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Whealbi
Wheat and barley Legacy for Breeding Improvement
Grant agreement number: FP7-613556
Collaborative Project
SEVENTH FRAMEWORK PROGRAMME
Deliverable D8.7
2nd report on training organisation
Due date: M54
Actual submission date: M54
Project start date: January 1st, 2014 Duration: 60 months
Workpackage concerned: WP8
Concerned workpackage leader: ARCADIA INTERNATIONAL
Dissemination level: PU
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Table of contents
1. SUMMARY .............................................................................................................................................. 3
2. TRAINING ORGANIZATION – GENERAL VIEW .......................................................................................... 4
3. REPORTS AND TRAINING DESCRIPTIONS ................................................................................................. 5
4. CONCLUSION ......................................................................................................................................... 10
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1. Summary
During the WHEALBI project, an important focus is given to the knowledge transmission. A large effort was dedicated to trainings, organized all along the project. Thus, this second deliverable about trainings summarizes the different trainings organized during the course of the project, and summarizes the main outputs (attendance, reached targets, evaluation…).
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2. Training Organization – General view The table below summarized the different trainings with organizer(s), date and location:
Title of the training course Organizer Date and Location
High-throughput and precision phenotyping for most relevant agronomic traits (abiotic stress tolerance, response to major disease, plant growth descriptors) (WP3)
CREA 18-20 April 2016, CREA, Italy
SNP discovery and analysis using next generation technologies: exome capture and RNAseq (WP2)
JHI (and contribution IPK and PTP)
19-20 May 2016, JHI Dundee, UK
Allele mining / genetic analysis (WP5)
University of Zurich 6-7 June 2017, Wageningen, NL
Databases, SNP calling and genetic analysis of multi-environment data (WP4)
Wageningen University, Helmholtz
Zentrum Muenchen, INRA
7-9 June 2017, Wageningen, NL
Crop Management and Development of Innovative Cropping Systems (WP7)
NIAB 29-30 May 2018, NIAB Cambridge,
UK
Wheat and Barley Pre-breeding (WP6)
KWS 30-31 May 2018, NIAB Cambridge,
UK
Reports about these trainings are presented on the WHEALBI website: http://www.whealbi.eu/science/trainings/
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3. Reports and training descriptions Below the main information and feedback from the participants of the trainings is presented.
WP2 – Genotyping – James Hutton Institute
The training: “SNP discovery and analysis using next generation technologies: exome capture and RNAseq” was organised by the The James Hutton Institute and the WHEALBI consortium the 19-20 May 2016 in Dundee (Scotland). The training was attended by 15 participants from all over Europe with young researchers (Ph.D and Post docs), researchers and students. The schedule was the same as announced in the deliverable 8.4, with three presentations the first day and five the second day, with sufficient time for discussions and practical questions.
19th May 2016 - Introduction – available approaches to SNP discovery (exome capture, RNA seq) - Mapping and variant calling (barley genome assembly, pseudomolecules and
pipelines for SNP calling) - Visualisation and databasing (Flapjack and MorexGenes)
20th May 2016
- Data utilisation – Applications for population genetics - QTLs and GWAS approaches - Combining SNP data with bioclimatic variables - eQTLsWider applications and the development of SNP assays (KASPs and 50K SNP
chips) - Targeted approaches for disease resistance genes an example from potato (REN seq)
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WP3 – Phenotyping – CREA The training: “High-throughput and precision phenotyping for most relevant agronomic traits (abiotic stress tolerance, response to major disease, plant growth descriptors)” was organized by CREA and the WHEALBI consortium the 18-20 April 2016 in Fiorenzuola d’Arda (Italy). The training was attended by 30 participants from all over Europe with breeders, young researchers (PhD and Post docs), researchers and students. The organisation was excellent with a strong mixing of courses and practice/ demos in the field. Evaluation of the training by the participants was high.
April 18th
- Short introduction on WHEALBI project (Luigi Cattivelli). - Phenotyping for low temperature tolerance in cereals: theory and practice (Fulvia
Rizza). - Phenotyping for canopy development in wheat and barley: 1 theoretical bases (Franz
Badeck). - Plant development and mutant-based analysis: visit to a mutant barley collection
(Michele Stanca).
April 19th
- Phenotyping for drought tolerance in wheat and barley: theory and practice (Yehoshua Saranga).
- High-throughput phenotyping for plant disease resistance (Patrick Schweizer). - Phenotyping for leaf disease in wheat: theory and practice (Simon Krattinger). - Smartphone-based application for plant phenotyping (Roberto Confalonieri). - Phenotyping for canopy development in wheat and barley: 2 a practical experience in
the WHEALBI field (Franz Badeck, Fulvia Rizza, Roberto Confalonieri). - Genotype to phenotype crop models (Pierre Martre).
April 20th
- Phenotyping for canopy development in wheat and barley: 3 bioinformatic analysis of collected data (Franz Badeck).
- Presentation from Lemnatec on new platforms for field phenotyping (TBC).
