Search Results (14)

Coffee berry disease (CBD), caused by Colletotrichum kahawae, significantly threatens global Coffee arabica production, leading to major yield losses. Traditional detection methods are often subjective and inefficient, particularly in resource-limited settings. While deep learning has advanced plant disease detection, most existing research targets leaf diseases, with limited focus on berry-specific infections like CBD. This study proposes a lightweight and accurate solution using a Compact Convolutional Transformer (CCT) for classifying healthy and CBD-affected coffee berries. The CCT model combines parallel convolutional branches for hierarchical feature extraction with a transformer encoder to capture long-range dependencies, enabling high performance on limited data. A dataset of 1737 coffee berry images was enhanced using bilateral filtering and color segmentation. The CCT model, integrated with a Multilayer Perceptron (MLP) classifier and optimized through early stopping and regularization, achieved a validation accuracy of 97.70% and a sensitivity of 100% for CBD detection. Additionally, CCT-extracted features performed well with traditional classifiers, including Support Vector Machine (SVM) (82.47% accuracy; AUC 0.91) and Decision Tree (82.76% accuracy; AUC 0.86). Compared to pretrained models, the proposed system delivered superior accuracy (97.5%) with only 0.408 million parameters and faster training (2.3 s/epoch), highlighting its potential for real-time, low-resource deployment in sustainable coffee production systems. Full article

The coffee berry borer (CBB) is the most destructive pest of coffee worldwide, with damages exceeding $500 M a year and affecting the livelihood of 25 million farmers. Coffee fruit rot (CFR) is described as an anthracnose disease; it can cause up to 80% loss of the crop on susceptible cultivars when conditions favor it. These two serious threats to coffee production have been studied separately, but a link between them was not shown until recently. Several recent studies show that CBB damage is associated with a higher incidence of fruit rot; CBBs carry Colletotrichum and Fusarium fungi, also found in rotted fruits, and can transmit disease to coffee fruits as they bore into them. Previous studies on the relationship between CBB and Fusarium did not take into account that Fusarium is involved in coffee fruit rot, so these recent findings shed new light on the relationship. Here we discuss this relationship and its implications, both ecological and practical. Full article

The application of marker-assisted selection in coffee breeding programs accelerates the identification and concentration of target alleles, being essential for developing cultivars resistant to multiple diseases. In this study, a population was developed from artificial crossings between Timor Hybrid and Tupi Amarelo, with the aim of promoting the pyramiding of resistance genes to the main diseases and pests of Coffea arabica: coffee leaf rust (CLR), coffee berry disease (CBD), cercospora, and leaf miner. Resistance was confirmed by nine molecular markers at loci associated with CLR (genes SH3, CC-NBS-LRR, RLK, QTL-GL2, and GL5) and with CBD (gene Ck-1). The resistance to CLR, cercospora, and leaf miner was evaluated using phenotypic diagrammatic scales. Mixed models estimated population superiority in 16 morphoagronomic traits over four agricultural years. The introgression of resistance alleles to CLR and CBD was identified in 98.6% of the population, with 29% showing pyramiding of five resistance genes. These pyramiding genotypes showed 100% resistance to the leaf miner and 90% to cercospora. The traits were grouped into univariate, bivariate, and trivariate repeatability models, with 11 significant ones. These results are indicative of genetic variability to be explored in the development of cultivars with multiple resistances and high agronomic potential. Full article

The main diseases that affect coffee production worldwide are coffee leaf rust (CLR) and coffee berry disease (CBD), caused by fungi Hemileia vastatrix and Colletotrichum kahawae, respectively. The identification of cultivars with stacking resistance genes is of paramount importance for the control of these diseases. This work aimed to profile the phenotypic and genetic resistance of 160 genotypes belonging to 36 commercial coffee cultivars from five Central American countries regarding resistance to races II and XXXIII of H. vastatrix through phenotypic evaluation and evaluations associated with the genetic loci of resistance to CLR and CBD by molecular markers. Of the 160 genotypes from Central America evaluated, 26.25% presented genes stacked to the three loci of resistance to CLR and the locus of resistance to CBD, and resistance to races II and XXXIII when inoculated with urediniospores. In addition, 14 genotypes were identified with the presence of the S_H3 gene, whose resistance has not yet been broken. This work revealed errors in passport data or hybridizations in cultivars and even possible resistance breakdown in the Catimor genetic group. These results are essential to the search for strategies in coffee genetic breeding programs. Full article

