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Basal Stem Rot (BSR) disease caused by Ganoderma boninense pathogen, is a significant disease in oil palm-producing countries. In Malaysia and Indonesia, the disease attacks on a massive scale in oil palm plantations. Various methods of assessment have been explored on the disease in oil palm plantations. However, none of the measures have yielded an absolute solution. Therefore, this research analysed BSR disease and the resulting plant physiology reaction through water use efficiency (WUE) in oil palm trees to provide a comprehensive understanding of both conditions. The study sought to evaluate WUE performance for mature oil palm trees in varying BSR disease severity and suggested a novel model assessment from WUE for BSR disease severity. Based on the overall result, the WUE parameters were affected by BSR severity in different levels, especially when being compared between healthy (T0) and affected (T1, T2, T3) categories. Secondly, the correlation between WUE with different variables, Photosynthetic Rate (Pr), Transpiration Rate (Tr), Temperature Leaf (TempL), Intercellular CO2 Concentration (Ci), Stomata Conductance (gs), and Chlorophyll Content (F), for frond 9 and frond 17 corresponded to the BSR disease severity. By performing a correlation analysis, a high correlation (0.5 and −0.5) was observed between these variables in both frond levels except in the Chlorophyll Content (F) variables (positive low correlation). Thirdly, the variables that contributed significantly to the WUE performance in mature oil palm included Pr, Tr, and Ci. Specifically, Pr was the highest value in both frond levels while Tr and Ci were inconsistent and ranked second and third place in different frond levels, respectively. Finally, the WUE model developed provides a significant result in BSR disease severity with RMSE (0.54–0.19, 0.48–0.32) for training and validation models respectively. The model order is sorted into Model 1, Model 2, Model 3, and Model 4 in ascending order based on the RMSE accuracy assessment. [ABSTRACT FROM AUTHOR]

Understanding the microbial communities in asymptomatic oil palm seedlings is crucial for developing disease-suppressive microbiota against basal stem rot (BSR) in oil palm. In this study, we compared the microbial communities in bulk soil, rhizosphere, and endosphere of control, asymptomatic, and symptomatic seedlings following inoculation with Ganoderma boninense. Our findings revealed significant shifts in microbial structure and interactions, particularly in asymptomatic seedlings. Both Actinobacteriota and Ascomycota were notably enriched in these samples, with Actinobacteriota identified as keystone taxa. Long-read shotgun metagenomics demonstrated that 67.4% of enriched Actinobacteriota taxa were unique to asymptomatic seedlings. Similarly, Ascomycota members showed significant enrichment, suggesting their potential role in BSR suppression. The consistent identification of these phyla across various analyses underscores their importance in disease resistance. This is the first report detailing the shifts in prokaryotic and fungal communities in asymptomatic and symptomatic seedlings, offering insights into potential disease-suppressive taxa across three compartments: bulk soil, rhizosphere, and endosphere of oil palm seedlings. [ABSTRACT FROM AUTHOR]

The determination of transcript accumulation values significantly affects gene expression in oil palm. Various genes are involved in pathogen infection, including probable 2‐oxoglutarate‐dependent dioxygenase At5g05600 (EgUnk3), zinc finger protein 2‐like (EgZFP2), and inositol polyphosphate multikinase beta‐like (EgIPK2b). Gene expression is typically measured using relative quantitative methods to calculate differences in quantitative values in the expression levels of targeted genes compared to a reference gene. However, the effectiveness of these methods in assessing the expression of EgUnk3, EgZFP2, and EgIPK2b, which are involved in Ganoderma boninense infection in oil palm seedlings, requires evaluation. This study aimed to establish an effective and straightforward method for analyzing the expression of EgUnk1, EgZFP2, and EgIPK2b genes in oil palm seedlings infected with G. boninense, utilizing Ct value correction through regression coefficients on the 2‐ΔΔCt and E‐ΔΔCt approaches. A correlation regression revealed values of 0.28, ‐0.32, and 0.29 for delta Ct of EgUnk1, EgZFP2, and EgIPK2b, respectively. However, a negative correlation in the Ct mean was corrected by linear regression for the targeted genes: ‐0.55, ‐0.81, and ‐0.29 for EgUnk1, EgZFP2, and EgIPK2b, respectively. The amplification factor (E) and efficiency value (R) using the EgActin gene were 1.95 and 94.92%, respectively. Normalization of log10 on the fold change value 2‐ΔΔCt and 1.95‐ΔΔCt approaches using the regression coefficient yielded consistent results for the EgUnk1, EgZFP2, and EgIPK2b genes. Overall, EgUnk3 and EgIPK2b genes exhibited downregulated expression in susceptible oil palm seedlings (‐0.60 for 2(‐ΔΔCt) and ‐0.58 for 1.95(‐ΔΔCt)), whereas EgIPK2b gene showed up‐regulated and the highest value in inoculated resistant seedlings (1.39 for 2(‐ΔΔCt) and 1.34 for 1.95(‐ΔΔCt)). Basal stem rot disease (BSR) in oil palm decreased EgUnk1 and EgIPK2b expression in susceptible seedlings but increased EgZFP2 gene expression in resistant ones. The results of this research provide valuable corrections to Ct values obtained directly from RT‐qPCR machines using simple linear regression. Consequently, the Ct values of target genes and reference genes exhibit smaller bias values, rendering gene expression levels more reliable.

