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Sustainable soil management to optimize water use and enhance nutrient uptake is a promising approach for decreasing the incidence of coffee leaf rust. This work analysed soil coverings, fertilizers and soil conditioners to optimize water usage and nutrients in coffee rust management. The experiment was set up in the field in January 2016, with seedlings of Coffea arabica ‘Mundo Novo IAC – 379‐19’, susceptible to rust. The experimental design was in randomized blocks with three replications and arranged in a 3 × 2 × 5 factorial scheme. We assessed the combination of three soil coverings (plastic film, Urochloa decumbens and bare soil), two fertilizer types (conventional and controlled release) and five soil conditioners (organic compound, coffee husk, agricultural gypsum, water‐retaining polymer and control without soil conditioner). The rust incidence and foliage progress curve were integrated into the area under the rust incidence or foliage progress curve. Additionally, we assessed the leaf area index and coffee yield. The association of U. decumbens with controlled‐release fertilizers and organic compound or coffee husk increased coffee foliage and yield despite higher disease incidence. [ABSTRACT FROM AUTHOR]

Coffee leaf rust (CLR), caused by Hemileia vastatrix, poses a significant threat to global coffee production, resulting in substantial economic losses. This study explores the effectiveness of triazole derivatives synthesized from glycerol in controlling CLR in conilon coffee (Coffea canephora). In vitro assays evaluated the inhibitory effect of triazole derivatives (4a–4q) at concentrations of 10, 25, 50, 75 and 100 ppm on H. vastatrix urediniospore germination, followed by greenhouse experiments to assess their preventive and curative potential. Preventive and curative sprayings of the four most efficient triazoles were conducted on seedlings inoculated with H. vastatrix at concentrations ranging from 0 to 400 ppm, evaluating severity, sporulation, incubation and latent periods. Triazole derivatives 4b, 4d, 4f and 4o effectively suppressed H. vastatrix urediniospore germination, achieving reductions between 9.9% and 78.8%. In greenhouse trials, these compounds demonstrated preventive efficacy by prolonging incubation and latent periods, reducing sporulation and mitigating rust severity, with triazole 4f exhibiting the highest efficiency. Furthermore, the derivatives showed effectiveness in curative treatments, particularly triazole 4f. Physiological analyses indicated no significant alterations in coffee plant metabolism, suggesting the safety of these compounds for agricultural use. Molecular docking studies elucidated their mechanism of action, suggesting their potential as antifungal agents by interacting with the HvCYP51 enzyme involved in ergosterol biosynthesis. Overall, the study underscores the promising efficacy of glycerol‐derived triazole derivatives in managing CLR, providing sustainable solutions for disease control in agriculture. [ABSTRACT FROM AUTHOR]

During surveys in the centres of origin of the coffee leaf rust (CLR), Hemileia vastatrix in Africa, as well as in its exotic range in Brazil, 23 isolates of the genus Cladosporium were obtained from uredinial pustules. Using a phylogenetic analysis of all isolates involving a combination of partial sequences of the internal transcribed spacer region of rDNA (ITS) and two gene regions: actin (act) and translation elongation factor-1a (tef1), 12 species were delimited; including four new species - Cladosporium chlamydosporiformans, C. hemileiicola, C. mucilaginosum and C. setoides. GCPSR criteria were employed for species recognition, supported by morphological and cultural characters. The potential of these purported mycoparasites is discussed in the context of biological control of CLR in Latin America. [ABSTRACT FROM AUTHOR]

IPR Pérola is a Coffea arabica cultivar developed from a cross between IAPAR 59 and Mundo Novo IAC 376-4. It features a dwarf-medium size, high yield, excellent cup quality, a medium-early ripening cycle, and large beans. Additionally, it boasts high resistance to coffee leaf rust. [ABSTRACT FROM AUTHOR]

Coffee leaf rust, caused by Hemileia vastatrix, is the most important disease affecting Coffea arabica. The use of molecular markers through marker-assisted selection (MAS) is an effective approach to develop cultivars with multiple and durable resistance, which is economically and environmentally beneficial for this disease control. In this work, a new molecular marker based on allele-specific polymerase chain reaction (AS-PCR) associated with the quantitative trait locus (QTL) of the linkage group 5 (LG5), which confers resistance to races I, II and pathotype 001 of H. vastatrix, was developed. The CaRHv10-AS marker was validated in a segregating genetic mapping population of 247 F2 genotypes and demonstrated selection efficiency greater than 97% for genotypes with resistance to three races. Thus, this work provides a fast, robust, and affordable molecular marker for use in MAS, facilitating the development of coffee plants with multiple resistance and ensuring sustainable coffee production. [ABSTRACT FROM AUTHOR]

Coffee leaf rust (CLR) is one of the most economically important diseases affecting Coffea arabica production, having a significant economic impact. Among the main goals of coffee breeding programs is the development of cultivars resistant to this disease. A source of resistance genes is Híbrido de Timor (HdT), a spontaneous hybrid originated from the cross between C. arabica and C. canephora. Previously, in a transcriptome study, the Ca TDF77 NBS-LRR gene from HdT involved in resistance to CLR was identified. Hence, our aim was to characterize the genomic region surrounding the Ca TDF77 NBS-LRR gene in Coffea spp. Furthermore, we aimed to analyze the transcriptional profile of this gene, in the C. arabica cultivar IAPAR 59, which is originated from HdT introgression and is resistant to CLR race II. The outcome delineated the gene's localization on chromosome 11 (canephora subgenome) of C. arabica, spotlighting intragenic polymorphisms between HdT and Arabica coffee susceptible to CLR race II. The genomic region surrounding the gene in Coffea spp. revealed a tandem structure and transposable elements. Notably, within IAPAR 59, the gene exhibited significant upregulation at 24 and 72 h post CLR infection, contrasting starkly with the susceptible genotype. This observation validates its role in fortifying the defense mechanism of this particular cultivar. This study enriches our understanding of the evolutionary dynamics of Coffea spp. genomes and also provides genomic resources instrumental in devising biotechnological strategies for resistance to CLR. [ABSTRACT FROM AUTHOR]

