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Periodic Report Summary 2 - WHEALBI (Wheat and barley Legacy for Breeding Improvement)

Project Context and Objectives:
To satisfy the demand of an expanding population, agriculture faces the challenge of delivering safer, high quality, and health-promoting food and feed in an economic, environmentally sensitive, and sustainable manner. A sustained effort is thus required to generate crops with higher and more stable yields across diverse and changing environments. Wheat and barley are key renewable resources and among the most important crops worldwide.
Wheat yields have been stagnating in the European Union (EU) since the mid-1990s (FAOSTAT2010). In a recent study in France, Brisson et al (2010) showed that this stagnation was mostly due to climate, i.e. increased frequency and severity of negative factors such as drought or high temperatures. These effects of climate are more severe in Southern European and are not expected to improve, whatever the climate scenario to occur.
In addition, intensification of agricultural practices is associated with increased crop damages caused by pests and diseases. Chemical control has been increasingly used and Europe is currently the number one user of pesticides in the world, with cereal cultivation accounting for 40% of this consumption. This situation leads to high production costs, emergence of resistance to pesticides, and environmental and human health concerns. The most sustainable alternative to pesticides is the use of crop varieties that are genetically resistant to pathogens. Thus, genetics is one of the principal of addressing the effects of both climate change, and societal demands for environmental sustainability and healthy products.
In order to flourish, breeding programmes in either large companies or small and medium size enterprises (SMEs) will need to select new varieties that are both adapted to changing environments and to more sustainable cropping systems while maintaining or improving yield. This implies more resilience to biotic and abiotic stresses, increased water and nitrogen use efficiency and higher stability of yield and grain quality. Agronomists and crop (eco)-physiologists must help define optimal combinations of traits, or so-called ideotypes. Crop management systems must also evolve to fit the improved properties of these new ideotypes. They will have to consider issues such as yield stability in adverse conditions, lower dependence on chemicals (fertilizers and pesticides), and maintenance of desirable grain composition under sub-optimal plant nutrition. Eco-physiology and gene (network) modelling will help define crop ideotypes for the future that are aligned to new crop management practices.
WHEALBI will develop and implement tools, methods and procedures to facilitate the characterisation of wild relatives and local varieties of wheat and barley as sources of genes for use in crop improvement. It will explore the application of modern molecular, computational and analytical tools to provide understanding of the evolutionary processes that have shaped the current diversity in the genepool and to predict exploitable value from unadapted germplasm. It will develop innovative methods to optimise the use of these resources in pre-breeding and breeding programmes. New ideotypes will be evaluated in innovative cropping systems under several climatic conditions. Particular attention will be paid to the usefulness of the developed tools and knowledge and their transfer to stakeholders, particularly SMEs, breeders as well as present and future farmers. The WHEALBI project will make use of a multidisciplinary approach, including genetics, genomics, ecophysiology, bioinformatics, biostatistics, agronomy and socio-economy to improve European production of wheat and barley, through increasing productivity, robustness and adaptation to changing environmental conditions. This will be achieved by improving the efficiency of wheat and barley breeding programmes and designing sustainable crop management systems adapted to new plant ideotypes.

