Periodic Reporting for period 1 - FRUITDIV (Exploiting the Untapped potential of Fruit tree Wild DIVersity for Sustainable Agriculture)
Okres sprawozdawczy: 2024-01-01 do 2025-06-30
FRUITDIV is a project designed to address a critical issue in the agricultural sector: the underutilization and conservation of crop wild relatives (CWRs), particularly those related to fruit trees. CWRs are wild plants that are genetically similar to domesticated crops, and they contain a wealth of untapped genetic diversity. This diversity can provide beneficial traits, such as resistance to pests and diseases, tolerance to drought and salinity, and adaptation to fluctuating climates.
Currently, the fruit industry relies on a narrow range of elite cultivars that, while high-yielding, are becoming increasingly vulnerable to new pests and diseases and are not well-suited for low-input, pesticide-free farming. Furthermore, the genetic resources of fruit tree CWRs are severely under-represented in European genebanks and are threatened by factors like climate change and habitat loss. Given the long lifespan of fruit trees and the years it takes to develop new varieties, there is an urgent need to harness the potential of CWRs to ensure sustainable fruit production in the future.
In this context, the overall goal of FRUITDIV is to better understand, conserve, and integrate the genetic diversity of fruit tree CWRs (specifically for Malus, Pyrus, and Prunus species) into breeding programs. This will help create more resilient and productive fruit crops, aligning with the goals of the European Green Deal to reduce pesticide use and boost biodiversity.
Currently, the fruit industry relies on a narrow range of elite cultivars that, while high-yielding, are becoming increasingly vulnerable to new pests and diseases and are not well-suited for low-input, pesticide-free farming. Furthermore, the genetic resources of fruit tree CWRs are severely under-represented in European genebanks and are threatened by factors like climate change and habitat loss. Given the long lifespan of fruit trees and the years it takes to develop new varieties, there is an urgent need to harness the potential of CWRs to ensure sustainable fruit production in the future.
In this context, the overall goal of FRUITDIV is to better understand, conserve, and integrate the genetic diversity of fruit tree CWRs (specifically for Malus, Pyrus, and Prunus species) into breeding programs. This will help create more resilient and productive fruit crops, aligning with the goals of the European Green Deal to reduce pesticide use and boost biodiversity.
The FRUITDIV project follows a multi-faceted pathway, moving from initial research and data collection to the development of practical tools and the dissemination of new plant material. In particular, during the first reporting period, FRUITDIV successfully inventoried both ex-situ (genebank) and in-situ (wild) CWR collections. A standardized protocol for passport data was created, and data from 2,310 ex-situ samples were compiled. Extensive in-situ sampling was conducted across 11 countries, collecting 3,010 mother trees and 1,516 seed samples, which exceeded targets. A comprehensive system for ABS (Access and Benefit-Sharing) compliance was established to ensure legal germplasm use, and initial phenotyping data was collected. FRUITDIV thus achieved the creation of vast genetic collections of fruit tree CWRs spanning a wide geographic area from Spain to Armenia, the development of standardized protocols for data collection and characterization, and the establishment of a robust ABS compliance framework. These results will form the foundation for genetic analysis and future breeding efforts.
From those ex-situ and in-situ collections, over 3,700 leaf samples were processed for DNA extraction. A pre-screening step was initiated using specific genetic markers to identify and exclude domesticated individuals or hybrids. This work is a crucial step toward building fruit tree CWR core-collections and will enable the project to proceed with advanced genomic analyses.
In the meantime, a core-collection for wild apricot was successfully reproduced and established at three different sites in Europe. Work is underway to propagate seeds from other CWRs. Significant phenotypic diversity was observed among the fruit tree CWRs, particularly in wild apricot, with promising results for traits like rooting ability and extended flowering periods. Disease resistance was also characterized in both controlled and open-field conditions, leading to the identification of superior genotypes. Preliminary analysis of metabolomic data for wild apricot is also being used to distinguish resistant from susceptible genotypes.