Ganoderma boninense , the causative agent behind basal stem rot (BSR) disease in oil palm, instigated a pressing need for innovative and ecologically sustainable strategies to counter its impact. Biological control strategies, particularly employing bio-fungicides, have emerged as environmentally friendly alternatives for managing oil palm plant diseases. This study delved into harnessing the biocontrol potential of Indigenous bacterial isolate by investigating and evaluating its bioactive compounds of ethyl acetate extract with the capacity to suppress G. boninense growth in oil palm plants. Molecular identification was utilized to identify of bacterial isolate using 16S rRNA primers (5′- AGA GTT TGA TCC TGG CTC AG– 3′) and (5′- GGA TAC CTT GTT ACG ACT T– 3′). The agar well diffusion technique and scanning electron microscopy (SEM) were utilized to assess the inhibitory effects of bacterial ethyl acetate extract against G. boninense. A comprehensive analysis of the bacterial ethyl acetate extracts was conducted by gas chromatography - mass spectrometry (GC–MS). Molecular identification confirmed that the bacterial isolate was Bacterium strain BS1727. By employing SEM, the ethyl acetate extracts had influenced on G. boninense mycelial architecture. The exposure to the bacterial ethyl acetate extracts induced degradation and morphological distortion of the mycelial structure, serving as an indicator of its impact on the mycelium's structural modulation. Noteworthy, the spectrum of bioactive compounds was a subset of aromatic hydrocarbons, encompassing volatile organic compounds (VOCs). Based on GC–MS analysis, among the VOCs, acetic acid butyl ester and toluene showed the highest relative peak areas, 46.34 % for acetic acid butyl ester and 31.82 % for toluene, respectively. Ethylbenzene had a relative peak area of 5.4 %, 1,1,2-trichloroethane 4.41 %, and allyldimethyl (prop-1-ynyl) silane 3.17 %. The remaining compounds were 6-undecyl-5,6-dihydro-2H-pyran-2-one, 3-decen-5-one, 2-methyl-, and o-cymene, with the relative peak areas were below 1 %. These findings explained the inherent capacity of antifungal compounds as a viable strategy in inhibiting the growth of G. boninense. [ABSTRACT FROM AUTHOR]

Ganoderma boninense is a white-rot fungus that causes basal stem rot (BSR) disease in the oil palm. Potential natural inhibitors, such as gallic acid, thymol, propolis, and carvacrol, were assessed for their antagonistic effects against G. boninense. These naturally occurring phenolic compounds have also been utilised to inhibit hydrolytic and ligninolytic enzymes produced by the pathogen. Mycelial inhibition was dose-dependent in the presence of different concentrations of phenolic compounds, including, for example, in cellulase enzyme inhibition (GA mg/mL = 94%, THY 0.25 mg/mL = 90%, PRO 3.5 mg/mL = 92.5%, and CARV 0.15 mg/mL = 90.3%). A significant difference was observed revealing that gallic acid had the greatest inhibitory effect on the secretion of hydrolytic and ligninolytic enzymes, especially at 40 mM GA (cellulase = 0.337 U/mL, amylase = 0.3314 U/mL, xylanase = 0.211 U/mL, laccase = 0.4885 U/mL, lignin peroxidase = 0.218 U/mL, and manganese peroxidase = 0.386 U/mL). The growth and secretion of enzymes (inhibitory action) are inversely proportional to the concentration of phenolic compounds. Phenolic compounds have a greater potential as inhibitory agents and suppress the production of hydrolytic and ligninolytic enzymes. The selected phenolic compounds were evaluated for their ability to alter the morphology and integrity of G. boninense mycelia. The reduction in cell viability of G. boninense has been explained by research on morphological disruption, such as branching patterns, hyphal length, and rigidity of fungal cells, which eventually interrupt the secretion of enzymes. These studies highlight the efficacy of phenolic compounds in treating Ganoderma. In addition, these findings proved that naturally occurring phenolic compounds could be a substitute for chemical controls and other synthetic fungicides to eradicate the occurrence of BSR in oil palms, thus avoiding a situation that is difficult to overcome. [ABSTRACT FROM AUTHOR]

Ganoderma boninense is a white-rot fungus that causes basal stem rot (BSR) disease in the oil palm. Potential natural inhibitors, such as gallic acid, thymol, propolis, and carvacrol, were assessed for their antagonistic effects against G. boninense. These naturally occurring phenolic compounds have also been utilised to inhibit hydrolytic and ligninolytic enzymes produced by the pathogen. Mycelial inhibition was dose-dependent in the presence of different concentrations of phenolic compounds, including, for example, in cellulase enzyme inhibition (GA mg/mL = 94%, THY 0.25 mg/mL = 90%, PRO 3.5 mg/mL = 92.5%, and CARV 0.15 mg/mL = 90.3%). A significant difference was observed revealing that gallic acid had the greatest inhibitory effect on the secretion of hydrolytic and ligninolytic enzymes, especially at 40 mM GA (cellulase = 0.337 U/mL, amylase = 0.3314 U/mL, xylanase = 0.211 U/mL, laccase = 0.4885 U/mL, lignin peroxidase = 0.218 U/mL, and manganese peroxidase = 0.386 U/mL). The growth and secretion of enzymes (inhibitory action) are inversely proportional to the concentration of phenolic compounds. Phenolic compounds have a greater potential as inhibitory agents and suppress the production of hydrolytic and ligninolytic enzymes. The selected phenolic compounds were evaluated for their ability to alter the morphology and integrity of G. boninense mycelia. The reduction in cell viability of G. boninense has been explained by research on morphological disruption, such as branching patterns, hyphal length, and rigidity of fungal cells, which eventually interrupt the secretion of enzymes. These studies highlight the efficacy of phenolic compounds in treating Ganoderma. In addition, these findings proved that naturally occurring phenolic compounds could be a substitute for chemical controls and other synthetic fungicides to eradicate the occurrence of BSR in oil palms, thus avoiding a situation that is difficult to overcome.

Detecting Ganoderma boninense in Indonesia is crucial for effectively controlling and mitigating the spread of basal stem disease in oil palm fields. While there is ongoing development of tolerant plants, no such plant has been successfully created yet. Consequently, researchers are actively studying detection methods for Ganoderma boninense. One established and highly accurate approach is the use of polymerase chain reaction (PCR) techniques for molecular detection. However, this method requires time‐consuming sample preparation, which can pose challenges in plantation settings. To address this problem, a portable lab‐on‐chip device has been introduced. This technology enables easy and automatic DNA retrieval from liquid samples by absorbing lysed DNA using magnetic beads. An efficient mechanism for manipulating the magnetic bead within the semiconductor has been successfully implemented. The extraction process typically takes around 15 minutes using a modified methodology on the chip device approach. The chip facilitates the retrieval of two samples with a capacity of 120 µL for each sample. The PCR method was utilized to validate the equivalence of the lab‐on‐chip device extraction to the standard extraction method. This represents a promising alternative for expedited and simplified detection of Ganoderma boninense in field conditions.

