1Indonesian Research Institute for Coconut and Palmae, Manado, Indonesia; 2CABI Bioscience, Bakeham Lane, Egham, UK

Background and objectives
The production of coconut and copra is an extremely important activity in Indonesia and across SE Asia/Pacific region with production of copra in Indonesia being 2,342,00 tonnes p.a. (26% of world production) from 3,418,00 acres. (32% of world coconut area). Of this, the great majority of production is by smallholders with coconut generally underplanted with other cash and food crops, notably doubling as a shade tree for cocoa. Budrot and premature nutfall, caused by Phytophthora species [1] (mainly P. palmivora), are the major disease problems affecting coconut in Indonesia and account for extensive losses of both stands and nut production. In some areas stand losses of 43% can occur due to bud rot (a decay in the terminal meristem, resulting in death of the palm) while premature nutfall, which is the more common disease, affects nut of 3-7 months old. From field observations and inoculation, studies some varieties have been found to be resistant in Sulawesi, but knowledge of the variation in the pathogen populations is required for successful resistance breeding programmes. Also, the development of molecular genetic tools for Phytophthora characterisation will enable the detection of individual isolates to support epidemiological studies in the field and hence, determine disease spread.

Materials and method
Over 150 Phytophthora isolates were obtained from diseased palms, buds and from soil samples under palm cultivation between 1990-98. These populations focused on disparate locations within Indonesia and extensive sampling of a few selected plantations in 1997/98. Representative isolates of closely related Phytophthora spp were also included for comparative purposes. Characterisation of strains focused on genomic fingerprinting of amplified fragment length polymorphisms (AFLPs). The method applied was adapted from Mueller et al. [2]: adapters were designed to a single restriction enzyme, Pst1; 2 and 3 base extensions to the adapter were used as PCR primers and the products were separated by standard agarose gel electrophoresis. Studies on classical morphological, physiological and mating type were also undertaken.

Results and discussion
At the outset of this research it was recognised from previous studies that P. palmivora was a fairly homogeneous pathogen, and hence, it would be necessary to develop a sensitive method of strain characterisation. The relatively new method of AFLP was selected as this offers sensitivity and reproducibility; facets that are hard to achieve in other PCR based methods. However, the commonly used methods of AFLP require electrophoresis of the amplified product on a denaturing gel such as those used for DNA sequencing. This equipment was not available, so an alternative AFLP method that produced fewer and larger PCR products that were visible by standard agarose gel electrophoresis was evaluated. This method gave highly sensitive and reproducible results. Initial studies identified significant genomic variants within the populations obtained. These data will be analysed with the aim of identifying biological groupings that delineate biogeographic distributions and functional traits such as pathogenicity, host range and morphology. This knowledge on the structure of indigenous populations will also underpin epidemiological studies on the spread and dynamics of populations within plantations.

1. Warokka JS & Thevenin JM 1994. In Coconut Phytphthora Workshop Proceedings, Manado, Indonesia 1992, CIRAD-CP, Montpellier, France, pp. 71-74.
2. Mueller UG, Lipari SE & Milgroom MG 1996. Molecular Ecology 5, 119-122.