Coffee Leaf Rust (CLR) is caused by Hemileia vastatrix in Coffea spp. It is one of the most dangerous phytopathogens for coffee plantations in terms of coffee productivity and coffee cup quality. In this review, we resume the problem of CLR in Mexico and the pathogenesis of H. vastatrix. The review abord plant-pathogen interactions which lead a compatible or incompatible interactions and result in CLR disease or resistance, respectively. The review abord Coffea spp. defense response pathways involved in H. vastatrix pathogenicity. Additionally, current measures to control H. vastatrix proliferation and germination were aborded focused on phytosanitary actions, and biological and chemical control. Finally, new trendlines to reduce the impact of CLR as nanoparticles and nanotechnology were analyzed. [ABSTRACT FROM AUTHOR]

Coffee leaf rust (CLR) is caused by the biotrophic pathogenic fungus Hemileia vastatrix. Despite being the most researched coffee disease, mysteries still exist relating to its epidemiology and biology. The objective of this work is to highlight past and present events concerning this prominent coffee disease. We start with an historical overview of the homeland of Coffea arabica, the Afromontane forest of south‐west Ethiopia, and then follow its journey across the globe linked to colonial trade and power struggles. We report the relevance of CLR to coffee production today, with a focus on the Americas and summarize unproven hypotheses in relation to the cause of recent epidemics. We present an original hypothesis concerning the first major outbreak occurring in 1869 in Ceylon (Sri Lanka), based on geopolitical connections to global trade. We review old and new options for management of the disease. The likelihood of a yet undetected alternate host of H. vastatrix is also considered as an additional piece of the epidemiological puzzle. Finally, we reflect on the interactions between H. vastatrix and a changing climate. By better understanding past events, linked to CLR, we may be better prepared for future outbreaks. [ABSTRACT FROM AUTHOR]

Coffee has immense value as a worldwide-appreciated commodity. However, its production faces the effects of climate change and the spread of severe diseases such as coffee leaf rust (CLR). The exploration of fungal endophytes associated with Coffea sp. has already found the existence of nearly 600 fungal species, but their role in the plants remains practically unknown. We have researched the diversity of leaf fungal endophytes in two Coffea arabica varieties: one susceptible and one resistant to CLR. Then, we conducted cross-infection essays with four common endophyte species (three Colletotrichum sp. and Xylaria sp. 1) and Hemileia vastatrix (CLR) in leaf discs, to investigate the interaction of the endophytes on CLR colonisation success and severity of infection. Two Colletotrichum sp., when inoculated 72 h before H. vastatrix, prevented the colonisation of the leaf disc by the latter. Moreover, the presence of endophytes prior to the arrival of H. vastatrix ameliorated the severity of CLR. Our work highlights both the importance of characterising the hidden biodiversity of endophytes and investigating their potential roles in the plant-endophyte interaction. [ABSTRACT FROM AUTHOR]

(1) The fungal genus Simplicillium (Cordycipitaceae: Hypocreales) has an extensive distribution and a broad spectrum of hosts and substrates. The species Simplicillium lanosoniveum is a mycoparasite with potential for biological control of coffee leaf rust, Hemileia vastatrix. Morphologically, Simplicillium closely resembles mycoparasitic and entomopathogenic Lecanicillium fungi, often resulting in misidentification. A fungal isolate was obtained from leaf-rust-infested coffee plants from Cienfuegos Province, Cuba. (2) Combined analyses of morphology and molecular markers (ITS, LSU, EF-1alpha) were used for fungal identification. (3) In the NJ, ML, and BI phylogenies which were reconstructed, the isolate LBSim-01 was located in the Simplicillium lanosoniveum clade. This species-level identification was supported by morphological features. (4) The isolate LBSim-01 was assigned to the species Simplicillium lanosoniveum. This is the first description of a Simplicillium fungus associated with coffee leaf rust in Cuba. The presented results hold implications for the biological control of this economically relevant plant disease. [ABSTRACT FROM AUTHOR]

Natural enemies of plant pathogens might play an important role in controlling plant disease levels in natural and agricultural systems. Yet, plant pathogen–natural enemy interactions might be sensitive to climatic changes. Understanding the relationship between climate, plant pathogens and their natural enemies is thus important for developing climate‐resilient, sustainable agriculture.To this aim, we recorded shade cover, daily minimum and maximum temperature, relative humidity, coffee leaf rust and its hyperparasite at 58 sites in southwestern Ethiopia during the dry and wet season for 2 years.Coffee leaf rust severity was positively related to the maximum temperature. Hyperparasite severity was higher when the minimum temperature was low (i.e. in places with cold night temperatures). While canopy cover did not have a direct effect on rust severity, it reduced rust severity indirectly by lowering the maximum temperature. Canopy cover had a direct positive effect on the hyperparasite severity during one surveying period.Synthesis and applications. Our findings highlight that coffee leaf rust and its hyperparasite are both affected by shade cover and temperature, but in different ways. On the one hand, these niche differences lead to the worrying prediction that levels of coffee leaf rust will increase, and its hyperparasite will decrease, with climate change. On the other hand, these niche differences between coffee leaf rust and its hyperparasite provide opportunities to develop strategies to manage the environment (such as shade cover and microclimate) in such a way that the rust is disfavoured and the hyperparasite is favoured. [ABSTRACT FROM AUTHOR]

