genomics and epigenomics in the post sequence era</td><td>75</td></tr><tr><td>Yield potential and resource efficiency</td><td>79</td></tr><tr><td>Improving tolerance to biotic and abiotic stress</td><td>85</td></tr><tr><td>High quality and safe cereals for food, feed and industry</td><td>117</td></tr><tr><td>Future challenges and innovations</td><td>122</td></tr><tr><td>Keynote lecture list</td><td>128</td></tr><tr><td>EUCARPIA Oral presentations list</td><td>129</td></tr><tr><td>Posters List</td><td>131</td></tr><tr><td>Author's index</td><td>134</td></tr><tr><td>EUCARPIA participants list</td><td></td></tr><tr><td>IWIW2 participants list</td><td></td></tr></table>
# INTRODUCTION TALK
## Introduction Talk

<figure><img src="image_39.png" /><figcaption>RAPHAEL DUMAIN</figcaption></figure>

raphael.dumain@bayer.com

Bayer CropScience

**Global context for wheat, Innovation & Bayer Activities**

### Context for wheat and the challenges to deliver innovation

Wheat is the staple food for 1/3 of the world population. Future demand for wheat will be driven by population growth and to meet this predicted demand, global annual wheat yield growth will need to increase from around 1% to 1.6% p.a. This significant production increase will need to be achieved in the context of expected negative impacts of climate change (-6% global yield for each 1 degree C temperature rise) and the need to improve input efficiency and environmental stewardship in agricultural production. The wheat planted area is not expected to grow (ref. FAO, Wheat Initiative) and is even declining in countries like the US. Improvements in agronomy and management practices have already addressed much of the gap between average yield and potential yield, in major producing regions. As the stability of wheat production worldwide is under environmental and economic pressures, there is a critical need to increase wheat yield through new varieties, hybrids, traits and other agronomic innovations.

Wheat improvement has been lagging behind other major crops such as corn and rice. The enhanced enabling resources and methodologies developed in the past decade in genomics (e.g. the IWGSC wheat genome reference sequence), molecular genetics (e.g MAGIC populations accelerating QTL identification) and biotechnology (e.g. genome editing of wheat powdery mildew genes), provide new platforms for accelerating wheat breeding. These platforms encourage investment, but the timelines remain long (16-20 years from discovery to market) and the risk is high, thereby necessitating the need for investment and risk sharing by multiple players to ensure success. Public/private partnerships are essential to meet the scientific challenges of trait improvement in wheat and ensure that innovation reaches all farmers worldwide as fast as possible.

Wheat today is almost exclusively an open-pollinated crop in all markets, with the exception of a small hybrid wheat business in parts of Europe. As an open-pollinated crop, farmers purchase new genetic material and then retain seed-lots on-farm to plant for the next year. Consequently, we estimate that ~70% of the global wheat planted area is “farm-saved” seed. The nature of wheat plant breeding to date, given the lower technology deployment versus other crops and the relatively low-income stream, has necessitated a key role for public breeding and led to a highly fragmented private breeding structure with many markets having country specific local breeding companies. These companies are able to operate at relatively low cost yet effectively address the local market with adapted varieties. A small number of companies have developed multi-regional breeding programs, including partnerships with local companies and in some countries with public institutions, providing some economies of scale. However, the need to develop locally adapted varieties limits the synergies that can be realized from this approach and the opportunities to generate revenues for private breeders remains limited. As a consequence of the lack of market attractiveness, public breeding has played a critical role in the global breeding effort with CGIAR/CIMMYT estimating ~60% of released varieties globally being from public breeding sources.
(Source: Impacts of International Wheat Improvement Research 1994-2014, CGIAR, CIMMYT, ICARDA: 2014 Global Wheat Impacts survey) whereas investment by private companies in wheat research has been sporadic and not long term oriented. Quoting from the assessment made by the Wheat Initiative organization in May 2013 which reflects the low level of private-corporate investment – “In the last 20 years, wheat has become an orphan crop in terms of research investments considering its importance for global food security. As of 2010, global investments in maize research, mostly in the US and Europe, were more than four times greater than in wheat research.” (Source: Wheat Initiative May 2013 - www.wheatinitiative.org)

Hybrid wheat offers the opportunity to provide farmers with higher yield stability and improved revenues. It has been identified as a game changing breeding method to improve the effectiveness of breeding for yield potential as part of the Wheat Initiative strategic research agenda. Investments in hybrid wheat have been undertaken by a number of companies over the past decades but in the absence of efficient enabling platforms hybrid wheat varieties have been very challenging to deliver. Bayer believes that the new genomic and phenotyping technologies developed in large part by public-private initiatives in the last decade will now enable a long-term sustainable business in hybrid wheat. However, the commercial development of such technology will only slowly impact the market given the logistics of wheat seed production and the likely premium in the market to support higher production costs.

## Bayer wheat research – Breeding and Traits

In the last years, Bayer committed to invest significantly in new capacities and programs to support wheat breeding and trait research as a long-term strategic plan to address the above challenges. As part of this investment, seven main breeding stations in Europe, North America and Australia were established and a major research program aiming at developing a hybrid wheat platform supplemented by project to improve traits underlying yield performance (in a so called crop efficiency program) has been deployed.

To produce Hybrid Wheat, Bayer has focused on developing a CMS based male sterility system for its future hybrid varieties. To date, Bayer reached several significant milestones and is continuing efforts to launch hybrids as soon as possible in the next decade. As for trait-based yield improvement, Bayer's research program is focused on deciphering and improving multiple genetics component of grain yield through genes involved in resource utilization, radiation use efficiency, transport of sugars and minerals to seeds, etc... These research efforts are intentionally designed to complement incremental improvements provided by breeding to increase yield and protect it from disease and insect loss. Bayer strategy is first to deploy traits that will enable the production of hybrids while continuing to provide native traits with durable resistance to major diseases such as rusts, followed by the delivery of the first non-GM CE traits to improve yield performance.

To support this strategy, significant investments are also made into enabling technologies. This includes supporting the production of a high quality reference genome sequence of bread wheat through international collaborations with the IWGSC and internal sequencing of elite parent materials, developing integrated databases and deploying precision phenotyping platforms. Bayer has also developed expertise for wheat in the areas of cell biology, gene editing, transcriptomics, and doubled haploid methodology. Finally, future areas of research may include a better understanding the interactions between the genetics components of the crop and biological compounds used in the fields to stimulate yield increase.

**Keywords:** Introduction, Context, Innovation, Hybrid, Bayer

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Session I

CHARACTERIZATION AND USE OF GENETIC
RESOURCES

Chair: François Balfourier, INRA, France
**Keynote Lecture**

<figure><img src="image_40.png" /><figcaption>**ANDREAS GRANER**</figcaption></figure>

graner@ipk-gatersleben.de

IPK, Germany

*Ex situ collections: getting dressed up for another green revolution*

Conventional crop breeding essentially rests on repeated cycles of crossing and selection. This approach has warranted the development of superior cultivars over the past decades. However, it is only sustainable, if the genetic diversity that is lost in the process of selection is adequately replenished by introducing novel diversity into the genepool. At present about 7 million seed samples are stored in far more than 1000 *ex-situ* collections worldwide. Arguably, the vast diversity resting on the shelves of genebanks has been tapped into only marginally. Benefitting from genomics technologies, the conservation management of individual collections can be optimized in order to maintain the authenticity and the integrity of a given accession, and to provide access to the genetically defined material.

At the highest level of resolution, informed access to genetic resources means that each genebank accession will be tagged with information on individual alleles along with their phenotypic effects. The majority of crop genomes are characterized by their large size and inherent complexity hampering molecular analysis, meiotic recombination and, sometimes, their amenability to genetic modification. However, these limitations have been increasingly overcome by technical advances in several key areas including (i) structural and functional genomics, (ii) phenotypic cataloging of accessions using automated imaging and (iii) novel biotechnological approaches that will provide entry points for crop improvement. While the application of novel technology opens up a wealth of entry points for genetic analyses, it also generates and amasses humongous streams of data. Therefore, integrated concepts of data management and analysis will need serious consideration when aiming at the exploitation of novel technologies for the systematic phenotypic and genotypic characterization of genebank collections.

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**Davide GUERRA** - Studying the genetic basis of barley adaptation to contrasting environments in the WHEALBI collection

Studying the genetic basis of barley adaptation to contrasting environments in the
WHEALBI collection

**Davide GUERRA**<fnref n="1" />, Daniela BUSTOS-KORTS<fnref n="2" />, Alessandro TONDELLI<fnref n="1" />, JR RUSSELL<fnref n="3" />, Ian DAWSON<fnref n="3" />,
Laura ROSSINI<fnref n="4" />, Noemi TRABANCO<fnref n="4" />, C FERRANDI<fnref n="4" />, S KYRIAKIDIS<fnref n="3" />, A BOOTH<fnref n="3" />, F STROZZI<fnref n="4" />, E NICOLAZZI<fnref n="4" />,
Stefano DELBONO<fnref n="1" />, Hakan OZKAN<fnref n="5" />, E ÇAKIR<fnref n="5" />, E YAKIŞIR<fnref n="5" />, Márta MOLNÁR-LÁNG<fnref n="6" />, Mária MEGYERI<fnref n="6" />,
Péter MIKÓ<fnref n="6" />, Luigi CATTIVELLI<fnref n="1" />, R WAUGH<fnref n="3" /> and Fred A VAN EEUWIJK<fnref n="2" />

Corresponding author: davide.guerra@crea.gov.it

The EU-funded WHEALBI (Wheat and barley Legacy for Breeding Improvement) project is taking a
multidisciplinary approach to identify, understand and utilise the genetic diversity available in wheat and barley
formally-bred cultivars, landraces and wild relatives. This is strategic to meet the challenge to increase crop yields
while reduce environmental impact. Here we focus on a carefully selected set of 403 barley accessions from extensive
*ex situ* collections which cover the geographical and agro-ecological adaptive range of barley cultivation.
Comprehensive molecular variant analysis by exome sequencing defined sets of 0.45 M and 1.9 M SNPs for GWAS
and allele mining approaches, respectively. Agronomic and life history traits were also collected from multi-
environment common garden experiments and provide unique datasets to decipher the genetic basis of adaptation to
environment. Genomic regions and candidate genes driving phenotypic differences for heading date, plant height,
grain weight, and awn length across a number of environments will be discussed. Relating the genomic diversity to
tested accessions' sites of origin and breeding history will define promising sources of alleles for European breeding
programmes.

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<footnote n="1">¹ CREA - Research Centre for Genomics and Bioinformatics Via San Protaso 302 Fiorenzuola d'Arda, 29017 Italy</footnote>

<footnote n="2">2 Wageningen University & Research - Biometris Droevendaalsesteeg 1 Wageningen, 6708PB Netherlands</footnote>

<footnote n="3">³ The James Hutton Institute Invergowrie Invergowrie, Dundee, DD2 5DA United Kingdom</footnote>

<footnote n="4">⁴ Parco Tecnologico Padano, Via Einstein, Loc C.na Codazza, 26900 Lodi, Italy</footnote>

<footnote n="5">5 University of Cukurova Faculty of Agriculture, University of Cukurova Department of Field Crops, Adana, 01330 Turkey</footnote>

<footnote n="6">⁶ Agricultural Institute, MTA ATK Brunszvik u. 2 Martonvásár, 2462 Hungary</footnote>
**Ernesto IGARTUA** - Association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

# Association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

Bruno CONTRERAS-MOREIRA<fnref n="1" />,<fnref n="2" />, Roberto SERRANO-NOTIVOLI<fnref n="1" />, Naheif E MOHAMED<fnref n="1" />,<fnref n="3" />, Carlos P CANTALAPIEDRA<fnref n="1" />, Santiago BEGUERÍA<fnref n="1" />, Ana M CASAS<fnref n="1" /> and Ernesto IGARTUA<fnref n="1" />

Corresponding author: igartua@eead.csic.es

Landraces are populations of crop plants adapted to a particular environment. Extant landraces are surviving genetic archives, keeping information of the selection processes experienced by them until settling in their current niches. Barley landraces were abundant in Spain and properly collected in germplasm banks over the last century. This study intends to establish relationships between genetic diversity of the landraces and the climate of their collection sites. A thorough study of a period of 30 years of past climate (1981-2010), extracted agro-climatic variables meaningful for cereal production at the collection sites of 135 barley landraces. Variables summarize temperature, precipitation, evapotranspiration, potential vernalization and frost probabilities at different moments of the year and time scales (season, month). A set of high-resolution maps of climatic variables, computed from over 2,000 temperature and 7,000 precipitation stations across peninsular Spain, was built to assess the relationship between barley accessions and the climate of the territory. SNP genotyping of the landraces was carried out combining Illumina Infinium assays and genotyping-by-sequencing, yielding 7,479 biallelic markers placed on the barley reference genome. These SNPS were then analysed to ascertain their association with agro-climatic variables at two levels of genetic diversity, with and without taking into account population structure. We report a number of associations that suggest the differential adaptation of the germplasm groups identified are dominated by reactions to cold temperature and frost. Several significant associations pointing at specific adaptations to agro-climatic features were found, and candidate genes underlying some of the main regions are proposed.

**Keywords:** agro-climatic indices, genome-wide association analysis, selection footprint, barley, adaptation

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<footnote n="1">¹ Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain</footnote>

<footnote n="2">² Fundación ARAID, Av. de Ranillas 1-D, planta 2ª, oficina B, 50018 Zaragoza, Spain</footnote>

<footnote n="3">³ Agronomy Department, Faculty of Agriculture, Sohag University, Sohag, Egypt</footnote>
**Marco MACCAFERRI** - SNP-based characterization of a wide collection of tetraploid wheat reveals extensive domestication sweeps and haplotypes associated to traits of breeding interest

SNP-based characterization of a wide collection of tetraploid wheat reveals extensive
domestication sweeps and haplotypes associated to traits of breeding interest

**Marco MACCAFERRI**<sup>1,2</sup>, **Anna M MASTRANGELO**<sup>2*</sup>, **Elisabetta MAZZUCOTELLI**<sup>3*</sup>, **Reem JOUKHADAR**<sup>4*</sup>,
**Raj K PASAM**<sup>4*</sup>, **Francesca DESIDERIO**<sup>2</sup>, **Sara MILNER**<sup>5</sup>, **Danara ORMANBEKOVA**<sup>1</sup>, **Simona CORNETI**<sup>1</sup>,
**Silvio SALVI**<sup>1</sup>, **Roberto TUBEROSA**<sup>1</sup>, **Neil S HARRIS**<sup>6</sup>, **Gabriella SONNANTE**<sup>7</sup>, **Benjamin KILIAN**<sup>8</sup>,
**Hakan OZKAN**<sup>9</sup>, **Pasquale DE VITA**<sup>2</sup>, **Daniela MARONE**<sup>2</sup>, **Domenica NIGRO**<sup>10</sup>, **Agata GADALETA**<sup>11</sup>,
**Mike PUMPHREY**<sup>12</sup>, **Weizhen LIU**<sup>12</sup>, **Michela JANNI**<sup>7,13</sup>, **Domenico DE PAOLA**<sup>7</sup>, **Krysta WIEBE**<sup>14</sup>,
**John M CLARKE**<sup>14</sup>, **Ron KNOX**<sup>15</sup>, **Assaf DISTELFELD**<sup>16</sup>, **Aldo CERIOTTI**<sup>17</sup>, **Nicola PECCHIONI**<sup>2</sup>,
**Curtis J POZNIAK**<sup>14</sup>, **Steven S XU**<sup>18</sup>, **Shiaoman CHAO**<sup>18</sup>, **Matthew J HAYDEN**<sup>4</sup> and **Luigi CATTIVELLI**<sup>3</sup>

The iSelect wheat 90K SNP array and the recently assembled Svevo durum wheat genome were used to characterize a world-wide tetraploid wheat collection and to project the genotyping data onto the golden-standard durum wheat genome. We report on the diversity pattern of 1,854 non-redundant accessions from all known *Triticum turgidum* subspecies, from wild emmer to modern durum wheat. The whole-genome genetic diversity survey relied on a common genotype-calling pipeline developed by AgriBio (c/o Matt Hayden) supported by 17 tetraploid linkage maps. The pipeline yielded 17,416 informative single-locus SNPs anchored to the Svevo genome. Among the wild emmer (WEW), domesticated emmer (DEW), durum wheat landraces (DWL), durum wheat cultivars (DWC), WEW showed the highest and most uniform average p10Mb diversity level across the whole genome, thus providing a

<footnote n="1">¹ Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy</footnote>

<footnote n="2">² CREA-Research Centre for Cereal and Industrial Crops, Foggia, Italy</footnote>

<footnote n="3">³ CREA-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda (PC), Italy</footnote>

<footnote n="4">⁴ Department of Economic Development, Jobs, Transport and Resources, Agribio Centre, La Trobe Research And Development Park, Bundoora, Vic 3083, Australia</footnote>

<footnote n="5">⁵ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Seeland, Germany</footnote>

<footnote n="6">⁶ Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada</footnote>

<footnote n="7">⁷ National Research Council - Institute of Biosciences and Bioresources, Bari, Italy</footnote>

<footnote n="8">⁸ Global Crop Diversity Trust (GCDT), Bonn, Germany</footnote>

<footnote n="9">⁹ Çukurova University, Faculty of Agriculture, Department of Field Crops, Adana, Turkey</footnote>

<footnote n="10">¹⁰ Department of Soil, Plant and Food Sciences, University of Bari 'Aldo Moro', Bari, Italy</footnote>

<footnote n="11">¹¹ Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Bari, Italy</footnote>

<footnote n="12">¹² Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA</footnote>

<footnote n="13">¹³ Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parma, Italy</footnote>

<footnote n="14">¹⁴ Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada</footnote>

<footnote n="15">¹⁵ Swift Current Research and Development Centre, Agriculture and Agro-Food Canada, Swift Current Saskatchewan, Canada</footnote>

<footnote n="16">¹⁶ School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel</footnote>

<footnote n="17">¹⁷ National Research Council - Institute of Agricultural Biology and Biotechnology, Milano, Italy</footnote>

<footnote n="18">¹⁸ United States Department of Agriculture, Agricultural Research Service, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Fargo, ND, USA</footnote>

<footnote>*authors contributed equally to this work</footnote>

<footnote>Corresponding author: [marco.maccaferri@unibo.it](mailto:marco.maccaferri@unibo.it)</footnote>
valuable reference for cross-comparisons with DEW, DWL and DWC. Extended genetic diversity depletions were found particularly in pericentromeric regions. Our results suggest that 38.2% of modern DW genome has been affected by genetic bottleneck/selection events leading to strong diversity depletions. However, we also report the presence of six extended regions of increased genetic diversity associated to DEW-DWL and DWL-DWC transitions. We also confirm the presence of an extended region on pericentromeric 4A chromosome characterized by genetic diversity depletion in WEW. Population structure of the collection have been studied in details using ADMIXTURE and fineSTRUCTURE, revealing multiple subsequent events of population differentiation associated to human-driven dispersal routes. This analysis provides the basis for a more informative re-sequencing towards a tetraploid pangenome. Sub-panels of this collection have already been used for GWAS analysis. I.e. the dicoccum, landrace and modern durum panels have been characterized for response to yellow rust, allowing us to identify highly significant GWAS-QTL (Liu et al. 2017 Theor Appl Genet. 130:649-667) that can be readily used in breeding. GWAS-QTLs for grain yield components (grain size and grain number per spike) have been identified using a subpanel of Mediterranean DW landraces. These resources allowed us to map QTLs at an improved resolution (1 cM confidence interval) and readily scan the genome for underlying candidate genes.

