WHEAt and barley Legacy for Breeding Improvement

WHEALBI NEWSLETTER
december 2018 - Issue 5

Edito

In 2018, WHEALBI project is coming to the end, at least officially. A closing annual meeting was organized in Edinburg UK, 24-25 October. Partners draw a survey of what has been achieved and what remains to be worked out, particularly for valorizing our results through publications and dissemination to stakeholders. In WP1, 512 barley and 512 wheat varieties of the WHEALBI panels have been (most) made available through INRA and IPK gene banks, together with passport data. Evaluation data in the “garden experiment” from WP3 will also be available soon on https://wheat-urgi.versailles.inra.fr/Projects/Whealbi.

Barley and wheat EXOME data from WP2 data have been exploited with the most recent approaches of population and quantitative genetics to infer the evolutionary history, domestication and selection effects on spatial and temporal structure of diversity and identify key genes for adaptive traits along the evolution of modern wheat and barley varieties. Two major manuscripts describing the results have been submitted in high standard scientific journals. Evaluation data in the field and in controlled conditions for disease, frost and drought tolerance, canopy development and adaptive phenology have also been analyzed together with polymorphisms in candidate genes to identify useful association. Particularly, a list of accessions with new resistance or tolerance to the main diseases will be delivered. A new software was developed in WP4 to achieve genome-wide association studies (GWAS) and genomic predictions with multi-environment data. Pending work in WP5 should identify new genes or haplotypes involved in resistance and other adaptive traits such as frost and drought tolerance, which would lead to new publications and disseminations in the coming years. Other deliverables are newly developed pre-breeding materials in WP6, such as barley and wheat lines with introgression of alien (other species) or exotic (e.g. old landraces) genetic materials into modern lines, which are easier to use in applied breeding programs. These newly developed materials have been characterized for both agronomic traits and molecular markers, and a list of best adapted lines selected from phenotypic and molecular data is being delivered. Extensive results of management trials in WP7 have been delivered. These trials were conducted in UK, Hungary and Italy with a subset of diverse barley and wheat lines to identify ideotypes most adapted to conservation agriculture or organic farming. WP7 also delivered a list of candidate traits and ideotypes for improving wheat adaptation and stability identified using SirrusQuality2 model. Finally, 6 trainings plus numerous dissemination events have been organized, such as the college project. 15 videos explaining the aims, goals and intermediate achievements of the project are available : https://www.youtube.com/watch?v=fH_6cmtZ7wk. A final conference was organized in Edinburgh 24-25th of October, attended by 70 persons all over Europe, and a final stakeholder meeting with members of the EU commission is organized in Brussels, December 4th, hosted by the European Seed Association.

Overall, we can say this project was successful in delivering a highly valuable corpus of data as a legacy for research and breeding. Particularly, exome data of 1000 accessions is the largest dataset produced to date worldwide, and we are proud that WHEALBI data have already been requested by numerous research consortium. It has been a pleasure, all along these five years, to be the coordinator of the WHEALBI project and to work with all the partners, and we wish to find other opportunities to keep working together.

Gilles Charmet, WHEALBI coordinator


Group picture at the Final Whealbi Conference, Edinburgh, 24th of October

A website explaining the goals and presenting the project results is available:

» WHEALBI.EU

Meeting Whealbi Consortium

We are now at the end of the WHEALBI project and each Work Package leader was interviewed to answer different questions about the main output obtained, the best and worst memories with the consortium, what they would two differently 5 years back and what drives their motivation...

“The main output of WP1 was selecting, collecting, and distributing the genetic resources used for all downstream activities of the project. The best memory is clearly the strong collaborative spirit, and as a bad point, I would say that the project wanted too much. If I was 5 years back? I would focus on one crop and thus use the resources of the project in a more focused manner. And probably implement a better tracking of the material. What next? We need to turn this work into profit for the crop innovation and have more systematic approaches for assessing the potential of genetic resources.”Nils Stein, WP1 leader, Group Leader at IPK Gatersleben

The variation data access portal developed previously in the frame of WP4 was adjusted to accommodate the variation data generated from the improved wheat reference sequence. This new portal version was made available thanks to the work of HMGU and can be accessed through https://pgsb.helmholtz-muenchen.de/whealbi. The portal enables researchers to interactively browse the variation data in their genomic and gene-annotation context. Detailed information about the quality of the variants (e.g. detected genotype of a sample) can be easily accessed. Specific gene models or variants can be searched by name and additional search options can/will be added if required or available. Access to the data base can be granted by requesting a username/password to the contact page.

Training ‘Databases, SNP calling and genetic analysis of multi-environment data’
http://www.whealbi.eu/about-the-allele-mining-genetic-analysis-data-analysis-trainings-of-june-2017/

During the 7-9 June 2017, a training about Databases, SNP calling and genetic analysis of multi-environment data was organized by Wageningen University, Helmholtz Zentrum München and INRA, in the framework of WP4. The organizers were pleased because of the high interest in this workshop, reaching more than 35 participants. Participants were diverse, consisting of plant breeders, students and researchers from various fields related to plant breeding.

Participants of the training ‘Databases, SNP calling and genetic analysis of multi-environment data’.

The workshop was subdivided in three parts. The first part involved a demo of the Whealbi database, teaching participants how to use the query options (taught by INRA). The second part consisted of a hands-on training of variant calling using a sub-sampling of the data generated in Whealbi (taught by Helmholtz Zentrum München and INRA). The main learning goal was to teach an actionable work-flow of variant detection from reference and raw sequence data to variation data. The third part of the workshop (8th and 9th June) covered the topics of spatial analysis of field trials, GxE analysis, QTL detection and GWAS (taught by Biometris, Wageningen University). The workshop ended with a discussion about advanced topics and genomic prediction. Participants had the opportunity to apply the concepts discussed in the lectures via computer exercises, giving them practical tools that can be used for their own research.

