Periodic Reporting for period 2 - BOLERO (Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks)
Période du rapport: 2024-04-01 au 2025-09-30
Climate change is threatening many crops, including fruit tree crops (FTC) such as coffee and cocoa.
Classic breeding method are expensive and last decades, and are therefore not adapted for tree crops.
One alternative, the grafting, could be the key to rapidly adapt coffee and cocoa cultures to climate change, specially for low input farming systems.
A global approach is developed in the framework of the project, both in field and controlled conditions, integrating "-omics" data (phenomics,genomics, metabolomic, transcriptomic, microbiomic...) to have a better understanding of root system architecture dynamic and plasticity.
Over the last 36months of the project, partners worked together to generate data and knowledge.
A database is under construction to store all the data and build some models.
De novo genome assemblies of Robusta accessions were initiated using PacBio sequencing.
Preliminary LCA assessments have shown that the effect of grafting trajectory.
Protocols, and new breeding strategies are designed and tested.
Results and strategies will be disseminated in the last year of the project, through demo plots, workshops, trainings, publications...
Classic breeding method are expensive and last decades, and are therefore not adapted for tree crops.
One alternative, the grafting, could be the key to rapidly adapt coffee and cocoa cultures to climate change, specially for low input farming systems.
A global approach is developed in the framework of the project, both in field and controlled conditions, integrating "-omics" data (phenomics,genomics, metabolomic, transcriptomic, microbiomic...) to have a better understanding of root system architecture dynamic and plasticity.
Over the last 36months of the project, partners worked together to generate data and knowledge.
A database is under construction to store all the data and build some models.
De novo genome assemblies of Robusta accessions were initiated using PacBio sequencing.
Preliminary LCA assessments have shown that the effect of grafting trajectory.
Protocols, and new breeding strategies are designed and tested.
Results and strategies will be disseminated in the last year of the project, through demo plots, workshops, trainings, publications...
Periode M18 - M36
WP1 : The root structure architecture (RSA) study of 8 coffee species was carried out in a high-throughput phenotyping system. 9 coffee species are under comparison in rhizotrons under controlled conditions and two contrasted Nitrogen amounts. A drought trial was performed with 5 coffee species in controlled conditions.
Eight coffee species were established in two plots to study RSA and plasticity in field conditions.
Robusta clones were grafted onto non-cultivated species, and transferred in field.
Genes involved in RSA and plasticity have been identified based on transcriptomic analysis.
A protocol enabling the rhizosphere, rhizoplane and endosphere to be studied has been implemented.
Almost all the data have been collected and will be analyzed within the last year of the project.
WP2: To measure the impact of anthropization on the plant microbiome, protocols for decoding the root microbiome of native and cultivated coffee and cocoa trees were developed. Field missions were carried out in three countries (Uganda, Vietnam, Nicaragua), samples collected, DNA extracted, and sequencing is running.
Metabolic models of interactions between plants and the root microbiome were generated and translated into a common database of biochemical reactions, enabling the discovery and analysis of interactions within microbial communities.
WP3: An interface for storing and exploiting phenotypic, metabolomic, genetic and metagenomic data, as well as experimental and field-scale metadata, is developed.
De novo genome assemblies were initiated for 8 representative genotypes.
Multi-trait genomic prediction using 9 traits and 300,000 markers, revealed a the genomic models to be applied to root-related traits in coffee.
Multivariate model based on composition and abundance data was developed to predict plant traits from microbial composition and abundance data.
WP4: Three factorial designs representing respectively 28 and 81 Robusta families and 12 families for cocoa were created in 2023 and 2024, seedlings were used as rootstock for commercial Robusta clones.
Trial in field has been establish, and a part of the plants were already excavated for further analysis (root architecture, biomass, Nirs...)
WP5:The survey to determine the agronomic performance of grafted and ungrafted coffee farms has been completed a. The survey of 802 farmers managing 1,321 coffee plots enables a number of specific studies to be carried out relating to the comparison of the profitability of grafted and ungrafted coffee. A protocol for estimating underground biomass has been tested . Preliminary LCA assessments have shown that the effect of grafting trajectory, i.e. grafting onto old rootstock versus young grafted plants, may be as important as other non-crop parameters.
A survey form for the evaluation of coffee and cocoa nurseries has been developed,. A technical manual for grafted mini-cuttings technology was shared and technology transfer and training for grafted rootstocks began in Vietnam.
WP6: By Month 36, all tasks in Work Package 6 were successfully completed, ensuring:
- Effective coordination and project management
- Transparent communication
- Wide dissemination of results
- Proactive risk management
- Adherence to ethical standards
Key Deliverables: 3
- Deliverable data management plan,
- Deliverable communication, dissemination, and exploitation plans.
