Dataset Information

Modelling coffee leaf rust risk in Colombia with climate reanalysis data.

ABSTRACT: Many fungal plant diseases are strongly controlled by weather, and global climate change is thus likely to have affected fungal pathogen distributions and impacts. Modelling the response of plant diseases to climate change is hampered by the difficulty of estimating pathogen-relevant microclimatic variables from standard meteorological data. The availability of increasingly sophisticated high-resolution climate reanalyses may help overcome this challenge. We illustrate the use of climate reanalyses by testing the hypothesis that climate change increased the likelihood of the 2008-2011 outbreak of Coffee Leaf Rust (CLR, Hemileia vastatrix) in Colombia. We develop a model of germination and infection risk, and drive this model using estimates of leaf wetness duration and canopy temperature from the Japanese 55-Year Reanalysis (JRA-55). We model germination and infection as Weibull functions with different temperature optima, based upon existing experimental data. We find no evidence for an overall trend in disease risk in coffee-growing regions of Colombia from 1990 to 2015, therefore, we reject the climate change hypothesis. There was a significant elevation in predicted CLR infection risk from 2008 to 2011 compared with other years. JRA-55 data suggest a decrease in canopy surface water after 2008, which may have helped terminate the outbreak. The spatial resolution and accuracy of climate reanalyses are continually improving, increasing their utility for biological modelling. Confronting disease models with data requires not only accurate climate data, but also disease observations at high spatio-temporal resolution. Investment in monitoring, storage and accessibility of plant disease observation data are needed to match the quality of the climate data now available.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

SUBMITTER: Bebber DP

PROVIDER: S-EPMC5095537 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Modelling coffee leaf rust risk in Colombia with climate reanalysis data.

Bebber Daniel P DP Castillo Ángela Delgado ÁD Gurr Sarah J SJ

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 20161201 1709

Many fungal plant diseases are strongly controlled by weather, and global climate change is thus likely to have affected fungal pathogen distributions and impacts. Modelling the response of plant diseases to climate change is hampered by the difficulty of estimating pathogen-relevant microclimatic variables from standard meteorological data. The availability of increasingly sophisticated high-resolution climate reanalyses may help overcome this challenge. We illustrate the use of climate reanaly ...[more]

PMID: 28080984

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Project description: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.

Dataset Information

Modelling coffee leaf rust risk in Colombia with climate reanalysis data.

Publications

Modelling coffee leaf rust risk in Colombia with climate reanalysis data.

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