We acknowledge the funding support of: Italian Ministry of Education and Research 251 through the Flagship InterOmics (PB05) project, CREA project Interomics, Fondazione in 252 rete per la ricerca agroalimentare (AGER) project From Seed to Pasta, FP7-KBBE Project 253 DROPS (ID244347), Genome Canada, Western Grain Research Foundation, Saskatchewan 254 Wheat Development Commission, Alberta wheat Development Commission, Saskatchewan 255 Ministry of Agriculture, the administrative support of Genome Prairie, Canadian Triticum 256 Applied Genomics (CTAG2), Binational Science Foundation (BSF) grant #2015409, USDA-257 Agricultural Research Service Current Research Information System project 3060-21000-258 037-00-D, German Federal Ministry of Food and Agriculture (2819103915), German 259 Ministry of Education and Research (031A536), and Natural Sciences and Engineering 260 Council of Canada (NSERC) (SPG 336119-06, RGPIN 92787).

**Keywords:** single nucleotide polymorphism, genetic diversity, GWAS, *Triticum turgidum* L. ssp. *durum* Desf., haplotype

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**Helmy M YOUSSEF** - Natural Diversity of Inflorescence Architecture Traces Cryptic Domestication Genes in Barley
*(Hordeum vulgare L.)*

# Natural Diversity of Inflorescence Architecture Traces Cryptic Domestication Genes in Barley (Hordeum vulgare L.)

**Helmy M YOUSSEF**<fnref n="1" />, Martin MASCHER<fnref n="1" />, Mohammad A AYOUB<fnref n="1" />, Nils STEIN<fnref n="1" />, Benjamin KILIAN<fnref n="2" />
and Thorsten SCHNURBUSCH<fnref n="1" />

Corresponding author: youssef@ipk-gatersleben.de

Many-grained mutants occurring spontaneously among their less well-endowed field mates may have appeared to early farmers as fortunate twists of fate foreboding wealth and abundance. In domesticated barley, the number of kernel rows in spike can be tripled by recessive mutant alleles at the Six-rowed spike 1 (vrs1) locus that abolish the suppression of lateral spikelet fertility. Genetic analyses of so-called intermedium barleys, where lateral spikelet development is intermediate between six-rowed and two-rowed types, and induced mutants have revealed that other genes can increase the size of florets and even stimulate occasional grain setting in lateral spikelets, in interaction with vrs1. Here, we show that a complete six-rowed phenotype occurs in a diverse panel of intermedium barley carrying wildtype Vrs1 in presence of the Int-c.a allele of the intermedium spike-c (int-c) gene, previously considered only as a modifier of lateral spikelet fertility. Int-c.a-type alleles had arisen before domestication and are associated with the enlargement of lateral florets in wild barley. Since Int-c.a cannot overcome the suppression of fertile lateral florets in the genomic background of wild barleys, we infer the existence of other gene loci at which novel alleles or allelic combinations were selected for after domestication to increase grain number of barley independently of Vrs1.

**Related publication:**

Youssef, H.M., Mascher, M., Ayoub, M.A. et al. (2017) Natural diversity of inflorescence architecture traces cryptic domestication genes in barley (*Hordeum vulgare* L.) *Genet Resour Crop Evol* 64: 843. https://doi.org/10.1007/s10722-017-0504-6

**Keywords:** Barley domestication, Int-c, intermedium barleys, spikelet fertility, Vrs1

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<footnote n="1">¹ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany</footnote>

<footnote n="2">² Bayer Crop Science NV, Ghent, Belgium</footnote>
**Constance LAVERGNE** - Introduction of *Aegilops sharonensis* cytoplasm into common wheat and production of addition / wheat - *Ae. sharonensis* lines translocation lines

# Introduction of *Aegilops sharonensis* cytoplasm into common wheat and production of addition / wheat – *Ae. sharonensis* lines translocation lines

**Constance LAVERGNE**<fnref n="1" />, Pierrick VARENNE<fnref n="2" />, Jérémy DERORY<fnref n="2" />, Alain MURIGNEUX<fnref n="2" />, Cai-yun YANG<fnref n="1" />, Duncan SCHOLEFIELD<fnref n="1" />, Stephen ASHLING<fnref n="1" />, Ian P KING<fnref n="1" /> and Julie KING<fnref n="1" />

Corresponding author: stxcl15@nottingham.ac.uk

Exploitation of heterosis, or hybrid vigour, is a promising solution for yield improvement in wheat (Triticum aestivum) to meet the challenge of feeding the growing population. Cytoplasmic male sterility (CMS) is one option to produce hybrid wheat on a large scale. Today the main CMS system is based on *T. timopheevii* cytoplasm. Nevertheless, a combination of several restorer genes seems to be required to reach a complete restoration of fertility when other CMS could be restored using one single restorer gene. *Aegilops sharonensis* Eig (Sharon goatgrass) is a diploid species (2n = 14, SshSsh), which together with Aegilops speltoides, belongs to the Sitopsis. It has been reported that *Ae. sharonensis* caused sterility when its cytoplasm was transferred into common wheat (Tsunewaki et al., 1976). *Ae. sharonensis* could therefore be a potential source of sterile cytoplasm for common wheat. Cytoplasm of *Ae. sharonensis* was introduced into common wheat by repeated backcrosses. The initial cross was carried out by pollinating several accessions of *Ae. sharonensis* with common wheat. *Ae. sharonensis* carries a gametocidal gene, Gc, on chromosome 4Ssh, which will be preferentially transmitted to the next generation. To eliminate chromosome 4Ssh, a wheat translocation line carrying a small fragment of chromosome 4Ssh on the distal end of chromosome 4B with the Gc gene knocked out (Friebe et al., 2003) was used as the recurrent parent. Alloplasmic, addition and wheat - *Ae. sharonensis* translocation lines were identified using genomic in situ hybridization (GISH). If some of the back crossed lines appear to be sterile, the next steps will be to find a restorer line against *Ae. sharonensis* cytoplasm together with a maintainer line, to have a complete CMS system.

**Related publication:**

Tsunewaki, K., Y. Mukai, T.R. Endo, S. Tsuji and M. Murata (1976) Genetic diversity of the cytoplasm in *Triticum* and *Aegilops*. *VI*. Distribution of the haploid-inducing cytoplasms. Jpn. J. Genet. 51:193-200

Friebe, B., P. Zhang, S. Nasuda, and B.S. Gill (2003) Characterization of a knock-out mutation at the Gc2 locus in wheat. Chromosoma 111:509-517

**Keywords:** *Ae. sharonensis*, hybrid wheat, Gametocidal gene, GISH, alloplasmic lines, CMS, wild relatives

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<footnote n="1">¹ University of Nottingham, Plant and Crop Sciences Division, School of Biosciences, Sutton Bonington Campus, LE12 5RD, UK</footnote>

<footnote n="2">² Centre de Recherche de Chappes, Route d'Ennezat, 63720 Chappes, France</footnote>
# GENOMICS AND EPIGENOMICS IN THE POST SEQUENCE ERA

Chair: Laura Rossini, University of Milano, Italy
Keynote Lecture

<figure><img src="image_41.png" /><figcaption>SCOTT ALLEN JACKSON</figcaption></figure>

sjackson@uga.edu

Center for Applied Genetic Technologies (CAGT)

Crop & Soil Sciences

College of Agricultural & Environmental Sciences

University of Georgia, US

Sources of variation in crop legumes - genetic, epigenetic and structural

Using two legume crops, common bean (Phaseolus vulgaris) and soybean (Glycine max), I will discuss efforts to understand and describe genetic/epigenetic variation and how that might affect plant improvement programs. Both crops have undergone extensive genetic bottlenecks due to domestication and, in soybean, the US germplasm can be traced to just a few founder lines, an extreme bottleneck. Polyploidy has resulted in diversity within domesticated soybean that is often overlooked, e.g. differentially methylated genes, presence-absence variation facilitated by genetic redundancy, and potentially, fixed hybridity between duplicated genes. Through comparisons between common bean and soybean, I will describe and discuss some of the genome-level mechanisms of generating novel variation and the results of polyploidy on genes and genome structure.

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**Luigi CATTIVELLI** - Durum wheat genome reveals the signature of 10,000 years of selection

Durum wheat genome reveals the signature of 10,000 years of selection

**Luigi Cattivelli**¹, Marco MACCAFERRI², Neil S HARRIS³, Sven O TWARDZIOK⁴, Heidrun GUNDLACH⁴,
Manuel SPANNAGL⁴, Danara ORMANBEKOVA⁴, Thomas LUX⁴, Verena PRADE⁴, Sara MILNER⁵,
Axel HIMMELBACH⁵, Martin MASCHER³, Paolo BAGNARESI¹, Primetta FACCIOLI¹, Paolo COZZI⁶,
Lauria MASSIMILIANO⁶, Barbara LAZZARI⁶, Alessandra STELLA⁶, Andrea MANCONI⁷, Matteo GNOCCHI⁷,
Raz AVNI⁸, Jasline DEEK⁸, Sezgi BIYIKLIOGLU⁹, Elisabetta FRASCAROLI², Simona CORNETI², Silvio SALVI²,
Roberto TUBEROSA², Gabriella SONNANTE¹⁰, Francesca DESIDERIO¹, Caterina MARÈ¹, Cristina CROSATTI¹,
Erica MICA¹, Hakan OZKAN¹¹, Pasquale DE VITA¹², Daniela MARONE¹², Reem JOUKHADAR¹⁴,
Raj K PASAM¹⁴, Elisabetta MAZZUCOTELLI¹, Domenica NIGRO¹⁵, Agata GADALETA¹⁵, Shiaoman CHAO¹⁶,
Justin FARIS¹⁶, Arthur TO MELO¹⁷, Mike PUMPHREY¹⁸, Nicola PECCHIONI¹², Luciano MILANESI⁷,
Krysta WIEBE¹⁹, Ron P MACLACHLAN¹⁹, John M CLARKE¹⁹, Andrew G SHARPE¹⁹, Kevin KOH²⁰,
Kevin YH LIANG²¹, Gregory J TAYLOR²¹, Ron KNOX²², Hikmet BUDAK²³, Anna M MASTRANGELO²⁴,
Steven S XU¹⁶, Nils STEIN⁵, Iago HALE⁷, Assaf DISTELFELD⁸, Matthew J HAYDEN¹⁴, Sean WALKOWIAK¹⁹,
Klaus FX MAYER⁴, Aldo CERIOTTI⁷ and Curtis J POZNIAK¹⁹

1 CREA-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda (PC), Italy

2 University of Bologna, Bologna, Italy

3 Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada

4 Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany

5 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Seeland, Germany

6 National Research Council - Institute of Agricultural Biology and Biotechnology, Milano, Italy

7 National Research Council - Institute of Biomedical Technologies, Segrate Milano, Italy

8 School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel

9 Montana State University, Bozeman, MT, USA

10 National Research Council - Institute of Biosciences and Bioresources, Bari, Italy

11 Çukurova University, Faculty of Agriculture, Department of Field Crops, Adana, Turkey

12 CREA-Research Centre for Cereal and Industrial Crops, Foggia, Italy

14 Department of Economic Development, Jobs, Transport and Resources, Agribio Centre, La Trobe Research And Development Park, Bundoora, Vic 3083, Australia

15 Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Bari, Italy

16 United States Department of Agriculture, Agricultural Research Service, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Fargo, ND, USA

17 Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, USA

18 Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA

19 Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

20 Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

21 Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada

22 Swift Current Research and Development Centre, Agriculture and Agro-Food Canada, Swift Current Saskatchewan, Canada

23 Montana State University, Bozeman, MT, USA
The domestication of wild emmer wheat ~10,000 years ago by early agrarian societies led to domesticated emmer and subsequently durum wheat through a process of selection for non-brittle rachis and free-threshing forms. Durum wheat became established as a prominent crop only ~1,500-2,000 years ago. We completed genome sequencing of the modern durum wheat cultivar Svevo, assembling the Illumina reads with DeNovoMAGIC software (NRGene, Israel) and scaffolding contigs using a high density genetic map and chromosome conformation capture sequencing (Hi-C). The final assembly covers 10.45 Gb and is characterized by a N50 of 6Mb. The comparison of this durum wheat assembly to a recently published wild emmer assembly allowed the identification of genome-wide modifications imposed by 10,000 years of selection and breeding on the genomic architecture of tetraploid wheat. The comparison revealed strong overall synteny, as well as several thousand regions subjected to copy number variation. The wheat iSelect 90K SNP Infinium assay was then employed to genotype a diversity panel of 1,854 tetraploid wheat accessions representing the main domestication- and breeding-related germplasm groups. Analysis of these data reevaluated the number of regions exhibiting strong signatures of genetic divergence associated with speciation, genetic drift, and selection events. Further, we projected onto the durum wheat genome about 1,500 QTL for morphological, phenological and quality traits, grain yield components, and disease resistance reported from published biparental mapping studies and GWAS. The durum wheat genome contains more than 66,000 genes. Among them, we annotated ~1,500 complete NBS-LRR genes, a family of genes known to be prominently involved in signaling and plant disease resistance. The availability of the complete genome of durum wheat will accelerate the identification and the isolation of new sources of disease resistance, as well as other genes that will contribute to breeding high-yielding and more resilient cultivars.

**Keywords:** Durum wheat, Genome sequencing

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Linking genomic and epigenomic features in hexaploid wheat genome

Juery CAROLINE<fnref n="1" />, Étienne PAUX<fnref n="1" /> and Frédéric CHOULET<fnref n="1" />

Corresponding author: caroline.juery@inra.fr

Because of its size, allohexaploid nature and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function and regulation. Such analyses have long been hampered by the lack of a high quality reference sequence. However, thanks to the efforts of the International Wheat Genome Sequencing Consortium (IWGSC), such sequences are now available and can be used to decipher the wheat genome. By conducting a wide range of analyses on the reference sequence of chromosome 3B, including gene and transposable element annotation, recombination, transcriptomics and structural variations studies, we revealed unexpected relationships between gene and genome structure and function, that cannot be explained at the sole genomic level. These include a strong partitioning of chromosome 3B, the existence of chromosomal domains encompassing clusters of co-expressed genes as well as co-regulation islands involving distant co-expression clusters. In order to investigate the role of epigenetics, we conducted ChIP-seq and RNA-seq experiments on various tissues and analyzed the presence of different histone modifications in view of the gene and genome organization and regulation. Results of this study will be presented.

**Keywords:** Genomic, Epigenomic, Wheat, Histone modification

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<footnote n="1">¹ INRA, UCA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales (GDEC), 5 chemin de Beaulieu, 63 039 Clermont-Ferrand cedex2, France</footnote>
**Cécile MONAT** - Hi-C and chromosome-scale assembly to detect large chromosomal rearrangements in wheat genomes

# Hi-C and chromosome-scale assembly to detect large chromosomal rearrangements in wheat genomes

**Cécile MONAT**¹, Sudharsan PADMARASU¹, Axel HIMMELBACH¹, Kobi BARUCH², Markus C KOLODZIEJ³, Thomas WICKER³, Kevin KOH⁴, Jennifer ENS⁴, Sean WALKOWIAK⁴, Kirby NILSEN⁴, Andrew G SHARPE⁴, Klaus FX MAYER⁵, Simon KRATTINGER³, Beat KELLER³, Martin MASCHER¹, Nils STEIN¹ and Curtis J POZNIAK⁴

1. IPK Gatersleben

2. IPK NRGene

3. IPK University of Zurich

4. IPK University of Saskatoon

5. Helmholtz Zentrum München

Corresponding author: monat@ipk-gatersleben.de

High-quality sequence assemblies of multiple individuals have emerged as important tools towards a deeper understanding of the full diversity within a species. The comprehensive and robust assessment of the different type of variation based on sequence assemblies can only be achieved through the collection of genome-wide sequence data with complementary technologies that retain information about physical linkage between sequence fragments. In the context of the Wheat Ten plus Genomes Project, in which we are assembling at pseudomolecules level wheat genomes with the final goal to get on overview of the wheat pan-genome, we are studying structural variation in bread wheat (*Triticum aestivum* L.). We have developed a pipeline to use chromosome capture (Hi-C) sequencing data to construct chromosome-scale sequence assemblies. Hi-C uses three-dimensional contact probabilities of chromatin in the nucleus to reconstruct the linear order of sequence scaffolds. The first step of our pipeline is the alignment of Hi-C data to a genetically anchored sequence assembly. Subsequently, residual misassemblies are detected and corrected and chromosome-scale physical genome maps are constructed from Hi-C contact matrices. Here, we present the outcome of this computational pipeline for three wheat cultivars. Highly contiguous sequence assemblies of three wheat genomes with scaffold N50 values > 10 Mb were constructed using the DeNovoMAGIC™ technology (NRGene, Ness Ziona, Israel) from paired-end and mate-pair Illumina data as well 10X Chromium linked-reads. These assemblies were ordered into 21 pseudomolecules representing > 95 % of the genome using Hi-C. Sequence alignments and Hi-C contact matrices revealed megabase-scale chromosomal rearrangements between cultivars such as inversions and inter-chromosomal translocations.

**Keywords:** genome assembly, pseudomolecules, wheat

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**Maria BÜERSTMAYR** - High-resolution mapping of the peri-centromeric region on wheat chromosome arm 5AS harboring the *Fusarium* head blight resistance QTL Qfhs.ifa-5A

# High-resolution mapping of the peri-centromeric region on wheat chromosome arm 5AS harboring the *Fusarium* head blight resistance QTL Qfhs.ifa-5A

**Maria BÜERSTMAYR**<fnref n="1" />, Barbara STEINER<fnref n="1" />, Petra SCHWARZ<fnref n="1" />, Christian WAGNER<fnref n="1" />, Klaus BRUGGER<fnref n="1" />,
Delfina BARABASCHI<fnref n="2" />, Andrea VOLANTE<fnref n="2" />, Giampiero VALE<fnref n="2" />, Luigi CATTIVELLI<fnref n="2" />
and Hermann BÜERSTMAYR<fnref n="1" />

Corresponding author: maria.buerstmayr@boku.ac.at

The relevant Qfhs.ifa-5A allele, contributing to enhanced *Fusarium* head blight resistance in wheat, resides in the pericentromeric interval of chromosome 5A (Buerstmayr et al. 2003). It is well documented that crossover events are distributed unevenly along chromosomes and almost absent around centromere. As an example, even among 3650 near isogenic recombinant inbred lines used for genetically fine-mapping Qfhs.ifa-5A, solely four individuals recombined within the C-5AS1-0.40 bin covering 40% of the physical length of 5AS. As a consequence, precisely locating of Qfhs.ifa-5A employing recombination dependent linkage mapping is practically impossible. To facilitate fine-mapping of Qfhs.ifa-5A we therefore used radiation hybrid (RH) mapping approach. RH mapping utilizes radiation to induce double strand breaks (DSBs) leading to deletions and these DSBs occur randomly and evenly distributed along a chromosome (Tiwari et al. 2016). We generated a radiation selfing (RS) panel by selfing plants from irradiated seeds of the experimental line NIL3 containing the Qfhs.ifa-5A resistance allele in the background of the cultivar Remus. In addition we generated a radiation hybrid (RH) panel by pollinating Chinese Spring (CS) Nullisomic-5A/Tetrasomic-5B plants with gamma-irradiated CS pollen. In total 5,157 radiation selfing and 276 radiation hybrid plants were screened for deletions on 5AS and plants containing deletions were analysed using 102 5AS specific DNA markers. Combining genotypic information of both panels yielded an 817-fold map improvement (cR/cM) for the centromeric bin and was 389-fold increased across the Qfhs.ifa-5A interval compared to the genetic map, with an average map resolution of 0.77 Mb/cR. Radiation induced deletion mapping demonstrated to be particularly efficient for high-resolution mapping of recombination poor stretches, such as pericentromeric regions. Selected RS lines will be used to associate losses of DNA stretches with the FHB phenotype and vice versa during evaluation in field tests, thus providing an unprecedented tool for fine localization of the Qfhs.ifa-5A gene locus. For more details please refer to Buerstmayr et al. (2017).