Project Results:
The WHEALBI project started on January 1st, 2014, but some tasks such as seed multiplication had been anticipated to ensure the respect of deliverables. During the first year, all work packages have established their work plan, and global coordination started during the Kick-off meeting in March, 2014.
The main actions and achievements made during the first and second reporting period are:
• In WP1, the panel of 512 barley and 512 wheat genotypes were compiled. All seeds were aliquoted and distributed on time to WP3. Seed samples were provided to WP7. JHI extracted DNA of all the accessions and forwarded samples to WP2. Seed samples are being re-multiplied to set-up the seed depository as defined in the DoW. It was suggested to skip out the maintenance of DNA stock, as DNA extraction is now simple and automated, so preserving seeds from pure seed lot is more relevant.
• In WP2, for both barley and wheat, capture and sequencing 512 exomes has been completed (Task 2.1; D2.1; M06) (Delayed by 12 months), and pipelines have been developed and used to identify indels and SNP variants in 443 (2 failed due to low reads after sequencing and 67 technical fails during capture) and 502 (10 failed due to low reads after sequencing) accessions, respectively. Raw reads were successfully mapped to available reference genomes (24 and 20.5 million reads mapped). SNPs and indels were identified for both barley and wheat, which have been distributed to partners for allele mining and genome wide analyses. Both datasets are the largest generated to date for barley and wheat. File transfer systems set up and all data distributed to relevant partners (Task 2.2; D2.2; M07) (Delayed by 12 months). For whole genome association and evolutionary studies, methods have been developed and successfully tested in pilot studies for both species (Task 2.3).
• In WP3, the garden experiment has been accomplished; the phenotypic data acquired highlights the wide genetic diversity present in the WHEALBI germplasm, suggesting that different genetic factors are responsible for the adaptation of each genotype to specific environmental conditions. The data are currently under analysis in the frame of WP4. The corresponding delivery has been submitted at M25. Task 3.1 also served as seed multiplication for the precision phenotyping activities. Seed distribution from partners involved in common garden experiments and those involved in phenotyping has been carried out within the timescales outlined in the proposal. The evaluation of drought tolerance in wheat by a field-based experiment has been limited by seed availability and converted to a mini-plots in tunnels. The first year of the field trial for the evaluation of barley canopy traits has been completed, field harvesting is ongoing and data analysis will follow. The screening for the wheat/barley diseases considered in WHEALBI is in progress in all cases. Overall, the experimental activity is on schedule with minimal deviation that should not impact on the deliverable.
• In WP4, the WHEALBI wheat and barley germplasm (WP1 data) were integrated in the information system. There was a minor delay in the achievement of MS4.1 because of the delayed availability of data from upstream tasks. The evaluation of imputation and IBD (Identity By Descent) calculation methods on WHEALBI data is pending because other WP are still working on the data generation. The evaluation of multi-trait and multi-environment models on WHEALBI data is still pending because other WP are still working on the data generation. A simulation that integrates genetic and crop growth models was done to evaluate multi-trait and multi-environment scenarios. The output of the simulations will be useful to propose strategies to analyse the data from WHEALBI experiments.
• The main objectives of WP5 so far were to identify new transcription factors implied in the regulation of the wheat seed storage proteins in Task 5.1 and the start of the allele-mining activities (Tasks 5.2, 5.3). So far in Task 5.1, the promoters of 4 genes SPA, MCB1, MYBS3 and SHP were annotated using a tool developed by INRA and work focused on the SHP promoter for the yeast-one-hybrid experiments. The promoter annotation of SHP, together with the use of orthologous promoter sequences from other monocotyledon species allowed the detection of eight motifs potentially able to bind transcription factors. These cis-motifs were used as bait in the yeast-one-hybrid screening and allowed the identification of four potential interactors able to regulate SHP expression: Roc8, TaHdZip, C3H protein 54 and an ERF5 like protein. These interactions have been validated by a one by one yeast hybrid assay using wild type and mutated versions of cis-motifs. Tasks 5.2 and 5.3 have very recently started in month 29 after the SNP data became available. Partners are currently evaluating the data for the specific genes of interest. Preliminary analysis of the data is promising.
• WP6 is running very well with only few minor delays. All three populations in task 6.1 are on track, and phenotyping and genotyping data has started to be generated. Finalisation of the KWS pre-breeding population together with further phenotyping of all populations will be the focus on the next reporting period. WU will start to play an important role in this task when genotyping data becomes available as well. The targeted introgression projects in task 6.2 have all worked through their challenges, which in hindsight were not unexpected. Although there are no guarantees that the various introgressions and translocations will have any practical importance, the resources developed will surely be valuable. The overall objective of WP6 is not to utilise the genetic resources assembled and characterised in WHEABLI. Rather, this work package will serve as inspiration for future use of the WHEABLI legacy, and for this Task 6.3 will play an important role. Modelling how best to use different approaches will be valuable in future pre-breeding projects, both academic and industrial.
• For WP7, in task 7.1, to calibrate the wheat simulation model SiriusQuality2, specific measures have been collected include weather, soil, management, phenology, canopy management and yield components. A ‘common set’ of measures has been agreed by participants (NIAB, ORC, MTA ATK and SIS) to be assessed on a common sub-set of genotypes at each participant site. Standardized protocols to measure these traits are being developed. A scientific paper (reported in the Journal of Experimental Biology) analysing physiological traits determining grain yield and protein in wheat as influenced by climate and crop management was published in 2015. For task 7.2 and 7.3, field experimental platforms under conservation management that include tillage approaches for conventional (plough tillage); deep non-inversion tillage (~20cm depth of disturbance) and shallow non-inversion tillage (~10cm depth of disturbance) each with contrasting nitrogen inputs (high and low) have been established on a replicated basis (3 replicates) at each partner site (NIAB, MTA ATK and SIS). A further field experimental platform under organic management that include tillage approaches for conventional (plough tillage) and shallow non-inversion tillage (~10cm depth of disturbance) has been established on a replicated basis (4 reps) at the partner site (ORC).
• For WP8, the dissemination plan outlined in the DoW was done as expected. The three main visible actions for the period were i) the set-up of the trainings (six are planned during the project, and two have been already performed, one on phenotyping (“Field phenotyping: how to phenotype for the most relevant agronomic traits”) organised at CREA in Italy the 18th – 20th April 2016, with 23 participants and one on genotyping (“SNP discovery and analysis using next generation technologies : exome capture and RNAseq”) organised at The James Hutton Institute in Scotland the 19-20 May 2016, which was attended by 15 participants. Both trainings were successful in terms of attendance and overall appreciation of the participants. (See:; ii) the planning and start of the college project (see :; and iii), the start of dissemination actions to the stakeholders (breeders, farmers, industries...), which was done during open days, field days, targeted conferences, and also through the newsletters which reached each time around 1000 stakeholders.
• The objectives for WP9 were to make sure that the rules of participation to this project were clear for all partners; to identify and overcome issues that may rise after the first year and ensure a smooth reporting. These objectives were met by the organisation of the annual meetings; by assisting the partners on the administrative and financial issues and by preparing the reporting process. Transversal issues concerning various WPs were discussed during the annual meetings at dedicated sessions and some more informal meetings (workshops, phone or video conferences) which allowed making progress on these points. The collaborative platform was updated, enabling sharing and exchange of ideas and documents between the partners. The platform was used to communicate all information related to the project to the partners, including deliverables, milestones, scientific data to be shared within the project, and templates for the reporting.
• Delays have occurred with getting the sequences data ready for the different WPs but the consortium is working on catching up with the delay in the second half or the project.