Microorganisms play a pivotal role in the growth and development of plants, making their interaction a promising avenue for managing plant diseases, including those affecting oil palm cultivation. In this study, endophytic microbes such as actinomycetes, bacteria, and fungi were isolated from healthy oil palm tissue in susceptible areas to serve as stock isolates. These isolates underwent in vitro evaluation to determine their efficacy in controlling Ganoderma boninense and to identify bioactive metabolites. Additionally, in planta tests were conducted using bioformulations. A dual culture assay was utilized to assess the inhibitory effects of three different stock isolates on G. boninense. To detect bioactive metabolites responsible for the inhibition, particularly phenazine and syringic acid, a series of procedures involving fermentation, extraction, and LC-MS analysis were employed. Furthermore, the efficacy of bioformulations employing various carriers and consisting of either microbial consortia was meticulously evaluated in a nursery setting. The main focus of this evaluation was to determine their capacity to effectively curb disease onset and maintain the vegetative growth of oil palm during the progression of G. boninense. Several strains of indigenous bacteria (Pseudomonas aeruginosa strain JQ-41, Serratia marcescens strain S16, Stenotrophomonas rhizophila strain CASMBAUDAL2), an actinobacterium (Streptomyces sp.), and a fungus (Trichoderma sp.) exhibited significant growth inhibition against G. boninense. Based on the results obtained from the LC-MS analysis of the ethyl acetate extract, it was revealed that the extract contains 2 compounds known as antifungal agents, namely phenazine and syringic acid. The most effective approach to mitigate infection involved the preventive application of bioformulations containing mixed bacterial isolates or microbial consortia. After 12 months of observation, these bioformulations demonstrated efficacy comparable to that of Marfu-P, a commercially available biofungicide for oil palm seedlings. The study establishes the effectiveness of endophytic bioformulations as a viable strategy to manage the onset of G. boninense disease, highlighting the potential of microorganisms as an alternative solution for controlling basal stem rot in the nursery. [ABSTRACT FROM AUTHOR]

Ganoderma boninense (G. boninense) is a soil-borne fungus threatening oil palm at the present. It causes basal stem rot disease on oil palm. Within six months, this fungus can cause an oil palm plantation to suffer a significant 43% economic loss. The high persistence and nature of spread of G. boninense in soil make control of the disease challenging. Therefore, controlling the pathogen requires a thorough understanding of the mechanisms that underlie pathogenicity as well as its interactions with host plants. In this paper, we present the general characteristics, the pathogenic mechanisms, and the host's defensive system of G. boninense. We also review upcoming and most promising techniques for disease management that will have the least negative effects on the environment and natural resources. [ABSTRACT FROM AUTHOR]

Oil palms (OP) produce palm oil, a unique commodity without commercial alternatives. A serious disease of OP is basal stem rot (BSR) caused by Ganoderma boninense Pat. Climate change will likely increase BSR, thereby causing mortality of OP and reduced yields of palm oil. Work is being undertaken to produce modified OP (mOP) to resist BSR, although this will take decades for full development, if successfully produced at all. mOP will not be 100% effective, and it would be useful to know the effect of mOP on the key parameters of BSR incidence, OP mortality, and yield loss. The current paper employed CLIMEX modeling of suitable climates for OP and modeling narratives for Indonesia and Thailand. Indonesia is the largest producer of OP and Thailand is a much smaller manufacturer, and it was informative to compare these two countries. The gains from using mOP were substantial compared to the current production of some other continents and countries. The current paper, for the first time, assessed how climate change will affect BSR parameters for conventional and mOP. Greater consideration of the potential benefits of mOP is required to justify investing in the technology. [ABSTRACT FROM AUTHOR]

Dazomet-micelle nanodelivery systems (DAMINs) were prepared using ionic surfactants: sodium dodecylbenzene sulfonate and sodium dodecyl sulfate; and non-ionic surfactant: Tween 80. Their physicochemical properties, crystallinity, size, thermal and morphology and their anti-fungicidal activity, toward the Ganoderma boninense also were evaluated and compared. The nanoparticle size of DAMINs was found to be dependent on surfactant type and their concentration which in turn played a crucial role in fungi inhibition. This study found that DAMINs prepared using sodium dodecylbenzene sulfonate (SDBS), DMBS gave the highest inhibitory activities with the lowest EC50 value of 4789 ug/L which is about ten times better compared to the one prepared using sodium dodecyl sulfate, Tween 80, DMDS and DMT, respectively, with the value of 31,598 and 21,083 ug/L, respectively. This is toward the new generation of nanofungicides of better efficacy. [ABSTRACT FROM AUTHOR]

Palm oil industry is an important economic resource for Malaysia. However, an oil palm tree disease called Basal Stem Rot has impeded the production of palm oil, which caused significant economic loss at the same time. The oil palm tree disease is caused by a fungus known as Ganoderma Boninense. Infected trees often have little to no symptoms during early stage of infection, which made early detection difficult. Early disease detection is necessary to allow early sanitization and disease control efforts. Using Terrestrial Laser Scanning technology, 88 grey-distribution canopy images of oil palm tree were obtained. The images were pre-processed and augmented before being used for training and testing of the deep learning models. The capabilities of the Convolution Neural Network deep learning models in the classification of dataset into healthy and non-healthy class were tested and the best performing model was identified based on the Macro-F1 score. Fine-tuned DenseNet121 model was the best performing model, recorded a Macro F1-score of 0.798. It was also noted that Baseline model showed a relatively remarkable macro-F1 score of 0.747, which was better than all the feature extractor models and some of the fine-tuned models. However, fine-tuned models suffered from model overfitting due to dataset limitations. For future work, it is recommended to increase the sample size and utilize other CNN architectures to improve the model performance and progress towards detecting Basal Stem Rot at the early stage of infection by classifying sample images into multiple classes.

