Periodic Reporting for period 1 - INCREASE (Intelligent Collections of Food Legumes Genetic Resources for European Agrofood Systems)
Berichtszeitraum: 2020-05-01 bis 2021-10-31
INCREASE objectives are defined in short as follows:
1. To improve management and sharing of food legume GenRes data through optimised databases and easily accessible tools
2. To produce a large amount of high-quality genotypic and phenotypic data
3. To develop Intelligent Collections for exploration of the GenRes diversity and design innovative conservation management approaches collaboratively
4. To generate new knowledge made easily available through web-based searching and visualisation tools to identify appropriate sources of germplasm
5. To develop, test and disseminate best practices for dynamic management of GenRes across worldwide institutions and initiatives
6. To develop decentralised information technology approaches for data sharing and germplasm conservation.
• Specific phenotyping and genotyping protocols for each species were developed, tested and made available to all partners, to characterise the GenRes during SSD development, subsequent seed increase cycles, field and controlled conditions experiments. Protocols for seed phenotyping of Intelligent Collections (visually and through digital images) and plants growing in controlled conditions during Primary Seed Increase were described in four scientific articles (papers for lentil, common bean and lupin are already published in Current Protocols in Plant Biology, while for chickpea the paper was ready for submission at the time of this Report). For molecular phenotyping, the required fresh tissues and samples were sent to relevant partners for all four crops in order to set up the suitable protocols for RNA extraction. All pipelines for DNA extraction were established, DNA extraction has started for all crops and almost completed for T-COREs. The DNA extraction from historical herbarium specimens obtained from the National Museum of Natural History of Paris was successfully tested on common bean from the 1700’, sequencing was performed using Illumina WGS protocol with excellent results. All pipelines for whole genome sequencing and genotyping, including bioinformatic, planned for platinum genome development and pangenome reconstruction, were established and tested.
The collected data on heterogeneous and SSD lines, including passport data, along with phenotypic and genotypic data available from characterisations on previous projects, were used to select the R-COREs and T-COREs. Seed increase cycles, starting from both heterogeneous and SSD seeds, to produce seeds to be distributed to all relevant partners started from the beginning of the project. Subsets of R-CORE and T-CORE lines were also used for specific phenotypic characterization, such as drought tolerance in controlled conditions for common bean and chickpea and intercropping maize-common bean. For common bean, the SSD list developed was also used to identify more than 1,000 lines used in the Citizen Science Experiment (CSE).
Data and genomic information from partners and collaborators were explored; indeed, the availability of germplasm and data from providers has been considered a crucial criterion for the sampling of the Intelligent Collections (T-core in particular). In parallel, pipelines, strategies and approaches for data analysis on the data soon available on the Intelligent Collections, taking into account characteristics of the different collections and specific features of each species, were discussed.
• The first round of the CSE, designed to test a fully decentralised approach to germplasm conservation, was launched. A tailored CSE App was developed assisting in data collection and processing Easy-STMA agreements, ensuring seed exchange with participants under a legal framework. The innovative App is paving the way for future PGRFA-related Citizen Science projects. This first CSE round was a great success with more than 3,000 registered participants overall Europe and more than 2,000 EU citizens receiving seeds, to conduct the experiment.
• Increased data quantity and quality in established information systems for crop GenRes;
• Innovative ways of sharing resources and services between gene banks/ in-situ conservation sites in Europe and beyond;
• Novel services for users within and outside the conservation communities;
• Economical and societal impacts by improving food legumes quality, adaptation and yield, boosting the competitiveness of European agriculture and food sector in line with new European plant protein plan recommendations, promoting the use of food legumes GenRes;
• Novel varieties for easier adoption of food legumes in the agroecosystem improving the agrobiodiversity with all its related positive consequences (e.g. sustainability, food security, economic returns, diversify products, human nutrition improvement, etc.);
• Environmental adaptation of food legumes to European environments including improved drought tolerance of chickpea and common bean; better adaptation to climate changes.