CDNA-SSR markers for molecular epidemiology of ganoderma boninense

Abstract

Basal stem rot (BSR) caused by Ganoderma boninense is the most devastating and yield-limiting disease for the oil palm industry in South-east Asia. Information on the population biology of G. boninense for testing important hypotheses concerning BSR infection is lacking. This article describes the development of the most discerning molecular marker to date, i.e. cDNA-SSR, in an attempt to evaluate the genetic diversity and epidemiology of G. boninense. The Belitung Island in Indonesia was chosen for this study because it has BSR disease spread in first generation plantings of oil palm, and geographically not connected to the Sumatra main island. There are considerable field experiences alongside the indepth genetic analyses presented here. The basidiocarps of Ganoderma collected from BSR and upper stem rot (USR) infected oil palm were confirmed as G. boninense by phylogenetic analysis. The marker data inferred that the G. boninense isolates were very diverse, with heterozygosity of 0.777, reflecting random mating and the outcrossing nature of this fungus. Clonal spread was not found in the present study and isolates were genetically different, from palm to palm. The hierarchical cluster analysis and distance-standardised principal coordinates analysis suggested G. boninense spread from the coastal region (north) to inland areas (south) on Belitung Island. Despite the very small sample size, the thorough analyses revealed major shortcomings and difficuties in developing a set of polymorphic cDNA-SSR markers for epidemiology of G. boninense.