Current Status and Management of Coffee Rust Disease

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Pest and Disease Management".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 45886

Special Issue Editor

Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Linking Landscape, Environment, Agriculture and Food Research Center (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
Interests: plant pathology; plant–microbe interactions; coffee leaf rust; coffee berry disease; plant defense responses; microbial mechanisms of pathogenicity
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Special Issue Information

Dear Colleagues,

Coffee is not only a vital presence in the daily life of a significant share of the world´s population, which consumes about 3 billion cups of coffee a day, but also the most important agricultural commodity. It is crucial to the economy of more than 50 countries and constitutes the major source of livelihood for between 12 and 25 million farmers worldwide. One of the main limiting factors for the sustainable farming of Arabica coffee, which currently represents 59% of the world’s coffee production, is coffee leaf rust (CLR), a disease caused by the biotrophic fungus Hemileia vastatrix. Since first historical burst of CLR in the 19th century, which caused the eradication of coffee cultivation in Sri Lanka, the disease has spread to all of the coffee cultivation areas in the world. The losses caused by CLR are estimated to be 1–2 billion U.S. dollars annually.

Coffee breeding for rust resistance has been one of the most suitable and sustainable strategies for controlling the disease. However, the pathogen’s high degree of variability and adaptability, together with the consequent occurrence of frequent shifts in pathotypes, has resulted in the gradual loss of resistance of some varieties. Furthermore, since 2008, there has been a serious cluster of outbreaks of CLR across the Americas, which has been associated with changes in meteorological patterns, in the rust fungus itself, and in the ecology of coffee farms. This scenario shows us that, despite all the progress made so far in CLR research, there remains an unceasing need to better understand the dynamics of H. vastatrix populations and the mechanisms controlling plant resistance and fungal pathogenicity in order to breed efficiently for durable resistance.

This Special Issue aims to describe recent advances in CLR research, particularly in different coffee-growing regions, and provide new directions for sustainable disease control strategies. We welcome all scientific work (original research articles, reviews, short communications, opinion and perspectives papers) addressing one or more of the following topics:

  • pathogen genetic diversity;
  • plant–pathogen effectors;
  • plant genetic resistance;
  • mechanisms of plant resistance and tolerance;
  • impact of climate changes on coffee leaf rust;
  • breeding strategies to achieve durable resistance; and
  • sustainable disease control strategies.

Dr. Maria Céu Lavado da Silva
Guest Editor

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Keywords

  • coffee
  • Hemileia vastatrix
  • coffee leaf rust
  • pathogen genetic diversity
  • plant genetic resistance
  • mechanisms of plant resistance and tolerance
  • durable resistance
  • sustainable disease control strategies.

Published Papers (9 papers)

