Heterotic potential and combining ability of Coffea arabica L

The use of hybrid vigor or heterosis in Coffea arabica L. cultivation has gradually been commercially explored worldwide since research has evolved in understanding this phenomenon and the vegetative propagation techniques or male-sterility making its use viable. Additionally, coffee producers adopting this technology have continuously increased. Therefore, we studied the existence and magnitude of heterosis and estimate the combining ability of parents in bi-parental crosses. The experiment was installed in 2019 using a randomized block design with three replications, with the experimental plot consisting of six plants. The experimental treatments consisted of 90 hybrids and 34 parental lines in which the grain yield in bags of processed coffee per hectare was evaluated according to the cumulative result of the first three harvests. Significant differences were observed between the 124 treatments, with the mean accumulated productivity values of the best hybrids surpassing those of the four most used commercial cultivars by more than 74 bags of coffee per hectare. The average yield mean heterosis was 64.2%, varying from - 26.1 to 184.4. Both the general combining ability (GCA) and the specific combining ability (SCA) were statistically significant, with the best-performing lines identified as potential parents being 'Acauã Novo', 'IAC 125 RN', 'MGS Liberdade', 'Catiguá MG2', and 'Sarchimor MG 8840'. Promising hybrids for commercial exploitation were identified with a productive advantage of 30% relative to the best commercial standard cultivar, reinforcing the potential of this technology for C. arabica L. cultivation future.

Integrated Metabolomics and Transcriptomics Analyses Reveal the Regulatory Mechanisms of Anthocyanin and Carotenoid Accumulation in the Peel of Coffea arabica

The color of coffee fruits is influenced by several factors, including cultivar, ripening stage, and metabolite composition. However, the metabolic accumulation of pigments and the molecular mechanisms underlying peel coloration during the ripening process of Coffea arabica L. remain relatively understudied. In this study, UPLC-MS/MS-based metabolomics and RNA sequencing (RNA-seq)-based transcriptomics were integrated to investigate the accumulation of anthocyanins and carotenoids in the peel of Coffea arabica at different ripening stages: green peel (GP), green-yellow peel (GYRP), red peel (RP), and red-purple peel (RPP). This integration aimed at elucidating the molecular mechanisms associated with these changes. A total of ten anthocyanins, six carotenoids, and thirty-five xanthophylls were identified throughout the ripening process. The results demonstrated a gradual decrease in the total carotenoid content in the peel with fruit maturation, while anthocyanin content increased significantly. Notably, the accumulation of specific anthocyanins was closely associated with the transition of peel colors from green to red. Integrated metabolomics and transcriptomics analyses identified the GYRP stage as critical for this color transition. A weighted gene co-expression network analysis (WGCNA) revealed that enzyme-coding genes such as 3AT, BZ1, and lcyE, along with transcription factors including MYB, NAC, and bHLH, which interact with PHD and SET TR, may regulate the biosynthesis of anthocyanins and carotenoids, thereby influencing peel pigmentation. These findings provide valuable insights into the molecular mechanisms underlying the accumulation of anthocyanins and carotenoids in Coffea arabica peel during fruit maturation.

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Climate risks and vulnerabilities of the Arabica coffee in Brazil under current and future climates considering new CMIP6 models

The susceptibility to climate change concerns the coffee market worldwide due to possible severe productivity losses. Brazil is the world's largest Arabica coffee producer and has crops in regions considered persistent climate change hotspots. Our study analyzed risks, vulnerabilities, and susceptibilities to pests and diseases in these regions under current and future climates and outlined adaptive measures to reduce future vulnerabilities. Ten risk indicators based on Arabica coffee requirements were proposed: water supply (Iw), base (TIB) and maximum temperature stresses (TImax), which delimit the temperature range where Arabica coffee grows and productivity is penalized outside both ranges, frost stress (TIfrost), diseases such as rust (DIrust), brown eye spot (DIbrown), and Phoma leaf spot (DIphoma), pests such as coffee berry borer (PIberry), coffee leaf miner (PIminer), and yield loss due to water stress (Iyg). Daily near-surface air temperature (minimum, mean, and maximum), relative humidity, precipitation, and global solar radiation were used from 16 General Circulation Models (GCMs) from the NASA Earth Exchange Global Daily Downscaled Projections (NEX-GDDP), which are derived from the Coupled Model Intercomparison Project Phase 6 (CMIP6) in three Shared Socioeconomic Pathways scenarios (SSP245, SSP370 and SSP585). All risk indicators were calculated for the current climate (1995-2014) and projected for the near (2041-2060), intermediate (2061-2080), and far future (2081-2100) in three SSPs and then classified into five risk classes (very low, low, moderate, high and very high). Our results indicated that due to increases in TImax and Iyg indicators, with high to very high risk in area and magnitude, Arabica coffee plantations will be negatively affected and economically unfeasible for about 35 % to 75 % of the studied area throughout the 21st century. Furthermore, the rust and the leaf miner will remain a concern in future climates due to increased temperatures and reduced relative humidity. The future of Arabica coffee crops in Brazil will depend on adopting effective adaptive measures and prudent agricultural strategies to address anticipated risks, including shifting crops to higher altitude areas, introducing more climate-resilient coffee cultivars/varieties, using agroforestry or intercropping systems, planting in closer spacing or higher density planting, and employing dripper or partial root-zone irrigation techniques.

