Botanic Gardens Trust, Sydney, Australia

Plant Pathology & Mycology 2008-2009

Dr Edward Liew - Manager Plant Pathology and Arthur Pinaria – PhD Student

On-going research in the plant pathology and mycology section includes documenting and describing foliar diseases of members of the Proteaceae and Myrtaceae, describing new species of the fungal genus Fusarium, understanding the biogeography and evolution of soil inhabiting and endophytic species of Fusarium, studying movement and distribution of economically significant Fusarium pathogens and investigating disease management strategies for a range of diseases incited by the water mould Phytophthora, including root rot of Wollemi Pine.

Research Highlight

Members of the Fusarium oxysporum species complex are some of the most economically significant soil borne plant pathogens, causing crop disease epidemics in over 150 plant species worldwide. F. oxysporum f.sp. vanillae causes vanilla stem and root rot, a devastating disease and a major constraint to vanilla cultivation in vanilla producing countries, including Indonesia. 

The Royal Botanic Gardens & Domain Trust’s pathology and mycology team have been an integral part of an international development program in building plant disease diagnostic and research capacity in North Sulawesi, Indonesia since 2001. With the foundational work of establishing laboratory and greenhouse facilities, conducting disease surveys and facilitating training workshops completed in the initial part of the program, in recent years the team have been focussing on research related to key diseases, one of which is vanilla stem and root rot.

Understanding the origins, movement and variations of the pathogen population is essential in ultimately establishing sustainable long term disease management strategies. To facilitate population analysis of this pathogen, we obtained a large collection of F. oxysporum f.sp. vanillae isolates, representing subpopulations of this pathogen from major vanilla growing regions throughout Indonesia. 
 
Our DNA fingerprinting analysis based on Randomly Amplified Microsatellites (RAMS) revealed a total of 16 haplotypes in the whole population. A large proportion of the individuals were clonal, i.e. genetically identical belonging to just two haplotypes, a common scenario for an asexual haploid fungus. The total number of 16 haplotypes was still unexpectedly high, indicating a significant amount of genetic diversity present. Analysis of the spatial dynamics of this pathogen indicated a high level of gene flow between subpopulations, although one geographical subpopulation was genetically well differentiated. These findings give a good indication of how the pathogen is spread throughout the different growing regions, the potential for further spread, and the type of control strategies needed.
 
On the other hand, these findings led us to wonder about the origin of the pathogen in Indonesia where vanilla is not native but a recently introduced crop. We then compared our isolates of F. oxysporum f.sp. vanillae with those from the Reunion and Comoro Islands, two well-established vanilla producing countries where the same disease has been observed, as well as from Mexico, where vanilla is believed to have originated. We found that most of the Indonesian haplotypes, including the large clonal ones, shared the same lineage as the isolates from Mexico and the Indian Ocean Islands. Three haplotypes, however, were shown to have derived from two separate lineages distinct from the main lineage. These distinct lineages coincided with lineages thought to be ancestral within the overall F. oxysporum species complex by other research groups and generally believed to be associated with the South East Asian region.

We demonstrated that the vanilla stem and root rot pathogen in Indonesia evolved from multiple unrelated lineages. It was most probably brought into Indonesia together with the introduction of the host plant or the various germplasms imported over the years. We also have evidence to suggest that a secondary source of the pathogen could be from the surrounding region or even evolved from within Indonesia.

vanilla-vines
Vanilla vines growing on Glyricidia shade trees. Photo: Arthur Pinaria

vanilla-stem-rot
Symptoms of vanilla stem and root rot include yellow and brown stem lesions progressing along the vine. Photo: Arthur Pinaria

culture
A culture of the vanilla stem and root rot pathogen, Fusarium oxysporum f.sp. vanillae, growing on a Petri dish. Photo: Arthur Pinaria

map
Map of Indonesia indicating the major vanilla growing provinces
sampled in our studies. Map: Dr Edward Liew

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