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Research

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22 pages, 5923 KiB  
Article
Coffee Rust Forecast Systems: Development of a Warning Platform in a Minas Gerais State, Brazil
by Edson Ampélio Pozza, Éder Ribeiro dos Santos, Nilva Alice Gaspar, Ximena Maira de Souza Vilela, Marcelo de Carvalho Alves and Mário Roberto Nogueira Colares
Agronomy 2021, 11(11), 2284; https://doi.org/10.3390/agronomy11112284 - 11 Nov 2021
Cited by 2 | Viewed by 2933
Abstract
This study aimed to develop a warning system platform for coffee rust incidence fifteen days in advance, as well as validating and regionalizing multiple linear regression models based on meteorological variables. The models developed by Pinto were validated in five counties. Experiments were [...] Read more.
This study aimed to develop a warning system platform for coffee rust incidence fifteen days in advance, as well as validating and regionalizing multiple linear regression models based on meteorological variables. The models developed by Pinto were validated in five counties. Experiments were set up in a randomized block design with five treatments and five replications. The experimental plot had six lines with 20 central plants of useful area. Assessments of coffee rust incidence were carried out fortnightly. The data collected from automatic stations were adjusted in new multiple linear regression models (MLRM) for five counties. Meteorological variables were lagged concerning disease assessment dates. After the adjustments, two models were selected and calculated for five counties, later there was an expansion to include ten more counties and 35 properties to validate these models. The result showed that the adjusted models of 15–30 days before rust incidence for Carmo do Rio Claro and Nova Resende counties were promising. These models were the best at forecasting disease 15 days in advance. With these models and the geoinformation systems, the warning platform and interface will be improved in the coffee grower region of the south and savannas of the Minas Gerais State, Brazil. Full article
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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18 pages, 22246 KiB  
Article
Marker-Assisted Pyramiding of Multiple Disease Resistance Genes in Coffee Genotypes (Coffea arabica)
by Dênia Pires de Almeida, Eveline Teixeira Caixeta, Karoliny Ferreira Moreira, Antonio Carlos Baião de Oliveira, Kátia Nogueira Pestana de Freitas, Antônio Alves Pereira, Renato Domiciano Silva Rosado, Laércio Zambolim and Cosme Damião Cruz
Agronomy 2021, 11(9), 1763; https://doi.org/10.3390/agronomy11091763 - 01 Sep 2021
Cited by 8 | Viewed by 2926
Abstract
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 [...] Read more.
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 F2:3 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 F3:4 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 F3:4 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
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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17 pages, 5084 KiB  
Article
Defense Response to Hemileia vastatrix in Susceptible Grafts onto Resistant Rootstock of Coffea arabica L.
by Edgar Couttolenc-Brenis, Gloria Carrión, Luc Villain, Fernando Ortega-Escalona, Martín Mata-Rosas and Alfonso Méndez-Bravo
Agronomy 2021, 11(8), 1621; https://doi.org/10.3390/agronomy11081621 - 16 Aug 2021
Cited by 1 | Viewed by 2783
Abstract
The use of resistant cultivars and fungicides are common methods to control coffee leaf rust (CLR), the main disease that affects the Arabica coffee crop. In this study, we evaluated the response of grafted and ungrafted plants during the early stage of Hemileia [...] Read more.
The use of resistant cultivars and fungicides are common methods to control coffee leaf rust (CLR), the main disease that affects the Arabica coffee crop. In this study, we evaluated the response of grafted and ungrafted plants during the early stage of Hemileia vastatrix infection. We used ungrafted plants of Oro Azteca (resistant cultivar) and Garnica (susceptible cultivar), and grafted plants, combining both as rootstock and graft (Garnica/Oro Azteca and Oro Azteca/Garnica). All plants were inoculated with H. vastatrix uredospores, and we quantified the development of fungal structures in the leaf tissue of inoculated plants using qRT-PCR to measure relative expression of two pathogenesis recognition genes (CaNDR1 and CaNBS-LRR) and three genes associated with the salicylic acid (SA) pathway (CaNPR1, CaPR1 and CaPR5). In Garnica grafted on Oro Azteca, the fungal structures recorded were significantly less than in Garnica ungrafted plants. In addition, the expression of defense-related genes in grafted plants was higher than in ungrafted plants. Our results indicate that the defense response to CLR is strongly influenced by the rootstock employed. Full article
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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11 pages, 2429 KiB  
Article
Behavior of Ten Coffee Cultivars against Hemileia vastatrix in San Ramón (Chanchamayo, Peru)
by Ricardo Borjas-Ventura, Leonel Alvarado-Huaman, Viviana Castro-Cepero, Diana Rebaza-Fernández, Luz Gómez-Pando and Alberto Julca-Otiniano
Agronomy 2020, 10(12), 1867; https://doi.org/10.3390/agronomy10121867 - 26 Nov 2020
Cited by 4 | Viewed by 2638
Abstract
The objective of this research was to know the behavior of ten coffee cultivars against Hemileia vastatrix in San Ramón (Chanchamayo, Peru). The test was carried out from April 2017 to March 2018 at the Coffee Germplasm Bank, at the Regional Development Institute [...] Read more.
The objective of this research was to know the behavior of ten coffee cultivars against Hemileia vastatrix in San Ramón (Chanchamayo, Peru). The test was carried out from April 2017 to March 2018 at the Coffee Germplasm Bank, at the Regional Development Institute “La Génova” (San Ramón, Chanchamayo) of La Molina National Agrarian University. 10 cultivars were selected (Catimor, Pache, Mundo Novo, Pacamara, Caturra, Catuaí, Bourbon, Typica, Maragogype and Geisha), each one with 5 plants (2 × 1 m) of seven years of age, installed under the shade of trees of Inga sp. (12 × 12 m). For the statistical analysis, it was worked as a Completely Random Design, considering each cultivar as a treatment and each plant as a repetition. The severity was evaluated throughout a year, in the lower, middle and upper third of each plant, using a graphic scale. For the months with high severity, a comparison of means obtained in each third of the plant and for each variety was made. Then, the severity means obtained in each cultivar were compared. The results showed that the severity was different in each of the ten cultivars evaluated. Throughout the year, the highest severity values corresponded to the months of April, May and June 2017. The severity was greater in the lower third and was decreasing until the upper third of the plant, presenting statistically significant differences. Maragogype, presented the highest severity (15.9%) and Pacamara the lowest (1.3%), values that were also statistically different. Full article
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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Review