Tryptophan synthase (TRPS) is a complex enzyme responsible for tryptophan biosynthesis. It occurs in bacteria, plants, and fungi as an αββα heterotetramer. Although encoded by independent genes in bacteria and plants, in fungi, TRPS is generated by a single gene that concurrently expresses the α and β entities, which are linked by an elongated peculiar segment. We conducted 1 µs all-atom molecular dynamics simulations on Hemileia vastatrix TRPS to address two questions: (i) the role of the linker segment and (ii) the comparative mode of action. Since there is not an experimental structure, we started our simulations with homology modeling. Based on the results, it seems that TRPS makes use of an already-existing tunnel that can spontaneously move the indole moiety from the α catalytic pocket to the β one. Such behavior was completely disrupted in the simulation without the linker. In light of these results and the αβ dimer's low stability, the full-working TRPS single genes might be the result of a particular evolution. Considering the significant losses that Hemileia vastatrix causes to coffee plantations, our next course of action will be to use the TRPS to look for substances that can block tryptophan production and therefore control the disease. [ABSTRACT FROM AUTHOR]

Nanoparticles (NPs) have a high surface/volume ratio and small size (100 ≤ nm, these characteristics allow its use in the management of plant diseases in small quantities. The objective of this study was to evaluate the efficiency of silver (Ag) and copper oxide (CuO) NPs in the control of coffee rust (Hemileia vastatrix Berkeley & Broome). The effect of these NPs at doses of 0, 50, 100, 200 and 400 mg/L on the germination of spores of H. vastatrix and the control of rust in coffee seedlings in a greenhouse was evaluated. The CuO NPs 250 mg/L was also compared with other commercial copper fungicides: copper hydroxide, cuprous oxide and copper chelate (Ethylenediamine tetraacetic acid - EDTA). The incidence and severity of rust were evaluated every seven days, after the appearance the first pustules and the data obtained were transformed into area under disease progress curve for incidence (AUDPCI) and severity (AUDPCS). The 400 mg/L dose of Ag and CuO NPs inhibited 99.8 and 98.4% of H. vastatrix spore germination, respectively. In the greenhouse, in the experiments with Ag and CuO NPs, the lowest AUDPCS was also observed at the dose of 400 mg/L with 97.5 and 92%, respectively. The efficacy of NPs CuO 250 mg/L was equal (p < 0.05) to cuprous oxide, with a reduction of 84.2 and 83.1% of AUDPCS, respectively. Therefore, the potential of Ag and CuO NPs to inhibit the germination of H. vastatrix spores and to control rust in coffee seedlings was verified. [ABSTRACT FROM AUTHOR]

Abstract Background Coffee is an important plantation crop in Indonesia. The coffee cultivation process was disrupted due to the fungus Hemileia vastatrix which causes rust disease. Biological control has the potential to suppress disease development. The diversity of antagonistic fungi such as Trichoderma in nature is very abundant, so it is necessary to explore and find Trichoderma which has the potential as a biological agent in controlling coffee leaf rust. The research aimed to obtain antagonist fungi that have the potential as biological agents in controlling coffee leaf rust naturally in the coffee plant ecosystem. Result Morphology of a local antagonist fungus isolate, coded TBK1, was identified as Trichoderma atroviride which had the potential to naturally control coffee leaf rust by H. vastatrix through a mycoparasitic mechanism. Conclusion In the Dieng Plateau, Banjarnegara Indonesia, an antagonistic fungus as a biological agent, T. atroviride, was found to control H. vastatrix coffee leaf rust.

The coffee industry faces coffee leaf rust caused by Hemileia vastratix, which is considered the most devastating disease of the crop, as it reduces the photosynthetic rate and limits productivity. The use of plant resistance inducers, such as chitosan, is an alternative for the control of the disease by inducing the synthesis of phytoalexins, as well as the activation of resistance genes. Previously, the effect of chitosan from different sources and physicochemical properties was studied; however, its mechanisms of action have not been fully elucidated. In this work, the ability of food-grade high-density chitosan (0.01% and 0.05%) to control the infection caused by the pathogen was evaluated. Subsequently, the effect of high-density chitosan (0.05%) on the induction of pathogenesis-related gene expression (GLUC, POX, PAL, NPR1, and CAT), the enzymatic activity of pathogenesis-related proteins (GLUC, POX, SOD, PPO, and APX), and phytoalexin production were evaluated. The results showed that 0.05% chitosan increased the activity and gene expression of ß-1,3 glucanases and induced a differentiated response in enzymes related to the antioxidant system of plants. In addition, a correlation was observed between the activities of polyphenol oxidase and the production of phytoalexin, which allowed an effective defense response in coffee plants. [ABSTRACT FROM AUTHOR]