Keratinolytic is a microorganism ability to degrade keratin substrates. Fungi are known to produce the enzyme keratinase. This research was carried out aiming to know the keratinolytic fungi potential in inhibiting Ganoderma boninense fungi. Five isolates of keratinolytic fungi coded A 31, A 18, A 12, K 18, and A 29 have antagonistic ability against G. boninense. A 12 and A 18 had the largest inhibitory diameter of 25.23 mm and 24 mm, respectively, after 7 days of incubation. The ability of A 12 and A 18 antagonisms was observed by testing the supernatant of keratinolytic fungi incubated in a feather meal broth medium. An 18 has the largest antagonism percentage of inhibition at 84.72% against G. boninense, followed by A12 (77.78%) and combination treatment of A 12 + A 18 (73.55%) after 7 days of incubation. Keratinolytic fungi can also grow on minimum salt chitin medium (MSCM) and produced a hydrolysis zone after 3 days of incubation. G. boninense hyphae abnormalities were observed by using a 100x magnification microscope. Moreover, hyphae lysis and dwarf, curved, rolled, and curly hyphae were also observed after giving treatment on A 12, A 18, and the combination treatment of both isolates. These results showed that both keratinolytic fungi isolates and the supernatant are powerful biocontrol agents against G. boninense. There is no previous research report on endophytic fungi inhibiting the growth of Ganoderma boninense. In the future, keratinolytic fungi can be applied in agriculture technology. [ABSTRACT FROM AUTHOR]

Oil palm is a key agricultural resource in Malaysia. However, palm disease, most prominently basal stem rot caused at least RM 255 million of annual economic loss. Basal stem rot is caused by a fungus known as Ganoderma boninense. An infected tree shows few symptoms during early stage of infection, while potentially suffers an 80% lifetime yield loss and the tree may be dead within 2 years. Early detection of basal stem rot is crucial since disease control efforts can be done. Laboratory BSR detection methods are effective, but the methods have accuracy, biosafety, and cost concerns. This review article consists of scientific articles related to the oil palm tree disease, basal stem rot, Ganoderma Boninense, remote sensors and deep learning that are listed in the Web of Science since year 2012. About 110 scientific articles were found that is related to the index terms mentioned and 60 research articles were found to be related to the objective of this research thus included in this review article. From the review, it was found that the potential use of deep learning methods were rarely explored. Some research showed unsatisfactory results due to limitations on dataset. However, based on studies related to other plant diseases, deep learning in combination with data augmentation techniques showed great potentials, showing remarkable detection accuracy. Therefore, the feasibility of analyzing oil palm remote sensor data using deep learning models together with data augmentation techniques should be studied. On a commercial scale, deep learning used together with remote sensors and unmanned aerial vehicle technologies showed great potential in the detection of basal stem rot disease.

Aims: This study was designed to examine the enzyme activity of selected virulent isolates of Ganoderma boninense against oil palm. In a separate in vitro assessment, the effect of macronutrients on the mycelial growth of four selected Ganoderma spp. was also tested. Methodology and results: The study involved a comparison of ligninolytic enzymes; lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac) profiling of eight isolates of G. boninense, categorized into three levels of aggressiveness, with two control isolates (G. boninense PER71 and G. tornatum NPG1) using solid-state fermentation (SSF). The Principal Component Analysis (PCA) revealed that the isolates had a significant production of ligninolytic enzymes on day 80. The most aggressive isolate, ET61 had the highest Lac production. As for the macronutrient test, mycelial growth for all the Ganoderma spp. was highly affected by potassium (K). Conclusion, significance and impact of study: The findings of this study elucidated the characteristics of G. boninense in relation to enzyme production for the degradation of oil palm lignin and the identification of essential nutrients involved in the survival and growth of Ganoderma spp. The study provides vital information on the pathogenic characteristics of G. boninense isolates involved in biomass degradation along with the role of nutrient on the growth of Ganoderma spp. that may influence basal stem rot (BSR) management in the field. [ABSTRACT FROM AUTHOR]

Basal Stem Rot (BSR), a disease caused by Ganoderma boninense (G. boninense), has posed a significant concern for the oil palm industry, particularly in Southeast Asia, as it has the potential to cause substantial economic losses. The breeding programme is currently searching for G. boninense-resistant planting materials, which has necessitated intense manual screening in the nursery to track the progression of disease development in response to different treatments. The combination of hyperspectral image and machine learning approaches has a high detection potential for BSR. However, manual feature selection is still required to construct a detection model. Therefore, the objective of this study is to establish an automatic BSR detection at the seedling stage using a pre-trained deep learning model and hyperspectral images. The aerial view image of an oil palm seedling is divided into three regions in order to determine if there is any substantial spectral change across leaf positions. To investigate if the background images affect the performance of the detection, segmented images of the plant seedling have been automatically generated using a Mask Region-based Convolutional Neural Network (RCNN). Consequently, three models are utilised to detect BSR: a convolutional neural network that is 16 layers deep (VGG16) model trained on a segmented image; and VGG16 and Mask RCNN models both trained on the original images. The results indicate that the VGG16 model trained with the original images at 938 nm wavelength performed the best in terms of accuracy (91.93%), precision (94.32%), recall (89.26%), and F1 score (91.72%). This method revealed that users may detect BSR automatically without having to manually extract image attributes before detection. [ABSTRACT FROM AUTHOR]

Oil palm plantation was first established in Malaysia in 1917. Since then, the oil palm industry in Malaysia flourished especially following the shifting of Deli Dura palm to Tenera palm in the 1960s, which contributed to a 30% increase in yield. However, the outbreak of basal stem rot disease caused by Ganoderma boninense has caused substantial yield losses. With no known cure to date, extensive molecular studies were conducted to better understand the underlying mechanism of G. boninense infection and the role of protein-coding genes as regulators in oil palms against G. boninense. The studies have demonstrated the importance of non-coding RNAs (ncRNAs) in the interaction between oil palm and G. boninense. However, there is still limited genome-scale identification for ncRNAs in oil palm (Elaeis guineensis jacq.) and its pathogen, G. boninense. In this study, we focused on the identification of small and medium-sized non-coding RNA using a computational approach and managed to predict 2,233 ncRNAs and 369 ncRNAs in the E. guineensis and G. boninense genomes, respectively. The identified ncRNAs include transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and microRNA (miRNA). Although the number may be far fewer than the real number, the predicted ncRNAs here represent an almost complete dataset of small and medium-sized ncRNA in both the E. guineensis and G. boninense genomes. The information obtained may be useful to tackle the issue of G. boninense attack on oil palm plantations. [ABSTRACT FROM AUTHOR]