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19 pages, 1384 KiB  
Review
Coffee Leaf Rust in Brazil: Historical Events, Current Situation, and Control Measures
by Gustavo Hiroshi Sera, Carlos Henrique Siqueira de Carvalho, Juliana Costa de Rezende Abrahão, Edson Ampélio Pozza, José Braz Matiello, Saulo Roque de Almeida, Lucas Bartelega and Deila Magna dos Santos Botelho
Agronomy 2022, 12(2), 496; https://doi.org/10.3390/agronomy12020496 - 17 Feb 2022
Cited by 18 | Viewed by 5057
Abstract
In this review of coffee leaf rust (CLR) in Brazil, we report: (i) the historical introduction of CLR in Brazil and the first control measures; (ii) favorable environmental conditions and times of year for the disease; (iii) breeding methods and strategies used for [...] Read more.
In this review of coffee leaf rust (CLR) in Brazil, we report: (i) the historical introduction of CLR in Brazil and the first control measures; (ii) favorable environmental conditions and times of year for the disease; (iii) breeding methods and strategies used for developing CLR-resistant cultivars; (iv) the levels, sources, and types of CLR resistance; (v) the development of Brazilian resistant cultivars; and (vi) chemical and cultural control methods. Most plantations are cultivated with susceptible cultivars, such as those of the Catuaí and Mundo Novo groups. Brazilian research institutes have developed dozens of cultivars with different levels of resistance, and significantly increased the planting of new resistant cultivars. The main sources of CLR resistance are genotypes from Híbrido de Timor, Icatu, BA series carrying the SH3 gene, and Ethiopian wild coffees. High CLR resistance is still observed in Sarchimor and SH3-carrying genotypes. Intermediate CLR resistance is observed in Ethiopian wild coffees and in Sarchimor and Icatu derivatives, where qualitative resistance has been supplanted by races of Hemileia vastatrix. Contact, mesostemic, and systemic fungicides are used for chemical control in Brazil. CLR incidence in Brazil begins to increase after the rainy season onset in November, reaches a peak in June, and remains high until August. Thus, chemical control is typically applied from December to April. Full article
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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30 pages, 2595 KiB  
Review
An Overview of the Mechanisms Involved in Coffee-Hemileia vastatrix Interactions: Plant and Pathogen Perspectives
by Maria do Céu Silva, Leonor Guerra-Guimarães, Inês Diniz, Andreia Loureiro, Helena Azinheira, Ana P. Pereira, Sílvia Tavares, Dora Batista and Vítor Várzea
Agronomy 2022, 12(2), 326; https://doi.org/10.3390/agronomy12020326 - 26 Jan 2022
Cited by 19 | Viewed by 6691
Abstract
Coffee is one of the most consumed beverages in the world. It is also one of the most globally traded commodities. Coffee leaf rust (CLR), caused by the biotrophic fungus Hemileia vastatrix, is the most important disease affecting Arabica coffee growing worldwide, [...] Read more.
Coffee is one of the most consumed beverages in the world. It is also one of the most globally traded commodities. Coffee leaf rust (CLR), caused by the biotrophic fungus Hemileia vastatrix, is the most important disease affecting Arabica coffee growing worldwide, leading to significant yield losses if no control measures are applied. A deep understanding of the complex mechanisms involved in coffee-H. vastatrix interactions, such as the pathogen variability and the mechanisms governing plant resistance and susceptibility, is required to breed efficiently for durable resistance and design new approaches for crop protection. Here we summarize our current understanding across multiple areas related to pathogen infection, variability and candidate effectors, breeding for disease resistance, and the various components of the coffee immune system, by reviewing a comprehensive body of research on CLR and the advances recently made. We also update information about the defense responses activated by the application of plant resistance inducers, a promising alternative to fungicides in the control of CLR. Moreover, we identify and discuss future directions for further research. Full article
