Hervé Etienne

The production of F1 hybrid Arabica varieties is a key strategy to improve the resilience, competitivity and sustainability of coffee cultivation. Indeed, under both full sun and agroforestry systems, these varieties have performed better than traditional varieties in terms of higher yields, cup quality, and enhanced tolerance to biotic and abiotic stresses, including remarkable adaptation to the shady conditions of agroforestry. Until recently, somatic embryogenesis was a key cloning methodology that made it possible to start propagating the first selected F1 hybrid. However, this in vitro method of multiplication is complex and costly, technically demanding and hence limited to a few high-tech micropropagation laboratories. Horticultural vegetative propagation techniques such as rooted mini-cuttings have been developed to reduce the cost. They provided a scalable solution for larger-scale dissemination by spreading it across numerous regional nurseries at less cost but still too high, thereby contributing to the popularization and adoption of F1 hybrids. More recently, a major innovation for the global coffee sector was the arrival of new Arabica F1 hybrids with similar agronomic performances but produced by seed and using male sterility. The cost of seed propagation is low, similar to the production of seedlings of conventional pure lines plus seeds are easy to disseminate, while clonal methods ensure total genetic uniformity so, depending on the production goals, local constraints and the target market, the two approaches may be complementary. This methodological paper focuses specifically on F1 hybrid Arabica coffee seed production. Changes to breeding strategies and the different propagation techniques used to develop and disseminate F1 hybrid varieties are described, together with the advantages and limitations, with emphasis on biotechnological approaches, horticultural clonal propagation methods and recent advances in male sterility systems. Technical aspects aimed at improving the use of seed gardens and optimizing hybrid seed production in coffee are reviewed. F1 hybrid seed technology represents a promising development for coffee breeding and propagation, allowing access to high-performing and more resilient cultivars, hence supporting farmer’s transition toward climate-smart and sustainable coffee production systems.

High-throughput drought phenotyping in perennial crops is limited by slow, costly, destructive, and labour-intensive methods that restrict genetic gain. Here, we developed and validated a portable near-infrared spectroscopy (NIRS) framework for drought phenotyping in Coffea canephora. The framework integrates variance decomposition, ensemble machine learning, the Drought Factor Index (DFI), and temporal trajectory modelling to distinguish drought responses among 22 genotypes under controlled water deficit. Leaf spectra were collected from both adaxial and abaxial surfaces using a handheld MicroNIR sensor (908–1676 nm), alongside predawn leaf water potential and chlorophyll fluorescence measured using conventional methods. Abaxial measurements reduced residual variance and improved the signal-to-noise ratio compared with adaxial measurements, identifying the abaxial surface as the preferred target for sensor deployment. Reduction of Repeatability Error–ASCA (REP-ASCA) partitioned spectral variance into biologically structured components. Drought treatment, genotype, and their interaction each explained significant proportions of spectral variance (p < 0.001). Ensemble machine learning models (Random Forest and XGBoost) accurately predicted predawn leaf water potential (R² = 0.82, RPD = 2.42, CCC = 0.90). In contrast, chlorophyll fluorescence and gas exchange traits were poorly predicted (R² < 0.15), revealing trait-specific sensing limitations imposed by the device’s restricted spectral range. Temporal modelling of NIRS-predicted water potential trajectories produced a slope-based classification metric that grouped genotypes as drought-tolerant, intermediate, or sensitive. Drought-tolerant classifications showed 75% concordance with DFI, demonstrating that NIRS can serve as an interpretable and scalable genotype-selection pipeline for climate-resilient coffee breeding, rather than merely as a static trait predictor.

In a few important plant families and genera, including Arecaceae, Fabaceae and the genus Coffea , the main seed storage polysaccharide is not starch but cell wall galactomannans. Such seeds are albuminous with a persistent copious living endosperm that accumulates galactomannans. However, our understanding of the regulation of endosperm maturation, cell wall formation and galactomannan biosynthesis in albuminous seeds remains very limited. To gain insights into these processes, a large RNA-seq dataset was produced (14 coffee species × 5 endosperm developmental stages) and scrutinized using gene coexpression network analysis. The network revealed tight transcriptional coordination of the core galactomannan biosynthetic machinery for sucrose import, glycolysis, nucleotide sugar synthesis and transport, arabinogalactan protein and cellulose synthesis, and regulation of the trans-Golgi network. The orchestration of galactomannan and oil accumulation during endosperm maturation appeared to be exerted by the transcription factors FUSCA3, WRINKLED1, SHINE2 and DREB2D. The latter was the only coexpression partner of galactomannan biosynthetic genes. Numerous key genes of galactomannan biosynthesis were significantly upregulated in coffee somatic embryos overexpressing DREB2D, which showed increased production of UDP-galactose and diversion towards raffinose family oligosaccharides. Further, most genes of the galactomannan coexpression module were identified as DREB2D target genes by DAP-seq analysis. Highlight: Gene coexpression network analysis of the maturing endosperm identified the AP2/ERF transcription factor DREB2D as a major regulator of galactomannan accumulation in the cell walls of albuminous coffee seeds.

