Plant pathogens are key threats to agriculture and global food security, causing various crop diseases that lead to massive economic losses. Palm oil is a commodity export of economic importance in Southeast Asia, especially in Malaysia and Indonesia. However, the sustainability of oil palm plantations and production is threatened by basal stem rot (BSR), a devastating disease predominantly caused by the fungus Ganoderma boninense Pat. In Malaysia, infected trees have been reported in nearly 60% of plantation areas, and economic losses are estimated to reach up to ~USD500 million a year. This review covers the current knowledge of the mechanisms utilized by G. boninense during infection and the methods used in the disease management to reduce BSR, including cultural practices, chemical treatments and antagonistic microorganism manipulations. Newer developments arising from multi-omics technologies such as whole-genome sequencing (WGS) and RNA sequencing (RNA-Seq) are also reviewed. Future directions are proposed to increase the understanding of G. boninense invasion mechanisms against oil palm. It is hoped that this review can contribute towards an improved disease management and a sustainable oil palm production in this region.

Basal stem rot (BSR) disease caused by pathogenic fungus Ganoderma boninense is a significant concern in the oil palm industry. G. boninense infection in oil palm induces defense-related genes. To understand oil palm defense mechanisms in response to fungal invasion, we analyzed differentially expressed genes (DEGs) derived from RNA-sequencing (RNA-seq) transcriptomic libraries of oil palm roots infected with G. boninense. A total of 126 DEGs were detected from the transcriptomic libraries of G. boninense-infected root tissues at different infection stages. Functional annotation via pathway enrichment analyses revealed that the DEGs were involved in the defense response against the pathogen. The expression of the selected DEGs was further confirmed using real-time quantitative PCR (qPCR) on independent oil palm seedlings and mature palm samples. Seven putative defense-related DEGs consistently showed upregulation in seedlings and mature plants during G. boninense infection. These seven genes might potentially be developed as biomarkers for the early detection of BSR in oil palm.

The coconut cadang-cadang viroid (CCCVd) is the causal agent of orange spotting (OS) disease in commercial oil palm (Elaeis guineensis) plantations in Malaysia. At present, the methods used to detect OS are time-consuming and can be inaccurate. Here, we describe the development of a rapid, sensitive and specific method of detecting CCCVd variants in oil palm leaves using a reverse transcription loop-mediated isothermal amplification (RT-LAMP) method. RT-LAMP detected CCCVd variants at a concentration of 2 ng mu l(-1) in less than 1 hr at 63 degrees C using total ribonucleic acid (RNA) of leaf extracts; whereas a minimum of 20 ng mu l(-1) was required to detect CCCVd using conventional polymerase chain reaction (PCR). The utility of RT-LAMP as OS detection in plantations was evaluated using symptomatic and asymptomatic oil palm leaf samples from nurseries and field sites. RT-LAMP successfully detected CCCVd in OS-infected samples. Leaves with OS-like symptoms caused by nutrient deficiencies or leaf spot disease other than OS produced a negative result. The RT-LAMP results were confirmed by conventional PCR, indicating that RT-LAMP is a valuable tool, sensitive and rapid method of diagnosing OS in oil palm plantations that could be performed by plantation personnel for OS disease management in oil palm plantations.