Coffee leaf rust (CLR) poses a significant threat to coffee crops worldwide, including those grown in Brazil. CLR thrives in climatic conditions ideal for coffee cultivation, which results in its constant presence in Brazilian coffee farms. The intensity of CLR exhibits variations as affected by interannual and spatial climate variability that shape epidemics. The aim of this study was to determine the agro-climatic favourability zones for CLR occurrence in the major coffee-producing regions of Brazil based on region-specific agro-climatic conditions. Climate data spanning from 1961 to 2015 at 46 sites were selected to represent the major coffee-producing regions. Using a CLR infection rate model, daily simulations were performed to calculate the cumulative infection rate (CIR) for each site and growing season, starting from 1st October to 30th June of the following year. Based on the CIR values, the sites and seasons were categorised into five favourability classes: Very Low, Low, Medium, High, and Very High. An Agro-Climatic Favourability index (ACFavindex) was developed, considering the frequency of seasons falling within each favourability class. A map displaying four distinct favourability zones across the studied regions was then obtained and showed that most of the traditional coffee-growing areas fell within the Medium to High Favourability zones for CLR. The obtained map, delineating CLR favourability zones, holds practical value for coffee growers, consultants, and policymakers alike. It can guide the selection of CLR-resistant coffee cultivars for new cultivation areas and aid in the development of effective disease control strategies. [ABSTRACT FROM AUTHOR]

Coffee leaf rust (CLR) is caused by the biotrophic fungus Hemileia vastatrix Berk. & Br., a disease of economic importance, reducing coffee yield up to 60%. Currently, CLR epidemics have negatively impacted food security. Therefore, the objective of the present research study is to show a current framework of this disease and its effects on diverse areas, as well as the biological systems used for its control, mode of action, and effectiveness. The use of essential plant oils and antagonistic microorganisms to H. vastatrix are highlighted. Terpenes, terpenoids, and aromatic compounds are the main constituents of these oils, which alter the cell wall and membrane composition and modify the basic cell functions. Beneficial microorganisms inhibit urediniospore germination and reduce disease incidence and severity. The antagonistic microorganisms and essential oils of some aromatic plants have great potential in agriculture. These biological systems may have more than one mechanism of action, which reduces the possibility of the emergence of resistant strains of H. vastatrix. [ABSTRACT FROM AUTHOR]

The aim of this work was to validate markers linked to the SH3 gene of coffee leaf rust (CLR) resistance and use them in assisted selection. Initially, we validated the markers in genotypes already known to carry SH3. Next, we performed phenotype and genotype evaluation for resistance to CLR in coffee plants growing under field conditions. We used Arabica coffee progenies derived from BA-10, which carries the SH3 gene due to introgression of C. liberica. Three SCAR markers (SP-M16-SH3, BA-48-21O-f, and BA-124-12K-f) and one SSR marker (Sat244) linked to SH3 gene were used to amplify the coffee plants' DNA. Our assessments of markers validation in resistant genotypes, SP-M16-SH3 and BA-124-12K-f, were efficient to identify the SH3 gene. These two markers were used to evaluate the progenies derived from BA-10 and were significantly linked to the phenotype evaluations. The SP-M16-SH3 marker was more efficient, with the advantage of being codominant. [ABSTRACT FROM AUTHOR]

Coffee (Coffea spp.) is the second most significant commodity worldwide, with C. arabica being its most representative species. The coffee crop is affected by different fungal diseases that reduce the photosynthetically active area of its leaves and the production of grains. In order of agronomic importance, the rust caused by the biotrophic pathogen Hemileia vastatrix is a disease difficult to manage due to its type of reproduction. Another no less important, Thread Blight, caused by the basidiomycetes Ceratobasidium noxium (Syn. Corticium koleroga) and C. chavesanum, affects all aerial tissues of plants. The third disease, Cercospora leaf spot caused by Cercospora coffeicola, infects both leaves and grains, making it difficult to manage. Although there is enough scientific information on Rust, very little is known about the etiology, symptomatology, life cycle, and management of Thread Blight and Cercospora leaf spot. High-resolution photographs and micrographs were used and related with available scientific information. In addition, current scientific information on each disease was compiled, and with that, the life cycles were developed. Likewise, this manuscript describes the management of the three diseases based mainly on the use of genetic, cultural, physical, biological, and chemical measures and their integration as a sustainable alternative in the coffee agroecosystem. Current and future challenges in coffee include the evaluation of cultivars, genetic diversity of Ceratobasidium spp. and C. coffeicola, plant-pathogen interactions, and agroecological management practices. [ABSTRACT FROM AUTHOR]

El café (Coffea spp.) es el segundo producto básico de mayor importancia a nivel mundial, siendo C. arabica su especie más representativa. El cultivo de café es afectado por diferentes enfermedades fúngicas que reducen el área fotosintéticamente activa de sus hojas y la producción de granos. Por orden de importancia se destacan la Roya causada por el patógeno biótrofo Hemileia vastatrix que es de difícil manejo por su tipo de reproducción. Otra no menos importante, el Mal de hilachas ocasionada por los basidiomicetos Ceratobasidium noxium (Sin. Corticium koleroga) y C. chavesanum, que afectan todos los tejidos aéreos de las plantas. La tercera enfermedad, la Cercosporiosis causada por Cercospora coffeicola infecta tanto hojas como granos lo que dificulta su manejo. Aunque hay basta información científica sobre la Roya, muy poco se conoce sobre la etiología, sintomatología, ciclo de vida y manejo de Mal de hilachas y Cercosporiosis. Se utilizaron fotografías y micrografías de alta resolución y se las relacionó con la información científica disponible. Además, se recopiló información científica actualizada sobre cada enfermedad, y con eso se elaboraron los ciclos de vida. Así mismo, en este manuscrito se describe el manejo de las tres enfermedades basado principalmente en el uso de medidas genéticas, culturales, físicas, biológicas y químicas, y su integración como una alternativa sostenible en el agroecosistema de café. Entre los principales desafíos actuales y futuros en café están la evaluación de cultivares, diversidad genética de Ceratobasidium spp. y C. coffeicola, interacciones planta-patógenos, y prácticas de manejo agroecológicas.