Supported by the Austrian Science Fund, project: SFB F3711

**Related publication:**

Buerstmayr et al. (2003) Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. II. Resistance to fungal penetration and spread. Theor Appl Genet 107:503-508. DOI:10.1007/s00122-003-1272-6

Buerstmayr et al. (2017) High-resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa-5A. Plant Biotechnol. J., in press. DOI: 10.1111/pbi.12850

Tiwari et al. (2016) A whole-genome, radiation hybrid mapping resource of hexaploid wheat. Plant J. 86, 195-207. DOI:10.1111/tpj.13153

**Keywords:** Radiation hybrid mapping, *Fusarium* head blight, *Triticum aestivum*, supressed recombination, gamma irradiation

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<footnote n="1">¹ Department of Agrobiotechnology Tulln, BOKU - University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria</footnote>

<footnote n="2">² Council for Agricultural Research and Economics (CREA), Genomics Research Centre, Fiorenzuola d'Arda, Italy</footnote>
**Romain DE OLIVEIRA** - Deciphering structural variations in the wheat genome using resequencing data

# Deciphering structural variations in the wheat genome using resequencing data

Romain DE OLIVEIRA<fnref n="1" />, Emeric DYNOMANT<fnref n="1" />, Hélène RIMBERT<fnref n="1" />, Hana SIMKOVA<fnref n="2" />, Jaroslav DOLEŽEL<fnref n="2" />, Frederica CATTONARO<fnref n="3" />, François BALFOURIER<fnref n="1" />, Étienne PAUX<fnref n="1" /> and Frédéric CHOULET<fnref n="1" />

Corresponding author: romain.de-oliveira@inra.fr

Structural variations (SVs) such as copy number and presence-absence variations (CNVs, PAVs) are polymorphisms that are known to be involved in the expression of phenotypes. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent advent of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild populations. Our project aims at characterizing SVs in a *Triticeae* diversity panel of 44 accessions from seven tetraploid and hexaploid *Triticeae* species. To cope with the wheat genome complexity, we developed strategies combining shotgun sequencing of sorted chromosomes 3B with bioinformatics tools and we studied SVs affecting not only genes but also transposable elements (TEs). Our results show that 14% of the genes are variable within this panel. In addition, they reveal a very high level of intra- and interspecific variability affecting TEs, contrasting with the weak polymorphism rate usually reported with SNPs. Chromosomal extremities are the regions where we see most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses.

**Keywords:** Structural variation, CNV, PAV, Wheat, Comparative genomics, bioinformatics

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<footnote n="1">¹ INRA, UCA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales (GDEC), 5 chemin de Beaulieu, 63 039 Clermont-Ferrand cedex2, France</footnote>

<footnote n="2">² IEB, Olomouc, Czech Republic</footnote>

<footnote n="3">³ IGA, Udine, Italy</footnote>
# YIELD POTENTIAL AND RESOURCE EFFICIENCY

CHAIR: FRANK ORDON, JKI, GERMANY
Keynote Lecture

<figure><img src="image_42.png" /><figcaption>JOHN FOULKES</figcaption></figure>

John.Foulkes@nottingham.ac.uk

University Nottingham, School Biosciences, Leics LE12 5RD, UK

Exploiting genetic diversity for enhancing yield potential and
resource efficiency in wheat

Matthew REYNOLDS<fnref n="1" />, Gemma MOLERO<fnref n="1" />, Carolina RIVERA AMADO<fnref n="1" />, Sivakumar SUKUMARAN<fnref n="1" />, Aleyda SIERRA GONZALEZ<fnref n="2" />, Reshmi GAJU<fnref n="2" />, Shaunagh SLACK<fnref n="2" />, Larry YORK<fnref n="2" />, Jayalath DE SILVA<fnref n="2" /> and Malcolm BENNETT<fnref n="2" />

Future genetic progress in wheat grain yield will depend on increasing biological yield (aboveground dry-matter per unit area) and maintaining, or ideally increasing, harvest index (grain yield/biomass; HI). In recent years the rate of genetic progress in HI has not increased; indeed, there is evidence for a trade-off with increasing biomass (Aisawi et al., 2015). Therefore, it is important to identify new avenues for increased grain partitioning in high biomass backgrounds. A Genome Wide Association Study (GWAS) was carried out focused on grain traits to enhance HI in a High Biomass Association spring wheat panel (HiBAP) at CIMMYT, Ciudad Obregon, Mexico in two years. Our analysis has identified marker-trait associations for key grain traits associated with HI and elucidated underlying mechanisms in relation to stem internode partitioning and fruiting efficiency (grains g-1 spike DM at anthesis). Future genetic progress in grain yield will depend on raising biomass without commensurate increases in N fertilizer inputs to minimize environmental impacts. In the BBSRC Wheat Improvement Strategic Programme (WISP) we quantified variation in grain yield, biomass and N-use efficiency (NUE) and associated traits in panels of diverse hexaploid wheat germplasm comprising landraces (Watkins collection) and synthetic-derived hexaploid under low N and high N conditions. Intensive phenotyping has revealed novel diversity in leaf photosynthetic rate and senescence-related traits associated with improved biomass under both high N and low N conditions. Mapping of Single Seed Descent (SSD) lines derived from Watkins landraces × UK elite cultivar Paragon crosses has revealed novel QTL for biomass and NUE and related traits. In the WISP mapping populations yield was mainly explained by genetic variation in N uptake under low N implying root traits were determining improved yield. Our recent work in the ERC Future Roots project has developed high-throughput platforms for field phenotyping of root system architecture for application in wheat breeding. The perspectives for future goals to raise yield potential and resource efficiency and the challenge to transfer traits into commercial varieties will be discussed.

**Related publication:**

Aisawi K, Reynolds M, Singh RP, Foulkes, MJ 2015. Crop Science 55, 1749-64

**Keywords:** Genetic diversity, yield, resource use, wheat, phenomics, GWAS

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<footnote n="1">¹ CIMMYT, Int. Apdo. Postal 6-641, 06600 Mexico, DF, Mexico</footnote>

<footnote n="2">² University Nottingham, School Biosciences, Leicestershire LE12 5RD, UK</footnote>
**Bruno CONTRERAS-MOREIRA** - Agronomic advantage of presence of *PpdH2* in winter barleys proven through a natural selection approach using GBS in pools of field-grown populations

# Agronomic advantage of presence of *PpdH2* in winter barleys proven through a natural selection approach using GBS in pools of field-grown populations

Bruno Contreras-Moreira¹,², Ana M CASAS¹, Carlos P CANTALAPIEDRA¹, M Pilar GRACIA¹ and Ernesto IGARTUA¹

¹ Aula Dei Experimental Station - CSIC and Fundación ARAID, Zaragoza, Spain

² Fundación ARAID, Zaragoza, Spain

Corresponding authors: bcontreras@eead.csic.es

Previous research suggests that winter barley in the Mediterranean region can benefit from the presence of a functional gene *PpdH2* which, in more northern latitudes, is typical only in spring cultivars. Previous evidence also indicates an agronomic advantage of reduced vernalization allele *VrnH1-4* in this same area.

A natural selection experiment was devised, using biparental RIL population SBCC097 x Plaisant. SBCC097 is an inbred line derived from a Spanish landrace, presenting an active PpdH2 allele and VrnH1-4. Plaisant is a typical winter cultivar, with a loss-of-function *ppdH2* allele and the winter *vrnH1* allele. Both parents have an active *VrnH2* allele, necessary to produce a winter growth habit.

Four bulks of 25 RILs each were assembled, stratified according to the four possible haplotypes resulting from the *PpdH2-VrnH1* combination, and ascertained using allele specific molecular markers. Bulks were carefully prepared for the whole series of trials, using the same amount of seed per each of the 25 constituent lines. Field trials were run for three years, at two sowing dates, standard (November) and late (February), in Zaragoza, Spain. Grain yield was superior for bulks having the active *PpdH2* allele, at both sowings, whereas yield advantage of VrnH1-4 allele was less general, restricted to late sowings and in interaction with *PpdH2*.

Besides the four bulks, a "metabulk" was constructed, using equal amounts of seed from the four bulks (hence, from the 100 lines). This metabulk was sown in the same field trials, at both sowing dates, with the difference that it was hand harvested every year, and the seed from each harvest was used for next season sowings. Thus, two series of metabulks, standard and late sowing, were actually subjected to natural selection for three years. The expectation was that the initial balanced contribution of the 100 lines would shift according to the reproductive fitness of the lines, i.e., lines producing more seeds would increase in frequency in the metabulks over the years.

After the field trials, the initial bulks and the final metabulks were genotyped, using double digest restriction-site associated DNA (ddRAD-Seq). For the initial bulks, DNA was extracted from each of the 25 constituent lines, and pooled in equal amounts. For the two final metabulks, DNA was extracted and pooled from three independent samples of 100 plants, thus providing true biological replicates. Parents were also genotyped.

After curation of the sequence reads and alignment to the current barley reference, 3087 markers were kept, which were used to analyse allele frequency shifts in the metabulks. Overall, there were more frequency shifts in the late sowing, with a majority of changes occurring in favour of the SBCC097 allele. In the standard sowings, the only significant shift occurred precisely in the *PpdH2* region, which showed a strong selection footprint towards the SBCC097 allele.

These experiments provide a double confirmation of the advantage of the presence of *PpdH2* in winter barleys, under a typical Mediterranean climate, validate the adaptation syndrome described for Spanish (and other Mediterranean) barleys, and demonstrate the validity of a DNA-pooling approach to answer relevant questions on crop adaptation.

**Keywords:** bulk, genotyping by sequencing, PpdH2, winter barley

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**Gaëtan TOUZY** - Improving water use efficiency in bread wheat by multi-trait multi-environment genome-wide association studies

# Improving water use efficiency in bread wheat by multi-trait multi-environment genome-wide association Studies

**Gaëtan TOUZY**<fnref n="1" />, Renaud RINCENT<fnref n="2" />, Willem KRUIJER<fnref n="3" />, Stéphane LAFARGE<fnref n="4" />, Katia BEAUCHÊNE<fnref n="1" />,
Fred A VAN EEUWIJK<fnref n="3" />, Jacques LE GOUIS<fnref n="2" /> and Sebastien PRAUD<fnref n="4" />

Corresponding author: g.touzy@arvalis.fr

Drought is one of the main abiotic stresses limiting bread wheat (Triticum aestivum L.) growth and productivity around the world. Many climate-based simulations have predicted an increase in the frequency and intensity of this abiotic stress. The delivery of new high yielding and stress-tolerant cultivars is now necessary and requires an improved understanding of the basis of the physiological and genetic response to drought.

A panel of 220 European elite cultivars, genotyped with the TaBW420K SNP chip, was evaluated in 39 field experiments; among them, specific drought field trials were conducted using monitored irrigation and rain shelters. Grain yield and yield components were scored for each trial. A crop model was run with detailed climatic data and soil water status, to identify the timing, intensity and history of stress for each genotype × trial combination.

A detailed study of genetic by environmental interactions (GxE) was conducted. By modelling water-deficit patterns, as Chenu et al. (2011), the trials were grouped in three scenarios: no stress, high stress at pre-anthesis stage, and moderate stress at post-anthesis stage. The grain yield loss in the two stressed scenarios ranged from 7 to 12% when compared to the no-stressed scenarios. A large genetic variability of grain yield was identified, with a genotypic coefficient of variation affecting the mean by ± 15%. In the same way, GxE interactions affected the grain yield mean by ± 12.5%. Reaction norm models were run using stress indicators to discriminate tolerant/sensitive varieties. Then, GWAS was performed with the stress-tolerant index and phenotypic values, using simple and multi-environment mixed models. Several quantitative traits loci (QTLs) were identified in the different stress scenarios and the allelic effects of these QTL were related to the environmental co-variables. Methods and results will be discussed especially those regarding the impacts of QTL×E interactions on stress indicators, grain yield and components and grain yield.

**Related publication:**

Chenu K, Cooper M, Hammer GL, Mathews KL, Dreccer MF, Chapman SC (2011) Environment characterization as an aid to wheat improvement: interpreting genotype-environment interactions by modelling water-deficit patterns in North-Eastern Australia. J Exp Bot 62: 1743–1755

**Keywords:** Drought stress, Genotype-by-environment interaction, GWAS

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<footnote n="1">¹ ARVALIS-Institut du végétal, 41240 Ouzouer-le-Marché, France</footnote>

<footnote n="2">² INRA, UCA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales (GDEC), 5 chemin de Beaulieu, 63 039 Clermont-Ferrand cedex2, France</footnote>

<footnote n="3">³ Wageningen University, 6700AA Wageningen, Netherlands</footnote>

<footnote n="4">⁴ BIOGEMMA, Centre de recherche de Chappes, Route d'Ennezat, 63720 Chappes, France</footnote>
# Implementing large-scale field phenotyping in genomic selection to accelerate wheat breeding

**Eric OBER**<fnref n="1" />, Robert JACKSON<fnref n="1" />, Chris GAYNOR<fnref n="2" />, Jaap BUNTJER<fnref n="2" />, Stefan HOJ-EDWARDS<fnref n="2" />, Alison BENTLEY<fnref n="1" />,
Phil HOWEL<fnref n="1" />, John HICKEY and IAN MACKAY<fnref n="1" />

Corresponding author: eric.ober@niab.com

The process of breeding new plant varieties can be accelerated and made less costly by applying new methods of genomic selection (GS). GS uses high density molecular markers and relatively inexpensive genotyping, in combination with phenotypic and pedigree data to increase the selection intensity and decrease the cycle time between initial crosses and finished varieties. Increased precision comes from both exploiting genetic relationships between traits and reducing the effect of environmental influences. However, a bottleneck in applying GS is the cost of phenotyping the requisite training population, which for commercial breeding programmes must be large (several thousand individuals). Robust prediction algorithms developed from the training population can be applied to reference populations without needing to repeat the phenotyping process. While yield is the fundamental phenotypic variable of interest, we test the idea that additional physiological and morphological traits can increase the predictive power of algorithms, akin to increasing the number of genetic markers. The time and cost of phenotyping can be reduced by using remote sensing methods, largely based on spectral reflectance from crop surfaces using RGB, multi- and hyperspectral cameras. In a collaborative project with four commercial breeding companies, we are testing these principles using a combination of ground-based measurements, UAV and aircraft platforms to derive phenotypic markers in a large population of 2992 wheat (Triticum aestivum) lines (44 elite crosses, 68 lines per cross) planted in two field locations in 2016 and in 2017. Further prediction precision can be obtained by taking into account environmental covariates that vary spatially across the trial area, such as apparent differences in soil texture and water holding capacity. Initial results show heritabilities of 0.37 to 0.54 for yield predicted from genomic data, with optimal correlations obtained with at least 60 BLUEs per cross. Predictive linear models based solely on phenomic data (dominated by remotely sensed variables) showed a correlation of 0.58 between training and focal sets. The utility of models combining genomic and phenomic markers will be discussed, and the implications for wheat breeding programmes implementing GS.

**Keywords:** wheat, genomic selection, phenotyping, remote sensing

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<footnote n="1">¹ National Institute of Agricultural Botany (NIAB)</footnote>

<footnote n="2">² Roslin Institute</footnote>
**Kerstin NEUMANN** - Non-invasive phenotyping reveals stress-adaptive and constitutive biomass QTL in cereals

# Non-invasive phenotyping reveals stress-adaptive and constitutive biomass QTL in cereals

**Kerstin NEUMANN**<fnref n="1" />, Yusheng ZHAO<fnref n="1" />, Sidram DHANAGOND<fnref n="1" />, Benjamin KILIAN<fnref n="2" />, Jochen C REIF<fnref n="1" />
and Andreas GRANER<fnref n="1" />

Corresponding author: neumannk@ipk-gatersleben.de

Future yield improvement is hampered by biotic and abiotic stresses due to climate change and accordingly, wheat and barley yields in Germany showed a strong fluctuation during the last 15 years. One factor is the increased frequency and severity of drought stress events, especially in spring during the vegetative growth phase - affecting the formation of biomass. Our experiments in different wheat and barley collections show a general reduction of ~30% in grain yield caused by a drought period in the vegetative stage. Understanding the genetics of biomass accumulation under well-watered and seasonal drought stress conditions can provide a basis for stabilizing or even increasing grain yield. By daily non-invasive imaging dynamics of biomass accumulation could be resolved, both phenotypically and genetically. To evaluate the genetics of biomass, an automated phenotyping system with controlled watering and non-invasive imaging was used to evaluate diverse wheat and barley collections under greenhouse conditions. Genome-wide association scans (GWAS) were applied to identify genetic markers associated with variation in biomass formation. Drought stress treatment started in the tillering phase and included a recovery period until the imaging period ended around tipping time. We obtained high heritabilities for biomass under both conditions in wheat and barley and over the whole observation period. GWAS revealed constitutive biomass QTL that are shared between drought and well-watered treatments and stress-adaptive QTL that occur only under the influence of drought stress.

**Related publication:**

NEUMANN K., ZHAO Y., CHU J., KEILWAGEN J., REIF J.C., KILIAN B., GRANER A. (2017): Genetic architecture and temporal patterns of biomass accumulation in spring barley revealed by image analysis. BMC Plant Biol. 17 (2017) 137. dx.doi.org/10.1186/s12870-017-1085-4.

**Keywords:** biomass, growth, drought, genome-wide association mapping

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<footnote n="1">¹ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Germany</footnote>

<footnote n="2">² Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany</footnote>
**Ulrike LOHWASSER** - Searching for frost tolerance in wheat (*Triticum aestivum* L.) – a genome wide association study

# Searching for frost tolerance in wheat (*Triticum aestivum* L.) – A genome wide association study

**Ulrike LOHWASSER**<fnref n="1" />, Fernando ARANA-CEBALLOS<fnref n="1" />, Michael KOCH<fnref n="2" />, Kerstin NEUMANN<fnref n="1" />
and Andreas BÖRNER<fnref n="1" />

Corresponding author: lohwasser@ipk-gatersleben.de

Wheat is one of the most important crops for human nutrition and is the most widely grown cereal crop in the world. Wheat yield stability has to be ensured in the context of climate change. Frost tolerance is essential for autumn-planted wheat to survive freezing temperatures during winter in temperate zones. It is a key trait with economic and agronomic importance but its molecular and genetic background (a complex trait with polygenic inheritance) is still poorly understood. The aims of the present study are (1) to investigate phenotypic variation for frost tolerance in a panel of 276 winter wheat accessions (2) to generate information about genetic variation and (3) to find molecular markers closely linked to the trait frost tolerance. Frost tolerance phenotype scores were collected from several locations in Germany and Russia during two seasons and were combined with the genotypic data in genome wide association studies (GWAS). The genotyping was done employing ILLUMINA infinium iSelect 90k wheat chip. The chip carries a total of 81,587 valid and functional SNPs. Finally, 17,900 polymorphic markers could be used for the genome wide analyses. SNP associations were performed using linear mixed models that evaluated the effects of SNPs with minor allele frequencies (MAF) > 10% individually, adjusting for kinship. GWAS analyses of the most significant SNP loci (highly significant associations, LOD>3) identified three and seven positive SNP associations on the chromosomes 1B and 5A, respectively. Haplotype analysis revealed that most of the significant SNP loci for these positions represent an advantage for the evaluated genotypes. Validation of SNPs and their respective haplotypes associated with frost tolerance together with candidate gene based-association studies, will be performed in future studies to determine the diagnostic value of markers for marker assisted selection in winter wheat breeding programs.