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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9 pages, 2279 KiB  
Review
Coffee Leaf Rust (Hemileia vastatrix) in Kenya—A Review
by Elijah Gichuru, Getrude Alwora, James Gimase and Cecilia Kathurima
Agronomy 2021, 11(12), 2590; https://doi.org/10.3390/agronomy11122590 - 20 Dec 2021
Cited by 17 | Viewed by 8282
Abstract
Coffee is one of the most important cash crops and beverages in the world. Production of coffee is limited by many factors, which include insect pests and diseases, among others. One of the most devastating coffee diseases in many coffee-producing countries is Coffee [...] Read more.
Coffee is one of the most important cash crops and beverages in the world. Production of coffee is limited by many factors, which include insect pests and diseases, among others. One of the most devastating coffee diseases in many coffee-producing countries is Coffee Leaf Rust caused by the fungus Hemileia vastatrix. Kenya is a coffee-producing country and has conducted studies to understand and manage the disease. Management strategies for the disease include the development and use of fungicide spray programs, cultural control practices, breeding resistant coffee varieties, and biological control agents. This paper reviews the status of the disease and management options applied in Kenya. Full article
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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14 pages, 590 KiB  
Review
Strategies for Coffee Leaf Rust Management in Organic Crop Systems
by Mário L. V. de Resende, Edson A. Pozza, Tharyn Reichel and Deila M. S. Botelho
Agronomy 2021, 11(9), 1865; https://doi.org/10.3390/agronomy11091865 - 17 Sep 2021
Cited by 16 | Viewed by 5539
Abstract
Coffee is a crop of great economic importance in many countries. The organic coffee crop stands out from other production systems by aiming to eliminate the use of synthetic fertilizers and pesticides. One of the most important limitations in the organic system is [...] Read more.
Coffee is a crop of great economic importance in many countries. The organic coffee crop stands out from other production systems by aiming to eliminate the use of synthetic fertilizers and pesticides. One of the most important limitations in the organic system is the management of diseases, especially coffee rust, which is considered the main disease of this crop. Coffee rust causes a production slump of up to 50%, significantly affecting the profitability of coffee growers. This work aims to review the integrated rust management in organic coffee crop in different producing countries. Regarding the disease management strategies, this review addresses the use of rust-resistant cultivars, cultural management, biological control, use of plant extracts, and chemical rust control by cupric fungicides. Considering the importance of the organic system, the increase in world coffee consumption, and the potential market for this kind of coffee, this review may help researchers and producers looking for alternative strategies to control rust in an organic coffee cultivation system. Full article
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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20 pages, 1007 KiB  
Review
Improving Pathogen Resistance by Exploiting Plant Susceptibility Genes in Coffee (Coffea spp.)
by Lei Cui, Katharina Hanika, Richard G. F. Visser and Yuling Bai
Agronomy 2020, 10(12), 1928; https://doi.org/10.3390/agronomy10121928 - 08 Dec 2020
Cited by 11 | Viewed by 5677
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Current Status and Management of Coffee Rust Disease)
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