Periodic Reporting for period 1 - INCREASE (Intelligent Collections of Food Legumes Genetic Resources for European Agrofood Systems) Reporting period: 2020-05-01 to 2021-10-31 Summary of the context and overall objectives of the project Food legumes are crucial for all agriculture-related societal challenges including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. In this regard, a key aspect is the transition to plant-based diets, largely based on food legumes. The characterisation, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and healthy food systems. INCREASE, focusing on chickpea, common bean, lentil and lupin, is implementing a new approach to conserve, manage and characterise genetic resources. Intelligent Collections, consisting of nested core collections, composed of single seed decent (SSD) purified accessions (i.e. inbred lines), are being developed, exploiting germplasm available both from gene banks, and on-farm, and subjected to different level of genotypic and phenotypic characterisation. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors (breeders, scientists, farmers, agri-food and non-food industry) exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE is testing, with a Citizen Science Experiment, an innovative system of conservation and use of genetic resources based on a decentralised approach for data management and dynamic conservation. By promoting the use of food legumes, improving quality, adaptation and yield, and boosting the competitiveness of the agriculture and food sector, INCREASE will have a major impact on economy and society, representing a case study of integrative and participatory approaches for conservation and exploitation of crop genetic resources.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 tools2. To produce a large amount of high-quality genotypic and phenotypic data3. To develop Intelligent Collections for exploration of the GenRes diversity and design innovative conservation management approaches collaboratively4. To generate new knowledge made easily available through web-based searching and visualisation tools to identify appropriate sources of germplasm5. To develop, test and disseminate best practices for dynamic management of GenRes across worldwide institutions and initiatives6. To develop decentralised information technology approaches for data sharing and germplasm conservation. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far • Passport (e.g. code, species, biological status, geographic coordinates, etc.), phenotypic and genotypic data of GenRes accessions were collected from INCREASE partners through a specifically developed template file in order to unequivocally identify datasets. A unique INCREASE code and a DOI code were assigned to every developed SSD line. Partners who provided seeds of heterogeneous accessions were also requested to assign a DOI, if not already available, to be linked to the new one assigned to the relative SSD line developed within INCREASE. • 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. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) • Enhanced GenRes status and increased effectiveness of conservation efforts, particularly in Europe; high quality, harmonised standards for GenRes management across Europe (and beyond); • 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. 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