Periodic Reporting for period 1 - BOLERO (Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks)
Berichtszeitraum: 2022-10-01 bis 2024-03-31
Some first results of the project after 18 months are worth highlighting
The root structure architecture (RSA) of 24 genotypes representing 8 coffee species was carried out in a high-throughput phenotyping system. The experiment considered two nitrogen conditions, mimicking low and high fertilization. Low nitrogen conditions significantly increased root system surface area, length and volume for some genotypes.
Using new species as rootstocks for Robusta could be an alternative . Two Robusta clones were grafted onto 6 non-cultivated species. The rate of succes was high for the 21 combinations tested, demonstrating no early problems of incompatibility during grafting between Robusta and the 6 species tested.
A protocol enabling the rhizosphere, rhizoplane and endosphere to be studied has been implemented for the first time in an FTC.
In order 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.
Metabolic models of interactions between plants and the root microbiome can be generated using different approaches. A pipeline is already available.
An application programming interface for storing and exploiting data, has been developed.
De novo genome assemblies of Robusta accessions were initiated using PacBio sequencing. A
An in-depth comparative analysis, using nine traits with 446 accessions and 300,000 genetic markers, revealed a clear classification of the different genomic models to be applied to root-related traits in coffee.
To predict plant traits from microbial composition and abundance data, a multivariate model based on composition and abundance data was developed.
In Vietnam, the survey of 802 farmers managing 1,321 coffee plots revealed that grafted coffee growers produced more coffee per hectare than non-grafted coffee growers.
Preliminary LCA assessments have shown that the effect of grafting trajectory.
Ethical considerations on genetic resources and exchange were explored at a workshop attended by around 25 participants.
The root structure architecture (RSA) of 24 genotypes representing 8 coffee species was carried out in a high-throughput phenotyping system. The experiment considered two nitrogen conditions, mimicking low and high fertilization. Low nitrogen conditions significantly increased root system surface area, length and volume for some genotypes.
Using new species as rootstocks for Robusta could be an alternative . Two Robusta clones were grafted onto 6 non-cultivated species. The rate of succes was high for the 21 combinations tested, demonstrating no early problems of incompatibility during grafting between Robusta and the 6 species tested.
A protocol enabling the rhizosphere, rhizoplane and endosphere to be studied has been implemented for the first time in an FTC.
In order 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.
Metabolic models of interactions between plants and the root microbiome can be generated using different approaches. A pipeline is already available.
An application programming interface for storing and exploiting data, has been developed.
De novo genome assemblies of Robusta accessions were initiated using PacBio sequencing. A
An in-depth comparative analysis, using nine traits with 446 accessions and 300,000 genetic markers, revealed a clear classification of the different genomic models to be applied to root-related traits in coffee.
To predict plant traits from microbial composition and abundance data, a multivariate model based on composition and abundance data was developed.
In Vietnam, the survey of 802 farmers managing 1,321 coffee plots revealed that grafted coffee growers produced more coffee per hectare than non-grafted coffee growers.
Preliminary LCA assessments have shown that the effect of grafting trajectory.
Ethical considerations on genetic resources and exchange were explored at a workshop attended by around 25 participants.
Year 1 :
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 6 coffee species.
Eight coffee species were established in two plots to study RSA and plasticity.
Robusta clones were grafted onto non-cultivated species.
Genes involved in RSA and plasticity have been identified .
A protocol enabling the rhizosphere, rhizoplane and endosphere to be studied has been implemented.
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).
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, has been 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.
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: Data management, communication, dissemination and exploitation plans have been developed.
Ethical considerations on genetic resources and exchange were explored at a workshop attended by around 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 6 coffee species.
Eight coffee species were established in two plots to study RSA and plasticity.
Robusta clones were grafted onto non-cultivated species.
Genes involved in RSA and plasticity have been identified .
A protocol enabling the rhizosphere, rhizoplane and endosphere to be studied has been implemented.
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).
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, has been 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.
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: Data management, communication, dissemination and exploitation plans have been developed.
Ethical considerations on genetic resources and exchange were explored at a workshop attended by around 25 participants.
Year 1 :
WP1: All the experiments conducted contribute to bringing new insights into RSA architecture and plasticity, to reach predicted impacts.
WP2: Our ambiiton is to know how root microbiome and genotypes shape the plasticity of root traits and how this impacts on the plant performance.
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.
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.
WP1: All the experiments conducted contribute to bringing new insights into RSA architecture and plasticity, to reach predicted impacts.
WP2: Our ambiiton is to know how root microbiome and genotypes shape the plasticity of root traits and how this impacts on the plant performance.
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.
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.