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Precipitation anomalies (mm) in 2012 compared to the climate (1981-2010) for Central America. CHIRPS data (Climate Hazards Group InfraRed Precipitation with Station data, Funk et al. 2014) from ftp://chgftpout.geog.ucsb.edu/pub/org/ chg/products/CHIRPS-latest. M: Mexico; G: Guatemala; ES: El Salvador; H: Honduras; N: Nicaragua; CR: Costa Rica; P: Panama; C: Colombia
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Coffee rust is a leaf disease caused by the fungus, Hemileia vastatrix. Coffee rust epidemics, with intensities higher than previously observed, have affected a number of countries including: Colombia, from 2008 to 2011; Central America and Mexico, in 2012–13; and Peru and Ecuador in 2013. There are many contributing factors to the onset of these e...
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Context 1
... This is shown in Fig. 5 for Guatemalan coffee areas, where, in 2012, minimum daily temperatures increased by 0.9 °C, whereas maximum daily temperatures decreased by 1.2 °C on average. Anomalies were also reported for the 2012 wet season mean precipitation and variability, with lower rainfall amounts and higher variability ( Amador et al. 2013; Fig. 6). However, seasonal analysis using the CHIRPS dataset (Funk et al. 2014) shows positive rainfall anomalies for April to June (second trimester, end of the dry season and start of the rains) and negative during July to September (third trimester and most of the rainy season) for Guatemala. Honduras, Nicaragua and the Costa Rican high- ...
Context 2
... positive rainfall anomalies for April to June (second trimester, end of the dry season and start of the rains) and negative during July to September (third trimester and most of the rainy season) for Guatemala. Honduras, Nicaragua and the Costa Rican high- lands showed some positive anomalies during the fourth tri- mester (October to December; Fig. 6). In addition, stronger than normal winds occurred in July, due to El Niño conditions during the second and third trimesters ( Amador et al. 2013). In Colombia, La Niña conditions prevailed during the period 2008-2011. In Chinchiná, increased rainfall, decreased sun- shine duration and a decreased diurnal temperature range (due to an ...
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... Trends and variability assessments across homogeneous climatic zones of Pakistan from 1961 to 2017 found widespread significant changes linked with warming (except in JJA) throughout most of the regions investigated ( Fig. 3 and Table 3). These findings were consistent with several earlier research conducted on regional and global scales (Avelino et al. 2015;Blöschl et al. 2019;Mondal et al. 2015;Ullah et al. 2019a). It can be inferred from the current increasing temperature trends that the current warming over Pakistan will increase with greater magnitudes in the future Ullah et al. 2020b). ...
Rising temperature has increased the frequency, severity, length, and timing of temperature extremes around the globe. The
current study examined the spatiotemporal variation of Tmin, Tmax, Tmean, and diurnal temperature range (DTR) over
homogeneous climatic zones of Pakistan, using observed monthly datasets from fifty stations for the period 1961–2017. The
nonparametric modified Mann–Kendall (MMK), Sen’s slope estimator (SSE), and sequential Mann–Kendall (SQMK) tests
were utilized to investigate the spatiotemporal trends. Cluster analysis and the L-moment approach were used to identify
the homogenous climatic regions. In general, seasonal and annual Tmin, Tmax, Tmean, and DTR increased significantly in
most sub-regions and the whole country, whereas JJA observed significant decreasing trends in Tmin, Tmax, and Tmean
in most sub-regions during 1961–2017. Furthermore, decreasing trends prevailed in seasonal and annual Tmin in most
sub-regions and the whole country during 1961–1989, whereas increasing trends were evident during 1990–2017. Tmean
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°C/decade, respectively, in the whole country during 1990–2017. The SQMK results indicate that Tmin, Tmax, Tmean, and
DTR observed an increasing trend in DJF and MAM from 1985 onwards, and most of the regions observed significant trends
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... g for robusta [177]. 2012 and 2014 [8]. The first CLR reports in Hawaii appeared in 2020 [66,4]. ...
... • desiccation of young shoots and branches, which reduces the production for the following years [8]. ...
... Direct impacts include decreased quantity and quality of yield. In some cases, more than 70% of the coffee production is lost [58,8]. Indirect impacts include increased costs to control the disease. ...
