Periodic Reporting for period 2 - INCREASE (Intelligent Collections of Food Legumes Genetic Resources for European Agrofood Systems)
Période du rapport: 2021-11-01 au 2023-04-30
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.
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 through a specifically developed template file in order to unequivocally identify datasets. A unique INCREASE code and a DOI code were assigned to each accession.
• Phenotyping protocols for each species were established and made available to all partners, to characterise the GenRes during SSD development, subsequent seed increase cycles, field and controlled conditions experiments. Protocols for phenotyping of seeds and of plants growing in controlled conditions during Primary Seed Increase were described in four scientific publications in Current Protocols in Plant Biology (DOIs: 10.1002/cpz1.133; 10.1002/cpz1.134; 10.1002/cpz1.191; 10.1002/cpz1.371). Regarding the molecular phenotyping, protocols for transcriptomics and metabolomics have been optimized and established for all four crops. Pipelines for DNA extraction were established, and DNA extraction has been completed for T-COREs, while it is currently ongoing for the R-COREs. A protocol for aDNA (ancient DNA) extraction was successfully tested on common bean historical herbarium specimen obtained from the National Museum of Natural History of Paris, that was sequenced using Illumina WGS. The protocol has been used to successfully extract aDNA from 67 herbarium specimens of different legume taxa, for which sequencing is ongoing. 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, and a manuscript describing this achievement is ready for submission. 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).
• The collected data on the GenRes, including passport, phenotypic and genotypic data available from sister projects, are used to establish the R-COREs, T-COREs and H-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. Subsets of R-CORE and T-CORE lines were used for phenotypic characterization under controlled conditions, such as drought stress, for common bean and chickpea and for intercropping maize-common bean. Several field trials have been carried out for the four species, during which the developed common phenotyping protocols have been employed. 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 7,500 samples, and to date, 1,200 RNA leaf samples from common bean and chickpea lines have been extracted and sent for sequencing. Nutritional and technological analyses are also ongoing.
• 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 two rounds have been launched in 2022 and 2023, reaching in total over 16,000 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.
• Phenotyping protocols for each species were established and made available to all partners, to characterise the GenRes during SSD development, subsequent seed increase cycles, field and controlled conditions experiments. Protocols for phenotyping of seeds and of plants growing in controlled conditions during Primary Seed Increase were described in four scientific publications in Current Protocols in Plant Biology (DOIs: 10.1002/cpz1.133; 10.1002/cpz1.134; 10.1002/cpz1.191; 10.1002/cpz1.371). Regarding the molecular phenotyping, protocols for transcriptomics and metabolomics have been optimized and established for all four crops. Pipelines for DNA extraction were established, and DNA extraction has been completed for T-COREs, while it is currently ongoing for the R-COREs. A protocol for aDNA (ancient DNA) extraction was successfully tested on common bean historical herbarium specimen obtained from the National Museum of Natural History of Paris, that was sequenced using Illumina WGS. The protocol has been used to successfully extract aDNA from 67 herbarium specimens of different legume taxa, for which sequencing is ongoing. 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, and a manuscript describing this achievement is ready for submission. 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).
• The collected data on the GenRes, including passport, phenotypic and genotypic data available from sister projects, are used to establish the R-COREs, T-COREs and H-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. Subsets of R-CORE and T-CORE lines were used for phenotypic characterization under controlled conditions, such as drought stress, for common bean and chickpea and for intercropping maize-common bean. Several field trials have been carried out for the four species, during which the developed common phenotyping protocols have been employed. 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 7,500 samples, and to date, 1,200 RNA leaf samples from common bean and chickpea lines have been extracted and sent for sequencing. Nutritional and technological analyses are also ongoing.
• 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 two rounds have been launched in 2022 and 2023, reaching in total over 16,000 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.
• 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.