Ganoderma species are common wood-rotting fungi that cause root and stem rot in most monocots, dicots, and gymnosperms. It influences plantation crops such as oil palm and rubber in Malaysia, but the effects vary greatly within the genus. Because of the complex chemistry of Ganoderma, extracting and identifying the physiologically active chemicals is often time-consuming and necessitates extensive bioassays. This study investigated the specific identification of the most infectious Ganoderma species using a sub-20-nm gold electrode. Three electrodes were created using chemically controlled etching (2, 10, and 20 nm). An AutoCAD mask containing nanogap pad electrodes was used to create a chrome glass surface, which was then translated and built. Following the successful construction of the device, the sensor was evaluated using a combination of conventional photolithography and a size reduction technique to imprint the nanogap design onto the gold surface. Ganoderma boninense target DNA was synthesised and surface-modified to enable interaction at extremely low molecular concentrations. The proposed device has a detection limit of 0.001 mol/L, which is seven times lower than the detection limits of currently available devices. The capacitance, conductivity, and permittivity of complementary, non-complementary, single mismatched, and targeted biomolecules changed during hybridization. This sensor correctly differentiated between all samples. The sensor's performance is further validated by comparing experimental data from the sensor to theoretical data from the sensor's corresponding circuit model. The two data sets are very similar. [ABSTRACT FROM AUTHOR]

Basal stem rot caused by Ganoderma boninense is the single major disease to affect oil palms in South Asia and Oceania. Although first described in commercial plantations some 90 years ago it remains a major constraint to oil palm planting, with disease occurence increasing with succesive plantings. There is a considerable volume of published research into the occurence, diagnostics and control of basal stem rot but much of this has been focused on individual plantings or local environments. In this manuscript we attempt to bring together reports from across the South Asia/Oceania regions to provide a comprehensive review of the current knowledge and to identify the key issues that still need to be addressed in order to achieve a comprehensive understanding of the disease and disease processes. [ABSTRACT FROM AUTHOR]

Oil palm infectious diseases have devastating economic implications for the Southeast Asian nations of Indonesia and Malaysia. Therefore, this paper reviews oil palm growth, related diseases, specifically Ganoderma sp. infection, and control methods. The literature was sourced from Scopus using the following keywords: Oil palm, palm oil, Ganoderma boninense, Ganoderma, Elaeis, basal stem rot, Elaies guineensis, fungi, Arecaceae, and microbiology. The majority (73.1%) of infection control methods focused on biological methods such as biological control agents (BCA), metabolites from BCAs, and the development of resistant oil palm varieties. The second most frequent subject included chemical control methods such as fungicides and fertilisers (25.6%), and only one study (1.3%) focused on a mechanical (cultural) control method (pulverisation). Trichoderma spp. were the most frequently studied BCA. Other BCAs included Pseudomonas aeruginosa, endophytes of oil palm, Pycnoporus sanguineus, Streptomyces, Hymenomycetes, Burkholderia cepacian, and Schizophyllum commune. Currently, there is no effective method to combat G. boninense infection. The reviewed biological, chemical, and mechanical control methods are available to the industry, leaving scope for future studies. [ABSTRACT FROM AUTHOR]

The globally vital oil palm, a major oil producer, confronts productivity challenges due to Ganoderma boninense (Gb), causing output decline. Chemical control efforts have proven ineffective, prompting exploration of microbial-based biocontrol. While single fungal biocontrol research exists, the impact of employing multiple biocontrols concurrently to combat Ganoderma and enhance oil palm growth remains uncharted. This study examined four soil-derived fungal isolates for their ability to antagonize Gb PER71 in vitro. Molecular identification categorized them as Talaromyces spp. and Penicillium sp. Moreover, all isolates were revealed to have at least three plant growth-promoting (PGP) traits and were shown to have phosphoric hydrolase, ester hydrolase, peptide hydrolase, and glycosidase activities which are essential for plant growth. Furthermore, the synergistic evaluation of fungal isolates was tested against Gb PER71. One out of six combinations of fungal isolates showed a synergistic effect in vitro, and two showed a synergistic effect in planta. The application of single and combined fungal isolates tested in planta also suppressed Gb PER71 and enhanced oil palm growth compared to control groups. The findings indicate the promising potential of these isolates as biocontrol agents (BCAs) and bioformulations against Gb in oil palm cultivation., (© 2024 Wiley‐VCH GmbH.)

Oil palms (OP) produce palm oil, a unique commodity without commercial alternatives. A serious disease of OP is basal stem rot (BSR) caused by Ganoderma boninense Pat. Climate change will likely increase BSR, thereby causing mortality of OP and reduced yields of palm oil. Work is being undertaken to produce modified OP (mOP) to resist BSR, although this will take decades for full development, if successfully produced at all. mOP will not be 100% effective, and it would be useful to know the effect of mOP on the key parameters of BSR incidence, OP mortality, and yield loss. The current paper employed CLIMEX modeling of suitable climates for OP and modeling narratives for Indonesia and Thailand. Indonesia is the largest producer of OP and Thailand is a much smaller manufacturer, and it was informative to compare these two countries. The gains from using mOP were substantial compared to the current production of some other continents and countries. The current paper, for the first time, assessed how climate change will affect BSR parameters for conventional and mOP. Greater consideration of the potential benefits of mOP is required to justify investing in the technology.

Ganoderma boninense is the major causal agent of basal stem rot (BSR) disease in oil palm, causing the progressive rot of the basal part of the stem. Despite its prominence, the key pathogenicity determinants for the aggressive nature of hemibiotrophic infection remain unknown. In this study, genome sequencing and the annotation of G. boninense T10 were carried out using the Illumina sequencing platform, and comparative genome analysis was performed with previously reported G. boninense strains (NJ3 and G3). The pan-secretome of G. boninense was constructed and comprised 937 core orthogroups, 243 accessory orthogroups, and 84 strain-specific orthogroups. In total, 320 core orthogroups were enriched with candidate effector proteins (CEPs) that could be classified as carbohydrate-active enzymes, hydrolases, and non-catalytic proteins. Differential expression analysis revealed an upregulation of five CEP genes that was linked to the suppression of PTI signaling cascade, while the downregulation of four CEP genes was linked to the inhibition of PTI by preventing host defense elicitation. Genome architecture analysis revealed the one-speed architecture of the G. boninense genome and the lack of preferential association of CEP genes to transposable elements. The findings obtained from this study aid in the characterization of pathogenicity determinants and molecular biomarkers of BSR disease. [ABSTRACT FROM AUTHOR]

Understanding oil palm’s cell wall lipid during pathogenic invasion, especially from Ganoderma fungus helps us to devise better strategies in managing Basal Stem Rot caused by the fungus effectively. However, as the lipids of plant’s cell wall is a delicate subject, while acquiring them in ample amount with decent quality for research purpose is an excruciating work, therefore it is crucial to develops an optimised method for acquisition. In this study, the effects of solvent ratio, extraction time, extraction temperature and biomass to solvent ratio pertaining effective lipids extraction from oil palm roots cell wall were investigated, aided with Central Composite design (CCD) of Response Surface Methodology (RSM) analysis to obtain optimum oil palm cell wall lipid extraction conditions. Using the projection of RSM model and validation of empirical evaluation, the results revealed that the optimum cell wall lipids yield was obtained under the following extraction conditions: 10 mL of solvent mixture (chloroform: methanol (2:1, v/v)) per gram tissue for 120 min with gentle agitation at 30˚C of extraction temperature. Ultimately, Fourier Transform Spectroscopy (FTIR) analysis was carried out to validate the successful and complete extraction were achieved using the optimised condition.