The project (code 0315953C) was funded by the German Federal Ministry of Education and Research (BMBF)

**Keywords:** wheat, frost tolerance, GWAS

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<footnote n="1">¹ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</footnote>

<footnote n="2">² Deutsche Saatveredelung AG (DSV), Germany</footnote>
Session IV

IMPROVING TOLERANCE TO BIOTIC AND ABIOTIC
STRESS

CHAIR: FIONA DOOHAN, UNIVERSITY OF DUBLIN, IRELAND
**Keynote Lecture**

**HERIBERT HIRT**

[heribert.hirt@kaust.edu.sa](mailto:heribert.hirt@kaust.edu.sa)

Center for Desert Agriculture, KAUST, Saudi Arabia and Institute of Plant Sciences Paris Saclay, France

<figure><img src="image_43.png" /></figure>

***Next green revolution: Plant endophytes to enhance stress tolerance and yield of crops***

We currently have more than 1 billion of undernourished people worldwide. This situation is not going to get better, unless we can increase food production by 50 % in the next decades. However, drought, salt and heat stress make up to more than 60 % of crop losses, so that improving abiotic stress resistance is one of the most important factors in securing food production. In the DARWIN21 project (http://www.darwin21.net), we isolate and employ endophytic desert microbes to enhance stress tolerance of plants. I will show that endophytic microbes isolated from desert plants can enhance yield of crops in adverse agriculture conditions, making beneficial microbes a powerful low-cost approach for subsistence farming in many under-producing areas of the world. To better understand the molecular processes in beneficial plant-microbe interactions, I will present the results from our molecular genetic approaches using as a model system *Arabidopsis thaliana*.

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**Ewen MULLINS** - Intensive field phenotyping to support breeding initiatives against *septoria tritici* blotch (STB) disease of wheat

# Intensive field phenotyping to support breeding initiatives against *septoria tritici* blotch (STB) disease of wheat

<u>Ewen MULLINS</u>¹, James Gerard HEHIR¹, Cliona CONNOLLY¹, Aoife O'DRISCOLL¹, Joseph P LYNCH¹,
Atikur RAHMAN¹, John SPINK¹, James KM BROWN², Stephen BYRNE¹, Petra KOCHAPPLEGREN¹
and Fiona DOOHAN³

¹ Teagasc, Ireland

² John Innes Centre, UK

³ University College Dublin, Ireland

Corresponding author: ewen.mullins@teagasc.ie

Zymoseptoria tritici, the causal agent of septoria tritici blotch (STB), remains a significant threat to European wheat production with the continuous emergence of fungicide resistance in Z. tritici strains eroding the economic sustainability of wheat production systems. For Irish wheat growers, STB is eroding the commercial viability of the national crop with wheat acreage dropping 40% in the last two years. In response, a national programme was established through the Virtual Irish Centre for Crop Improvement (VICCI) to investigate the aspects of the wheat-STB biotic interaction with a view to supporting commercial wheat breeders in delivering elite lines with higher STB resistance scores. One aspect of VICCI has focused on the pre-symptomatic phase (latent period, LP) after which the pathogen switches to an aggressive necrotrophic stage, when lesions bearing pycnidia quickly manifest on the leaf. As minimal knowledge on the possible role of the LP in supporting the resistance/susceptibility of wheat exists, the goal of this study was to investigate the spatial and temporal association between the LP and disease progression across three locations (Ireland - Waterford, Carlow; UK - Norwich) that represent commercially high, medium and low STB pressure environments. Completed over two seasons (2013-2015) with commercial cultivars, the potential of the LP in stalling STB epidemics was significant as identified with cv. Stigg, whose high level of partial resistance was characterised by a lengthened LP (~36 days) under the high disease pressure environment of Waterford. However, once the LP concluded it was followed by a rate of disease progression in cv. Stigg that was comparable to that observed in the more susceptible commercial varieties. Complementary analysis via logistic modelling of intensive disease assessments and qPCR-based quantifications of STB biomass made at Carlow and Waterford in 2015, further highlighted the value of identifying wheat germplasm in breeding programmes that support an extension of the LP. In parallel to this study we have been field phenotyping the NIAB MAGIC population for STB response under Irish conditions and have included the DiverseMAGIC population for 2,018 assessments. Data recorded on these multi-parent mapping populations will enable QTL associated with STB resistance to be identified, and integrated into genome-wide selection strategies for forward selection during varietal development.

**Related publication:**

Hehir et al. (2017) Plant Pathology. http://onlinelibrary.wiley.com/doi/10.1111/ppa.12780/full

**Keywords:** wheat, STB, resistance

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Yvan MOËNNE-LOCCOZ - Interactions of plant-beneficial rhizosphere bacteria according to cereal genotype

# Interactions of plant-beneficial rhizosphere bacteria according to cereal genotype

<u>Yvan MOËNNE-LOCCOZ</u><fnref n="1" />, Jordan VALENTE<fnref n="1" />, Marie-Lara BOUFFAUD<fnref n="1" />, Brigitte GOUESNARD<fnref n="2" />, Jacques LE GOUIS<fnref n="3" />,
Daniel MULLER<fnref n="1" /> and Claire PRIGENT-COMBARET<fnref n="1" />

Corresponding author: yvan.moenne-loccoz@univ-lyon1.fr

Roots of wheat and other cereals interact with a huge range of soil microorganisms, which colonize the rhizosphere and/or root tissues. This root-associated microbial community (sometimes termed the root microbiome) is important to consider because it includes both deleterious and symbiotic microorganisms. Therefore, it has a significant impact on plant growth, health and tolerance to stress. In this context, understanding root microbiome assembly and dynamics is of fundamental interest and could help design microbiome-based strategies for crop management. To address this issue, the significance of cereal genotype for root-microbiome interactions was studied. A relationship was found when comparing rhizobacterial communities with the phylogenetic distance between the corresponding plant genotypes, but this relationship held true only for a fraction of the community. It prompted us to assess how plant hosts selected for specific bacteria with plant-beneficial potential. This type of screening showed that the ability to interact with plant-beneficial bacteria had been largely counter-selected in modern wheat cultivars, yet it had been retained in some of them. The implications for plant-microbe interactions and breeding will be discussed.

**Related publication:**

Vacheron, J., G. Desbrosses, M.-L. Bouffaud, B. Touraine, Y. Moënne-Loccoz, D. Muller, L. Legendre, F. Wisniewski-Dyé, C. Prigent-Combaret. 2013. Plant growth-promoting rhizobacteria and root system functioning. Frontiers in Plant Science 4:356.

Bouffaud, M.-L., M.-A. Poirier, D. Muller, Y. Moënne-Loccoz. 2014. Root microbiome relates to plant host evolution in maize and other Poaceae. Environmental Microbiology 16:2804-2814.

Bruto, M., C. Prigent-Combaret, D. Muller, Y. Moënne-Loccoz. 2014. Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Scientific Reports 4:6261.

Bouffaud, M.-L., S. Renoud, Y. Moënne-Loccoz, D. Muller. 2016. Is plant evolutionary history impacting recruitment of diazotrophs and nifH expression in the rhizosphere? Scientific Reports 6:21690.

Vacheron, J., E. Combes-Meynet, V. Walker, B. Gouesnard, D. Muller, Y. Moënne-Loccoz, C. Prigent-Combaret. 2016. Expression on roots and contribution to maize phytostimulation of 1-aminocyclopropane-1-decarboxylate deaminase gene acdS in Pseudomonas fluorescens F113. Plant and Soil 407:187-202.

Cormier, F., J. Foulkes, B. Hirel, D. Gouache, Y. Moënne-Loccoz, J. Le Gouis. 2016. Breeding for increased nitrogen use efficiency: a review for wheat (*Triticum aestivum* L.). Plant Breeding 135:255-278.

Lemanceau, P., M. Blouin, D. Muller, Y. Moënne-Loccoz, Y. 2017. Let the core microbiota be functional. Trends in Plant Science 22:583-595.

**Keywords:** Rhizosphere, microbial community, microbiome, PGPR, phytoprotection, phytostimulation, QTL

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<footnote n="1">¹ UMR Microbial Ecology, Université Lyon 1/CNRS/INRA/VetAgro Sup, 69622 Villeurbanne, France</footnote>

<footnote n="2">² UMR INRA 1334 AGAP, 34000 Montpellier, France</footnote>

<footnote n="3">³ INRA, UCA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales (GDEC), 5 chemin de Beaulieu, 63 039 Clermont-Ferrand cedex2, France</footnote>
**Laeticia WILLOCQUET** - Developing phenotyping methods for quantitative host plant resistance using simulation modelling and ROC curves

# Developing phenotyping methods for quantitative host plant resistance using simulation modelling and ROC curves

**Laeticia WILLOCQUET**<fnref n="1" />, Serge SAVARY<fnref n="1" /> and Jonathan YUEN³

Corresponding authors: laetitia.willoquet@inra.fr

Components of resistance (CRs) constitute a conceptual stepping stone for resistance expression, from QTL (the geneticist's scale) to the cultivated field (the breeder's target). We propose an approach to identify predictors for field resistance, and to determine thresholds for genotype selection associated to sensitivity and specificity of the identified predictors. In a first stage, we use a process-based epidemiological simulation model that includes the effects of CRs on monocyclic parameters such as infection efficiency, latent period, infectious period, lesion expansion, and sporulation intensity. These effects correspond to relative resistances, RR, ranging from 0 (susceptible) to 1 (resistant genotype). This model enables sensitivity analyses on the effects of RR on simulates epidemics, which allow identifying CRs which affect most the speed of epidemics. This translates into a first result useful for breeding: the identification of traits (CRs) to target in phenotyping for field resistance. Each of the RR of these traits represents a predictor for field resistance. In a second stage, epidemics are simulated considering genotypes displaying increasing levels of RR. The familiar decision framework for chemical control "spray / do not spray", with cases as epidemics and controls as non-epidemics, is translated into a decision framework for the breeder "retain / reject the genotype" where cases are resistant genotypes and controls are susceptible genotypes. Analyses using this framework allow identifying a value of RR to target in phenotyping according to levels of sensitivity or specificity using ROC curves. This approach can be applied to wheat diseases such as rusts and septoria to develop phenotyping methods for field resistance.

**Related publication:**

Willoquet L, Savary S, Yuen J. 2017. Multiscale phenotyping and decision strategies in breeding for resistance. Trends in Plant Science 22: 420-432. DOI: 10.1016/j.tplants.2017.01.009

**Keywords:** phenotyping, host plant resistance, plant disease epidemiology, breeding

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<footnote n="1">¹ AGIR, INRA, Université de Toulouse, INPT, INP- EI PURPAN, Castanet-Tolosan, France</footnote>

<footnote n="2">² Swedish University of Agricultural Sciences, Uppsala, Sweden</footnote>
**Hermann BÜERSTMAYR** - Genomics assisted improvement of *Fusarium* head blight resistance in bread wheat, durum wheat and triticale

# Genomics assisted improvement of *Fusarium* head blight resistance in bread wheat, durum wheat and triticale

Hermann BÜERSTMAYR¹, Marc LEMMENS¹, Sebastian MICHEL¹, Jose Esteban Moreno AMORES¹, Marine OLLIER¹, Noemie PRAT¹, Christian WAGNER¹, Maria BÜERSTMAYR¹ and Barbara STEINER¹

1 BOKU - University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology Tulln, Institute of Biotechnology in Plant Production, 3430 Tulln, Austria

Corresponding author: hermann.buerstmayr@boku.ac.at

*Fusarium* Fungi are among the most feared pathogens of small grain cereals, particularly wheat. Resistance to *Fusarium* is therefore a top priority for resistance breeding, and receives high attention in research. The search string: TS=(*Fusarium* AND resistance AND wheat) in the ISI Web of Knowledge finds in the time frame 2000-2017 more hits than any other wheat disease.

Apart from yield losses, the contamination of the crop with mycotoxins is the major issue associated with *Fusarium* head blight (FHB). *Fusarium* is an opportunistic pathogen, which preferentially penetrates and colonizes cereal florets during the flowering period. Environmental conditions which either favor or hamper the fungus and the status of the plant during flowering have therefore a huge impact on disease establishment and development.

Resistance to FHB can be classified into passive (morphological and developmental) factors and active (physiological, biochemical) factors, both of which play a role.

Typical passive resistance factors are plant height and the extent of anther extrusion during flowering. Based on previous comparative mapping studies we discovered that 1) anther extrusion is a clearly quantitative trait, 2) higher degree of anther extrusion is associated with reduced FHB susceptibility and 3) plant height genes, Rht-B1b and even more pronounced Rht-D1b are associated with increased FHB susceptibility and reduced anther extrusion, which could partly explain their effect on lowering FHB resistance.

The famous FHB resistance allele Fhb1, which was discovered in Chinese germplasm, residing on chromosome 3B, most likely has a different function. Fhb1 has not been linked to height or flowering traits. In our results, we always find Fhb1 associated with increased resistance to Fusarium spreading, and simultaneously to the toxin deoxynivalenol (DON). We could recently show that Fhb1 improves field resistance to FHB also in durum wheat and in triticale. Further tests on the functional characterization of Fhb1 in relation to DON detoxification are currently underway.

Apart from few large effect QTL for FHB resistance a great proportion of resistance is most likely due to numerous small effect genes. Breeders can make use of these small effect genes as well. Resistance selection utilizes often a skillful combination of phenotypic testing in provocation nurseries and of genome wide selection using genomic prediction approaches.

**Related publication:**

Prat N, Guilbert C, Prah U, Wachter E, Steiner B, Langin T, Robert O, Buerstmayr H (2017) QTL mapping of *Fusarium* head blight resistance in three related durum wheat populations. Theor Appl Genet 130:13-27 doi:10.1007/s00122-016-2785-0

Steiner B, Buerstmayr M, Michel S, Schweiger W, Lemmens M, Buerstmayr H (2017) Breeding strategies and advances in line selection for *Fusarium* head blight resistance in wheat. Tropical Plant Pathology 42:165-174 doi:10.1007/s40858-017-0127-7

Lemmens M, Steiner B, Sulyok M, Nicholson P, Mesterhazy A, Buerstmayr H (2016) Masked mycotoxins: does breeding for enhanced *Fusarium* head blight resistance result in more deoxynivalenol-3-glucoside in new wheat varieties? World Mycotoxin Journal 9:741-754 doi:10.3920/wmj2015.2029

Buerstmayr M, Buerstmayr H (2016) The Semidwarfing Alleles Rht-D1b and Rht-B1b Show Marked Differences in Their Associations with Anther-Retention in Wheat Heads and with *Fusarium* Head Blight Susceptibility. Phytopathology 106:1544-1552 doi:10.1094/phyto-05-16-0200-r

Buerstmayr M, Buerstmayr H (2015) Comparative mapping of quantitative trait loci for *Fusarium* head blight resistance and anther retention in the winter wheat population Capo x Arina. Theor Appl Genet 128:1519-1530 doi:10.1007/s00122-015-2527-8

**Keywords:** *Fusarium* head blight, resistance, wheat; triticale, durum wheat, food safety, feed safety

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Javier SANCHEZ-MARTIN - GWAS reveals new race-specific resistance genes to powdery mildew in wheat

# GWAS reveals new race-specific resistance genes to powdery mildew in wheat

Javier SANCHEZ-MARTIN<fnref n="1" />, Thomas MÜLLER<fnref n="1" /> and Beat KELLER<fnref n="1" />

Corresponding author: javier.sanchezmartin@botinst.uzh.ch

Wheat powdery mildew, caused by *Blumeria graminis* f.sp. *tritici* (Bgt), is among the most important and persistent diseases of wheat and compromises its global production. To counter the disease, breeding for wheat powdery mildew resistance has been the main mean to control wheat powdery mildew. Quantitative resistance (QR) based on the joint action of several genes is of great importance. However, its use in breeding is very limited due to its multi-genetic nature, and, therefore, difficulty to select. Conversely, major resistance (R) genes have been extensively used in breeding as most of these genes show a simple dominant Mendelian inheritance, enabling an easy and rapid way to introgress resistance. R genes are also called race-specific resistance genes because they confer resistance to some but not all powdery mildew races through the recognition of pathogen effectors by proteins that generally have nucleotide-binding and leucine-rich repeats (NLRs). However, R-mediated resistance tends to be short-lived under agricultural conditions, as newly evolving pathogen races frequently defeat this type of resistance by modifying effectors recognized by the NLRs. Consequently, to ensure genetic resistance, a constant search and transfer of new R genes is necessary to counter the continuous evolution of virulence of the wheat powdery mildew.

To discover new sources of race-specific resistance against powdery mildew we performed a genome-wide association study (GWAS) using the WHEALBI collection of 506 geo-referenced inbred European and Middle Eastern wheat accessions genotyped by whole exome sequencing technology. The GWAS identified four genomic regions in chromosomes 1B, 1D, 2B and 5D associated with powdery mildew resistance. To identify candidate R genes, a genomic region of ~1Mb around the most significant SNP call for each association signal was defined. Afterwards, all open reading frames that potentially encoded proteins falling into those genomic regions were screened for NLR domains using InterProScan in search of full-length NLR type genes.

Strong associations were found for SNPs linked with the recently cloned Pm2a gene in chromosome 5D. Further haplotyping analysis and long-range PCR amplification and sequencing of the complete Pm2a coding region for the accessions showing polymorphism unveiled a new allele, temporarily named Pm2j. The Pm2j allele recognizes the AvrPm2 gene of the pathogen in the heterologous system *Nicotiana benthamiana* proving its biological functionality. Finally, the significant association of SNPs in chromosome 1D did not overlap with documented R genes conferring resistance to powdery mildew. Two predicted R genes in very close proximity to the peak signal show a high association between the haplotypes and the phenotypes and their functional validation is ongoing.

The identification and validation of a new allele in the Pm2 locus and two novel R genes in chromosome 1D demonstrates the power of GWAS for the rapid identification of major genes conferring resistance to powdery mildew. These results will enhance understanding of powdery mildew resistance and assist breeding for resistant wheat varieties.

**Keywords:** wheat, powdery mildew, GWAS, NLR genes, gene isolation

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<footnote n="1">¹ Department of Plant and Microbial Biology, University of Zürich, Switzerland</footnote>
**Ali NIAZ** - Novel rye-wheat translocations in *Thinopyrum intermedium* wheat introgression lines enhancing *Wheat streak* mosaic virus resistance

# Novel rye-wheat translocations in *Thinopyrum intermedium* wheat introgression lines enhancing Wheat streak mosaic virus resistance

**Ali NIAZ**<fnref n="1" />,<fnref n="2" />, JS HESLOP-HARRISON<fnref n="1" />, Robert A GRAYBOSC<fnref n="3" /> and Trude SCHWARZACHER<fnref n="1" />

Corresponding author: niazalitk25@gmail.com

Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance genes in wheat is a cost-effective and environmentally safe strategy for disease control. PCR-based markers and genomic in situ hybridization (GISH) were applied to identify alien chromatin in four genetically diverse populations of wheat lines incorporating chromosome segments from Thinopyrum intermedium and Secale cereale (rye). Out of twenty experimental lines, ten carried Th. intermedium chromatin as 4Ai#2S.4DL translocation, one carried Th. intermedium chromatin on another D-genome chromosome, while seven lines were positive for alien chromatin (Th. intermedium or rye) on chromosome 1B. The newly described rye 1RS chromatin was associated with WSMV-resistance and has recombined with the 1BS arm. Under field conditions, 1RS chromatin alone showed some resistance, while 1RS chromatin together with the Th. intermedium 4Ai#2S offered superior resistance. Three translocation breakpoints between 1BS and alien chromatin of 1RS were recovered. Repetitive DNA probes proved excellent cytological markers for the detection of Th. intermedium 4Ai#2S arm in both alien-wheat lines and Th. intermedium genome. Labelled genomic Th. intermedium DNA hybridized to the rye 1RS chromatin under high stringency conditions, indicating micro-collinearity of the cereals group-1 and presence of potentially novel orthologous resistance and quality genes on Th. intermedium group-1. The presence of cryptic 1RS alien fragments may explain the difficulty of developing well-adapted lines carrying Wsm1. The results will facilitate development of agronomically desirable WSMV-resistant germplasm.