Coffee has immense value as a worldwide-appreciated commodity. However, its production faces the effects of climate change and the spread of severe diseases such as coffee leaf rust (CLR). The exploration of fungal endophytes associated with Coffea sp. has already found the existence of nearly 600 fungal species, but their role in the plants remains practically unknown. We have researched the diversity of leaf fungal endophytes in two Coffea arabica varieties: one susceptible and one resistant to CLR. Then, we conducted cross-infection essays with four common endophyte species (three Colletotrichum sp. and Xylaria sp. 1) and Hemileia vastatrix (CLR) in leaf discs, to investigate the interaction of the endophytes on CLR colonisation success and severity of infection. Two Colletotrichum sp., when inoculated 72 h before H. vastatrix, prevented the colonisation of the leaf disc by the latter. Moreover, the presence of endophytes prior to the arrival of H. vastatrix ameliorated the severity of CLR. Our work highlights both the importance of characterising the hidden biodiversity of endophytes and investigating their potential roles in the plant-endophyte interaction.

Coffee production is negatively affected by coffee leaf rust, a disease caused by the fungus Hemileia vastatrix. As a natural product-based alternative to chemically control the disease, this study evaluated the effect of two chitosan-coated nanoemulsions prepared from Cymbopogon citratus essential oil (EO) and the thymol: pyruvic acid (1:1) natural deep eutectic solvent (NADES) on the in vitro germination of H. vastatrix urediospores and on the in vivo control of the disease in Coffea arabica plants under greenhouse conditions. Both nanoformulations inhibited urediospores in vitro germination but only that prepared with EO did it significantly more than its free form active ingredient (the observed reduction was around 60 %). On the other hand, the in vivo experiment showed that the EO and NADES chitosan-coated nanoemulsions offered similar and significant protection for Coffea arabica plants against leaf rust; the disease severity level was found to be less than 2.6 % after 81 days from the application of the treatments to the plants (comparable to the cooper oxychloride, which is one of the commercial fungicides traditionally used), while the free components did not (9.0–13.3 % of severity level by day 81, such as the control). This is the first report demonstrating that chitosan-coated nanoemulsions, containing NADES or EO, protect coffee plants against H. vastatrix infection and can be two alternatives for sustainable pest management. Furthermore, this study contributes to broadening the prospects for using hydrophobic NADES in the design of biopesticides. [Display omitted] • Natural deep eutectic solvents inhibit the germination of urediospores. • Lemongrass oil and a eutectic solvent were nanoemulsified and chitosan-coated. • Chitosan-coated nanoemulsions showed a slow release of monoterpene over 36 days. • Nanostructured systems protect coffee plants from rust under greenhouse conditions. [ABSTRACT FROM AUTHOR]

Rust is the main disease affecting Coffea arabica, the most economically important coffee species. The objective of this study was to analyze C. arabica cultivars with different levels of rust resistance, including bean size, raw bean appearance, final sensory scores (FSS), and aroma and taste nuances of the coffee cup. The experiment was designed in randomized blocks (RBD) with three replications and 20 treatments (cultivars), totaling 60 experimental plots. The rust-susceptible cultivars IPR 100, Rubi MG 1192, and Topázio MG 1190 were compared with 17 rust-resistant cultivars. Cultivars IPR 103, MGS Aranãs, and Saíra II presented the highest percentages of high sieves, highest scores of raw bean appearance, and low percentages of mocha-type beans. All cultivars had FSS above 82 and were classified as specialty coffees. The cultivars with the highest FSS (Arara and Catiguá MG2) showed a greater diversity of coffee cup aroma and flavor nuances. Rust-resistant Arabica coffee cultivars are promising for the physical quality of beans and have potential for the specialty coffee market.

Obtaining resistance cultivars for leaf miner and leaf rust are the main important strategy of Brazil’s national coffee breeding program. The narrow genetic basis, and founder effect consequences, lead to challenges in quantifying and detecting genetic diversity for these traits. Biotechnology tools allied with classical breeding strategies are powerful in detecting variability and deploying a precision selection. The selection based on the genetic merit of an individual obtained from thousands of single nucleotide polymorphism effects is known as genomic selection. The ordinal scale principally makes the resistance evaluation of the leaf rust and leaf miner of the score, categorizing the phenotypes following the discrete (ordinal) distribution. Hence, this distribution can be better analyzed by threshold models. Our goals were to optimize genomic prediction models for coffee resistance to leaf rust and leaf miner via threshold models and compare pedigree and genomic relationship matrices to underlying prediction models. We have observed that the genomic model with the genomic relationship matrix performed better for all scenarios. For the traits with at least five degrees of scores, the threshold models performed better, whereas for a trait with ten degrees of scores, we see no advantage to using a threshold model for genomic prediction. [ABSTRACT FROM AUTHOR]

Endophyte microorganisms live in symbiosis inside of plant healthy tissues. These fungi help their hosts to tolerate pathogen affectation, pest damage, and to adapt to extreme conditions of salinity and temperatures. The coffee leaf rust, Hemileia vastatrix Berkeley & Broome, affects coffee crop, and its management is based on chemical fungicide application. In view of the world agriculture challenges, it is necessary to develop sustainable strategies. The endophytic fungi represent a potential for biological control of plant diseases. [ABSTRACT FROM AUTHOR]