This research aimed to determine the potential of endophytic Trichoderma sp originated from oil palm plant tissue as a biological control agent and its molecular identification. The potency assay was carried out using a completely randomized design consisting of three isolates of Trichoderma sp. from different plant tissues (TR01 from root tissue, TS01 from stem tissue, and TM01 from midrib tissue) with inhibitory ability parameters. The inhibition of the growth of G. boninense was performed at the concentration of 15% and 20%, and the molecular identification of Trichoderma sp. endophyte isolates was analyzed using BLAST software. The results showed that Trichoderma sp. TM01 isolate had larger inhibitory than the other isolates on days 3 and 4 by 60% and 68%. TM01 isolate also showed inhibition to the growth of the G. boninense at 15% and 20%, with the percentage of inhibition reaching 71.79% and 82.05%. Based on phylogenetic analysis, the three endophytic isolates of Trichoderma sp. were closely related to Trichoderma virens.

Aims: The basal stem rot disease in oil palm is caused by the pathogenic Ganoderma boninense, which is infectious after mating and forming dikaryotic hyphae. This study was aimed to generate a mating-type biomarker for the detection of pathogenic Ganoderma species. Methodology and results: Mating-type region of Ganoderma was amplified using polymerase chain reaction (PCR) and primers flanking the mating-type region of other basidiomycetes. Amplified fragments were sequenced and were identified as the Ganoderma pheromone receptor gene of matB locus called the gprb2 gene. Using this biomarker, the pheromone receptor gene was detected in a total of 107 pathogenic Ganoderma spp. while the gene was not detected in the non-pathogenic Ganoderma lucidum. Phylogenetic tree analyses of the gene fragment encoding the partial amino acid sequence of gprb2 showed clades of close evolutionary relationship among the 107 pathogenic Ganoderma spp. Phylogenetic analyses using deduced amino acid sequences of the Ganoderma pheromone receptor b2 gene, gprb2 with homologous pheromone receptors of other basidiomycetous fungi revealed high conservation of this pheromone receptor within their respective taxonomy. Conclusion, significance and impact of study: A potential mating-type biomarker was successfully identified that could detect pathogenic Ganoderma spp. The research findings will be helpful in oil palm screening to detect pathogenic Ganoderma spp. and gain further insight into the role of the mating-type loci of Ganoderma towards its pathogenesis in causing the basal stem rot disease of oil palm. [ABSTRACT FROM AUTHOR]

Abstract Fleiss et al. (CABI Agri Biosci 3:59, 2022) suggest that palm oil yield from Malaysia oil palm will not be affected substantially by increased temperature from climate change with evidence from a misinterpretation of a paper co-authored by the current author. This current comment article provides evidence that suggest that yields will be much lower in the future.

Oil palm (Elaeis guineensis) is considered as a golden crop and is also one of the main contributors to the economy of Malaysia. Unfortunately, Basal Stem Root (BSR) disease caused by Ganoderma boninense remains a major obstacle to oil palm cultivation and production. Hendersonia toruloidea (GanoEF1) is a biocontrol agent and also a novel strain isolated from oil palm plantation soil. Here, we use five-month-old oil palm seedlings and study five treatments to control the disease. Sixty-five (65) compounds from different treatments were selected as the main compounds to be tested, including three types of plant sterols. Release of specific compounds could be used to better understand more the mechanism of endophytic fungi and of the biocontrol to successfully control and suppress G. boninense in oil palm. Phytosterols (β-sitosterol, stigmasterol, and campesterol) were expressed at higher levels in infected than in uninfected seedlings. Other methods which could be used as an indicator to detect plant stress associated with the presence of G. boninense is through the determination of total expression of superoxide dismutase (SOD) and catalase (CAT) in oil palm. Few other studies show a good correlation between stress levels, reactive oxygen species (ROS), and level of SOD and CAT in plant. In this study, we confirm that Hendersonia GanoEF1 plays an important role to control and suppress the BSR disease. [ABSTRACT FROM AUTHOR]

An approach to metabolomics profiling of non-infected and Ganoderma boninense (G. boninsense) infected oil palm roots crude extracts that utilize gas chromatography-mass spectrometry (GC–MS) and multivariate statistics of principal component analysis (PCA) have been tested. This combination has provided a rapid approach in investigating the changes in the metabolite variations of non-infected and infected oil palm roots at 14 and 30 days post-infection. The extracts were prepared by using 80% (v/v) of methanol. In identifying the metabolites responsible for each differentiation, PCA model was generated in loading bi-plot. Dimethyl benzene-1,4-dicarboxylate, methyl 3-(3,5-ditert-butyl-4-hydroxyphenyl)propanoate, ergost-5-en-3-ol, (3β), stigmast-5-en-3-ol, (3β), stigmasterol, methyl hexadecanoate, methyl (9Z,12Z)-octadeca-9,12-dienoate, methyl octadecanoate, 2-(hydroxymethyl)-2-nitropropane-1,3-diol, methyl (Z)-octadec-6-enoate and (E)-icos-5-ene were found more abundant in G. boninense infected roots than in non-infected roots. Steroidal compounds and fatty acid derivatives which has been determined in the non-infected and G. boninense infected roots regulate a variety of responses to the G. boninense. The abundant of these metabolites in G. boninense infected roots are due to the crucial roles in pathogen defence.

