Coffee stands as a vital pillar of Colombia’s economic prosperity, constituting approximately 7% of the nation’s agricultural GDP. Moreover, it serves as a significant contributor to national agricultural employment, with direct jobs stemming from coffee cultivation comprising 26% of the total agricultural workforce. This underscores the pivotal role coffee plays in shaping Colombia’s social and economic landscape, solidifying its position as the primary origin of mildly washed coffees for global consumers. However, Colombia’s coffee production grapples with the challenge of operating amidst persistently rainy conditions, fostering an environment conducive to fungal diseases. This, compounded by environmental, economic, commercial, and safety constraints for disease control, creates a multifaceted scenario that continuously tests disease management strategies. Addressing this complex dynamic demands a crop protection framework that seamlessly integrates efficient and sustainable methodologies. Such methodologies should prioritize outbreak prevention, cost-effectiveness, adherence to national and international regulations, and the preservation of environmental and human health. Integrated disease management emerges as a solution capable of optimizing productivity tailored to the unique conditions of each plot. By mitigating the impact of pathogens while responsibly utilizing and conserving natural resources, this approach safeguards the well-being of both producers and consumers alike.

Coffee berry disease is caused by Colletotrichum kahawae, a quarantine fungus still absent from most coffee-producing countries. Given the potential adverse effects on coffee berry production, it is a severe worldwide threat to farmers and industry. Current biosecurity management focuses on exclusion by applying quarantine measures, including the certification of coffee plants and their products. However, methods for detecting C. kahawae by National Plant Protection Organization (NPPO) laboratories still need approval. This research aims to functionally demonstrate, standardize, and validate a method for detecting and discriminating C. kahawae from other Colletotrichum species that may be present in coffee plant samples. The method proposes to use an end-point PCR marker for the mating type gene (MAT1-2-1) and a confirmatory test with a real-time quantitative PCR (qPCR) marker developed on the glutamine synthetase gene. The C. kahawae amplicons for the Cen-CkM10 qPCR marker exhibited specific melting temperature values and high-resolution melt profiles that could be readily differentiated from other tested species, including their relatives. Given the fungus’s quarantine status, specificity was tested using artificial mixtures of DNA of C. kahawae with other Colletotrichum species and coffee plant DNA. The described method will enable NPPOs in coffee-producing and exporting countries, especially Colombia, to prevent this pathogen's entry, establishment, and spread. [ ] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Coffee leaf rust, caused by the fungusHemileia vastatrix(Basidiomycota; Pucciniomycota),is a devastating disease spread worldwide. To improve the available genomes, we use PacBio HiFi sequencing enhanced by Dovetail Omni-C chromatin conformation capture to assemble a highly contiguous 747.98 Mb genome of an isolate collected fromCoffea arabica.

CLR (Hemileia vastatrix) is the disease with the greatest economic and social impact on coffee production in the world, causing losses of up to 50% of productivity in susceptible varieties without proper and timely management. The department of Huila is the current largest producer with approximately 19% of production, going from 136,000 ha planted in 2012 with 61% in susceptible varieties, to about 150,000 ha in 2020 and 30% in susceptible varieties, mainly in the southern area of ??the department, indicating the advancement of the department's coffee sector. However, there is still an important area under threat from coffee rust, which must be controlled and reduced. The objective of this work was to validate the chemical management strategy for rust in commercial crops of the susceptible variety Caturra in the south of the department of Huila (Colombia). The evaluation was carried out in two commercial crops of var. Caturra at two altitudes at 1.410 and 1.280 m, where each batch was divided into three plots to monitor the blooms and the percentage of incidence of the disease from 2016 to 2018. The validation criteria consisted of: fixed calendars (CC1), adjustment of the main flowering (CC2), farmer (CA3), and finally without disease control (SC4). The incidence in critical periods was above 30% of the level of economic damage, directly accompanying the physiology of production. The criteria (CC1-CC2) and with the use of the recommended fungicide showed a lower incidence (AUDPC) compared to the other criteria evaluated, presenting a positive effect on the control of the disease, allowing a retention of foliage and delaying the curve of the disease reducing to 30% the incidence in critical periods. In addition, the risk of Colombian coffee growing has increased in recent years, especially due to the climatic variability that generates advances or delays in the peaks of the disease and generating reductions in the incubation periods.

El propósito de este documento es proporcionar una herramienta para identificar los síntomas asociados a CBD en el campo. La detección temprana de brotes de la enfermedad permitirá una respuesta rápida y efectiva para aplicar medidas cuarentenarias de contención y erradicación de cualquier incursión de CBD en Colombia.

Coffee leaf rust, caused by the obligate biotrophic fungus Hemileia vastatrix , remains the most destructive disease of coffee worldwide. Although genomic and transcriptomic studies have identified a large number of candidate effectors, experimental evidence supporting their biological roles during infection remains limited. Here, we integrated functional assays, temporal expression profiling during coffee infection and subcellular localization analyses to investigate the biological properties of 44 H. vastatrix effector candidates (HvECs). Using the Pseudomonas fluorescens EtHAn effector delivery system in Nicotiana benthamiana , 15 HvECs consistently suppressed pattern‐triggered immunity (PTI), indicating that immune suppression is a widespread property among the H. vastatrix effector repertoire, as assessed in this heterologous system. Five HvECs also attenuated AvrB‐triggered effector‐triggered immunity (ETI), and three suppressed both PTI and ETI, suggesting that a subset of HvECs targets conserved regulatory nodes shared by these interconnected immune pathways. Temporal expression profiling revealed sequential deployment of HvECs throughout infection, with distinct subsets predominating during pre‐biotrophic development, host penetration or biotrophic colonization, consistent with stage‐specific functions during fungal pathogenesis. Subcellular localization analyses further showed that HvECs preferentially accumulated in the nucleus or chloroplasts, compartments known as central hubs of plant immune regulation. This study provides the most comprehensive functional characterization of H. vastatrix effector candidates to date, establishes a biologically informed framework for prioritizing candidates for future identification of avirulence determinants recognized by SH resistance genes, and advances our understanding of how the coffee rust fungus orchestrates immune suppression across time and cellular space during pathogenesis.