Fungal diseases cause significant damages in crops and thus threaten global
food security. Fungicides are widely used, despite their negative impact on the environment and human health. In addition, they induce resistance that limits their long-term use. Alternative and sustainable control methods therefore need to be developed. This thesis contributes to this issue through a mathematical modelling approach. The models represent the seasonal dynamics of plant-fungus interactions and integrate a biological control method using hyperparasite releases.
The results obtained allowed to determine the quantity and frequency of releases necessary to control the disease. These results were applied to coffee leaf rust, a major coffee disease. Coffee being an important cash crop which provides a living for numerous small producers, controlling coffee leaf rust is a major socio-economic issue.
... Unfortunately, chemical-free strategies to manage or reduce the impacts of M. citricolor, as well as other pathogens, are very limited. Current approaches include farmers organizing for early detection of diseases, replacing the existing coffee plants with resistant varieties, and transitioning from synthetic fungicides to microorganism-derived compounds or biological control (Avelino et al. 2015). The latter has been favored in part by international certification agencies and international consumer markets, driving the coffee farmers to switch to greener practices (Pinto et al. 2014, Bravo-Monroy et al. 2016. ...
Aims:
The American leaf spot, caused by Mycena citricolor, is an important disease of coffee (Coffea arabica), mostly in Central America. Currently, there are limited pathogen control alternatives that are environmentally friendly and economically accessible. The use of fungi isolated from the plant endomycobiota in their native habitats is on the rise because studies show their great potential for biological control. To begin to generate a green alternative to control M. citricolor, the objectives of the present study were to (i) collect, identify, screen (in vitro and in planta), and select endophytic fungi from wild Rubiaceae collected in old-growth forests of Costa Rica; (ii) confirm endophytic colonization in coffee plantlets; (iii) evaluate the effects of the endophytes on plantlet development; and (iv) corroborate the antagonistic ability in planta.
Methods and results:
Through in vitro and in planta antagonism assays, we found that out of the selected isolates (i.e., Daldinia eschscholzii GU11N, Nectria pseudotrichia GUHN1, Purpureocillium aff. lilacinum CT24, Sarocladium aff. kiliense CT25, Trichoderma rifaii CT5, T. aff. crassum G1C, T. aff. atroviride G7T, T. aff. strigosellum GU12, and Xylaria multiplex GU14T), Trichoderma spp. produced the highest growth inhibition percentages in vitro. Trichoderma isolates CT5 and G1C were then tested in planta using Coffea arabica cv. caturra plantlets. Endophytic colonization was verified, followed by in planta growth promotion and antagonism assays.
Conclusions:
Results show that Trichoderma isolates CT5 and G1C have potential for plant growth promotion and antagonism against Mycena citricolor, reducing incidence and severity, and preventing plant mortality.
... Smallholder farmers, typically with landholdings of 5 hectares or less, dominate production across most of the main cultivation regions [4,5]. Specifically, In Colombia, the second-largest coffee producer in the world and the focus of this study, smallholder farms are the main coffee growing method [6]. ...
... The CTR spread, as well as the coffee trees' berries production, depend on multiple environmental and climate processes [85,86,87]. In particular, temperature, humidity, and rain are considered to be the primary ecological properties to have a direct influence on the CTR pandemic spread [88,6,89]. Formally, these three processes are represented using three time-series vectors C T (t), C H (t), and C R (t), respectively. Due to the complexity of associating these three ecological processes with the tree level CTR pandemic spread, we utilize a machine learning approach to learn the association between the two. ...
... Hence, if we consider the increase in costs in moving from one to two hectares, assuming that the cost shown in Table 1 is for the first hectare, and the amount of coffee bags will increase from 21.4 to 42.8, when the scale coefficient α is 0.6, we will get (according to the rule (T C v /T C v+1 ) = (Q v /Q v+1 ) α ) that the total cost will increase by $11711 to reach $5028.8. However, these costs are only correct for a season without 4 https://easyhomecoffee.com/does-coffee-grow-all-year-round/ 5 https://federaciondecafeteros.org/wp/coffee-statistics/?lang=en 6 The data is obtained from https://www.meteoblue.com/en/weather/archive/climatePredictions/colombia_colombia_ 3686120 7 https://federaciondecafeteros.org/wp/listado-noticias/colombian-coffee-production-closed-2019-at-14-8-million-bags/?lang=en a CTR outbreak. ...