Coffee berry disease (CBD) is not present in the Americas and presents a potential risk for growing coffee. Therefore, Colombia, which has been in scientific cooperation with the Centro de Investigação de Ferrugens do Cafeeiro (CIFC) of Portugal for more than 30 years, has been evaluating the genetic resistance of nine populations of C. arabica to 13 isolates of Colletotrichum kahawae JM Waller and PD Bridge, which are diverse in terms of aggressiveness and geographical origin. The phenotypes observed in the interaction between C. arabica and C. kahawae were used to develop a statistically reliable scale (p-value ≥ 0.001) to categorize resistance in C. arabica into five classes, and this scale was used to classify the nine populations of C. arabica evaluated. The results allowed us to corroborate the potential of Timor Hybrid CIFC 1343 (TH CIFC 1343) as a source of genetic resistance to CBD and to identify new genetic sources not yet explored for the development of varieties in Colombia that may eventually mitigate the effects of CBD in the face of increasing rainfall events and minimum temperatures due to climate change, which can favor disease development. Additionally, the results suggest that the existence of races in the C. arabica–C. kahawae complex is probable, and a selection of genotypes was identified as a possible differential series of races in C. kahawae. Full article

The genus Aspergillus contains several species that are important plant pathogens. Plant pathogenic Aspergillus spp. affect agricultural crops in the field as well as after harvest, often associated with corn ear rot, cotton boll rot, peanut yellow mold, black mold of onion and garlic, fruit rot on grapes, pomegranates, olives, citrus, and apples. Coffee berries and coffee beans as well as tree nuts are also frequently infected by Aspergillus spp. Some of the plant pathogenic Aspergillus spp. are also mycotoxigenic, produced mycotoxin in the plant tissues leading to contamination of agricultural products. Over the years, reports of plant diseases caused by Aspergillus in various crops have increased, suggesting they are commonly encountered plant pathogens. This review focuses on agricultural crops or cultivated plants infected by Aspergillus spp. The compilation of plant pathogenic Aspergillus spp. provides information to mycologists, particularly those involved in plant pathology and crop protection, with updated information on plant diseases caused by various species of Aspergillus. The updated information also includes the locality or location, province, state and the country. The knowledge on the prevalence and geographic distribution of plant pathogenic Aspergillus spp. is beneficial in the application of crop protection. Full article

The effects of coffee (Coffea arabica L.) berry pulp extracts (CBP extracts) on the improvement of diabetes, obesity, and non-alcoholic fatty liver disease (NAFLD) were evaluated using various in vitro antioxidant activity assays and through a high-fat diet-induced mild diabetic obese mouse model. After an 84-day oral administration of CBP extracts (400–100 mg/kg), bioactivities were evaluated. The in vitro analysis showed the highest DPPH^● scavenging activity of 73.10 ± 4.27%, ABTS^● scavenging activity of 41.18 ± 1.14%, and SOD activity of 56.24 ± 2.81%, at a CBP extract concentration of 1000 µg/mL. The in vivo analysis of the CBP extracts showed favorable and dose-dependent anti-obesity, anti-diabetic, NAFLD, nephropathy, and hyperlipidemia refinement effects through hepatic glucose enzyme activity, 5′-AMP-activated protein kinase (AMPK) up-regulation, antioxidant activity, lipid metabolism-related gene expression, and pancreatic lipid digestion enzyme modulatory activities. This study shows that an appropriate oral dosage of CBP extracts could function as a potent herbal formulation for a refinement agent or medicinal food ingredient to control type 2 diabetes and related complications. Full article

Background: Dietary (poly)phenol consumption is inversely associated with cardiovascular disease (CVD) risk in epidemiological studies, but little is known about the role of the gut microbiome in this relationship. Methods: In 200 healthy females, aged 62.0 ± 10.0 years, from the TwinsUK cohort, 114 individual (poly)phenol metabolites were measured from spot urine using ultra-high-performance liquid chromatography–mass spectrometry. The associations between metabolites, the gut microbiome (alpha diversity and genera), and cardiovascular scores were investigated using linear mixed models adjusting age, BMI, fibre, energy intake, family relatedness, and multiple testing (FDR < 0.1). Results: Significant associations were found between phenolic acid metabolites, CVD risk, and the gut microbiome. A total of 35 phenolic acid metabolites were associated with the Firmicutes phylum, while 5 metabolites were associated with alpha diversity (FDR-adjusted p < 0.05). Negative associations were observed between the atherosclerotic CVD (ASCVD) risk score and five phenolic acid metabolites, two tyrosol metabolites, and daidzein with stdBeta (95% (CI)) ranging from −0.05 (−0.09, −0.01) for 3-(2,4-dihydroxyphenyl)propanoic acid to −0.04 (−0.08, −0.003) for 2-hydroxycinnamic acid (FDR-adjusted p < 0.1). The genus 5-7N15 in the Bacteroidetes phylum was positively associated with the same metabolites, including 3-(3,5-dihydroxyphenyl)propanoic acid, 3-(2,4-dihydroxyphenyl)propanoic acid, 3-(3,4-dihydroxyphenyl)propanoic acid), 3-hydroxyphenylethanol-4-sulfate, and 4-hydroxyphenylethanol-3-sulfate)(stdBeta (95% CI): 0.23 (0.09, 0.36) to 0.28 (0.15, 0.42), FDR-adjusted p < 0.05), and negatively associated with the ASCVD score (stdBeta (95% CI): −0.05 (−0.09, −0.01), FDR-adjusted p = 0.02). Mediation analysis showed that genus 5-7N15 mediated 23.8% of the total effect of 3-(3,4-dihydroxyphenyl)propanoic acid on the ASCVD score. Conclusions: Coffee, tea, red wine, and several vegetables and fruits, especially berries, are the most abundant food sources of phenolic acids that have the strongest associations with CVD risk. We found that the gut microbiome, particularly the genus 5-7N15, partially mediates the negative association between urinary (poly)phenols and cardiovascular risk, supporting a key role of the gut microbiome in the health benefits of dietary (poly)phenols. Full article