**Related publication:**

http://www.nature.com/hdy/journal/v117/n2/full/hdy201636a.html

**Keywords:** Wheat alien introgression, fluorescent in situ hybridization, chromosomes, molecular markers, *Thinopyrum intermedium*, Wheat streak mosaic virus

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<footnote n="1">¹ University of Leicester, Department of Biology, UK</footnote>

<footnote n="2">² Hazara University Mansehra, Pakistan</footnote>

<footnote n="3">³ USDA-ARS & Department of Agronomy & Horticulture, University of Nebraska, USA</footnote>
**Pierre-Antoine PRÉCIGOUT** - Questioning the sustainability of quantitative physiological resistance: epidemiological and evolutionary responses of foliar fungal pathogens to changes in wheat plant traits

# Questioning the sustainability of quantitative physiological resistance: epidemiological and evolutionary responses of foliar fungal pathogens to changes in wheat plant traits

Pierre-Antoine PRÉCIGOUT¹, Corinne ROBERT¹ and David Claessen²

1 UMR ECOSYS INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France

2 Institut de Biologie de l'Ecole Normale Supérieure, CNRS-ENS-INSERM UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris

Corresponding author: pierre-antoine.precigout@inra.fr

Crop pathogens are known to rapidly adapt to agricultural practices. Although cultivar resistance breakdown and resistance to pesticides have been broadly studied, little is known about the adaptation of crop pathogens to more quantitative traits such as quantitative resistance. Quantitative resistance could be more sustainable than gene for gene resistance because it exerts a lower selective pressure on pathogens and relies on a variety of plant traits (and probably genes) rather than on a single one. Using a modelling approach, in this study we address the epidemiological and evolutionary responses of the pathogen to changes in several plant traits that impact epidemic development. With the model, we study life history evolution of biotrophic fungal pathogens of wheat. We focus on a single pathogen life history trait, the latent period, which directly determines the amount of resource allocated to growth and reproduction alongside the speed of canopy colonization. We investigate the evolutionary response of pathogens to changing several plant traits such as leaf metabolite concentration, leaf dimension and leaf lifespan. These plant traits impact epidemic development: disease severity is predicted to increase with metabolite content and leaf lifespan. We compare predictions of latent period evolution based on different “empirical” fitness measures such as annual spore production or within-season exponential growth rate, with predictions based on the more rigorous concept of invasion fitness from adaptive dynamics theory. For each of the studied plant traits, we use pairwise invisibility plots to identify evolutionarily stable strategies of the latent period (ESS). The ESS latent period responds differently to the different plant traits: it is longer on plants with long-lasting leaves and shorter on plants with bigger leaves leading to denser canopies. Our results further reveal that early canopy colonization during crop development might be a critical factor determining the issue of between-strain competition and shaping pathogen adaptation in the context of plant quantitative resistance. Finally, we argue that landscape-level heterogeneity may induce maladaptation of the pathogen that may be useful in stalling the evolutionary breakdown of quantitative resistance.

**Related publication:**

Précigout, P-A., Claessen, D., and Robert, C. (2017). Crop Fertilization Impacts Epidemics and Optimal Latent Period of Biotrophic Fungal Pathogens. Phytopathology PHYTO-01-17-001

**Keywords:** modelling, epidemiology, plant traits, ecophysiology, evolutionary ecology, plant pathogenic fungi, latent period, brown rust

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Session V

HIGH QUALITY AND SAFE CEREALS FOR FOOD,
FEED AND INDUSTRY

Chair: Dario Fossati, Agroscope Switzerland
Keynote Lecture

<figure><img src="image_44.png" /><figcaption>TATSUYA IKEDA</figcaption></figure>

tmikeda@affrc.go.jp

NARO, Western Region Agricultural Research Center, Fukuyama, Hiroshima,
Japan

Importance of international collaboration on wheat quality
and safety

Wheat quality and safety are very important for various end-use products. The Expert Working Groups (EWG) on improving wheat quality for processing and health was established under the Wheat Initiative (WI) in 2015 for maintaining and improving wheat quality and safety under varying environmental conditions. Our expert group focuses on wheat quality and safety in the broad sense, including seed proteins, allergens, carbohydrates, nutrition including micronutrients, processing and food safety. To share our data and advance our knowledge about the wheat quality and safety, it is important to standardize our methods and share standard cultivars representing allelic and phenotypic variations. We discuss to found a joint working group with ICC to standardize methods. For sharing standard cultivars, we selected standard cultivar sets representing the low-molecular-weight glutenin subunit alleles of bread and durum wheat. These sets have already become available for researchers at the CIMMYT gene bank. We are also working on developing other master sets for particular quality traits including carbohydrate diversity and low allergen content. We also have been collaborating with the EWG on Wheat Information System (WheatIS) to build connections between the Wheat Gene Catalogue and genome resources to facilitate the utilization of the genomic data for wheat breeding. I would like to discuss with participants the further promotion of international collaboration.

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**Sebastian MICHEL** - Multiple to conquer: Simultaneous selection for grain yield and baking quality in genomics-assisted wheat breeding

# Multiple to conquer: Simultaneous selection for grain yield and baking quality in genomics-assisted wheat breeding

**Sebastien MICHEL**<fnref n="1" />, Franziska LÖSCHENBERGER<fnref n="2" />, Christian AMETZ<fnref n="2" />, Ellen SPARRY<fnref n="3" />
and Hermann BÜERSTMAYR<fnref n="1" />

Corresponding author: sebastian.michel@boku.ac.at

Genomic selection has been implemented in many national and international breeding programs in recent years. Numerous studies have shown the potential of this new breeding tool, few have however taken the simultaneous selection for multiple traits into account that is though common practice in applied breeding programs.

The simultaneous improvement of grain yield and baking quality is thereby a major challenge in wheat breeding due to the well-known negative trade-off. Accordingly, we investigated the potential and limits of multi-trait selection for this particular trait complex utilizing vast phenotypic and genomic data collected in a commercial wheat breeding program where genomic selection is implemented since 2012.

The accuracy of across-year predictions of both preliminary and multi-environment trials could be significantly improved when combining phenotypic and genomic information in a genomics-assisted selection approach, which surpassed both genomics-based and classical phenotypic selection methods. Genomic predictions for quality traits could furthermore be improved when additionally considering traditional measurements for indirect selection such as protein content and sedimentation value from the head-row stage.

Using these enhanced genomics-assisted breeding methods two strategies were compared, which 1) aimed to select high-quality genotypes with acceptable yield potential, and 2) develop high-yielding varieties, while maintaining baking quality characteristics. Different genomic selection indices were developed, whereby protein quality related to loaf volume and crumb structure was represented by dough rheological parameters. Forward prediction across years revealed that twice the response to selection could be achieved by genomics-assisted compared to phenotypic selection with both breeding strategies when considering protein yield as target criterion. Simultaneous selection for grain yield, protein content and protein quality showed a lower trade-off between grain yield and protein quality than protein content suggesting that it is feasible to develop varieties that combine superior yield potential with comparably high end-use quality, thus utilizing available nitrogen resources more efficiently.

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<footnote n="1">¹ University of Natural Resources and Life Sciences, Vienna</footnote>

<footnote n="2">² Saatzucht Donau GesmbH. & CoKG</footnote>

<footnote n="3">³ C & M Seeds</footnote>
**Suong CU** - Genome-wide association studies of zinc, iron, copper, manganese and phosphorus in wheat (*Triticum aestivum* L.) grain and rachis at two developmental stages

# Genome-wide association studies of zinc, iron, copper, manganese and phosphorus in wheat (*Triticum aestivum* L.) grain and rachis at two developmental stages

Suong CU<fnref n="1" />, James STANGOULIS<fnref n="1" />, Alison NICOLSON<fnref n="1" />, Georgia GUILD<fnref n="1" /> and Govindan VELU<fnref n="2" />

Corresponding authors: suong.cu@flinders.edu.au

Globally, zinc and iron are two micronutrients that are most lacking in diets. The resulting micronutrient malnutrition can have detrimental impacts on overall health and wellbeing and affects approximately one third of the world's population, particularly young children [1-3]. Enhancing the densities of these minerals in bread wheat (*Triticum aestivum* L.) is a breeding objective to help alleviate these problems. A targeted biofortification breeding program initiated at the International Maize and Wheat Improvement Center (CIMMYT) established an association-mapping (AM) panel. This panel consists of 330 lines harbouring rich genetic diversity from resources possessing high Zn and Fe such as Triticum spelta, landraces and synthetic wheat [4]. Significant variation for grain Zn and Fe concentrations were found within the panel grown at various locations in India and Mexico [4, 5]. In this study, the panel was grown in Obregon (Mexico) over two seasons (2014-15 and 2015-16). Rachis and grain samples were taken at ten days after anthesis and at physiological maturity for the analysis of mineral concentrations. Phenology traits including days to heading, days to maturity and thousand kernel weight were also measured. Genome-wide association studies (GWAS) were carried out for five mineral concentrations, namely zinc, iron, copper, manganese and phosphorus with and without using phenology traits as covariates. For grain samples at physiological maturity, 40 to 60 significant marker-trait associations (MTA) (p< 0.001) were identified for each nutrient. Markers that showed pleiotropic effects on two or more nutrients were found on chromosomes 1B, 2D, 3B, 4A, 5B, 6B and 7B, of which those on chromosome 5BL were significantly associated with all five nutrients. Several significant MTAs were also identified for the nutrients in the rachis and grain at 10 days after anthesis. The genetic basis underlying the mechanisms that control the mineral concentrations at different developmental stages will be discussed.

**Related publication:**

Borrill, P., et al., Biofortification of wheat grain with iron and zinc: integrating novel genomic resources and knowledge from model crops. *Frontiers in Plant Sciences*, 2014. 5: p. 53.

Velu, G., et al., Biofortification strategies to increase grain zinc and iron concentrations in wheat. *Journal of Cereal Science*, 2014. 59(3): p. 365-372.

WHO The world health report 2002 - Reducing Risks, Promoting Healthy Life. 2002: Geneva.

Velu, G., et al., Genomic prediction for grain zinc and iron concentrations in spring wheat. *Theoretical and Applied Genetics*, 2016. 129(8): p. 1595-1605.

Velu, G., et al., Performance of biofortified spring wheat genotypes in target environments for grain zinc and iron concentrations. *Field Crops Research*, 2012. 137(Supplement C): p. 261-267.

**Keywords:** GWAS, iron, zinc, nutrition

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<footnote n="1">¹ College of Science and Engineering, Flinders University, SA 5042, Australia</footnote>

<footnote n="2">² International Maize and Wheat Improvement Center (CIMMYT), Apdo postal 6-641, Mexico</footnote>
**Simon GRIFFITHS** - Biochemical and genetic analysis of arabinoxylan fibre in wheat grain

**Biochemical and genetic analysis of arabinoxylan fibre in wheat grain**

Alison LOVEGROVE<fnref n="2" />, Amy PLUMMER<fnref n="2" />, Abigail WOOD<fnref n="2" />, Diana PASSMORE<fnref n="2" />, Ondrej KOSIK<fnref n="2" />, Jackie FREEMAN<fnref n="2" />,

Till PELLNY<fnref n="2" />, Rowan MITCHELL<fnref n="2" />, Mehmet ULKER<fnref n="3" />, Marianna RAKSZEGI<fnref n="4" />, Zoltan BEDO<fnref n="4" />,

Marie-Reine PERRETANT<fnref n="5" />, Gilles CHARMET<fnref n="5" />, Luzie WINGEN<fnref n="1" />, Michelle LEVERINGTON<fnref n="1" />, **Simon GRIFFITHS**<fnref n="1" />,

and Peter SHEWRY<fnref n="2" />

Corresponding authors: [simon.griffiths@jic.ac.uk](mailto:simon.griffiths@jic.ac.uk)

Wheat is the most important source of dietary fibre in western diets, with the major component being arabinoxylan (accounting for about half of the total fibre in whole grain and about 70% in white flour). AX fibre occurs in insoluble and soluble forms, which may differ in their health benefits with soluble fibre being particularly important in modulating glycaemic response. Work carried out under the EU Healthgrain programme identified the Chinese breadmaking wheat cultivar Yumai 34 as having the highest content of AX in flour out of 150 diverse genotypes, with about half of this being water-soluble (compared with about 25% in most wheats). Analysis of AX structure by enzyme fingerprinting (digestion with endoxylanase followed by HP-AEC of the released oligosaccharides (AXOS)) also shows that the high content and solubility of AX in Yumai 34 are associated with structural differences. To determine the molecular basis for the high contents of total and soluble AX in Yumai 34, and to facilitate their exploitation by wheat breeders, we have analysed four populations (2RIL and 2DH) from crosses between Yumai 34 and either lines with normal fibre content (Ukrainka, Claire, Altai) or high fibre content (Valoris). We have mapped QTL for either viscosity of aqueous extracts (as a proxy for soluble AX) or total AX (by enzyme fingerprinting) and identified a major QTL, allowing the identification of candidate genes and the establishment of markers for selection.

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<footnote n="1">¹ JIC, UK</footnote>

<footnote n="2">² Res, UK</footnote>

<footnote n="3">³ Yuzuncu Yil University, Van, Turkey</footnote>

<footnote n="4">⁴ Centre for Agricultural Research, MTA Agrártudományi Kutatóközpont Martonvásár, Hungary</footnote>

<footnote n="5">⁵ INRA, UCA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales (GDEC), 5 chemin de Beaulieu, 63 039 Clermont-Ferrand cedex2, France</footnote>
Session VI

FUTURE CHALLENGES AND INNOVATIONS

Chair: Roberto Tuberosa, University of Bologna, Italy
**Keynote Lecture**

**PETER ROGOWSKY**

peter.rogowsky@ens-lyon.fr

RDP, INRA, Univ Lyon, Lyon 69000, France

<figure><img src="image_45.png" /></figure>

***CRISPR-Cas9 technology in plant science***

CRISPR-Cas9 technology has raised considerable interest among plant scientists, both in basic science and plant breeding. Presently the generation of random mutations at a predetermined site of the genome is well mastered just like the targeted insertion of transgenes, although both remain restricted to species or genotypes amenable for plant transformation. On the other hand, true gene editing, i. e. the deliberate replacement of one or several nucleotides of the genome in a predetermined fashion, is limited to some rather particular examples that generally concern genes allowing positive selection, for example tolerance to herbicides. Therefore, further technological developments are necessary to fully exploit the potential of gene editing in enlarging the gene pool beyond the natural variability available in a given species. In principle the technology can be applied to any quality related, agronomical or ecological trait, under the condition of upstream knowledge on the genes to be targeted and the precise modifications necessary to improve alleles. Published proof of concepts concern a wide range of agronomical traits, the most frequent being disease resistance, herbicide tolerance and the biochemical composition of harvested products. The regulatory status of the plants obtained by CRISPR-Cas9 technology raises numerous questions, in particular with regard to the plants that carry in their genomes the punctual modifications caused by the presence of the Cas9 nuclease but not the nuclease itself. Without clarification by the competent authorities, CRISPR-Cas9 technology would continue to be a powerful tool in functional genomics, but its potential in plant breeding would remain untapped.

**Keywords:** CRISPR-Cas9, plant breeding, genome editing, plant transformation

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**Fred VAN EEUWIJK** - Statistical methodology for modelling genotype by environment interactions in QTL mapping and genomic prediction, with applications to barley and wheat

# Statistical methodology for modelling genotype by environment interactions in QTL mapping and genomic prediction, with applications to barley and wheat

**Fred VAN EEUWIJK**¹, Daniela BUSTOS-KORTS¹, Martin BOER¹, Marcos MALOSETTI¹, Willem KRUIJER¹
and EU-Whealbi consortium

¹ Wageningen University & Research - Biometris, Netherlands

Corresponding author: fred.vaneeuwijk@wur.nl

The most popular statistical methodology for QTL mapping and genomic prediction in plant breeding consists in some variations on linear mixed models with fixed QTL and random polygenic terms. The random polygenic effect is structured by a genotype x genotype matrix of relations to which both pedigree and marker information can contribute. In QTL mapping this random genetic effect is used as a correction term for background genetic variation in the search for QTLs, while in genomic prediction this term is the principal term producing the predictions. QTL and genomic prediction models for analysis of single traits and/or single environments are widely applied. Generalizations to multiple environments and traits while accounting for genotype by environment interactions are less common. Fixed QTL effects need to be defined in an environment specific way, while random polygenic effects need to be structured in a parsimonious way. For the latter, typically Kronecker products of structuring matrices on genotypes and environment are used. The computational requirements for fitting multi-environment mixed models strongly complicate model building and inference. For barley and wheat data from the EU-Whealbi project we present a mixed model framework for multi-environment QTL mapping and genomic prediction giving special attention to model building strategies, inference and interpretation.

**Related publication:**

Malosetti, M., Ribaut, J. M., & van Eeuwijk, F. A. (2013). The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis. *Frontiers in physiology*, 4.

Millet, E. J., Welcker, C., Kruijer, W., Negro, S., Coupel-Ledru, A., Nicolas, S. D., ... & Presterl, T. (2016). Genome-wide analysis of yield in Europe: allelic effects vary with drought and heat scenarios. *Plant physiology*, 172(2), 749-764.

Thoen, M. P., Davila Olivas, N. H., Kloth, K. J., Coolen, S., Huang, P. P., Aarts, M. G., ... & Bucher, J. (2017). Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping. *New Phytologist*, 213(3), 1346-1362.

**Keywords:** Adaptation, Genotype by environment interaction, genomic prediction, GWAS, multi-environment analysis, multi-trait analysis

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**Andreas HUND** - Zooming into GxE by means of modern field phenotyping techniques

Zooming into GxE by means of modern field phenotyping techniques

**Andreas HUND**¹, Norbert KIRCHGESSNER¹, Lukas KRONENBERG¹, Jonas ANDEREGG¹, Steven YATES¹, Kang YU², Christoph GRIEDER³ and Achim WALTER¹

1 ETH Zurich

2 KU Leuven

3 Agroscope

Corresponding author: andreas.hund@usys.ethz.ch

The combination of genomic prediction, modern crop phenotyping and modelling, will allow selecting crops in a way that was never possible before. Automated, sensor-based phenotyping techniques are well established under controlled conditions. Such techniques are now increasingly implemented in the field. This is an important step forward considering the large difficulties to mimic the field environment under controlled conditions. High throughput field phenotyping will completely alter the way we see plants. In the early days of quantitative genetics, mainly simple, static traits could be measured. Today, non-destructive, high throughput phenotyping offers the possibility to quantify allelic effects and their response to altering environmental conditions throughout the growing season.

We will demonstrate this concept using the example of wheat evaluated in the ETH field phenotyping platform (FIP; http://www.kp.ethz.ch/infrastructure/FIP.html). This unique prototype for automated, image-based crop phenotyping enables to follow the development of hundreds of plots. We evaluated a diverse panel of more than 300 genotypes consisting of the GABI wheat panel and important Swiss varieties. The overall aim within this project was to achieve a year-round phenotyping of wheat. We aimed to achieve a deeper understanding of wheat development during early growth (Grieder, Hund, and Walter 2015; Yu et al. 2017), stem elongation (Kronenberg et al. 2017) and senescence (See poster of Jonas Anderegg at this conference) including the response of these wheat genotypes to temperature and other environmental covariates. We will supply an overview of the heritability of the different traits assessed throughout the growing season and their dependencies. We will also highlight the major loci determining developmental processes across stages.