Potential Impact:
The WHEALBI project specifically will deliver:
• A publicly accessible collection of 1024 geo-referenced inbred wheat and barley accessions chosen from across the geographic range;
• Deep sequence (5-20X) of the exomes of the same wheat and barley accessions highlighting genetic variation;
• Life history trait and phenotypic data from all wheat and barley accessions grown in multiple environments across Europe;
• Phenotypic data of a selected subset of wheat and barley accessions from a high-throughput/precision phenotyping platform;
• A data repository and management system containing all of the above data;
• An interpretation of the observed patterns of diversity in relation to geography and environment;
• A list of candidate genes and alleles involved in key traits such as grain quality, frost and drought tolerance and resistance against fungal diseases;
• Pre-breeding pipelines to integrate new useful variation into applied breeding programmes, including those from old varieties and wild relatives;
• Identification of new sustainable crop management systems and their economic evaluation at both farm and EU levels;
• Identification of best ideotypes suited for innovative sustainable cropping systems, with reduced environmental impact (in terms of pollution, energy use, greenhouse gas emissions);
• Advice to policy makers at EU level on project related impacts (e.g. in relation to support agriculture, agro-environment and other CAP - Common Agricultural Policy - related issues).

As consequence of the WHEALBI activities a number of downstream effects will be promoted.

Development of breeding tools to support the breeding sector
The tools that will be developed in WHEALBI and the proof of concept made on the exome sequences will place EU research and industry in an ideal position to valorise future developments in genomics. This will help maintain EU scientists and breeders in the first circle of top world achievements in cereal genomics.

Development of new varieties with increased genetic variation and improved agronomic, processing and nutritional characteristics to support the farming sector
Succeeding in filling the “yield gap” of European wheat and barley production will help to maintain the gross value of major cereals production. With a reasonable figure of 30 kg/ha/year on average, across all EU countries, this would lead to about 50 more million tons in the decade following WHEALBI, i.e. a gross value of around 10 billion euros, and is certainly crucial for the maintenance of EU export capacity.

Widening the range of available adapted cereal genotypes
The efficient exploitation of untapped biodiversity of small grain cereal genetic resources, including wild relatives and landraces, through genome based methods will ensure the potential of long-term genetic progress, particularly for specific adaptive traits to crop management systems which have been little considered up to now.

Environmental impact of new varieties grown in improved and/or novel management practices
Development of new varieties with durable resistance to diseases will enable farmers to reduce the use of fungicides, saving around 500 million euros per annum while maintaining yield and safer production of grains. This output will enable farmers to comply with the IPM requirements.
Adopting tilling conservation on at least 50% of the EU cereals growing areas will stop the degradation and even improve the soil organic matter content. In addition to the positive impact on soil erosion and fertility, this will lead to the sequestration of substantial quantities of carbon.

Contribution to food security through more productive, diversified and resilient European cereal production
WHEALBI outcomes will enable EU agriculture to maintain its cereal production at a high level with more limited year to year variations. This will have positive impact on world production stability, limiting the volatility of cereal prices which has dramatic consequences on farmer incomes and consumers well-being, particularly in developing countries, but also on poor people in developed ones.

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