Fungal endophytes are a special group of symbionts that invade the internal environment of the host organism without causing any pathogenic symptoms. They increase the vigor of the plant while protecting them from several biotic and abiotic stress conditions such as herbivory, disease, and drought. In this study, endophytic fungi were isolated from fig (Ficus carica), a beneficial plant belongs to the family of Moraceae. This study was conducted to determine the potential of fungal endophytes of F.carica as biocontrol agents against selected phytopathogens Ganoderma boninense, Magnaporthe oryzae, and Fusarium verticillioides. Besides, endophytic fungi isolates were also screened to assess their ability as a phosphate-solubilizing agent. Results obtained revealed that a total of 11 fungal endophytes was successfully isolated from leaf, root, and stem samples of F.carica. The cultural-morphological identifications were carried out on the unknown fungal isolates. For the antagonistic test, S2-1 and R3-4 show a promising potential against those phytopathogens with more than 20% Percentage Inhibition Radial Growth (PIRG). Endophyte S2-1 exhibits the competition mechanism, while R3-4 expresses the antibiosis mechanism in suppressing the mycelium growth of phytopathogens. As for phosphate solubilization, 8 of 10 isolates show positive results as phosphate solubilizer with the highest PSI value 3.02±0.05 (S2-4).

Ganoderma, a genus of polypore white rot fungus with some species such as G. lucidum and G. sinense have been reported with remarkable biological activities and used as traditional medicine for long. On the other hand, G. boninense is recognized as an important oil palm pathogen which causes intensive losses in oil palm industry. Hence, this study reveals the potential of antimicrobial properties of G. boninense fruiting bodies extract using different solvents. Ethyl acetate extract demonstrated a broad spectrum pathogens inhibition activity, followed by hot water > acetone > methanol > ethanol > chloroform. Ethyl acetate extract also shown the strongest growth inhibition against Proteus mirabilis (14.20 ± 0.40 mm). Lowest MIC (0.625 mg/ml) was observed in methanol extract against Coagulase-Negative Staphylococci. LC-MS analysis identified the extracts of G. boninense putatively contains natural occurring derivatives of alkaloid, fatty acid, heterocyclic compounds and glycosides. G. boninense may potential as the future drug. However, further investigation is required to understand this fungus in depth.

Oil palm plantation in Indonesia is significantly affected by basal stem rot disease caused by the pathogenic fungus Ganoderma boninense. Tolerant oil palm cultivars toward G. boninense have been developed through a breeding program accelerated by the implementation of the CRISPR/Cas9 technology. This study was conducted to perform a gene knockout (KO) of oil palm that confers a putative defense‐related trait toward G. boninense. A plasmid pCRISPR_EMLP containing modules, i.e., 35S‐CaMV‐promoter‐driven CRISPR/Cas9, U6‐promoter‐driven sgRNA to the target EgEMLP gene (EL695076), and hygromycin resistance gene as the selectable marker, was established for Agrobacterium‐mediated delivery into oil palm calli (OPC). The transformed OPCs were regenerated and screened in DF (de Fossard) media containing hygromycin. The working concentration of hygromycin was successfully optimized for selection at 20 ppm. Through PCR‐based selection using HYG primers, we succeeded in discerning positive transformed OPC clones. The sequenced PCR products of genomic DNA as the template amplified using EMLP1 primers showed a point mutation, causing a frameshift in the edited EgEMLP and premature stop codon. Furthermore, in silico modeling demonstrated that the mutation resulted in a change in the C‐terminal region, affecting the tertiary protein structure. Moreover, electrophoresis analysis of PCR products of cDNA as the template from transformed OPC clones showed several samples with faint or undetected bands. This indicated that the CRISPR/Cas9 module induced a mutation that could destabilize the transcribed mRNA, e.g., premature degradation. Altogether, this study has successfully implemented CRISPR/Cas9 gene editing in oil palm in a model gene that is responsible for putative defense‐related traits toward the pathogenic fungus G. boninense.

Basal Stem Rot (BSR), a disease caused by Ganoderma boninense (G. boninense), has posed a significant concern for the oil palm industry, particularly in Southeast Asia, as it has the potential to cause substantial economic losses. The breeding programme is currently searching for G. boninense-resistant planting materials, which has necessitated intense manual screening in the nursery to track the progression of disease development in response to different treatments. The combination of hyperspectral image and machine learning approaches has a high detection potential for BSR. However, manual feature selection is still required to construct a detection model. Therefore, the objective of this study is to establish an automatic BSR detection at the seedling stage using a pre-trained deep learning model and hyperspectral images. The aerial view image of an oil palm seedling is divided into three regions in order to determine if there is any substantial spectral change across leaf positions. To investigate if the background images affect the performance of the detection, segmented images of the plant seedling have been automatically generated using a Mask Region-based Convolutional Neural Network (RCNN). Consequently, three models are utilised to detect BSR: a convolutional neural network that is 16 layers deep (VGG16) model trained on a segmented image; and VGG16 and Mask RCNN models both trained on the original images. The results indicate that the VGG16 model trained with the original images at 938 nm wavelength performed the best in terms of accuracy (91.93%), precision (94.32%), recall (89.26%), and F1 score (91.72%). This method revealed that users may detect BSR automatically without having to manually extract image attributes before detection.

Featured Application: Major improvements in yield and disease resistance have come from plant selection and breeding. The proposed method provides a better management due to its capability to detect the asymptomatic G. boninense infection. It can improve the sustainability of palm oil production which thus protects the environment and communities in palm oil-producing regions. Breeding programs to develop planting materials resistant to G. boninense involve a manual census to monitor the progress of the disease development associated with various treatments. It is prone to error due to a lack of experience and subjective judgements. This study focuses on the early detection of G. boninense infection in the oil palm seedlings using near infra-red (NIR)-hyperspectral data and a support vector machine (SVM). The study aims to use a small number of wavelengths by using 5, 4, 3, 2, and 1 band reflectance as datasets. These results were then compared with the results of detection obtained from the vegetation indices developed using spectral reflectance taken from the same hyperspectral sensor. Results indicated a kernel with a simple linear separation between two classes would be more suitable for G. boninense detection compared to the others, both for single-band reflectance and vegetation index datasets. A linear SVM which was developed using a single-band reflectance at 934 nm was identified as the best model of detection since it was not only economical, but also demonstrated a high score of accuracy (94.8%), sensitivity (97.6%), specificity (92.5%), and area under the receiver operating characteristic curve (AUC) (0.95). [ABSTRACT FROM AUTHOR]