- Deliverable on ethical considerations for genetic resources.
Key workshop :
- Ethical considerations on genetic resources and exchange were explored at a workshop attended by 25 participants.
WP1 : The root structure architecture (RSA) study of 8 coffee species was carried out in a high-throughput phenotyping system. 9 coffee species are under comparison in rhizotrons under controlled conditions and two contrasted Nitrogen amounts. A drought trial was performed with 5 coffee species in controlled conditions.
Eight coffee species were established in two plots to study RSA and plasticity in field conditions.
Robusta clones were grafted onto non-cultivated species, and transferred in field.
Genes involved in RSA and plasticity have been identified based on transcriptomic analysis.
A protocol enabling the rhizosphere, rhizoplane and endosphere to be studied has been implemented.
Almost all the data have been collected and will be analyzed within the last year of the project.
WP2: To measure the impact of anthropization on the plant microbiome, protocols for decoding the root microbiome of native and cultivated coffee and cocoa trees were developed. Field missions were carried out in three countries (Uganda, Vietnam, Nicaragua), samples collected, DNA extracted, and sequencing is running.
Metabolic models of interactions between plants and the root microbiome were generated and translated into a common database of biochemical reactions, enabling the discovery and analysis of interactions within microbial communities.
WP3: An interface for storing and exploiting phenotypic, metabolomic, genetic and metagenomic data, as well as experimental and field-scale metadata, is developed.
De novo genome assemblies were initiated for 8 representative genotypes.
Multi-trait genomic prediction using 9 traits and 300,000 markers, revealed a the genomic models to be applied to root-related traits in coffee.
Multivariate model based on composition and abundance data was developed to predict plant traits from microbial composition and abundance data.
WP4: Three factorial designs representing respectively 28 and 81 Robusta families and 12 families for cocoa were created in 2023 and 2024, seedlings were used as rootstock for commercial Robusta clones.
Trial in field has been establish, and a part of the plants were already excavated for further analysis (root architecture, biomass, Nirs...)
WP5:The survey to determine the agronomic performance of grafted and ungrafted coffee farms has been completed a. The survey of 802 farmers managing 1,321 coffee plots enables a number of specific studies to be carried out relating to the comparison of the profitability of grafted and ungrafted coffee. A protocol for estimating underground biomass has been tested . Preliminary LCA assessments have shown that the effect of grafting trajectory, i.e. grafting onto old rootstock versus young grafted plants, may be as important as other non-crop parameters.
A survey form for the evaluation of coffee and cocoa nurseries has been developed,. A technical manual for grafted mini-cuttings technology was shared and technology transfer and training for grafted rootstocks began in Vietnam.
WP6: By Month 36, all tasks in Work Package 6 were successfully completed, ensuring:
- Effective coordination and project management
- Transparent communication
- Wide dissemination of results
- Proactive risk management
- Adherence to ethical standards
Key Deliverables: 3
- Deliverable data management plan,
- Deliverable communication, dissemination, and exploitation plans.
- Deliverable on ethical considerations for genetic resources.
Key workshop :
- Ethical considerations on genetic resources and exchange were explored at a workshop attended by 25 participants.
WP1: All the experiments conducted contribute to bringing new insights into RSA architecture and plasticity, to reach predicted impacts.
WP2: Our ambition is to know how root microbiome and genotypes shape the plasticity of root traits and how this impacts plant performances, by sequencing thousands of samples from field.
WP3 contributes to develop statistical and metabolic network models based on genotyping, microbiome and root phenotypic data, to create new integrative breeding strategies.
Works in WP4 contributes to explore a large intraspecific genetic diversity of Robusta and of T. cacao for their RSA and plasticity, used as rootstock for commercial Robusta clones.
WP5 contributes to a comprehensive assessment of grafted farming systems, connecting environmental performances with soil organic carbon content. T
The WP6 (ethical considerations), contributes to the co-developing together with the main stakeholders of the value chain of an open-source instrument to promote and facilitate the exchange of the genetic material.
WP2: Our ambition is to know how root microbiome and genotypes shape the plasticity of root traits and how this impacts plant performances, by sequencing thousands of samples from field.
WP3 contributes to develop statistical and metabolic network models based on genotyping, microbiome and root phenotypic data, to create new integrative breeding strategies.
Works in WP4 contributes to explore a large intraspecific genetic diversity of Robusta and of T. cacao for their RSA and plasticity, used as rootstock for commercial Robusta clones.
WP5 contributes to a comprehensive assessment of grafted farming systems, connecting environmental performances with soil organic carbon content. T
The WP6 (ethical considerations), contributes to the co-developing together with the main stakeholders of the value chain of an open-source instrument to promote and facilitate the exchange of the genetic material.