Inheritance of Resistance to Bacterial Halo Blight and Bacterial Leaf Spot in Arabica Coffee

Developing coffee cultivars resistant to multiple diseases by combining resistance genes is a top priority in breeding programs. To create cultivars resistant to diseases and nematodes, we transferred genes for resistance to bacterial infections caused by Pseudomonas coronafaciens pv. garcae, which causes bacterial halo blight (BHB), and P. amygdali pv. tabaci, which causes bacterial leaf spots (BLS), into Arabica coffee. Genetic analyses were conducted on breeding populations to estimate the number and function of genes that confer resistance to BHB and BLS. In total, 2,109 plants in the F2 generation and reciprocal backcrosses were inoculated with P. coronafaciens pv. garcae, while 1,996 plants were inoculated with P. amygdali pv. tabaci. Results showed that resistance to both pathogens had a heritability of 0.99, and the segregations of resistance indicated that each disease was controlled by a single dominant gene. The analyses also revealed that the resistance genes for BHB and BLS were linked, with an average distance of 10.75 cM between them on the same chromosome.

Small RNAs: Promising Molecules to Tackle Climate Change Impacts in Coffee Production

Over the centuries, human society has evolved based on the ability to select and use more adapted species for food supply, which means making plant species tastier and more productive in particular environmental conditions. However, nowadays, this scenario is highly threatened by climate change, especially by the changes in temperature and greenhouse gasses that directly affect photosynthesis, which highlights the need for strategic studies aiming at crop breeding and guaranteeing food security. This is especially worrying for crops with complex phenology, genomes with low variability, and the ones that support a large production chain, such as Coffea sp. L. In this context, recent advances shed some light on the genome function and transcriptional control, revealing small RNAs (sRNAs) that are responsible for environmental cues and could provide variability through gene expression regulation. Basically, sRNAs are responsive to environmental changes and act on the transcriptional and post-transcriptional gene silencing pathways that regulate gene expression and, consequently, biological processes. Here, we first discuss the predicted impact of climate changes on coffee plants and coffee chain production and then the role of sRNAs in response to environmental changes, especially temperature, in different species, together with their potential as tools for genetic improvement. Very few studies in coffee explored the relationship between sRNAs and environmental cues; thus, this review contributes to understanding coffee development in the face of climate change and towards new strategies of crop breeding.

"« Coffee agroforestry business-driven clusters »: an innovative social and environmental organisational model for coffee farm renovation

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.

Description of an Arabica Coffee Ideotype for Agroforestry Cropping Systems: A Guideline for Breeding More Resilient New Varieties

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.

Shaded-Coffee: A Nature-Based Strategy for Coffee Production Under Climate Change? A Review

Coffee is deemed to be a high-risk crop in light of upcoming climate changes. Agroforestry practices have been proposed as a nature-based strategy for coffee farmers to mitigate and adapt to future climates. However, with agroforestry systems comes shade, a highly contentious factor for coffee production in terms of potential yield reduction, as well as additional management needs and interactions between shade trees and pest and disease. In this review, we summarize recent research relating to the effects of shade on (i) farmers' use and perceptions, (ii) the coffee microenvironment, (iii) pest and disease incidence, (iv) carbon assimilation and phenology of coffee plants, (v) coffee quality attributes (evaluated by coffee bean size, biochemical compounds, and cup quality tests), (vi) breeding of new Arabica coffee F1 hybrids and Robusta clones for future agroforestry systems, and (vii) coffee production under climate change. Through this work, we begin to decipher whether shaded systems are a feasible strategy to improve the coffee crop sustainability in anticipation of challenging climate conditions. Further research is proposed for developing new coffee varieties adapted to agroforestry systems (exhibiting traits suitable for climate stressors), refining extension tools by selecting locally-adapted shade trees species and developing policy and economic incentives enabling the adoption of sustainable agroforestry practices.