Coffee tree leaf rust is a prevalent botanical disease that causes a worldwide reduction in coffee supply and its quality, leading to immense economic losses. While several pandemic intervention policies (PIPs) for tackling this pandemic are commercially available, they seem to provide only partial epidemiological relief for farmers. In this work, we develop a high-resolution economical-epidemiological model that captures the pandemic's spread in coffee tree farms and its associated economic impact. Through extensive simulations for the case of Colombia, a country that consists mostly of small-size coffee farms and is the second-largest coffee producer in the world, our results show that it is economically impractical to sustain any profit without directly tackling the pandemic. Furthermore, even in the hypothetical case where farmers perfectly know their farm's epidemiological state and the weather in advance, any pandemic-related efforts can only amount to a limited profit of roughly 4% on investment. In the more realistic case, any pandemic-related efforts are expected to result in economic losses, indicating that major disturbances in the coffee market are anticipated.
... Over the following decades, CLR led to the collapse of the coffee industry in several Asian countries, such as India and Indonesia (Java Island) was also dramatically affected. CLR disease causes premature leaf fall due to direct damage, weakening and favouring dieback of branches, decreasing the photosynthetic capacity and vigour of the infected coffee plants [1,9,10]. The introduction of coffee species with higher tolerance to CLR, following its devastating impact on C. arabica plantations, led to the resurgence of coffee production in Asia. ...
To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, the whole genome of 42 coffee genotypes was sequenced and de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid Híbrido de Timor (HDT). Individual reads were aligned on the C. arabica reference to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled to discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (inherited from C. canephora ). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. This is the first time that specific DNA variants allow discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.
... Cup quality combined with disease resistance is one of the main objectives of genetic breeding of coffee trees. The species C. arabica is the one most severely attacked by the fungus Hemileia vastatrix, the etiological agent of coffee leaf rust, symptoms of which range from defoliation to branch death (Avelino et al. 2015). Rust may limit coffee production in Brazil up to 50% depending on the genotype resistance level (Capucho et al. 2013). ...
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.
... Direct impacts include decreased quantity and quality of yield. In some cases, more than 70% of the coffee production is lost [25,26]. Indirect impacts include increased costs to control the disease. ...
Fungal diseases cause serious damages in crop worldwide. In particular, coffee leaf rust (CLR), caused by fungus Hemileia vastatrix attacks coffee leaves and reduces coffee yield. This paper presents a multi-seasonal model of the CLR development in the coffee plantation with continuous dynamics during the rainy season and a discrete event to represent the simpler dynamics during the dry season. Biological control using predators through one or more discrete introduction events over the year is then added. Analytical and semi-numerical studies are performed to identify how much and how frequently predators need to be introduced through the definition of a threshold value, as a function of various parameters. We show that the best strategy to efficiently control the disease depends on the predator mortality: low mortality parasites need be released only once a year, while high mortality parasites should be released more frequently to ensure their persistence in the plantation. This work hence provides qualitative and quantitative bases for the deployment of predator-based biocontrol, a promising alternative to fungicides for rust control.
... The use of fungicides, in addition to reducing the producer's profits, has adverse effects on both the environment and the consumer [7][8][9]. In the absence of fungicide control, coffee leaf rust can develop and lead to a loss in yield of 30-50% [8,10]. Coffee berry disease (CBD) (caused by C. kahawae), a disease restricted to Africa, has led to production losses of 50-80% when disease management was not implemented. ...
... This strategy can be used to accumulate resistance alleles against the same and/or different diseases for generating broad-spectrum resistance and ensuring the durability of disease resistance [12,13]. In resistance allele pyramided cultivars, it is more complex for pathogens to overcome the multiple resistance alleles because they require multiple virulence gene mutations [10] to facilitate the infection. ...
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.
... Both questions have been studied within the "disease triangle" framework (Stevens, 1960). In this sense, scientists and farmers have studied the pathogen's properties such as its genetics (Carvalho et al., 2011), the host resistance and phenology (Avelino et al., 1993;Silva et al., 2006), and disease environmental drivers such as the temperature, humidity or precipitation (Avelino et al., 2015). Nevertheless, there is a large amount of variability in the intensity and timing of the different epidemiological phases of the coffee rust epidemic that remains unexplained, even between neighbouring coffee plots with the same environmental and biotic conditions (Li et al., 2022). ...
