Oil palm (Elaeis guineensis Jacq.) is a cornerstone of the global vegetable oil industry, with Indonesia as the leading producer. Oil palm cultivation faces a serious challenge from basal stem rot (BSR), a destructive disease predominantly caused by the pathogenic fungus Ganoderma boninense Pat. In addition to BSR, Ganoderma also induces upper stem rot (USR). Both diseases cause worsening yield losses, accelerating palm collapse, and shortening plantation lifespans. Despite the implementation of various control strategies, including land preparation, early detection, and biocontrol agents, the spread of these diseases has remained largely unrestricted. A critical knowledge gap concerning the genetic diversity of Ganoderma and its geographical distribution hinders the development of effective control measures, including the breeding of planting material with true tolerance to Ganoderma. This study investigates the genetic diversity and population structure of Ganoderma spp. across five provinces in Sumatra, Indonesia. A total of 228 pathogenic isolates were collected from living oil palm and identified as Ganoderma by sequencing of the internal transcribed spacer (ITS) regions. North Sumatra was identified as a hotspot with an average infection rate of 27.3% across sampling sites, followed by Riau (1.1%), Aceh (1.0%), West Sumatra (0.4%), and Jambi (0.1%). Of these, 166 isolates were identified as Ganoderma boninense (72.8%), 19 as Ganoderma orbiforme (8.3%), and 43 as Ganoderma sp. (18.9%). The results demonstrate that Ganoderma, particularly G. boninense, is the source of both USR and BSR, which primarily spread by basidiospores. Although, other transmission routes, such as root-to-root contact and infected plant debris, are also recognized as important in its epidemiology. Phylogenetic analysis further revealed genetic variations among the isolates, which is characteristic of a sexually reproducing organism. The Ganoderma isolates were clustered into four major clades based on the phylogenetic tree analysis. These clades included both USR- and BSR-causing types, which were found across five different provinces. Further analysis via genome-based sequencing (GBS) will provide a more detailed view of the pathogen population structure. These findings improve our understanding of Ganoderma spp. distribution and diversity, providing critical data for transmission epidemiology. Furthermore, this research serves as a foundation for developing more effective management strategies and fostering oil palm tolerance to BSR, ultimately enhancing the long-term sustainability of the oil palm industry.
Keywords: Basal Stem Rot; Upper Stem Rot; Elaeis guineensis; Ganoderma boninense; molecular identification.