**Related publication:**

Grieder, Christoph, Andreas Hund, and Achim Walter. 2015. "Image Based Phenotyping during Winter: A Powerful Tool to Assess Wheat Genetic Variation in Growth Response to Temperature." Functional Plant Biology 42 (4):387. https://doi.org/10.1071/FP14226.

Kronenberg, Lukas, Kang Yu, Achim Walter, and Andreas Hund. 2017. "Monitoring the Dynamics of Wheat Stem Elongation: Genotypes Differ at Critical Stages." Euphytica 213 (7): UNSP 157. https://doi.org/10.1007/s10681-017-1940-2.

Yu, Kang, Norbert Kirchgessner, Christoph Grieder, Achim Walter, and Andreas Hund. 2017. "An Image Analysis Pipeline for Automated Classification of Imaging Light Conditions and for Quantification of Wheat Canopy Cover Time Series in Field Phenotyping." Plant Methods 13 (March):15. https://doi.org/10.1186/s13007-017-0168-4.

**Keywords:** Phenotyping, wheat, canopy development, association mapping, abiotic stress

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# Optimum breeding schemes for line breeding in wheat

C Friedrich H LONGIN¹

¹ State Plant Breeding Institute, University of Hohenheim

Corresponding author: friedrich.longin@uni-hohenheim.de

Many new technologies are available for wheat breeding, for instance genomic selection (GS) or the use of doubled haploids (DHs). However, the question arise whether these technologies are of interest maximizing the selection gain in routine breeding. Particularly, costs in DH technology are still high compared to single seed descent (SSD) programs. Similarly, for GS, costs are still high and prediction abilities across breeding cycles low. I have therefore run computer simulations testing different breeding schemes under a given budget. The input variables are based on a survey between the members of the expert working group “Breeding Methods” of the International Wheat Initiative and orientate at recent elite wheat breeding in Central Europe.

Although DHs are considerably more expensive to produce than SSD lines, breeding schemes with DHs have a higher annual selection gain than breeding schemes with SSDs as long as the DH scheme is faster than the SSD scheme. If DH breeding schemes require several cycles of multiplication of seeds before yield testing, however, they are as slow as SSD schemes and have a lower annual selection gain than SSD schemes. Thus, the choice to use DHs or not should mainly be driven by the feasibility of a fast DH scheme.

Genomic prediction ability of grain yield across different breeding cycles is relatively low for wheat (r ~ 0.3). However, even with this low prediction ability, breeding schemes using one-stage genomic selection followed by one-stage phenotypic selection yield a higher annual selection gain than breeding schemes relying on two stages of phenotypic selection due to the shortened breeding cycle length with GS. The prediction ability, and thus also the selection gain, can be further improved by selective genotyping. This requires the phenotypic test of 5-15% poor lines, but seems to improve the prediction ability across breeding cycles (Zhao et al. 2012). My simulations clearly suggest that already small increases in the prediction ability justifies the phenotyping of a small proportion of poor lines maximizing annual selection gain and increasing further the potential of GS in elite breeding programs.

**Related publication:**

Zhao, Y., M. Gowda, C.F.H. Longin, T. Würschum, N. Ranc, and J.C. Reif. 2012. Impact of selective genotyping in the training population on accuracy and bias of genomic selection. Theoretical and Applied Genetics 125:707-713.

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**Daniela BUSTOS-KORTS** - A synthesis of crop growth and statistical genetic modelling to evaluate phenotyping strategies in wheat

# A synthesis of crop growth and statistical genetic modelling to evaluate phenotyping strategies in wheat

**Daniela BUSTOS-KORTS**¹,², Marcos MALOSETTI¹, Martin BOER¹, Scott CHAPMAN³, Karine CHENU⁴
and Fred A VAN EEUWIJK¹

¹ Biometris, Wageningen University and Research Centre, The Netherlands

² C.T. de Wit Graduate School for Production Ecology & Resource Conservation (PE&RC), The Netherlands

³ CSIRO Agriculture and Food, Brisbane, Australia

⁴ The University of Queensland, CPS, Queensland Alliance for Agriculture and Food Innovation, Toowoomba, Australia

Corresponding author: daniela.bustoskorts@wur.nl

Complex target traits like yield show low genomic prediction accuracy because they frequently suffer from low heritability and are regulated by a large number of loci with small effects. Yield can be decomposed into a number of underlying genetically-correlated traits. As genetically-correlated traits are informative with respect to each other, modelling yield simultaneously with its component traits allows to achieve higher prediction accuracy compared to single-trait genomic prediction. Phenotyping additional traits implies an investment that does not always pay off by a larger prediction accuracy. Therefore, it is crucial for breeders to estimate in advance whether their phenotyping strategy for additional traits is likely to increase prediction accuracy of the target trait. This is especially relevant for high throughput phenotyping (HTP). HTP makes the phenotyping of additional traits affordable but may suffer from large measurement error. A large measurement error in the additional trait may lead to no contribution to the accuracy of the target trait. A strategy to evaluate the potential of phenotyping strategies is by combining crop growth models and statistical-genetic models to characterize trait correlations and heritability over time. Simulated data of intermediate and target traits during the growing season is a useful resource to evaluate; i) multi-trait prediction using traits measured during the whole growing season and ii) yield predictions from traits measured early in the growing season. In this presentation, we propose a decision support tool based on the combination of statistical-genetic and crop growth models to design an effective phenotyping schedule across the Australian TPE for wheat. We compare different strategies to integrate traits over time (i.e. penalized splines and nonlinear regression model), using an Australian wheat panel simulated with APSIM to grow over a sample of 40 environments representing water deficit patterns present in the Australian TPE.

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**Renaud RINCENT** - Genomic prediction of genotype by environment interactions by coupling genetic and physiological modelling

# Genomic prediction of genotype by environment interactions by coupling genetic and physiological modellingt

**Renaud RINCENT**<fnref n="1" />, Jacques LE GOUIS<fnref n="1" />, Pierre MARTRE<fnref n="1" />, Fred A VAN EEUWIJK<fnref n="2" /> and Marcos MALOSETTI<fnref n="2" />

Corresponding author: renaud.rincent@inra.fr

Genomic prediction (GP) models can be used to predict the performances of unphenotyped individuals thanks to their genotypic information. This approach was shown to be efficient for many species, but its interest in crops is limited by the presence of genotype x environment interactions (GEI): the ranking of the varieties often depends on the environments.

Recent studies proposed to adapt GP models to predict GEI by using environmental covariates. In the same way that molecular information is used to link the genotypes, the environmental covariates are used to link the environments. In these models environments with similar limiting factors are supposed to interact similarly with the varieties.

We propose here to evaluate and improve these approaches by using ecophysiological modelling. The prediction efficiency of different strategies were compared in a dataset comprising 220 elite wheat varieties, phenotyped for yield components in around 40 environments and genotyped with the TaBW420K SNP array within the BreedWheat project.

We show that the use of environmental covariates increased prediction accuracy in comparison to additive models, and that crop models were efficient to derive environmental covariates more relevant than those directly obtained with pedoclimatic information.

Acknowledgements: we thank the BreedWheat program (ANR-10-BTBR-0003) for the production of this dataset and the Agreenskills+ program for the stay of R. Rincent in Wageningen University.

We thank the BreedWheat program (ANR-10-BTBR-0003) for the production of this dataset and the Agreenskills + program for the stay of R. Rincent in Wageningen University

**Keywords:** *Triticum aestivum* L., genomic prediction, genotype by environment interactions, crop modelling

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<footnote n="1">¹ UMR INRA/UCA 1095 GDEC, Clermont Ferrand, France</footnote>

<footnote n="2">² Wageningen University</footnote>
**Philipp BOEVEN** - Rare and wanted! How to breed for favorable male floral traits required for hybrid wheat?

# Rare and wanted! How to breed for favorable male floral traits required for hybrid wheat?

**Philipp BOEVEN**¹, C Friedrich H LONGIN², Tobias WÜRSCUM², Willmar L LEISER², Erhard EBMEYER³,
Sonja KOLLERS³ and Julia RUDLOFF³

¹ Limagrain Field Seeds

² University of Hohenheim, State Plant Breeding Institute

³ KWS LOCHOW GMBH

Corresponding author: Philipp.Boeven@limagrain.de

The exploitation of heterosis in wheat promises to boost grain yield and yield stability. To make the 10 % mid-parent heterosis for grain yield in wheat also economically competitive, however, a number of issues need to be solved. Hybrid seed production of wheat is largely hampered by its low cross-pollination ability resulting in high seed production costs and lines with favorable male floral traits are displaying a severe bottleneck. We employed 31 wheat male lines and evaluated the hybrid seed set on two female tester lines. We observed a large genetic variance and high heritability estimates underscoring the possibility of selecting for increased hybrid seed set. Unfortunately, testing large numbers of candidates for seed set in crossing blocks under field conditions is cumbersome and is highly affected by secondary traits like plant height or heading date. Therefore, we evaluated trait correlations with more easy to screen indirect male floral traits. Visual anther extrusion appeared most promising showing a high association with seed set. We further evaluated genomics-assisted breeding strategies for indirect male floral traits. To this end, we employed a large panel of 209 winter wheat lines assessed for male floral traits, and genotyped with genome-wide markers as well as for Rht-B1 and Rht-D1. We found a complex genetic architecture underlying all observed male floral traits and Rht-D1 was identified as the only major QTL. Consequently, we evaluated genomic prediction approaches and fitting the identified major- and medium-effect QTL as fixed effects yielded the highest prediction accuracies and outperformed marker-assisted selection. Finally, we integrated our findings in an initial concept to breed for favorable male floral traits in wheat. Our results show that the redesign of the wheat floral architecture as required for efficient hybrid wheat breeding is challenging, but a combination of phenotypic and genomics-assisted selection can solve this issue in the following years.

**Related publication:**

Boeven PHG, Longin CFH, Leiser WL, Kollers S, Ebmeyer E, Würschum T (2016) Genetic architecture of male floral traits required for hybrid wheat breeding. Theor Appl Genet 129:2343-2357. doi:10.1007/s00122-016-2771-6

**Keywords:** Hybrid wheat, male floral traits, phenotyping, genomics-assisted breeding

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**Funmi LADEJOBI** - Differentially penalized regression improves genomic prediction of wheat flowering time

# Differentially penalized regression improves genomic prediction of wheat flowering time

**Funmi LADEJOBI**<fnref n="1" />, Ian MACKAY<fnref n="1" />, Julian M HIBBERD<fnref n="2" />, Matthieu BOGARD<fnref n="3" /> and Alison BENTLEY<fnref n="1" />

Corresponding author: funmi.ladejobi@niab.com

Several models have been proposed for genomic prediction. Of these, ridge regression best linear unbiased prediction (RR-BLUP) is based on the assumption that all genotyped markers make equal genetic contributions to phenotypic variation. However, information from known marker-trait association and candidate genes is generally of greater significance to the phenotype under test and can be used to improve the accuracy of prediction. In this study, Differentially Penalized Regression (DiPR), a modification of standard RR-BLUP was used to make predictions of flowering time in an association mapping panel and a multi-parent advanced generation inter-cross (MAGIC) population. Predictive genetic markers for flowering time from an ongoing FSOV (fonds de soutien à l'obtention végétale) project, candidate adaptive gene markers, and genome-wide molecular markers were genotyped and genomic prediction conducted using DiPR to differentially weight all markers. Each marker set was also used independently and as a combined genotype data matrix to predict flowering time. Overall, the DiPR model performed better than single or combined marker sets for predicting flowering in both the association mapping panel and MAGIC population. This work demonstrates the importance of weighting genetic information to include key candidate gene and QTL markers in order to improve the accuracy of genomic selection.

**Keywords:** Genomic prediction, candidate genes, differentially penalized regression

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<footnote n="1">¹ The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK; Department of Plant Sciences, University of Cambridge, Cambridge, UK</footnote>

<footnote n="2">² Department of Plant Sciences, University of Cambridge, Cambridge, UK</footnote>

<footnote n="3">³ ARVALIS Institut du Végétal, Rue de Noetzlin, Bat. 630, F-91405 Orsay, France</footnote>
POSTERS
SESSION I. CHARACTERIZATION AND USE OF GENETIC RESOURCES
PI-01 - Hermann BÜERSTMAYR - Comparative genetic analysis of common bunt and dwarf bunt resistance in winter wheat

Comparative genetic analysis of common bunt and dwarf bunt resistance in winter wheat

Hermann BÜERSTMAYR<fnref n="1" />, Almuth Elise MUELLNER<fnref n="1" />, Babur ESHONKULOV<fnref n="1" />,<fnref n="2" />, Julia HAGENGUTH<fnref n="1" />,<fnref n="3" />,
Bernadette PACHLER<fnref n="1" />,<fnref n="4" />, Herbert HUSS<fnref n="5" /> and David HOLE<fnref n="6" />

Corresponding author: [hermann.buerstmayr@boku.ac.at](mailto:hermann.buerstmayr@boku.ac.at)

Bunts of wheat were a serious threat to wheat before the advent of effective fungicides. With the recent increase in organic wheat production, bunt diseases re-emerge as relevant wheat diseases. The major bunt pathogens in Europe are *Tilletia tritici* and *Tilletia laevis* causing common bunt and *Tilletia controvversa* causing dwarf bunt. Infested wheat crops display varying levels of yield losses and quality losses due to the fishy smell of bunt spores caused by trimethylamine. Most current cultivars are bunt susceptible. Resistance to bunt diseases is therefore of increasing relevance, particularly for organic wheat production.

We evaluated three mapping populations for bunt resistance descending from crosses of parents with high resistance to common bunt and dwarf bunt crossed with a susceptible winter wheat cultivar. The resistant parents were Bonneville, Blizzard and PI199333. Bonneville, Blizzard are North American winter wheats with unknown resistance, and PI119333 is a landrace which is described as carrier of the gene Bt12. Susceptible parent was the Austrian cultivar Rainer.

Mapping populations were evaluated in nurseries inoculated with either common bunt or dwarf bunt, using local spore mixes. Bunt severity was evaluated in percent infected spikes per plot. Parents and populations were genotyped using a 15k Illumina SNP array. Phenotypic data were highly informative with broad sense heritability for common bunt severity of 0.94-0.97 and for dwarf bunt severity of 0.83-0.85. Marker data were used for linkage map construction and QTL mapping.

Both large effect and small effect QTL were detected. Blizzard and Bonneville share a large effect QTL for common bunt and dwarf bunt resistance on chromosome 1A (R2 19.5-28), and a large effect QTL for common bunt resistance on 1B (R2 29.6-34). Several smaller effect QTL for dwarf bunt resistance mapped to 2D, 7A and 7B. The Bt12 donor line PI119333 was tested for common bunt resistance only and possesses common bunt resistance QTL on 7D (R2 42.9) and 4B (R2 10.5).

In summary, several large effect alleles for resistance to dwarf bunt and/or common bunt were detected and mapped. These are promising targets for marker assisted selection in order to rapidly introgress bunt resistance into regionally adapted wheat cultivars.

**Keywords:** common bunt, dwarf bunt, resistance, QTL, mapping, wheat, *Tilletia*

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<footnote n="1">¹ University of Natural Resources and Life Sciences Vienna - BOKU</footnote>

<footnote n="2">² Agricultural University Samarkand, Usbekistan</footnote>

<footnote n="3">³ University Goettingen, Germany</footnote>

<footnote n="4">⁴ Saatzucht-Donau, Austria</footnote>

<footnote n="5">⁵ LFZ Raumberg, Austria</footnote>

<footnote n="6">⁶ Utah State University, USA</footnote>
**PI-02 - Nicholas FRADGLEY** - The NIAB Diverse MAGIC wheat population: a community resource for QTL mapping

# The NIAB Diverse MAGIC wheat population: a community resource for QTL mapping

Nicholas FRADGLEY<fnref n="1" />, Alison BENTLEY<fnref n="1" />, Keith GARDNER<fnref n="1" />, Phil HOWELL<fnref n="1" />, Ian MACKAY<fnref n="1" />, Mike SCOTT<fnref n="2" />,
Richard MOTT<fnref n="2" /> and James COCKRAM<fnref n="1" />

Corresponding author: nick.fradgley@niab.com

Development of experimental mapping populations enables dissection of complex traits in crops and underpins
modern plant breeding. Plant Multi-parent Advanced Generation Inter-Cross (MAGIC) populations have now been
constructed in many crop species. The advantages of MAGIC include greater genetic diversity captured from the
multiple parents as well as multiple rounds of inter-crossing maximising recombination and minimising population
structure.

The 'NIAB Diverse' MAGIC wheat population has recently been developed from 16 founders, chosen to capture over 90% of the genetic diversity of UK adapted wheat varieties based on markers. These included both elite and historic varieties originating from several different northern European countries.

596 RILs (Recombinant Inbred Lines) have recently been genotyped at F7, and a genetic map is under development.
Preliminary results from the first year of replicated yield trials indicated high power to detect QTLs in heritable traits
such as flowering time and height, and further analysis on a larger number of traits including yield and yield
components is ongoing. These results confirm the NIAB Diverse MAGIC population as an excellent resource for
genetic dissection of complex traits.

The population is being developed as community resource. A replicated yield trial will be available for phenotyping
at NIAB-Cambridge in the 2018 season, and the population is available on request. Basic phenotype data and the
founder/progeny genotype data will also be available, along with the associated genetic map and QTL analysis pipeline
under development at UCL. Please contact nick.fradgley@niab.com for further information.

The MAGIC CARPeT' (MAGIC: Community Access to Resources, Protocols and Training) project is funded by the Biotechnology and Biological Sciences Research Council (BBSRC) under grants BB/M011666/1 (NIAB) and BB/M011585/1 (UCL)

**Related publication:**

Mackay, I., Powell, W. 2007. Methods for linkage disequilibrium mapping in crops. Trends Plant Sci., 12:57-63.

Allen, A. M., Winfield, M. O., Burridge, A. J., Downie, R. C., Benbow, H. R., Barker, G. L. A., Wilkinson, P. A., Coghill, J., Waterfall, C., Davassi, A., Scopes, G., Pirani, A., Webster, T., Brew, F., Bloor, C., Griffiths, S., Bentley, A. R., Alda, M., Jack, P., Phillips, A. L. Edwards, K. J. 2017. Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol J. 15:390-401.

**Keywords:** wheat, multi-founder populations, MAGIC, QTL mapping, community resources

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<footnote n="1">¹ NIAB</footnote>

<footnote n="2">² UCL</footnote>
**PI-03 - Mariateresa LAZZARO** - From heritage to modern germplasm: evaluation of competitive ability, molecular characterization and genome-wide association in common wheat

# From heritage to modern germplasm: evaluation of competitive ability, molecular characterization and genome-wide association in common wheat

Mariateresa LAZZARO<fnref n="1" />, Paolo LAINO<fnref n="2" />, Matteo DELL'ACQUA<fnref n="1" />, Stefano DELBONO<fnref n="2" />, Mario Enrico PÈ<fnref n="1" />,
Luigi CATTIVELLI<fnref n="2" /> and Patrizia VACCINO<fnref n="2" />

Corresponding author: patrizia.vaccino@crea.gov.it

Traits such as tillering capacity, biomass accumulation before the stem elongation phase, final plant height, and flag leaf morphology are functional in determining the competitiveness of a crop against weeds. The use of competitive germplasm is a fundamental weed control strategy in organic and low-input agriculture. The trade-off between productivity in weed-free situations and competitive ability is a main obstacle to the release of competitive cultivars (Andrew et al., 2015). Yield potential remains a primary criterion for cultivar choice by farmers, therefore it would be desirable to prioritize traits that confer higher competitive ability without incurring in considerable grain yield reduction in the absence of weed competition.