In the same period, FRUITDIV focused on creating a robust data infrastructure for CWR multi-omics. It finalized high-quality genome assemblies for several wild relatives and refined pipelines for pangenome construction, paving the way for future advanced genomic studies that will benefit fruit tree breeding. The project is also actively using CWRs for pre-breeding, with ongoing crosses and a clear strategy for trait introgression. The identification of target traits and the use of predictive models are key steps toward efficiently developing new, resilient fruit varieties.
In order to gather invaluable local and traditional knowledge linked to fruit tree CWRs, a questionnaire was developed, translated, and distributed EU-wide. Guidelines were issued to standardize the collected data. A concept note was prepared for upcoming workshops, and a literature review on legal frameworks for preserving local knowledge was launched. The groundwork for a series of workshops has been laid, which will further engage stakeholders and enrich the project's findings.
From those ex-situ and in-situ collections, over 3,700 leaf samples were processed for DNA extraction. A pre-screening step was initiated using specific genetic markers to identify and exclude domesticated individuals or hybrids. This work is a crucial step toward building fruit tree CWR core-collections and will enable the project to proceed with advanced genomic analyses.
In the meantime, a core-collection for wild apricot was successfully reproduced and established at three different sites in Europe. Work is underway to propagate seeds from other CWRs. Significant phenotypic diversity was observed among the fruit tree CWRs, particularly in wild apricot, with promising results for traits like rooting ability and extended flowering periods. Disease resistance was also characterized in both controlled and open-field conditions, leading to the identification of superior genotypes. Preliminary analysis of metabolomic data for wild apricot is also being used to distinguish resistant from susceptible genotypes.
In the same period, FRUITDIV focused on creating a robust data infrastructure for CWR multi-omics. It finalized high-quality genome assemblies for several wild relatives and refined pipelines for pangenome construction, paving the way for future advanced genomic studies that will benefit fruit tree breeding. The project is also actively using CWRs for pre-breeding, with ongoing crosses and a clear strategy for trait introgression. The identification of target traits and the use of predictive models are key steps toward efficiently developing new, resilient fruit varieties.
In order to gather invaluable local and traditional knowledge linked to fruit tree CWRs, a questionnaire was developed, translated, and distributed EU-wide. Guidelines were issued to standardize the collected data. A concept note was prepared for upcoming workshops, and a literature review on legal frameworks for preserving local knowledge was launched. The groundwork for a series of workshops has been laid, which will further engage stakeholders and enrich the project's findings.
FRUITDIV has moved beyond the current state of the art in several key areas. The project is establishing extensive, standardized ex-situ and in-situ genetic collections of fruit tree crop wild relatives (CWRs) across 11 countries, far exceeding previous efforts. This has created a foundation for breeding programs that didn’t exist before.
A crucial achievement is the development of a robust ABS compliance framework to ensure the legal and ethical use of this germplasm. FRUITDIV is also a leader in fruit tree CWR data management, having established a central database, finalized high-quality genome assemblies for several wild relatives, and refined pipelines for taxon pangenome construction.
This work directly supports pre-breeding by enabling targeted crosses between crop and wild relatives, trait introgression, and the use of predictive models to identify desirable alleles present in CWR and to be introduced in crops. The project has successfully deployed the first CWR core-collections, starting with wild apricot, at multiple sites and identified superior genotypes with promising traits like disease resistance and grafting or rooting ability. By integrating metabolomic data and traditional knowledge from local stakeholders, FRUITDIV is pioneering a comprehensive approach to CWR utilization that combines genetic science with on-the-ground expertise.
A crucial achievement is the development of a robust ABS compliance framework to ensure the legal and ethical use of this germplasm. FRUITDIV is also a leader in fruit tree CWR data management, having established a central database, finalized high-quality genome assemblies for several wild relatives, and refined pipelines for taxon pangenome construction.
This work directly supports pre-breeding by enabling targeted crosses between crop and wild relatives, trait introgression, and the use of predictive models to identify desirable alleles present in CWR and to be introduced in crops. The project has successfully deployed the first CWR core-collections, starting with wild apricot, at multiple sites and identified superior genotypes with promising traits like disease resistance and grafting or rooting ability. By integrating metabolomic data and traditional knowledge from local stakeholders, FRUITDIV is pioneering a comprehensive approach to CWR utilization that combines genetic science with on-the-ground expertise.