Global climate change is increasing pest and pathogen pressures on plant communities, deteriorating optimal plant functioning. In plant communities, root functional trait expression and microbial communities are important indicators of plant functioning belowground, and, when confronted with pathogens aboveground, can simultaneously reflect plant defence strategies. Yet, while research is continuing to emerge on the response of root functional traits and microbial processes to pathogens aboveground, little work has investigated these interactions in tree‐crops, or the role organic amendments play in moderating these relationships. The main objective of this study is to disentangle the dynamic effects of pathogens and amendments on root functional traits (i.e. specific root length and area, root diameter, root length density, root nitrogen and root carbon to nitrogen ratio) and root endophytic fungal communities. As a model, we use Coffea arabica (coffee) variety Caturra along a gradient of coffee leaf rust – a foliar disease prominent in coffee systems – under contrasting but widespread amendment regimes in biodiverse agroforestry systems. We found that root trait expression varies along established conservation and collaboration gradients, where fungal endophyte community composition varies significantly as a function of root traits. Belowground resource acquisition strategies do not change with foliar disease incidence, suggesting they may be decoupled. Rather, amendment regimes differentially shape root trait expression and microbial communities, where coffee plants under organic amendments, regardless of foliar disease incidence, expressed greater acquisitive traits and enhanced collaboration with symbiotic fungi. This is an important first step in disentangling the dynamic inter‐relationships between plant traits, endophytes and pathogens, generating new questions on the role of amendments in sustainable pathogen management in biodiverse agroecosystems. [ABSTRACT FROM AUTHOR]

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Rust is the main disease affecting Coffea arabica, the most economically important coffee species. The objective of this study was to analyze C. arabica cultivars with different levels of rust resistance, including bean size, raw bean appearance, final sensory scores (FSS), and aroma and taste nuances of the coffee cup. The experiment was designed in randomized blocks (RBD) with three replications and 20 treatments (cultivars), totaling 60 experimental plots. The rust-susceptible cultivars IPR 100, Rubi MG 1192, and Topázio MG 1190 were compared with 17 rust-resistant cultivars. Cultivars IPR 103, MGS Aranãs, and Saíra II presented the highest percentages of high sieves, highest scores of raw bean appearance, and low percentages of mocha-type beans. All cultivars had FSS above 82 and were classified as specialty coffees. The cultivars with the highest FSS (Arara and Catiguá MG2) showed a greater diversity of coffee cup aroma and flavor nuances. Rust-resistant Arabica coffee cultivars are promising for the physical quality of beans and have potential for the specialty coffee market. [ABSTRACT FROM AUTHOR]

Coffee leaf rust (CLR) is caused by Hemileia vastatrix and is the most critical phytosanitary problem for coffee production. So far, no biocontrol agents (BCAs) have been registered, and the selection of native agents is required. The present work evaluates the enzymatic activity of chitinase (3.2.1.14), glucanase (3.2.1.6), and protease (3.4.21.92) in three native CLR mycoparasite isolates from Chiapas, Mexico. Isolates were grown for 10 days on inducing substrate and on urediniospores collected in coffee plantations in Chiapas, Mexico. Isolate CERI-530 exhibited higher chitinase (38,178 ± 2950 U/mg) and glucanase (9720 ± 282 U/mg) activity in the presence of CLR, and chitinase and glucanase zymogram analysis revealed a typical 50 kDa band. Isolate CERI-701 showed additional 40, 30 and 20 kDa chitinase bands in the presence of CLR. Protease activity was visualized for all isolates, also in the presence of CLR. It was found that hydrolytic enzymes play an important role in the CLR-mycoparasite interactions for the strains of our study. Strain CERI-542 spores and supernatant significantly decreased CLR urediniospore germination. Observation under scanning electron microscope revealed that CERI-542 was the most aggressive CLR mycoparasite and had the ability to destroy CLR urediniospores, which also suggests that different action mechanisms are at work. The present study is a first step towards a deeper understanding of the interactions between native mycoparasites and CLR, and reports for the first time the formation of a covering over the urediniospores as part of these interactions. [ABSTRACT FROM AUTHOR]

Coffee leaf rust (CLR) is caused by the biotrophic fungus Hemileia vastatrix Berk. & Br., a disease of economic importance, reducing coffee yield up to 60%. Currently, CLR epidemics have negatively impacted food security. Therefore, the objective of the present research study is to show a current framework of this disease and its effects on diverse areas, as well as the biological systems used for its control, mode of action, and effectiveness. The use of essential plant oils and antagonistic microorganisms to H. vastatrix are highlighted. Terpenes, terpenoids, and aromatic compounds are the main constituents of these oils, which alter the cell wall and membrane composition and modify the basic cell functions. Beneficial microorganisms inhibit urediniospore germination and reduce disease incidence and severity. The antagonistic microorganisms and essential oils of some aromatic plants have great potential in agriculture. These biological systems may have more than one mechanism of action, which reduces the possibility of the emergence of resistant strains of H. vastatrix.