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WP4/WP5– Data Integration & Allele and Pathways Mining – UZH/DLO/ INRA-UGRI/ HMGU The two trainings “Allele mining / genetic analysis” & “Databases, SNP calling and genetic analysis of multi-environment data” were organised by the WHEALBI consortium (with special involvement of the University of Zurich, Wageningen University, Helmholtz Zentrum Muenchen, INRA) and hosted by Wageningen University the 6 and 7 June 2017. These trainings were attended by 25 and 38 persons respectively, with very diverse profiles, from Ph.D and Post-docs to many representatives from private companies. They were both very practical with time dedicated to practices with computers. Tuesday 6th June
- Introduction to the workshop and the basis of allele mining - Navreet Bhullar, ETHZ – Focused identification of diverse alleles from large
germplasm collections - Luigi Cattivelli, CREA – Mining genes controlling frost tolerance in barley: allelic
variation and copy number variation - Patrick Schweizer , IPK – Potentially useful alleles for powdery mildew resistance in
barley – a case study - Martin Mascher, IPK – Allele mining wild barley exomes: how many genes does it
take to make you six-rowed? - Javier Sanchez-Martin, UZH – Allele mining to increase disease resistance in cereals - Thomas Müller: Don’t fear the command line – Introduction to useful tools
Wednesday 7th June
- Thomas Müller: Computer lab: in silico allele mining (including coffee break). - Michael Alaux, INRA - Whealbi databases: Introduction - Thomas Letellier, INRA - Overview of germplasm, phenotype and ontologies data - Thomas Letellier, Mathilde Lainé, INRA - Whealbi databases: Live demo with use
cases - Michael Seidel, HMGU - SNP calling
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WP6 – Pre-breeding – KWS The training “Wheat and Barley Pre-breeding” was organised by KWS and the WHEALBI consortium and hosted at NIAB in Cambridge the 30-31 May 2018. It was a large success (28 people attended with a lot of young breeders and more than 10 speakers came from all over the world) and the evaluation of the training by participants was very high. Many results from improved pre-breeding techniques for wheat and barley were shown during the different presentations (examples from different private breeders, programs in Australia, South Africa, etc). With the field visits at KWS, trainees had the opportunity to see precisely how pre-breeding is done in a company like KWS and how old varieties and genetic resources and more precisely how the WHEALBI resources are used to bring more diversity in European cultivars of wheat and barley. 30 May Welcome, Whealbi and KWS (Jacob Lage, KWS)
- Setting the scene, and experiences from trait focused pre-breeding (Professor Richard Trethowan, University of Sydney)
Session 1: Novel source of genetic diversity - The role of IP and Nagoya in pre-breeding: why should we care? (Paul Olson, KWS) - Value of landraces to plant breeding (Joanne Russell, James Hutton Institute) - From QTL mapping to introgression to validation (Tamar Krugman, Haifa University) - Use of cytogenetics in pre-breeding (Marta Molnar, retired from Martonvasaar)
31 May Session 2: Tools in pre-breeding
- The role of Magic and NAM populations in applied pre-breeding (Gilles Charmet, INRA)
- Peri-centric haplotype pre-breeding (Peter Werner, KWS) - Physiology based pre-breeding (Scott Boden, John Innes Centre) - Use of modelling in pre-breeding (Daniela Bustos Korts, Wageningen)
Session 3: Conventional pre-breeding in a modern era - Combining winter and spring pools in hybrid breeding – lessons from a commercial
hybrid programme in South Africa (Francois Koekemoer, Sensako) - Role of pre-breeding in hybrid pool development (Yann Mannes, Syngenta) - Introgression of novel AB&D-genome diversity into elite UK winter wheat germplasm:
lessons learnt (Phil Howell, NIAB) - Pre-breeding in a commercial context (Jacob Lage, KWS) - KWS visit
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WP7 – Innovative Crop Management - NIAB The training “Crop Management and Development of Innovative Cropping Systems” was organised by NIAB in Cambridge the 29-30 May 2018. The training was attended by 10 persons from all over Europe with breeders, young researchers and students. During the two days of the training, people had the opportunity to discover new cropping techniques, new filed measure instruments and the different trials that NIAB performs at the Innovation Farm with innovative cropping systems and WHEALBI varieties. 29 May
- Welcome (Nathan Morris, NIAB) - Innovative conservation crop management practices (Nathan Morris, NIAB) - Innovative organic crop management practices – (Ambrogio Costanzo, ORC) - Crop physiology (Eric Ober, NIAB) - Quantitative Genetics – (Ian Mackay, IM Plant Consultancy) - Overview and discussion
30 May
- Field Visit (Nathan Morris + Lydia Smith, NIAB) - Field visit to include NIAB Innovation Farm facilities and WHEALBI demo plots. - Wider field tour at Cambridge
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4. Conclusion All these different trainings, each linked with a specific work package of the WHEALBI project, allowed to share knowledges and results from the project to young breeders, future researchers, and to the scientific European community. A special emphasis was put to attract young scientists (priority access to the trainings), young breeders and these trainings were widely open to private companies (for technology transfer, WP3 and WP6 for instance) and breeders academies (KWS breeding academy). Thanks to a large advertising around these trainings through many different channels (stakeholder database, social networks, direct contacts to other EU project and breeding companies), most of the trainings were full. The feedbacks we received from the participants were always good. This encouraged us all along the project to continue to provide high level trainings and shows that stakeholders were interested by this training approach, which is highly recommended in European projects. The dissemination around these trainings, mainly made through the website and social networks, allowed to reach and inform a larger public:
YouTube Channel: https://www.youtube.com/channel/UCkwqKlC8tgGgB768ZprZtyw?view_as=subscriber
Twitter: https://twitter.com/whealbi
LinkedIn: https://www.linkedin.com/company/whealbi/