Genome-wide association studies (GWAS) on competitive ability traits may be important for further advancing the knowledge about the genetic determination of the competition ability, and could be useful for increasing the information about the trade-off for yield and capability to resist to other stresses in common wheat.

In the present work, a *Triticum aestivum* collection summarizing the process of common wheat breeding in Italy during the latest hundred years was genetically characterized and screened for four traits related to competitiveness against weeds (above ground biomass accumulation before stem elongation phase, tillering index, plant height and flag leaf morphology) and two yield-related traits (grain yield and thousand kernel weight). The work was conducted with the aim to: (i) study the trends in four competitive ability traits and select genotypes with high competitive ability potential and with a combination of productivity and competitiveness adequate to organic and low-input systems; (ii) study the structure of the collection at molecular level and identify the main differences between heritage and modern germplasm; (iii) identify marker-trait associations (MTAs) for traits related to crop-weed interference.

The collection showed high phenotypic variability and molecular diversity. Accessions with high value for all competitiveness traits studied were identified, belonging mostly to the heritage germplasm. The accessions with the lowest grain yield to plant height trade-off were also identified. The genetic characterization highlighted a trend of polymorphism loss passing from heritage to modern germplasm and the presence of unique polymorphisms in both groups. This result underlines the importance of studying both heritage and elite germplasm. Marker-trait associations for all the evaluated traits were identified, both confirming associations already reported in the literature and describing new genomic regions that may disclose new breeding perspectives in common wheat.

The research was sponsored by the Italian Ministry of Agriculture in the framework of the Project RGV-FAO

**Related publication:**

Andrew, I.K.S., Storkey, J., Sparkes, D.L., 2015. A review of the potential for competitive cereal cultivars as a tool in integrated weed management. Weed Res. n/a-n/a. doi:10.1111/wre.12137

**Keywords:** Competitiveness, Crop-weed interaction, GWA (genome wide association), MTA (marker trait association), QTL (quantitative trait locus), *Triticum aestivum* L.

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<footnote n="1">¹ Scuola Superiore Sant'Anna, Institute of Life Sciences, Piazza Martiri della Libertà 33, 56127, Pisa, Italy</footnote>

<footnote n="2">² Consiglio per la Ricerca in agricoltura e l'analisi dell'economia Agraria, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy</footnote>
PI-04 - Natalia TIKHENKO - Reconstruction of the triticale genome in the progeny of incompatible crosses

Reconstruction of the triticale genome in the progeny of incompatible crosses

Natalia TIKHENKO<fnref n="1" />,<fnref n="2" />, Martin MASCHER<fnref n="1" />, Twan RUTTEN<fnref n="1" />, Angelika SENULA<fnref n="1" />, Myroslava RUBTSOVA<fnref n="1" />, Natalia TSVETKOVA<fnref n="3" />, Axel HIMMELBACH<fnref n="1" /> and Andreas BÖRNER<fnref n="1" />

Corresponding author: tikhenko@ipk-gatersleben.de

The wild and cultivated relatives of family Gramineae are source of useful alleles for wheat improvement. Rye (Secale cereale L.) is a close relative of wheat (Triticum aestivum L.) that provides a vast genetic variation for commercially important traits such as stress tolerance, biomass, yield and photosynthetic potential not only for triticale, but also for wheat itself. This biodiversity is not yet sufficiently utilized in wheat and triticale breeding programs and only a limited number of the modern cultivars of wheat contain wild species in their pedigree. Postzygotic isolating mechanisms between the Triticum and Secale genera ensure that not every cross between wheat and rye results in a hybrid plant. Such postzygotic barriers as embryonic lethality and hybrid sterility, which are controlled by a pairs of complementary incompatible alleles of both parents, significantly limit the possibility of obtaining primary triticale and lead to a sharp decrease in the efficiency of hybridization of parental forms. The proposed approach allows to overcome these barriers effectively and to obtain highly fertile forms of primary triticale based on incompatible combinations. The use of GBS analysis of genotypes of the offsprings from such incompatible crosses made it possible to evaluate the role of somaclonal and combinative variability in the stabilization of new forms and to classify the rearrangements of the genomes of both parents in offsprings with different fertility levels.

This study was funded by the German Research Foundation (grant number BO 1423/17-1/603175).

**Related publication:**

Tikhenko N D, Tsvetkova N V, Lyholay A N, Voylokov A V. Identification of complementary genes of hybrid lethality in crosses of bread wheat and rye. Results and prospects. Russ. J. Genet. Appl. Res. 7 (2017) 153-158. dx.doi.org/10.1134/s2079059717020149

Tikhenko N, Poursarebani N, Rutten T, Schnurbusch T, Börner A Embryo lethality in wheat-rye hybrids: dosage effect and deletion bin mapping of the responsible wheat locus. Biol. Plant. 61 (2017) 342-348. dx.doi.org/10.1007/s10535-016-0691-6

Tikhenko N, Rutten T, Senula A, Rubtsova M, Keller E R J, Börner A The changes in the reproductive barrier between hexaploid wheat (Triticum aestivum L.) and rye (Secale cereale L.): different states lead to different fates. Planta 246 (2017) 377-388. dx.doi.org/10.1007/s00425-017-2694-8

Tikhenko N, Rutten T, Tsvetkova N, Voylokov A, Börner A (2015) Hybrid dwarfness in crosses between wheat (Triticum aestivum L.) and rye (Secale cereale L.): a new look at an old phenomenon. Plant Biol 17: 320-326.

Tikhenko N., N. Tsvetkova, S. Priyatkina, A. Voylokov & A. Börner. (2011) Gene mutations in rye causing embryo lethality in hybrids with wheat - allelism test and chromosomal localization. Biol Plantarum 55 (3): 448-452.

**Keywords:** postzygotic incompatibility, embryo lethality, embryo rescue, chromosome doubling, hybrid sterility, postzygotic incompatibility, wheat-rye hybrids, GBS analysis.

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<footnote n="1">¹ Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, D-06466, Stadt Seeland OT Gatersleben, Germany</footnote>

<footnote n="2">² SPb Branch Vavilov Institute of General Genetics, RAS, 199034, St. Petersburg, Russia</footnote>

<footnote n="3">³ St. Petersburg State University, 199034, St. Petersburg, Russia</footnote>
PI-05 - Mathilde LAINÉ - BreedWheat GWAS data in GnpIS information system

BreedWheat GWAS data in GnpIS information system

Mathilde LAINÉ<fnref n="1" />, Thomas LETELLIER<fnref n="1" />, Raphaël FLORES<fnref n="1" />, Nacer MOHELLIBI<fnref n="1" />, Cyril POMMIER<fnref n="1" />, Sophie DURAND<fnref n="1" />, Anne-Françoise ADAM-BLONDON<fnref n="1" />, Hadi QUESNEVILLE<fnref n="1" />, Frédéric SAPET<fnref n="2" />, Agathe MINI<fnref n="2" />, Stéphane LAFARGE<fnref n="2" />, Étienne PAUX<fnref n="3" />, François BALFOURIER<fnref n="3" />, Jacques LE GOUIS<fnref n="3" /> and Michael ALAUX<fnref n="1" />

Corresponding author: mathilde.laine@inra.fr

BreedWheat project (https://breedwheat.fr/) aims to support the competitiveness of the French wheat breeding sector, answering to societal challenges for a sustainable and quality production. Moreover, the BreedWheat project characterize yet poorly exploited genetic resources to expand the diversity of the elite germplasm. Finally, new breeding methods are developed and evaluated for their socioeconomic impact.

The URGI (Research Unit in Genomics Info) is an INRA research unit in genomics and bioinformatics dedicated to plants and their parasites. It develops and maintains an information system in genomics and genetics: GnpIS (Steinbach et al., Database 2013, doi: 10.1093/database/bat058).

BreedWheat data available in GnpIS are genetic resources (collection of 5,232 accessions), polymorphisms (724,020 SNPs from 10 sources), genotyping (Affymetrix Axiom TaBW420K array), phenotyping (48,000 micro-plots in 21 locations) and Genome Wide Association Study (775,621 association results calculated from phenotyping and genotyping values): https://wheat-urgi.versailles.inra.fr/Projects/BreedWheat.

GnpIS interface allows to display association values (with links to metadata, phenotyping and genotyping related values), these data can be filtered according to several criteria (eg p-val) and visualized graphically (QQplot, boxlplot based on genotyping alleles, Manhattan plot mapped to IWGSC RefSeq v1.0).

**Related publication:**

Steinbach et al., Database 2013, doi: 10.1093/database/bat058

**Keywords:** BreedWheat, GnpIS, GWAS, Association, Phenotyping, Genotyping, Genetic Resources

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<footnote n="1">¹ INRA, UR1164 URGI - Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, Versailles, 78026, France</footnote>

<footnote n="2">² Biogemma, route Ennezat, Chappes, 63720, France</footnote>

<footnote n="3">³ INRA, UCA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales (GDEC), 5 chemin de Beaulieu, 63 039 Clermont-Ferrand cedex2, France</footnote>
PI-06 - Laura PASCUAL - Genomic variability of Spanish Durum wheat landraces

Genomic variability of Spanish Durum wheat landraces

Laura PASCUAL<fnref n="1" />, Matilde LÓPEZ-FERNÁNDEZ<fnref n="1" />, Elena BENAVENTE<fnref n="1" />, Magdalena RUIZ<fnref n="2" /> and Patricia GIRALDO<fnref n="1" />

Corresponding author: laura.pascual@upm.es

One of the main goals for the XXI century breeding is the development of cultivars that can maintain current yields under unfavorable conditions. Wheat landraces that have been grown under diverse and extreme local conditions include variability that will be necessary to achieve this objective. Several recent international initiatives are characterizing local wheat germplasm collections. However, Spanish landraces, representing a really wide diversity of eco-climatic conditions, are absent or only represented by a small number of accessions.

The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research (CRF-INIA) holds a collection with 591 landraces of durum wheat (subsp. *turgidum*, *durum* and *dicoccum*). Based upon agro-ecological distribution, passport data and agro-morphological characterisation a core set up to 190 accessions was selected to represent the diversity in the national collection. This sample includes nine different Spanish durum wheat populations, according to previous molecular data.

We have performed GBS on the set of 190 accessions using the DArTseq technology. We have identified more than 90K DArTs (absence/presence) polymorphisms, and among the sequence obtained more than 50K SNPs. More than 50% of the markers have been mapped in the available bread wheat genome (TGACv1). These markers have been used to explore the genetic diversity present in the collection at genomic level, and the population structure obtained compared with previous analysis. Furthermore, to fully exploit the potential of durum wheat Spanish landraces, the collection is being phenotyped for a wide set of traits in order to conduct GWAs analysis.

**Keywords:** Durum wheat, DArTseq

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<footnote n="1">¹ Universidad Politécnica de Madrid</footnote>

<footnote n="2">² Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria</footnote>
**PI-07 - Davide GUERRA** - Allele mining for frost tolerance in barley unveiled untapped alleles and copy number variants of CBF and Vrn-H1 genes

Allele mining for frost tolerance in barley unveiled untapped alleles and copy
number variants of CBF and *Vrn-H1* genes

**Davide GUERRA**<fnref n="1" />, A FRICANO<fnref n="1" />, Alessandro TONDELLI<fnref n="1" />, G BRETANI<fnref n="2" />, Laura ROSSINI<fnref n="2" />, Fulvia RIZZA<fnref n="1" />, F BADECK<fnref n="1" />, JA MILIC<fnref n="3" />, E FRANCIA<fnref n="3" />, C FERRANDI<fnref n="4" />, F STROZZI<fnref n="4" />, E NICOLAZZI<fnref n="4" /> and Luigi CATTIVELLI<fnref n="1" />

Corresponding author: davide.guerra@crea.gov.it

In temperate cereals, a transcriptome reprogramming in response to low-freezing temperature relies on the action of the key family of CBFs (C-Repeat Binding Factors) transcription factors. In barley, more than 13 HvCBFs map to the major QTL FR-H2, making them as the best candidates to explain frost tolerance. A second major QTL controlling phenotypic variation in frost resistance is FR-H1, located 40 Mbp apart from FR-H2 and coincident to *Vrn-H1* vernalization response locus.

To identify new alleles governing frost tolerance, the allelic variation of specific HvCBF and *Vrn-H1* genes was assayed through exome capture and sequencing of a collection of 403 barley accessions spanning a wide geographic range and including modern and old cultivars, landraces and wild relatives. Analysis of the whole exome sequence data outputted more than 64 million genome-wide raw SNPs mainly in barley coding sequences.

This dataset along with curated annotation of the CBF and *Vrn-H1* genes allowed us to uncover SNP variants in HvCBF2, HvCBF3, HvCBF4, HvCBF9, HvCBF10, HvCBF14 and *Vrn-H1* and to predict functional effects at the protein level. Furthermore, whole exome sequencing was exploited to detect copy number variants (CNV) and insertions/deletions at FR-H2 and *Vrn-H1* loci.

To validate this set of high confidence structural variants in silico approaches, qRT-PCR analysis and dataset querying for known gene deletions or duplications in barley genome were used. This work allowed to unveil different patterns of CNV affecting the FR-H2 locus, most of which encompass HvCBF2, HvCBF4 and HvCBF9 genes as well as several novel deletions in the promoter and in the first intron of *Vrn-H1*. Finally, an accurate phenotyping experiment was carried out to verify the impact of the novel CBF loci on frost tolerance.

This work provides a snapshot of the existing genetic diversity for FR-H2 and *Vrn-H1*/FR-H1 loci and paves the way for efficiently exploiting the natural genetic diversity of barley germplasms.

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<footnote n="1">¹ CREA - Research Centre for Genomics and Bioinformatics Via San Protaso 302 Fiorenzuola d'Arda, 29017 Italy</footnote>

<footnote n="2">² Università degli studi di Milano - DISAA, V Celoria 2, 20133 Milano, Italy</footnote>

<footnote n="3">³ Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy</footnote>

<footnote n="4">⁴ Parco Tecnologico Padano, Via Einstein, Loc C.na Codazza, 26900 Lodi, Italy</footnote>
**PI-08 - Jonas ANDEREGG** - Hyperspectral assessment of senescence dynamics and its relationship to grain yield and grain protein content in a high-yielding environment

# Hyperspectral assessment of senescence dynamics and its relationship to grain yield and grain protein content in a high-yielding environment

Jonas ANDEREGG<fnref n="1" />, Kang YU<fnref n="1" />, Helge AASEN<fnref n="1" />, Frank LIEBISCH<fnref n="1" /> and Andreas HUND<fnref n="1" />

Corresponding author: jonas.anderegg@usys.ethz.ch

The stay-green phenotype (i.e. a prolonged maintenance of green leaf area after anthesis) has been linked to increased yield in several crops. In wheat, potential yield is still considered to be predominantly limited by sink strength, which is largely determined up until and including a short period after anthesis. However, individual grain weight is an important yield component which is predominately regulated post-anthesis and is affected by both the onset of senescence and the rate of the process. In particular, the efficiency of remobilization processes in the course of senescence has been proposed as a possible target to improve grain yield (GY) and grain protein content (GPC), as well as their stability across environments.

The effects of senescence dynamics on GY and GPC as well as senescence dynamics per se are strongly influenced by environmental conditions and have not been studied in detail on a large number of genotypes in high-yielding environments such as the Swiss plateau region. For genetic studies and a better understanding of the effects on GY and GPC, senescence dynamics need to be measured accurately on a large number of genotypes in several contrasting environments at high temporal resolution.

Here, hyperspectral reflectance measurements of a set of > 300 wheat genotypes in two years were used to compare the widely used normalized difference vegetation index (NDVI) to passive-sensor derived narrow-band indices and full-spectrum analysis to predict senescence-related traits. Phenotypic correlations between GY, GPC and senescence dynamics were also investigated.

**Keywords:** Senescence, Hyperspectral reflectance, Vegetation index

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<footnote n="1">¹ Crop Science Group, Institute of agricultural sciences, ETH Zurich, Zurich, Switzerland</footnote>
PI-09 - Salar SHAAF - Integrated genetic approaches to modify canopy architecture for improved barley biomass and yield

Integrated genetic approaches to modify canopy architecture for improved barley biomass and yield

Salar SHAAF<fnref n="1" />, Noemi TRABANCO<fnref n="1" />, Paolo PESARESI<fnref n="1" />, Roberto CONFALONIERI<fnref n="2" />, Livia PALEARI<fnref n="2" />, Alessandro TONDELLI<fnref n="3" />, Davide GUERRA<fnref n="3" />, Fulvia RIZZA<fnref n="3" />, Moritz JÖST<fnref n="4" />, Christian KAPPEL<fnref n="4" />, Michael LENHARD<fnref n="4" />, Beata CHMIELEWSKA<fnref n="5" />, Agnieszka JANIAK<fnref n="5" /> and Laura ROSSINI<fnref n="1" />

Corresponding author: laura.rossini@unimi.it

In barley, genetic improvement of grain yield traditionally has been based on changes in plant architecture aimed at increasing harvest index and partitioning of biomass from straw to grains. With the increasing demands for renewable energy sources, plant biomass such as cereal straw is becoming more attractive. Barley straw is characterized by the largest content of carbohydrates among cereals, making it a valuable resource for its potential conversion into biofuels and other products. The BarPLUS consortium, a multidisciplinary group of scientists from different countries, is working to find genes, alleles, and candidate lines related to barley architecture and photosynthesis to maximize barley biomass and yield (https://barplus.wordpress.com/). In this framework, the major focus of our research group is optimizing tillering, leaf size and angle through integration of different genetic approaches exploiting both induced and natural allelic variation. Using a forward genetics approach, we screened the HorTillus population-derived from chemical mutagenesis of the barley cultivar "Sebastian"- under both field and controlled conditions and identified mutants with increased tillering and/or erect leaves: these are being targeted for mapping-by-sequencing in order to isolate the underlying genes. In parallel, we are analyzing natural genetic variation in biomass-related traits by genome wide association analysis on a set of 240 diverse barley accessions using exome capture data provided by the WHEALBI consortium (http://www.whealbi.eu/). Based on a preliminary analysis, heritability estimates revealed a substantial genetic component influencing leaf size and angle and several markers were found to be significantly associated with these traits. Through extensive literature search, bioinformatics analysis and comparative genomics, we identified a total of 48 candidate genes potentially involved in biomass-related traits. The sequences of these genes are being explored for mining functional variants in 403 barley accessions taking advantage of WHEALBI exome capture data. A subset of the candidate genes has been also subjected to TILLING to identify lines carrying mutated alleles. These resources will be characterized phenotypically to evaluate their effect on biomass traits. Together, this research will provide valuable knowledge and resources for potential improvement of barley biomass and yield.