Coffee leaf rust (CLR) is the most important disease in coffee and is caused by Hemileia vastatrix. The use of a diagrammatic scale helps people more effectively evaluate rust severity and improves disease measurement by evaluators. Our goal was to develop a new scale with colored pictures and seven disease levels (0; 0.1–1.0; 1.1–2.0; 2.1–5.0; 5.1–10.0; 10.1–25.0; >25.0%) and then compare the severity results of CLR on arabica coffee leaves with those based on three other scales. Three evaluations were performed by ten different evaluators. The first assessment was performed without a scale. On the same day, raters performed four assessments with each of the four diagrammatic scales. The third evaluation was performed at seven-day intervals. We analyzed the statistics with linear regression and Lin's concordance correlation. The evaluators using the proposed scale improved the precision, accuracy and reproducibility of the evaluations and reduced residual distribution when compared to the evaluators who did not use the proposed diagrammatic scale or who used the other scales. Overall, the proposed diagrammatic scale is a tool that can assist users in producing a disease estimate close to the real value of CLR on arabica coffee leaves. [ABSTRACT FROM AUTHOR]

Hemileia vastatrix (HV) is the pathogen responsible for the coffee leaf rust (CLR) disease that has spread globally. CLR causes losses of up to a billion dollars annually and affects all types of crops regardless of their production regime (organic or inorganic). Additionally, smallholders produce approximately 80% of coffee in developing countries. The condition causes losses of up to a billion dollars annually. It affects all types of crops regardless of their production regime (organic or inorganic). Approximately 80% of coffee is produced by smallholders in developing countries. Until the 90s, shaded-production systems and native varieties were encouraged; however, the rapid spread of CLR has forced farmers to migrate towards inorganic schemes, mainly due to a lack of knowledge about natural alternatives to pesticides that can be implemented to control HV. Therefore, the purpose of this article is to compile the currently existing options, emphasizing two key factors that guarantee efficient rust control: selective fungicidal activity against HV and the nutrition of coffee crops. Thus, by comprehending how these natural compounds (such as plant, bacteria, fungi, animals, or algae metabolites) impact coffee rust proliferation. Furthermore, since a various range of biochar effects contributes to the control of foliar fungal pathogens through modification of root exudates, soil properties, and nutrient availability, which influence the growth of antagonist microorganisms, we present a review of the pathogen-suppressive effects of biochar, and new control strategies suitable for organic schemes can be developed. [ABSTRACT FROM AUTHOR]

Context: Landscape structure influences the spread of plant pathogens, including coffee leaf rust, a fungal disease affecting the coffee industry. Rust transmission is likely affected by landscape structure through the dispersal of wind-borne spores. Previous studies found positive associations between rust incidence and the proportion of pasture cover, suggesting deforestation may facilitate spore dispersal. Objectives: We explored the links between landscape structure and coffee rust by modeling the spread of rust transmission. We investigated how (1) spatial clustering of coffee farms, (2) proportion of landscape deforestation, and (3) clustering of deforestation affects the speed of rust transmission. Methods: We developed a probabilistic model to simulate within-patch and between-patch transmission in simulated and real landscapes. We modeled within-patch transmission using a probabilistic cellular automata model and between-patch transmission using a random walk with spore movement inhibited by canopy cover. Results: Clustering of coffee farms is the primary driver of rust transmission. Deforestation is a secondary driver of rust spread: outbreaks spread more rapidly in landscapes where deforested areas are evenly dispersed throughout the landscape. When applied to real landscapes in Costa Rica, the model yields the same trends as simulated landscapes and suggests increased amounts of coffee near the starting location of the outbreak are correlated with more rapid rust spread. Conclusions: It is essential to consider landscape structure when managing the spread of crop diseases. Increasing the spacing between coffee farms and reducing forest fragmentation in coffee-growing regions can benefit biodiversity conservation and reduce the economic impacts of coffee rust. [ABSTRACT FROM AUTHOR]

Here we describe the proteome of the fungus Hemileia vastatrix by label free mass spectrometry (LC–MS/MS). H. vastatrix is the causal agent of coffee rust disease, causing great economic losses in this crop. The objective of our work was to identify H. vastatrix proteins potentially involved in host colonization and infection, by exploring the shotgun proteomics approach. A total of 742 proteins were identified and are associated with several crucial molecular functions, biological processes, and cellular components. The proteins identified contribute to a better understanding of the metabolism of the fungus and may help identify target proteins for the development of specific drugs in order to control coffee rust disease. All data can be accessed at the Centre for Computational Mass Spectrometry – MassIVE MSV000087665 -https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=cc71ad75f767451abe72dd1ce0019387

This research focused on the incidence and population genetics of coffee leaf rust (CLR) fungus, Hemileia vastatrix , to estimate the possible original source(s) and subsequent migration pathways of wind-borne and human-aided spores in three main coffee production regions (Northwest, Central Highlands, and Southeast) in Vietnam. In southern Vietnam (Central Highlands and Southeast), Coffea canephora covers the majority area, while Catimor lines of C. arabica accounts for 95% of the coffee plantations in northwestern Vietnam. Field surveys conducted at eighty-five plantations, show coffee leaf samples infected by the rust fungus across forty-one plantations. Catimor varieties exhibited high levels of susceptibility with severe rust symptoms, while robusta varieties had varying degrees of susceptibility. We analyzed 863−869 base pairs of internal transcribed spacer (ITS) region from 83 samples (41 sequences from Vietnam, 2 from Thailand, and the remaining 40 from American countries); and fifty-two haplotypes consisting of 123 polymorphic sites were detected. Although the analysis of molecular variance (AMOVA) indicates significant genetic differentiation in the H. vastatrix populations in Vietnam, there was no clear genetic structure with respect to the three geographic areas surveyed. Based on the haplotype network, NeighborNet analysis, and geographical distribution patterns of the haplotypes, five haplotypes were identified as early established, from which most other haplotypes in Vietnam were derived. The early established haplotypes were found in the highest frequency in Northwest Vietnam. This finding corresponds to the earliest record of CLR in Vietnam. The phylogenetic network analysis also illustrated that H. vastatrix had expanded from the northwest to southern Vietnam. Pairwise genetic distance analysis and the geophylogenetic tree also suggests that CLR was first established in the Northwest. In addition, some scattered individuals on the principal coordinate analysis (PCoA) diagram and several separated haplotypes in the phylogenetic networks indicated that other branches of CLR in Vietnam were initiated in the Central Highlands. Hemileia vastatrix from these branches have been spreading in southern Vietnam. [ABSTRACT FROM AUTHOR]