In this study, marker-assisted recurrent selection was evaluated for pyramiding resistance gene alleles against coffee leaf rust (CLR) and coffee berry diseases (CBD) in Coffea arabica. A total of 144 genotypes corresponding to 12 hybrid populations from crosses between eight parent plants with desired morphological and agronomic traits were evaluated. Molecular data were used for cross-certification, diversity study and resistance allele marker-assisted selection (MAS) against the causal agent of coffee leaf rust (Hemileia vastatrix) and coffee berry disease (Colletotrichum kahawae). In addition, nine morphological and agronomic traits were evaluated to determine the components of variance, select superior hybrids, and estimate genetic gain. From the genotypes evaluated, 134 were confirmed as hybrids. The genetic diversity between and within populations was 75.5% and 24.5%, respectively, and the cluster analysis revealed three primary groups. Pyramiding of CLR and CBD resistance genes was conducted in 11 genotypes using MAS. A selection intensity of 30% resulted in a gain of over 50% compared to the original population. Selected hybrids with increased gain also showed greater genetic divergence in addition to the pyramided resistance alleles. The strategies used were, therefore, efficient to select superior coffee hybrids for recurrent selection programs and could be used as a source of resistance in various crosses. Full article

Robusta coffee is mostly grown in Africa and Asia and parts of tropical America, but not yet in Colombia. The crop has potential in lowland areas of this traditional Arabica coffee producer. Compared to Arabicas grown in highland areas, the Robustas have more drought and heat tolerance. However, they differ in flavor and have higher caffeine levels. With natural resistance to some of the major pests and diseases of other coffees, such as rust and berry borers, they thrive under harsh conditions. The genetic improvement of Robusta coffee requires the understanding of its genetic resources and a good breeding strategy. This review discusses the traits of interest and selection criteria for breeding and recommends methods of varietal development for Robusta in Colombia. Most of the traits of importance in breeding are quantitative and of low or intermediate heritability. Robusta is an outcrossing species and can suffer from inbreeding depression, so mass and recurrent selection are used, followed by the clonal propagation of best plants. Colombia has limited germplasm only from the Congolese group, so the SG1/Conilon and SG2 genotypes should be introduced with quarantine. Issues to address include the timing of flowering, asynchronous fruit maturation, chemical composition and sensory quality, as well as bean size. Variability for abiotic stress tolerance exists in Robusta genotypes and needs further study. New methods of breeding include hybrid development and recurrent selection. Having adapted varieties of Robusta coffee should promote production in Colombia, as it has in regions of Brazil, and would complement Arabica coffee for this traditional and major producer. Full article

The use of resistant cultivars is the most effective strategy for controlling coffee leaf rust caused by the fungus Hemileia vastatrix. To assist the development of such cultivars, amplified fragment-length polymorphism (AFLP) markers linked to two loci of coffee resistance to races I and II as well as pathotype 001 of H. vastatrix were converted to sequence-characterized amplified region (SCAR) and cleaved amplified polymorphic site (CAPS) markers. In total, 2 SCAR markers and 1 CAPS marker were validated in resistant and susceptible parents as well as in 247 individuals from the F₂ population. The efficiency of these markers for marker-assisted selection (MAS) was evaluated in F_2:3 and backcross (BCrs₂) populations genotyped with the developed markers and phenotyped with race II of H. vastatrix. The markers showed 90% efficiency in MAS. Therefore, the developed markers, together with molecular markers associated with other rust resistance genes, were used for F_3:4 and BCrs₃ coffee selection. The selected plants were analyzed using two markers associated with coffee berry disease (CBD) resistance, aiming for preventive breeding. MAS of F_3:4 and BCrs₃ individuals with all resistance loci was feasible. Our phenotypic and genotypic approaches are useful for the development of coffee genotypes with multiple genes conferring resistance to coffee leaf rust and CBD. Full article

