H2020 INCREASE Project: Smart collections of food legume genetic resources for European agri-food systems

Type Project
Status Firmado
Execution 2020 -2026
Assigned Budget 6.999.999,5 €
Scope Europeo
Main source of financing H2020
Project website Proyecto INCREASE

Description

Legumes are crucial for sustainability, food security, and human health, according to the new European Protein Strategy for innovation in protein crop production in Europe. The EU-funded INCREASE project will improve the management and use of legume genetic resources. To address this challenge, it will expand their use, meeting users' needs regarding accessibility, quality, and quantity of available information.

The project will focus on four main legumes: chickpea, common bean, lentil, and lupin. In short, INCREASE will strengthen Europe in the field of legume genetic resources and, at the same time, represent an important model and tool for all crop genetic resources.

Description of activities

Passport, phenotypic, and genotypic data for GenRes accessions were collected from INCREASE partners using a template file specifically developed to uniquely identify the datasets. Each accession was assigned a unique INCREASE code and DOI.
Phenotyping protocols were established for each species and made available to all partners to characterize GenRes during SSD development, subsequent seed increase cycles, and field experiments under controlled conditions. Protocols for phenotyping seeds and plants grown under controlled conditions during Primary Seed Increase were described in four scientific publications in Current Protocols in Plant Biology (DOI: 10.1002/cpz1.133; 10.1002/cpz1.134; 10.1002/cpz1.191; 10.1002/cpz1.371). Regarding molecular phenotyping, transcriptomics and metabolomics protocols have been optimized and established for the four crops. DNA extraction pipelines were established, and DNA extraction has been completed for T-COREs and is currently ongoing for R-COREs. A protocol for aDNA (ancient DNA) extraction was successfully tested on a historic herbarium specimen of common bean obtained from the National Museum of Natural History in Paris, which was sequenced using Illumina WGS. The protocol has been used to successfully extract aDNA from 67 herbarium specimens of different legume taxa, whose sequencing is ongoing. All pipelines for whole-genome sequencing and genotyping, for high-quality genome assembly, and for pan-genome reconstruction were established and tested. A first common bean pan-genome has been assembled, and a manuscript describing this achievement is ready for submission. A novel technique for genotyping large genomes in lentils has been developed and successfully tested, and a paper describing the development of this technique was published in Genome Research (DOI: 10.1101/gr.277628.122).
Data collected in GenRes, including passport, phenotypic, and genotypic data available from sister projects, are used to establish the R-CORE, T-CORE, and H-CORE lines. Several seed breeding cycles were conducted, starting with heterogeneous and SSD seeds, and seeds were distributed to all partners relevant to their activities. Subsets of R-CORE and T-CORE lines were used for phenotypic characterization under controlled conditions, such as water stress, for common bean and chickpea, and for intercropping maize and common bean. Several field trials were conducted for the four species, during which the developed common phenotyping protocols were employed. From more than 16,000 samples collected for transcriptomic and metabolomic studies, metabolite profiling was performed by GC-MS and/or LC-MS on 7,500 samples. To date, 1,200 leaf RNA samples from common bean and chickpea lines have been extracted and submitted for sequencing. Nutritional and technological analyses are also underway. INCREASE designed and tested a fully decentralized approach to germplasm conservation, distributing 1,126 SSD common bean lines across Europe for citizen cultivation and characterization. Following the success of the first round of the Citizen Science Experiment, two further rounds were launched in 2022 and 2023, reaching a total of over 16,000 registrations from European citizens. Since the start of the project, a custom-made Citizen Science application has been developed and improved, facilitating data collection and processing of Easy-STMA agreements, ensuring seed exchange between participants within a legal framework. This innovative application lays the groundwork for future Citizen Science projects related to PGRFA.

Contextual description

Food legumes are crucial for all societal challenges related to agriculture, 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, primarily based on food legumes.