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<footnote n="1">¹ Università degli Studi di Milano, DiSAA, Via Celoria 2, Milano, Italy</footnote>

<footnote n="2">² Università degli Studi di Milano, DESP, Cassandra Lab, Italy</footnote>

<footnote n="3">³ CREA-GPG, Via San Protaso, 29017 Fiorenzuola d'Arda (PC), Italy</footnote>

<footnote n="4">⁴ Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany</footnote>

<footnote n="5">⁵ Department of Genetics, University of Silesia in Katowice, 40-032 Katowice, Poland</footnote>
**PI-10 - Gianluca BRETANI** - Genome scan to detect loci involved in culm morphological traits in a diverse barley collection

# Genome scan to detect loci involved in culm morphological traits in a diverse barley collection

Gianluca BRETANI<fnref n="1" />, Salar SHAAF<fnref n="1" />, A HOTTI<fnref n="1" />, Alessandro TONDELLI<fnref n="2" />, Luigi CATTIVELLI<fnref n="2" />, Stefano DELBONO<fnref n="2" />,
R WAUGH<fnref n="3" />, B THOMAS<fnref n="3" />, JR RUSSELL<fnref n="3" />, H BULL<fnref n="3" />, R KEITH<fnref n="3" />, Ernesto IGARTUA<fnref n="4" />, Ana M CASAS<fnref n="4" />,
M Pilar GRACIA<fnref n="4" />, Alan H SCHULMAN<fnref n="5" /> and Laura ROSSINI<fnref n="1" />

Corresponding author: laura.rossini@unimi.it

Barley (*Hordeum vulgare* L.) is ranked fourth in worldwide cereal production and is used for animal feed, as malt and food for humans, and as biomass for biofuel production. Although the introduction of semi-dwarfing genes greatly improved stem sturdiness and harvest index, new plant ideotypes are needed to face the increasingly frequent extreme climatic events that threaten barley production. Morphological and anatomical features of the cereal culm have been linked to lodging resistance and biomass increase in rice and wheat, but information on the genetic basis of such traits is scarce in barley. As part of the ClimBar project, the objective of our studies is to explore and dissect natural genetic variation for culm traits in barley, using a germplasm collection of 233 diverse barley accessions. This germplasm panel was genotyped by exome capture sequencing, which provides an ideal basis for genome-wide association studies (GWAS). Our main focus was the second (basal) internode as a critical site for lodging in barley. Phenotypic data were collected from field-grown plants at both dough stage (Zadok 83) in Italy and at pre-harvest growth stage (Zadok 90) in four European countries with different climatic conditions. Straw culms were dissected and scanned images collected. Green culm sections were stained with Safranin and photographed using a stereomicroscope. ImageJ was used to extract quantitative data for culm diameter, culm wall thickness, and culm circularity. The number of vascular bundles from green culm images were also counted. Statistical analyses indicated the existence of significant genetic variation for the studied traits as supported by high heritability values. For GWAS, 176,000 SNPs from exome sequencing were considered, applying a minor allele frequency ≥0.05. Marker-based Principal Component Analysis (PCoA) indicated the presence of population structure mainly due to spike row type (2-rowed vs. 6-rowed), an important trait associated with domestication in barley. GWAS identified genomic regions associated with the studied traits and potential candidate genes. In addition, trial-dependent associations were detected, possibly due to the existence of GxE interactions for the traits. Samples from a second year of field trials (2017) are being processed and will be used to run integrated analyses and evaluate the stability of identified associations. Regions of special interest will be analysed to further select putative candidate genes and carry out allelic diversity studies.

This work was supported by the FACCE JPI CLIMBAR project. http://plen.ku.dk/english/research/plant_soil/breeding/quality/climbar/

**Keywords: *Hordeum vulgare*, GWAS, culm architecture**

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<footnote n="1">¹ Università degli Studi di Milano, DiSAA, Via Celoria 2, Milano, Italy</footnote>

<footnote n="2">² CREA-GPG, Via San Protaso, 29017 Fiorenzuola d'Arda (PC), Italy</footnote>

<footnote n="3">³ JAMES HUTTON INSTITUTE, Invergowrie, Dundee DD2 5DA, Scotland, UK</footnote>

<footnote n="4">⁴ EEAD-CSIC, Avenida Montañana, 1005, 50059 Zaragoza, Spain</footnote>

<footnote n="5">⁵ Natural Resources Institute Finland (Luke) and Institute of Biotechnology, University of P.O.B. 65, FI-00014 Helsinki, Finland</footnote>
PI-11 - Edina TÜRKÖSI - 7BS.7HL wheat_barrow robertsonian translocation line with increased salt tolerance and β -glucan content

7BS.7HL wheat_barrow robertsonian translocation line with increased salt tolerance
and β -glucan content

András CSEH<fnref n="2" />, Edina TÜRKÖSI<fnref n="1" />, Éva DARKO<fnref n="3" />, Marianna RAKSZEGI<fnref n="4" /> and Márta MOLNÁR-LÁNG<fnref n="1" />

Corresponding author: turkosi.edina@agrar.mta.hu

One of the main challenge of current crop breeding is to improve yield stability and grain quality. Along with food production it is highly influenced by the conservation of biodiversity and responsible use of genetic resources. The modern wheat cultivars have excellent yield potential, and the new breeding programs put emphasis on breeding cultivars with better nutritional components (e.g. dietary fibres, essential amino acids), high resistance against diseases and better capacity of adaptation. Barley (*Hordeum vulgare* L., 2n=2x=14, HH) carries genes for abiotic stress tolerance and has good nutritional parameters. Cytologically stable, compensating wheat/alien translocations are promising gene sources for wheat improvement.

A QTL for salinity tolerance during germination was mapped on 7H chromosome. Salt stress analysis during germination of the Asakaze komugi/Manas 7HL ditelosomic addition line suggests that the 7HL chromosome arm is a good candidate for improving salinity tolerance of wheat during germination. In addition, a QTL responsible for β-glucan content of the seeds was mapped on chromosome 7H.

The present study was initiated to develop compensating Robertsonian translocations involving wheat chromosome 7B and barley chromosome 7H and to analyse its effect on salt tolerance of the genotype developed and β-glucan content of the seeds. A 7B monosomic stock of 'Rannaja' wheat was crossed with the disomic Asakaze/Manas wheat/barley 7H addition line. Plants carrying monosomic centric fusion were selected from F3 generation and the barley chromosome arm was identified using molecular markers. Fluorescent in situ hybridization using wheat specific repetitive DNA probes (pSc119.2, Afa family and pTa71) were used to identify wheat chromosome arm involved in the Robertsonian translocation. The F4 progenies homozygous for the presence of wheat/barley translocation were investigated from the viewpoint of salt tolerance and β-glucan content. The 7BS.7HL recombinant line exhibited higher salt tolerance both during germination and in the early developmental stages than the wheat parents. The expression of HvCslF6 barley gene in the wheat background and increased (1,3;1,4)-β-D-glucan content of this line proving that the 7BS.7HL translocation line could be of potential importance for improving β-glucan of wheat. The 7BS.7HL line is multiplied in field trials.

The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under the grant agreement no. FP7-613556, Whealbi project (http://www.whealbi.eu/project/project), the MTA KEP 5/2016 (Hungarian Academy of Sciences) and by National Research, Development and Innovation Office (K112226). AC gratefully acknowledges support from a Marie Skłodowska-Curie Fellowship Grant (H2020-MSCA-IF-2016-752453)

**Related publication:**

Darko, E., Janda, T., Majlath, I., Szopko, D., Dulai, S., Molnar, I., Turkosi, E., Molnar-Lang, M. (2015): Salt stress response of wheat-barley addition lines carrying chromosomes from the winter barley "Manas". EUPHYTICA 203:(3) pp. 491-504.

Türkösi, E., Cseh, A., Darkó, É., Molnár-Láng, M. (2016): Addition of Manas barley chromosome arms to the hexaploid wheat genome.
BMC GENETICS 17: Paper 87.

<footnote n="1">¹ Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences 2462 Martonvásár, Hungary</footnote>

<footnote n="2">² Molecular Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences 2462 Martonvásár, Hungary</footnote>

<footnote n="3">³ Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences 2462 Martonvásár, Hungary</footnote>

<footnote n="4">⁴ Cereal Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences 2462 Martonvásár, Hungary</footnote>
Darko, E., Gierczik, K., Hudák, O., Forgó, P., Pál, M., Türkösi, E., Kovács, V., Dulai, S., Majláth, I., Molnár, I., Janda, T., Márta Molnár-Láng (2017): Differing metabolic responses to salt stress in wheat-barley addition lines containing different 7H chromosomal fragments PLOS ONE 12:(3) Paper e0174170. 20 p.

**Keywords:** wheat/barley Robertsonian translocation, monosomic stock, wheat/barley disomic addition line, salt tolerance, β-glucan content

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PI-12 - Martina ROSELLÓ - Dissecting the QTLome for protein content in durum wheat Mediterranean landraces

Dissecting the QTLome for protein content in durum wheat Mediterranean
landraces

Martina ROSELLÓ<fnref n="1" />, José Miguel SORIANO<fnref n="1" />, Fanny ÁLVARO<fnref n="1" />, Dolors VILLEGAS<fnref n="1" /> and Conxita ROYO<fnref n="1" />

Corresponding author: martina.rosello@irta.cat

Durum wheat (*Triticum turgidum* L. var. durum) was originated in the Fertile Crescent (10,000 BP) and spread over the Mediterranean Basin developing into local landraces specifically adapted to their growing regions. The wide genetic diversity and high level of polymorphism in quality genes of landraces can be used as a source of genetic variation quality traits in breeding programs (Nazco et al., 2012). Additionally, the decrease of protein content in durum wheat cultivars as a consequence of the release of high yielding cultivars (Subirà et al. 2014) make the use of landraces as a source of protein content.

The aim of this study was the identification by association mapping (AM), of molecular markers linked to protein content (PC, %) in a set of 169 durum wheat Mediterranean landraces. Experiments were carried out during the 2007, 2008 and 2009 harvesting seasons in north-eastern Spain, under rainfed conditions. PC analysis was performed as reported previously by Nazco et al. (2012). Phenotypic data was fitted to a linear mixed model to produce the best linear unbiased predictors (BLUPs). The durum wheat PstI/TaqI array v2.0 was used for genotyping the panel and 872 markers were ordered according to the consensus map of durum wheat developed by Maccaferri et al. (2014). AM was performed using a Mixed Linear Model and marker trait associations (MTA) were considered significant using a threshold of -log10(P) > 3. False discovery rate (FDR) was calculated for each trait.

Four 4 MTAs were significant for the PC in the 3 years and their calculated mean. The marker wPt-2737 was detected in 3 associations including the mean across years with a -10log(P) over the FDR threshold and explaining a high percentage of the phenotypic variance explained (Table 1).

To compare the associations reported in our collection with previously mapped QTLs, a meta-analysis was performed. A total of 70 QTLs for grain protein content, from 18 studies, were projected onto a durum wheat consensus map (Maccaferri et al. 2014). In total 15 meta-QTLs were identified and 23 QTLs remained as singletons. The marker wPt-2737 was located within a MQTL, while wPt-1140, wPt-7355 and tPt-5342 identified new genomic regions controlling PC.

<table><caption>Table 1. Significant marker trait associations (-10log(P)>3) obtained for protein content in 169 durum wheat Mediterranean landraces.</caption><thead><tr><td>Marker</td><td>Year</td><td>Chromosome</td><td>Position (cM)</td><td>p-value</td><td>-10logP</td><td>Marker R2</td><td>Effecta</td></tr></thead><tbody><tr><td>wPt-2737</td><td>2007</td><td>7B</td><td>68.9</td><td>3.87E-04</td><td>3.41</td><td>0.08</td><td>0.71</td></tr><tr><td>wPt-2737</td><td>2008</td><td>7B</td><td>68.9</td><td>7.99E-04</td><td>3.10</td><td>0.07</td><td>0.55</td></tr><tr><td>wPt-2737</td><td>Mean</td><td>7B</td><td>68.9</td><td>2.98E-05</td><td>4.53*</td><td>0.11</td><td>0.53</td></tr><tr><td>wPt-1140</td><td>2007</td><td>2B</td><td>133.4</td><td>7.01E-05</td><td>4.15</td><td>0.10</td><td>1.71</td></tr><tr><td>tPt-5342</td><td>2008</td><td>4B</td><td>16.5</td><td>4.25E-04</td><td>3.37</td><td>0.08</td><td>-0.78</td></tr><tr><td>wPt-7355</td><td>2007</td><td>4A</td><td>59.8</td><td>9.26E-04</td><td>3.03</td><td>0.08</td><td>0.74</td></tr></tbody></table>

Study funded by the projects AGL-2006-09226-C02-01 and AGL2015-65351-R from the Spanish Ministry of Economy and Competitiveness (MINECO) and CERCA Programme / Generalitat de Catalunya. Martina Roselló is recipient of an INIA-FPI PhD-grant

**Related publication:**

Maccaferri, M., et al. (2014). BMC Genomics, 15(1), 873.

Nazco, R., et al. (2012). Euphytica, 185(1), 1-17.

Subirà, J., et al. (2014). Crop & Pasture Science 65, 16-26.

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<footnote n="1">¹ Av. Alcalde Rovira i Roure, 191 - 25198 Lleida, Spain</footnote>

<footnote>*(False Discovery Rate>4.24); a (allele presence effect).</footnote>
**PI-13 - Roberto TUBEROSA** - Development and characterization of a whole-genome radiation hybrid panel from reference tetraploid wheat cultivar Svevo

# Development and characterization of a whole-genome radiation hybrid panel from reference tetraploid wheat cultivar Svevo

Roberto TUBEROSA<fnref n="1" />, Martina BRUSCHI<fnref n="1" />, VK TIWARI<fnref n="2" />, Marco MACCAFERRI<fnref n="1" />, Silvio SALVI<fnref n="1" /> and BS GILL<fnref n="2" />

Corresponding author: roberto.tuberosa@unibo.it

The recent release of high-quality sequence information from hexaploid wheat (IWGSC 2014) coupled with the availability of high-density consensus maps for tetraploid wheat (Maccaferri et al. 2014) has accelerated marker and gene discovery in durum wheat (Triticum durum), thus facilitating the genetic dissection of agronomic traits. This notwithstanding, the construction of genetic maps remains a bottleneck for the investigation of the durum wheat genome. In this context, the development of physical mapping resources to facilitate the assembly of BAC contigs in future sequencing projects of durum wheat is becoming a primary necessity. Radiation hybrid (RH) mapping is a promising recombination-independent mapping approach, which involves the use of radiation-induced chromosomal breakage and marker segregation to reconstruct marker order (Tiwari et al. 2016). In this study, for the first time, a RH panel for tetraploid wheat was developed for reference durum genotype Svevo: the Svevo-Whole-Genome Radiation Hybrid (Sv-WGRH) panel. The Sv-WGRH panel was developed at Kansas State University (USA), according to the protocol reported by Tiwari et al. (2016). Freshly dehiscing pollen of Svevo was irradiated with γ-rays (10-Gy) and this was used to pollinate ~150 emasculated spikes of Senatore Cappelli (used as the female parent), which produced ~1300 RH1 seeds, each representing an independent RH event. Greenhouse planting of 1000 RH1 seeds resulted in ~730 RH1 plants, each representing a RH line of the Sv-WGRH panel. Initial assessment of the panel was performed on the DNA of 613 RH1 plants by means of 23 SSR markers. Results indicated that average marker retention frequency of the panel is ~87%, with 35% of RH1 lines having a retention frequency between 20 and 90%. Approximately 175 RH1 plants were obtained from planting 269 RH1 seeds in the greenhouse at DipSA UNIBO. DNA of these RH1 lines will be genotyped by means of the GBS technique in order to construct a physical map. This RH panel is an important resource contributing towards the assembly of the genome sequence of durum wheat and other tetraploid wheats and supporting positional cloning of important genes and QTLs in durum wheat.

**Keywords:** Durum wheat, physical map, radiation hybrid, sequencing, SSR markers

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<footnote n="1">¹ Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy</footnote>

<footnote n="2">² Department of Plant Pathology Kansas State University, Throckmorton Hall, Manhattan, Kansas, USA</footnote>
PI-14 - Radim SVAČINA - *Ph2* gene mapping through development and phenotyping of deletion lines in bread wheat

*Ph2* gene mapping through development and phenotyping of deletion lines in bread wheat

Radim SVAČINA<fnref n="1" />, Magdaléna MALUROVÁ<fnref n="1" />, Miroslava KARAFIÁTOVÁ<fnref n="1" />, Pierre SOURDILLE<fnref n="2" />, Takashi R ENDO<fnref n="3" />,
Jaroslav DOLEŽEL<fnref n="1" /> and Jan BARTOŠ<fnref n="1" />

Corresponding author: svacina@ueb.cas.cz

Wheat (*Triticum aestivum* L.) emerged by hybridization of three closely-related species. Thus its genome consists of three highly similar sub-genomes (A, B and D) called homoeologs. The coexistence of similar homoeologous chromosomes led to establishment of a diploid-like system of homologous chromosome pairing mainly genetically controlled by two *Ph* (for pairing homoeologous) genes: *Ph1* and *Ph2*. *Ph2* was mapped to a distal region of 80 Mbp on the short arm of chromosome 3D. Mutants for this gene were developed and it was observed that *Ph2* has only a small effect on homoeologous wheat-chromosome pairing suppression. On the other hand, pairing of wheat and alien chromosomes was witnessed after removal of *Ph2* gene in hybrids derived from crosses between wheat and closely related species such as rye (*Secale cereale*). This discovery suggests a capability of *Ph2* gene to be used as a new breeding tool by introgression of alien genes into wheat gene pool. Positional cloning of *Ph2* would thus be of interest. However, the size of the actual deletion (80 Mb) hampers the identification of any candidate and it would be useful to reduce the deletion to a maximum of a few Mb.

The goal of the project is to scale down the *Ph2* gene region by deletion mapping up to 5 Mbp radius, so more precise mapping by radiation deletion lines can be performed. We have established a new set of deletion lines for a short arm of chromosome 3D, which is being currently extended. We focused on a distal 80 Mb part of a short arm of chromosome 3D, which is the pinpointed area of *Ph2* gene presence. We used the 2C gametocidal chromosome from *Aegilops cylindrica* as a tool for the development of the deletion lines after monosomic introduction into ‘Chinese Spring’ cultivar of wheat. Some gametocidal chromosomes introduced into wheat are inherited preferably by causing sterility of gametes in which they are absent. The sterility is caused by the ability of these chromosomes to induce genomic rearrangements. In some cases, these changes are not lethal, thus giving the opportunity to transfer aberration into progeny.

The novel deletion lines were characterized by molecular markers. These lines will now be crossed with rye to see if we observe the *ph2* mutant corresponding phenotype.

This work has been supported by the Czech Science Foundation (grant award 17-05341S) and the Ministry of Education, Youth and Sports of the Czech Republic (award LO1204 from the National Program of Sustainability I)

**Keywords:** *Ph2*, deletion lines, chromosome 3D, phenotyping

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<footnote n="1">¹ Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, Olomouc, 783 71, Czech Republic</footnote>

<footnote n="2">² INRA, UCA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales (GDEC), 5 chemin de Beaulieu, 63 039 Clermont-Ferrand cedex2, France</footnote>

<footnote n="3">³ Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194, Japan</footnote>
PI-15 - Rubén Gómez RUFO - Genetic structure of Mediterranean wheat landraces assessed with SNP markers

Genetic structure of Mediterranean wheat landraces assessed with SNP markers

Rubén Gómez RUFO ¹, Fanny ÁLVARO¹, Conxita ROYO ¹ and José Miguel SORIANO ¹

1 Av. Alcalde Rovira Roure, 191, 25198 Lleida

Corresponding author: rubenrufogomez@gmail.com

Wheat is one of the most important grain crops in the world, being the hexaploid wheat (Triticum aestivum L.) the 95% of world wheat production. Landraces represent a valuable source of genetic diversity and are well adapted to local environmental conditions. Landraces may provide new alleles for the improvement of commercially valuable traits, being very useful especially in breeding for suboptimal environments as the Mediterranean Basin. Knowledge of genetic diversity is essential for understanding the relationships between cultivars and for the use of landraces in breeding programmes.

In this study, the genetic structure of a collection of 170 wheat landraces from 24 Mediterranean countries was ascertained using the wheat 15K SNP array. A total of 10,458 markers resulted polymorphic among the 170 genotypes. A model-based cluster method (Bayesian algorithm) using STRUCTURE software allocated 83.5% of the accessions in three subpopulations related to their geographic origin: North Africa and West of Mediterranean, East of Mediterranean and South Europe and North of Mediterranean.

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