... Dispersal is the process by which spores are transported from one place to another, across different scales, ranging from the intraleaf, interleaf, or even the interplot scale (Becker and Kranz, 1977;Boudrot et al., 2016;Vandermeer et al., 2018). Overall, the intensity of an epidemic is highly related to the rates of infection and dispersal during each season (Avelino et al., 2015). Analysis of dispersal is thus called for, and, by its very nature, must incorporate a spatial approach (Avelino et al., 2012). ...
One central issue in coffee-leaf rust (Hemileia vastatrix) epidemiology is to understand what determines the intensity and the timing of yearly infections in coffee plantations. However, most experimental and theoretical studies report infection as an average at the plot level, obscuring the role of potentially key factors like rust dispersal or the planting pattern. Here, we first review the rust epidemic patterns of different sites, which reveal large variability in the duration and magnitude of the different epidemiologic phases. We then present a spatially explicit and parametrised model, where the host population is subdivided into discrete patches linked through spore dispersal, modeled as simple diffusion. With this model, we study the role of the planting arrangement, the dispersal intensity and plant-level variables on the maximum average tree infection (MATI) and its timing. Our results suggest that the epidemic timeline can be divided into two phases: a time lag and a growth phase per se. The model shows that the combination of the dispersal magnitude and plant aggregation modifies the MATI and the time to MATI, mainly by preventing some plants from reaching their maximum peak during the epidemic. It also affects the epidemic curves, which can have a stepped, or a rather smooth pattern in plots with otherwise similar conditions. The initial rust infection modulates the time lag before the epidemic and the infected leaf-fall rate drastically changes the MATI. These findings highlight the importance of explicitly considering the spatial aspects of coffee agroecosystems when measuring and managing rust infection, and help us to further understand the spatio-temporal dynamics of ecological systems in general.
... Coffee leaf rust (CLR) is one of the diseases that Volumen 35 (2023) BIOAGRO N° 1 causes the most damage to coffee plants (Gichuru et al., 2012) since it can cause from 30 to 100 % yield loss (Piato et al., 2020). CLR is caused by the fungus Hemileia vastatrix, a parasite that affects the coffee leaves by infecting the lower surface (Avelino et al., 2015), where it produces large colonies of orange spores, leading to premature leaf fall (Talhinhas et al., 2017). In recent years, high intensity coffee rust epidemics have affected several Latin American countries, including Peru in 2013 (Avelino et al., 2015), with losses of approximately 60 % of the total harvest (Julca et al., 2019). ...
... CLR is caused by the fungus Hemileia vastatrix, a parasite that affects the coffee leaves by infecting the lower surface (Avelino et al., 2015), where it produces large colonies of orange spores, leading to premature leaf fall (Talhinhas et al., 2017). In recent years, high intensity coffee rust epidemics have affected several Latin American countries, including Peru in 2013 (Avelino et al., 2015), with losses of approximately 60 % of the total harvest (Julca et al., 2019). This crisis revealed the lack of technical training in the agronomic management of plantations for smallholder coffee farmers that allows them to implement measures against CLR (Borjas et al., 2020). ...
Coffee leaf rust (CLR) is a fungal infection which is devastating susceptible coffee plantations throughout the South American region in the last years. The objective of this study was to analyze the effects of shade trees management and pruning in two coffee varieties against coffee leaf rust in the Peruvian Amazon. The experimental design was a randomized complete block with factorial scheme 2A×2B×4C with 16 treatments and four repetitions, making a total of 64 experimental units, in which each experimental unit had 16 coffee plants. The studied factors were agroforestry system (A), coffee varieties (B), and pruning methods (C). The data were statistically examined by analysis of variance and mean comparisons using Tukey test. It was found that plant growth was favored by the use Inga shade and recepa pruning in Typica variety. Also, the use of polyculture-shaded coffee with about 40 % of shadow, and recepa, a pruning method which consists of cutting the stem of the coffee plants at 40 cm from the ground, reduce the incidence and severity of CLR in coffee plants. The incidence and severity of CLR was lower in the Typica variety as comparted to Pache variety. This study confirms that a shadow management and pruning coffee plants stimulate the growth of new branches and reduce incidence and severity of CLR in coffee plantations.