The characterization, maintenance, and exploitation of food legume genetic resources (GenRes), hitherto largely untapped, form the basis for the development of both sustainable agriculture and healthy food systems. INCREASE, focusing on chickpea, common bean, lentil, and lupin, is implementing a novel approach to conserve, manage, and characterize GenRes. Smart Collections, consisting of nested core collections of purified single-seeded progeny (SSD) accessions, are being developed by exploiting available germplasm from genebanks and on-farm, and subjected to varying levels of genotypic and phenotypic characterization.

Phenotyping and gene discovery activities will address, through a participatory approach, the needs of diverse stakeholders (breeders, scientists, farmers, agri-food and non-food industries), also leveraging the power of massive metabolomics and transcriptomics, as well as artificial intelligence and smart tools. Furthermore, INCREASE is testing, through a Citizen Science Experiment (CSE), an innovative system for the 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 agricultural and food sector, INCREASE has a major impact on the economy and society, representing a case study of integrative and participatory approaches to the conservation and exploitation of crop GenRes. INCREASE aims to:

Improve the management and sharing of GenRes data on food legumes through streamlined databases and easily accessible tools.
Produce a large amount of high-quality genotypic and phenotypic data.
Develop Smart Collections for exploring GenRes diversity and collaboratively design innovative conservation management approaches.
Generate new knowledge that is readily available through web-based search and visualization tools to identify appropriate germplasm sources.
Develop, test, and disseminate best practices for dynamic GenRes management across institutions and initiatives around the world.
Develop decentralized information technology approaches for data sharing and germplasm conservation.

Objectives

INCREASE will improve the management and use of food legume genetic resources, which are crucial for sustainability, food security, and human health, as recognized by the new European Protein Plan for innovation in this sector in Europe. To address this challenge, INCREASE will expand the use of food legume genetic resources by focusing on user needs in terms of accessibility, quality, and quantity of available information.

INCREASE, which works with four important food legumes (chickpeas, common beans, lentils, and lupins) with significant innovation value for EU agriculture and the food industry, will be based on four pillars:

Innovative data management solutions to develop benchmark standards for data exchange and integration into core infrastructure, with decentralized data entry, defined methodologies and best practices for exploiting new information, as well as the development of easy-to-use visualization tools.
Development of novel tools and principles for germplasm management, based on the development of "Smart Collections" as a set of nested core collections of different sizes that represent the full diversity of each crop.
Adoption of cutting-edge genotyping and phenotyping technologies combined with the potential of Artificial Intelligence focused on traits of interest to users.
An international effort involving non-European partners and international organizations will expand the scope and ambition of INCREASE, facilitating the integration of available data and genetic resources for European users. We will develop a citizen science experiment, primarily aimed at disseminating the project among stakeholders and citizens.

Overall, INCREASE will strengthen Europe in the field of legume genetic resources and, at the same time, represent an important model and tool for all crop genetic resources.

Additional information

Improved status of GenRes and increased effectiveness of conservation efforts, particularly in Europe; high-quality harmonized standards for GenRes management across Europe (and beyond).
Increased quantity and quality of data in the information systems established for GenRes crops.
Innovative ways of sharing resources and services between genebanks/in situ conservation sites in Europe and beyond.
New services for users inside and outside conservation communities.
Economic and social impacts through improved quality, adaptability, and performance of food legumes, boosting the competitiveness of European agriculture and food sectors in line with the new recommendations of the European Plant Protein Plan, and promoting the use of GenRes food legumes.
New varieties for easier adoption of food legumes in the agroecosystem, enhancing agrobiodiversity with all its associated positive consequences (e.g., sustainability, food security, economic returns, product diversification, improved human nutrition).
Environmental adaptation of food legumes to European environments and climate change, including improved drought tolerance of chickpea and common bean.

Coordinators

UNIVERSITA POLITECNICA DELLE MARCHE (UNIVPM)

Otros links

H2020 INCREASE Project: Smart collections of food legume genetic resources for European agri-food systems

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