Intelligent Collections of Food Legumes Genetic Resources for European Agrofood Systems

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 (GenRes), 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 GenRes. Intelligent Collections, consisting of nested core collections of single seed descent (SSD) purified accessions, are being developed, exploiting germplasm available 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 (CSE), an innovative system of decentralized and dynamic conservation and use of GenRes, by promoting the use of food legumes, improving quality, adaptation and yield, and boosting the competitiveness of the agriculture and food sector, INCREASE has a major impact on economy and society, representing a case study of integrative and participatory approaches for conservation and exploitation of crop GenRes.
INCREASE aims to:
1. Improve management and sharing of food legume GenRes data through optimised databases and easily accessible tools;
2. Produce a large amount of high-quality genotypic and phenotypic data;
3. Develop Intelligent Collections for exploration of the GenRes diversity and design innovative conservation management approaches collaboratively;
4. Generate new knowledge made easily available through web-based searching and visualisation tools to identify appropriate sources of germplasm;
5. Develop, test and disseminate best practices for dynamic management of GenRes across worldwide institutions and initiatives;
6. Develop decentralised information technology approaches for data sharing and germplasm conservation.

• Passport, phenotypic and genotypic data of GenRes accessions were collected from INCREASE partners and used to establish the sets of accessions to be included in INCREASE COREs. Several seed increase cycles, starting from both heterogeneous and SSD seeds were accomplished and seeds have been distributed to all relevant partners for their activities.
• Phenotyping protocols for each species were established and used to characterise the GenRes during SSD development, subsequent seed increase cycles, field and controlled conditions experiments. Regarding the molecular phenotyping, protocols for transcriptomics and metabolomics have been optimized and established for all four crops. DNA extraction has been completed for R-COREs (lines for which SSD seeds are available) and T-COREs. Ancient DNA (aDNA) extraction was successfully carried out on historical herbarium specimens obtained from the National Museum of Natural History of Paris; common bean samples were sequenced using Illumina WGS. All pipelines for whole genome sequencing and genotyping, for high-quality genome assembly and for pangenome reconstruction, were established and tested. A first common bean pangenome has been assembled (DOI: 10.1038/s41467-024-51032-2). A novel technique for genotyping of large genomes has been successfully developed and tested in lentil and an article, describing the development of this technique, was published in Genome Research (DOI: 10.1101/gr.277628.122).
• Phenotypic characterizations were carried out during seed increase cycles, multi-location field trials, drought stress tails for common bean and chickpea, interaction with Rhizobia trials for all the fours crops and for intercropping maize-common bean. Out of more than 16,000 samples collected for transcriptomic and metabolomics studies, metabolite profiling using both GC-MS and or LC-MS have been carried out on 14,000 samples, and to date, 2,000 RNA leaf samples from all the species have been extracted and sent for sequencing and 1,200 leaf samples from common bean and chickpea lines were already sequenced. Nutritional and technological analyses were also carried out.
• Data analyses are ongoing, related to phenotypic and genotypic characterization of the different INCREASE collections, to identification of genetic control of important traits (i.e. resistance/ tolerance to abiotic stresses, adaptation to different environments, nutritional traits), to development of genomic tools to help breeders in using GenRes for breeding as well as in conducting selection programmes.
• INCREASE designed and tested a fully decentralised approach to germplasm conservation, by distributing 1,126 SSD common bean lines all over Europe, to be grown and characterized by Citizens. Following the success of the first round of the Citizen Science Experiment, other three rounds have been launched in 2022, 2023 and 2024, reaching in total over 23,000 registrations by European Citizens. A tailored Citizen Science App was developed and improved since the beginning of the project, assisting in data collection and processing Easy-STMA agreements, ensuring seed exchange with and among participants under a legal framework. The innovative app is paving the way for future PGRFA-related Citizen Science projects.

• 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);
• Environmental adaptation of food legumes to European environments and to the climate changes, including improved drought tolerance of chickpea and common bean.