Coffee agroforestry systems could reconcile agricultural and environmental objectives. While pests and diseases can reduce yield, their interactions with shade and nutrition have been rarely researched, and are particularly lacking in perennial systems. We hypothesized that intermediate shade levels could reduce coffee pests while excess shade could favor fungal diseases. We hypothesized that organic rather than mineral fertilization would better synchronize with nutrient uptake and higher nutrient inputs would be associated with reduced pest and disease damage due to higher plant vigor, yet effects would be less obvious in shaded plots as coffee growth would be light-limited. Using three-year-old trees of Coffea canephora var. Robusta (robusta coffee) in the Ecuadorian Amazon, we compared a full-sun system with four shading methods creating different shade levels: (1) Myroxylon balsamum; (2) Inga edulis; (3) Erythrina spp.; or, (4) Erythrina spp. plus Myroxylon balsamum. Conventional farming at either (1) moderate or (2) intensified input and organic farming at (3) low or (4) intensified input were compared in a split-plot design with shade as the main plot factor and farming practice as the sub-plot factor. The infestation of the following pests and disease incidences were evaluated monthly during the dry season: brown twig beetle (Xylosandrus morigerus), coffee leaf miner (Leucoptera coffeella), coffee berry borer (Hypothenemus hampei), anthracnose disease (Colletotrichum spp.), thread blight (Pellicularia koleroga), and cercospora leaf spot (Cercospora coffeicola). Coffee berry borer and brown twig beetle infestation were both reduced by 7% in intensified organic treatments compared to intensified conventional treatments. Colonization of coffee berry borer holes in coffee berries by the entomopathogenic fungus Beauveria bassiana was also assessed. Brown twig beetle infestation was significantly higher under full sun than under Inga edulis, yet no other shade effects were detected. We demonstrate for the first time how intensified input use might promote pest populations and thus ultimately lead to robusta coffee yield losses. Full article

Coffee (Coffea spp.) is an economically important crop widely cultivated in (sub) tropical countries worldwide. Commercial coffee production relies mainly on two related species, namely C. arabica and C. canephora. Due to their perennial growth habit, cultivation practices, and narrow genetic diversity, coffees are constantly exposed to many diseases and pests. Coffee leaf rust (Hemileia vastatrix Berk. et Br.), coffee berry disease (Colletotrichum kahawae Bridge and Waller), and coffee wilt disease (Gibberella xylarioides Heim and Saccas/Fusarium xylarioides) are the top fungal diseases affecting C. arabica and C. canephora production areas worldwide. In many regions, chemical-based control measures are widely used and are the only way to control the diseases. Developing resistant cultivars is one of the prerequisites for increasing sustainable market demand and agriculture. However, desired and required resistance traits are not always available in the gene pool. Furthermore, from other crops it is clear that dominant resistance genes introduced into varieties are not durable because of pathogen variability and the emergence of new races of the different pathogens. Utilization of altered susceptibility genes (S genes) offers a novel and alternative strategy for the breeding of durable and broad-spectrum resistance. The S gene encodes a host factor that facilitates a compatible interaction with the pathogen, and impairment of S genes leads to loss-of-susceptibility. In this review, guidelines for effective identification, characterization, and utilization of dysfunctional S genes are proposed to aid breeding activities in order to introduce durable resistance in Coffea spp. Several candidate S genes likely contributing to the susceptibility of Colletotrichum spp., Fusarium spp., and Meloidogyne spp. are discussed. With the rapid development of genetic engineering techniques, including CRISPR-associated systems, we now have the potential to accelerate the application of S genes to achieve durable resistance in coffee. Full article

The genus Colletotrichum has witnessed tremendous variations over the years in the number of species recognized, ranging from 11 to several hundreds. Host-specific fungal species, once the rule, are now the exception, with polyphagous behavior regarded as normal in this genus. The species Colletotrichum kahawae was created to accommodate the pathogens that have the unique ability to infect green developing coffee berries causing the devastating Coffee Berry Disease in Africa, but its close phylogenetic relationship to a polyphagous group of fungi in the C. gloeosporioides species complex led some researchers to regard these pathogens as members of a wider species. In this work we combine pathological, morphological, cytogenomic, biochemical, and molecular data of a comprehensive set of phylogenetically-related isolates to show that the Coffee Berry Disease pathogen forms a separate species, C. kahawae, and also to assign the closely related fungi, previously in C. kahawae subsp. cigarro, to a new species, C. cigarro comb. et stat. nov. This taxonomic clarification provides an opportunity to link phylogeny and functional biology, and additionally enables a much-needed tool for plant pathology and agronomy, associating exclusively C. kahawae to the Coffee Berry Disease pathogen. Full article