The development of disease resistant coffee cultivars is of paramount importance to increase grain yield and decrease production costs. The lack of information on how the new cultivars resist the attack of diseases and pests is a limiting factor in the selection of the best cultivars. Thus, the objective of the present work was to select superior genotypes of the Big Coffee VL group for resistance to Hemileia vastatrix and Cercospora coffeicola. The experiment consisted of 18 progenies pre-selected from a group of 100 genetic materials, for the trait of productivity. The experiment was carried out in a randomized block design, with six blocks and one plant per experimental plot, totaling 108 individuals. The selected coffee plants were evaluated for 10 months for injuries caused by coffee leaf rust and brown eye spot using commonly used diagrammatic scales. During the evaluated months, the genotypes G10, P32 and M22 were more tolerant to rust and brown eye spot. Thus, they are good candidates for genetic improvement programs with the objective of producing larger grains and adding resistance to the main diseases of arabica coffee. [ABSTRACT FROM AUTHOR]

Coffea arabica is the most economically important coffee species worldwide. However, its production is severely limited by diseases such as rust. The mechanisms underlying constitutive defense responses in coffee are still poorly understood, compared with induced defense mechanisms. We aimed to characterize constitutive defense responses of thirteen cultivars of C. arabica. Cultivars were classified under field conditions according to the level of resistance to rust: resistant (R), moderately resistant (MR), and susceptible (S). Based on this classification, the stability of eight reference genes (RGs) was evaluated. The most stable RGs were EF1α, APT1, and 24S. We also evaluated the expression of CaWRKY1, CaPAL1, CaCAD1, and CaPOX1, and activities of PAL, CAD, and POX, which are involved in lignin biosynthesis, and leaf content of total phenolic compounds and lignin. Gene expression and enzymatic activity were not correlated with defense metabolites in the R cultivar group but showed a negative correlation with phenolic compounds in MR cultivars. Cultivar S showed positive correlations of gene expression and enzyme activity with phenolic compounds. These results may assist coffee breeding programs regarding selection of genotypes and in optimization of rust resistance. [ABSTRACT FROM AUTHOR]

The coffee leaf rust, Hemileia vastatrix, is the most destructive coffee-growing disease and the most important economically. More aggressive outbreaks of the disease were recently reported worldwide, including in Mexico, where coffee production showed a 40% decrease. This work aimed to determine the environmental conditions that favor release and air transport of the H. vastatrix urediniospores in coffee crops in Veracruz. The monitoring of airborne coffee leaf rust urediniospores was performed using three types of aerobiological traps at different heights: Hirst Spore Trap (HST, 1.5 m), Passive Spore Trap (PST 1.5, 3, 6, and 9 m), and Sedimentation Spore Sampler (SSS 1 m) from January 2014 to October 2015, in two plots in Veracruz, Mexico. The airborne urediniospores counts exhibited a bimodal distribution. Low concentrations that increase over time are evident from January to April, decreasing abruptly in May and June, only to rise again in August, reaching the highest record for airborne urediniospores during the mid-summer drought phenomenon. Dispersal of coffee rust urediniospores is mainly influenced by temperature, rain, wind, and humidity in leaves. They can reach heights in the air up to 9 m (above the canopy) in shade coffee crops. The dispersal of pathogens in the atmosphere comprises complex processes interconnected; their knowledge allows better comprehensive management of them. [ABSTRACT FROM AUTHOR]

This research focused on the incidence and population genetics of coffee leaf rust (CLR) fungus, Hemileia vastatrix, to estimate the possible original source(s) and subsequent migration pathways of wind-borne and human-aided spores in three main coffee production regions (Northwest, Central Highlands, and Southeast) in Vietnam. In southern Vietnam (Central Highlands and Southeast), Coffea canephora covers the majority area, while Catimor lines of C. arabica accounts for 95% of the coffee plantations in northwestern Vietnam. Field surveys conducted at eighty-five plantations, show coffee leaf samples infected by the rust fungus across forty-one plantations. Catimor varieties exhibited high levels of susceptibility with severe rust symptoms, while robusta varieties had varying degrees of susceptibility. We analyzed 863−869 base pairs of internal transcribed spacer (ITS) region from 83 samples (41 sequences from Vietnam, 2 from Thailand, and the remaining 40 from American countries); and fifty-two haplotypes consisting of 123 polymorphic sites were detected. Although the analysis of molecular variance (AMOVA) indicates significant genetic differentiation in the H. vastatrix populations in Vietnam, there was no clear genetic structure with respect to the three geographic areas surveyed. Based on the haplotype network, NeighborNet analysis, and geographical distribution patterns of the haplotypes, five haplotypes were identified as early established, from which most other haplotypes in Vietnam were derived. The early established haplotypes were found in the highest frequency in Northwest Vietnam. This finding corresponds to the earliest record of CLR in Vietnam. The phylogenetic network analysis also illustrated that H. vastatrix had expanded from the northwest to southern Vietnam. Pairwise genetic distance analysis and the geophylogenetic tree also suggests that CLR was first established in the Northwest. In addition, some scattered individuals on the principal coordinate analysis (PCoA) diagram and several separated haplotypes in the phylogenetic networks indicated that other branches of CLR in Vietnam were initiated in the Central Highlands. Hemileia vastatrix from these branches have been spreading in southern Vietnam.