Background: Worldwide coffee production, especially Arabica coffee, is threatened by climatic change, plants diseases and vulnerability of smallholders. Meanwhile, consumers’ demand for socially and environmentally sustainable products is steadily increasing, driving the engagement of stakeholders in agro-ecological and social initiatives. Here we present a new organizational model, the “Coffee agroforestry business-driven cluster” (CaFC), which aims at preserving ecosystems while offering producers a fair income. Based on an original local micro value-chain dedicated to sustainable production of high-quality Arabica coffee under agroforestry systems, the CaFC model stands out by addressing the issues around plantation renovation, a crucial process that requires considerable investments from producers. Methods: Based on a pilot project in Nicaragua, we illustrate how the operational principles of CaFC can be applied in a real setting. Using data shared by key stakeholders involved in the project, we assess the profitability of the CaFC model by comparing different scenarios and applying sensitivity analysis. We then reflect on the reproducibility of the model in other contexts, building on lessons learned from ongoing implementations in Vietnam and Cameroon. Results: For producers renovating their plantations, the CaFC model consistently outperforms other scenarios, offering high quality premiums coupled with capacity building, access to highly productive varieties that perform well under agroforestry systems and adapted credit with favourable repayment schemes. Implementation in Vietnam and Cameroon show that the model can be successfully replicated with some adaptation to local contexts. These cases also highlight the importance of mutual interests, trust and communication in enabling collaboration between stakeholders. Conclusions: The CaFC model has great potential for positive environmental and economic impact and offers strong incentives for stakeholders involved in its resulting micro value-chain. The concept was initially developed in Nicaragua for coffee but could also be adapted in other countries or even to other commodities such as cocoa.

Climate change (CC) is already impacting Arabica coffee cultivation in the intertropical zone. To deal with this situation, it is no longer possible to manage this crop using industrial agriculture techniques, which has been the main strategy implemented since the Green Revolution. Developing a more sustainable agriculture system that respects people and the environment is essential to guarantee future generations’ access to natural resources. In the case of Arabica coffee, the solution has been found. Agroforestry is proposed as an ecosystem-based strategy to mitigate and adapt to CC. At least 60% of Arabica coffee is produced in agroforestry systems (AFSs), which are the most sustainable way to produce coffee. Nevertheless, AFS coffee cultivation is currently uncompetitive partly because all modern varieties, selected for full-sun intensive cropping systems, have low yields in shaded environments. Here we review the reasons why agroforestry is part of the solution to CC, and why no breeding work has been undertaken for this cropping system. Based on the literature data, for breeding purposes we also define for the first time one possible coffee ideotype required for AFS coffee cultivation. The four main traits are: (1) productivity based on F1 hybrid vigor, tree volume and flowering intensity under shade; (2) beverage quality by using wild Ethiopian accessions as female progenitors and selecting for this criterion using specific biochemical and molecular predictors; (3) plant health to ensure good tolerance to stress, especially biotic; and (4) low fertilization to promote sustainable production. For each of these traits, numerous criteria with threshold values to be achieved per trait were identified. Through this research, an ecosystem-based breeding strategy was defined to help create new F1 hybrid varieties within the next 10 years.

Background: Worldwide coffee production, especially Arabica coffee, is threatened by climatic change, plants diseases and vulnerability of smallholders. Meanwhile, consumers’ demand for socially and environmentally sustainable products is steadily increasing, driving the engagement of stakeholders in agro-ecological and social initiatives. Here we present a new organizational model, the “Coffee agroforestry business-driven cluster” (CaFC), which aims at preserving ecosystems while offering producers a fair income. Based on an original local micro value-chain dedicated to sustainable production of high-quality Arabica coffee under agroforestry systems, the CaFC model stands out by addressing the issues around plantation renovation, a crucial process that requires considerable investments from producers. Methods: Based on a pilot project in Nicaragua, we illustrate how the operational principles of CaFC can be applied in a real setting. Using data shared by key stakeholders involved in the project, we assess the profitability of the CaFC model by comparing different scenarios and applying sensitivity analysis. We then reflect on the reproducibility of the model in other contexts, building on lessons learned from ongoing implementations in Vietnam and Cameroon. Results: For producers renovating their plantations, the CaFC model consistently outperforms other scenarios, offering high quality premiums coupled with capacity building, access to highly productive varieties that perform well under agroforestry systems and adapted credit with favourable repayment schemes. Implementation in Vietnam and Cameroon show that the model can be successfully replicated with some adaptation to local contexts. These cases also highlight the importance of mutual interests, trust and communication in enabling collaboration between stakeholders. Conclusions: The CaFC model has great potential for positive environmental and economic impact and offers strong incentives for stakeholders involved in its resulting micro value-chain. The concept was initially developed in Nicaragua for coffee but could also be adapted in other countries or even to other commodities such as cocoa.