Study on First Establishments, Expansion Pathways, and Management of Coffee Leaf Rust Disease in Vietnam

概要

Leaf rust is a devastating fungal disease in coffee production worldwide. The epidemics of
coffee leaf rust (CLR) were not random occurrences in the world but closely related to the
historical cultivation of coffee, wind, and human activities in the past. Historically, large
numbers of research related to CLR conducted globally indicate the paramount importance of
this disease in coffee production. Even though Vietnam, the global second-biggest producer,
has a long history of coffee production since 1857, and the rust was first detected in northern
Vietnam in 1890; however, coffee leaf rust has only been indicated in several reports. The actual
occurrence, and distribution of the disease as well as the causative pathogenic agent have not
been investigated. On the other hand, studies on controlling the disease are still being omitted
in Vietnam. Fungicides including Qo inhibitors (QoI) were applied in Vietnam and other
countries to control this disease. QoIs resistance has occurred in other rust fungi recently
reminds us of the necessity to investigate the fungicide-resistant matter in this fungus. Therefore,
the purpose of this study is to investigate the current situation of rust, evaluate the genetic
differentiation in the genome of pathogenic agents, and then, propose the appropriate
approaches to control this disease in Vietnam.
Three regions were chosen for the survey, i.e., the Southeast, Central Highlands, and
Northwest. Samples of CLR were collected, evaluated for disease severity and then identified
pathogenic agents based on morphological features and nuclear ribosomal DNA internal
transcribed spacer (rDNA-ITS) region. After that, based on genetic variation in the ITS region,
possible original sources and subsequent expansion pathways of wind-borne and human-aided
urediniospores of the CLR fungus were estimated. Furthermore, to investigate the mutation in
CYTB gene, three polymerase chain reaction (PCR) primer pairs were designed to amplify
exons 2 to 4 and applied to dried specimens from Vietnam.
Field surveys conducted at eighty-five plantations across three main coffee planting regions
showed coffee leaf samples infected by the rust fungus in forty-one plantations from South to
North, and from low altitudes to high mountainous areas. The field observation also indicated
that all coffee species and cultivars planted in Vietnam now are susceptible to rust disease.
Especially, Coffea arabica cv. Catimor varieties exhibited high levels of susceptibility with
severe rust symptoms, while Coffea canephora varieties had varying degrees of susceptibility.
Urediniospores of all isolates had tightly clustered spines on the borderline between echinulate
and smooth areas and similarity values in ITS region from 96% to 100% with Hemileia vastatrix.
Therefore, the pathogenic agent causing CLR disease in Vietnam was identified as H. vastatrix.
Further analyses of ITS region from 83 samples (41 sequences from Vietnam, 2 from Thailand,
and the remaining 40 from American countries) indicated that H. vastatrix populations from
Vietnam and those from Central and South American countries (Mexico and Brazil) have very
close relationships. In addition, there is no clear genetic structure in H. vastatrix population
with respect to the geographic regions surveyed.The low genetic distance recorded between
populations in Vietnam proves that the probability of migration between these regions was high.
Moreover, most ancestral haplotypes are present in the Northwest, and the percentage of those
ancestral haplotypes in the Northwest is larger than that in other regions. The phylogeographic
tree of these isolates also showed that H. vastatrix in the Northwest had a close genetic
relationship with those from other regions in Vietnam. Therefore, the Northwest was
hypothesized as the first establishment of CLR in Vietnam. Besides, based on the haplotype
network and neighborNet analysis, other branches of CLR in Vietnam were initiated in the
Central Highlands. Analyses of the CYTB gene of H. vastatrix isolates from Vietnam showed
no nucleotide mutations in exons 2 and 3. ...

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