Symposium ‘Genotype to Phenotype Modelling of Plant Adaptation’ organized in Wageningen
A symposium on genotype to phenotype modelling in relation to adaptation and GxE took place in Wageningen the 16th of November 2017. The symposium was co-organized by WUR-Biometris and Whealbi, with a program subdivided in three sessions.

The first session focused on the importance of collecting, generating and characterizing the genetic variation for traits contributing to adaptation. During this session, Gilles Charmet (coordinator of the EU-Whealbi project) gave an overview about the project objectives and achievements. He also discussed the potential of genetic resources like the ones in the Whealbi wheat and barley collections as source of valuable alleles to obtain well-adapted varieties. The second session focused on strategies for phenotypic characterization across environments. A number of modelling approaches to integrate phenotypic data from the field and high throughput phenotyping platforms with genetic/genomic data were discussed. Finally, we discussed statistical and crop growth modelling approaches to connect genotypes and phenotypes across environments.


Speakers at the symposium ‘Genotype to Phenotype Modelling of Plant Adaptation’. From left to right: Chris Schön (TUM), Scott Chapman (CSIRO), Charlie Messina (DuPont-Pioneer), Francois Tardieu (INRA), Ep Heuvelink (WUR), Cris Wijnen (WUR), Fred van Eeuwijk (WUR), Daniela Bustos-Korts (WUR), Willem Kruijer (WUR), Gilles Charmet (INRA).

More than 80 people joined this symposium allowing a fruitful discussion.

More details about the program can be found via this link:

https://www.wur.nl/en/Expertise-Services/Research-Institutes/plant-research/Biometris-1/Genotype-to-Phenotype-Modelling-of-Plant-Adaptation.htm

Participants at the symposium ‘Genotype to Phenotype Modelling of Plant Adaptation’

Annual meetings

The 2017 annual meeting was organized in Israel by the University of Haifa in March 2017. Videos presenting the field visits and interviews of consortium members are available at:

https://www.youtube.com/channel/UCkwqKlC8tgGgB768ZprZtyw/videos

The 2018 annual meeting will be organized by JHI in Scotland 23-25th of October 2018. This final annual meeting will discuss internal issues to the project and is not open to the broad community.

2018 trainings

During the course of the WHEALBI project, an important focus is given to the knowledge transmission. After the Allele mining and genetic analysis trainings organised in 2017 at Wageningen, the two last trainings will be organised by the Workpackages 6 and 7 in May 2018 in Cambridge:

  • WHEALBI WP7 workshop: Crop management and Development of Innovative Cropping Systems
    Organizer: NIAB
    Cambridge, 29-30 May 2018
  • WHEALBI WP6 workshop: Wheat and Barley Pre-BreedingOrganizer: KWS
    Cambridge, 30-31 May 2018

Detailed programs are available at:
http://www.whealbi.eu/trainings-crop-management-innovative-cropping-systems-practical-assisted-pre-breeding-may-2018-cambridge/

Both trainings have a limited number of attendees (35 each) and can be attended independently. Inscription will favour young researchers (Ph.Ds and post-doc) and private companies. Please register through the WHEALBI website and wait for confirmation (end of March) to book your travel. For more infos: contact@whealbi.eu.

The college project

To communicate around WHEALBI project and show the importance of genetic resources for the future of agriculture, 5 European agriculture colleges and universities, coming from 5 different countries (Italy, France, UK, Germany and Hungary) were involved in the dissemination of the project.
Each of the participating university was asked to conduct for one year the same trial containing 16 wheat and 16 barley (showing high diversity: different origins, landraces or modern varieties…), the set of varieties coming from the pool of varieties studied in the WHEALBI project.
The students investigated for one year the genetic diversity contained in this pool of varieties, with the opportunity to exchange observations and questions with the other European students observing the same varieties, but in a different environment.

This project gave us the opportunity to explain to the students the functioning of Europe and the Europe of Research, how a European research project works with the detailed example of WHEALBI, and gave them the chance to work on a concrete case with crop genetic diversity and discuss the importance of genetic resources for breeding.

Students have been involved in 2016-2017 and lot of data, material, interaction have been produced. The full description of the project and the results are available in the deliverable: http://www.whealbi.eu/d8-5-farmer-colleges-field-trials/

Visit in Italy at the “Istituto Tecnico Agrario e Chimico Scarabelli – Ghini” April 2017 – first results of the College project

Dissemination of Whealbi videos: Youtube channel & social networks

A number of videos have been released in 2017 and published on different social networks with a short description explaining the WHEALBI project.

Each link below presents a different WHEALBI page of a social network:

New videos recorded until the end of the project will be broadcasted in the different social networks – don’t forget to register to get informations !

Other news and initiatives

Eucarpia Cereal Section Meeting, 2018

INRA, the WHEALBI coordinating institute, is organizing the next meeting (symposium) of EUCARPIA, cereal section (https://symposium.inra.fr/eucarpia-cereal2018/ ).

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.

he meeting takes place in Clermont-Ferrand, 19-21 march, 2018. Registrations are still open until beginning of February 2018. This meeting will give WHEALBI consortium the opportunity to present some highlights on WHEALBI results.

This project has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement n°FP7-613556

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