Ganoderma boninense (G.boninense) is the causal agent of basal stem rot (BSR) which significantly reduced the productivity of oil palm plantations in Southeast Asia. At early stage, the disease did not show any physical symptoms that could be seen with naked eyes resulted in detection difficulties. To date, there was no effective detection for this disease, and conventional methods such as manual and laboratory-based required trained specialists as well as time-consuming. Therefore, this study was conducted using hyperspectral remote sensing to investigate the differences in spectral reflectance of young leaf (frond one (F1) of healthy and G. boninense infected oil palm seedlings. The seedlings were inoculated with G. boninense pathogen at five months old. At five months after inoculation, 558 spectral signatures of F1 were extracted from acquired hyperspectral images. Noise removal was done to the extracted spectral signatures to remove outliers in the data. Then, the spectral signatures were averaged and plotted to observe the differences. Differences in reflectance of healthy and G. boninense infected seedlings were seen evidently in the near-infrared (NIR) region. Thus, this study showed evidence that F1 spectral reflectance has the ability to detect early stage of G. boninense infection at oil palm seedlings.

Cerato-platanin (CP) proteins are small extracellular proteins that play essential roles in the plant-pathogen interactions of some economically important filamentous fungi. At present, there is a lack of information about the roles of CP proteins secreted by Ganoderma boninense , the causal agent of basal stem rot disease in African oil palm, during the early host-pathogen interaction. This work studies the properties and roles of two CP proteins from G. boninense strain PER71. Using bioassay-guided fractionation and nano-LC-MS/MS analysis, we identified peptide matches for G. sinense ZZ0214-1 CP-like and other elicitor proteins in the culture filtrate of G. boninense strain PER71. We found that GbCP2 and GbCP6, two out of nine CP gene models identified in the fungal genome of G. boninense strain PER71, exhibited potential effector properties. We further validated their effector properties by isolating and characterising their coding regions. Interestingly, GbCP6 showed a significant expression level at 11 days post inoculation, indicating its significance in fungal pathogenesis. On the other hand, GbCP2 did not show differential expression at any sampling point, suggesting a different function or role in the pathogenicity of G. boninense. This study identifies GbCP6 as a potential biomarker for early detection of basal stem rot disease in oil palm. [Display omitted] • Ganoderma boninense secretes hypersensitive response-inducing elicitor proteins. • Nine cerato-platanin homologs are present in the G. boninense fungal genome. • GbCP2 and GbCP6 are effector proteins with potential implications in pathogenesis. • GbCP6 emerges as a potential early biomarker for basal stem rot disease. [ABSTRACT FROM AUTHOR]

Abstrak Rendahnya produktivitas lahan pertanian di Indonesia berkaitan dengan serangan penyakit tanaman, contohnya penyakit layu Fusarium pada tanaman tomat dan busuk pangkal batang pada tanaman kelapa sawit yang disebabkan oleh Ganoderma boninense. Penelitian sebelumnya telah berhasil mengisolasi aktinomisetes dari tanah Arboretum Universitas Riau, namun belum diketahui kemampuannya dalam menghambat jamur Fusarium oxysporum f.sp lycopersici dan Ganoderma boninense. Penelitian ini bertujuan untuk menguji 32 isolat aktinomisetes terhadap jamur target dengan metode difusi agar. Aktinomisetes potensial yang terpilih, dilanjutkan untuk produksi senyawa antifungi dengan lama waktu fermentasi yang berbeda (4, 5, dan 6 hari) dan diuji dengan metode difusi kertas cakram. Hasil penelitian uji aktivitas antifungi dengan metode difusi agar menunjukkan 31 isolat aktinomisetes mampu menghambat pertumbuhan jamur F. oxysporum f.sp lycopersici dan isolat A2.01 memiliki zona hambat tertinggi yaitu sebesar 36,10 mm. Sebanyak 28 isolat aktinomisetes mampu menghambat jamur G. boninense dan isolat D2.28 memiliki zona hambat tertinggi, yaitu sebesar 45,71 mm. Isolat aktinomisetes Arboretum Universitas Riau sebagian besar dapat menghambat pertumbuhan kedua jamur target dengan metode difusi agar, namun hasil uji senyawa antifungi isolat potensial dengan metode difusi kertas cakram belum mampu membentuk zona hambat. Isolat aktinomisetes potensial dapat diaplikasikan menggunakan kultur langsung secara in vivo. Abstract The low productivity of agricultural land in Indonesia occurred because of plant diseases attack such as Wilt Fusarium in tomato plant and Basal Stem Rot disease in palm oil caused by Ganoderma boninese. Previous research had successfully isolated the actinomycetes from soil of Arboretum University of Riau However, the antifungal potency of those isolates against Fusarium oxysporum f. sp lycopersici and Ganoderma boninense had not been known. This research aimed to screening 32 actinomycetes isolates against the fungal target by using agar diffusion method. The selected actinomycetes were continued to produce crude antifungal by different duration of fermentation (4, 5 and 6 days) using disc diffusion method. The result of the antifungal activity using agar diffusion method showed that there were 31 isolates that able to inhibit the F. oxysporum f. sp lycopersici and isolate A2.01 showed the highest inhibition zone by 36.10 mm. There were 28 isolates that able to inhibit the G. boninense and isolate D2.28 showed the highest inhibition zone by 45.71 mm. Almost all of the isolate was able to inhibit both of two fungals targets with diffussion agar method, but the crude antifungal compound of the potential isolate by disc diffusion method could not inhibit both of the fungal targets. The potential actinomycetes isolate was suggested to be applied as a culture directly in vivo.

Ganoderma boninense is the major causal agent of basal stem rot (BSR) disease in oil palm, causing the progressive rot of the basal part of the stem. Despite its prominence, the key pathogenicity determinants for the aggressive nature of hemibiotrophic infection remain unknown. In this study, genome sequencing and the annotation of G. boninense T10 were carried out using the Illumina sequencing platform, and comparative genome analysis was performed with previously reported G. boninense strains (NJ3 and G3). The pan-secretome of G. boninense was constructed and comprised 937 core orthogroups, 243 accessory orthogroups, and 84 strain-specific orthogroups. In total, 320 core orthogroups were enriched with candidate effector proteins (CEPs) that could be classified as carbohydrate-active enzymes, hydrolases, and non-catalytic proteins. Differential expression analysis revealed an upregulation of five CEP genes that was linked to the suppression of PTI signaling cascade, while the downregulation of four CEP genes was linked to the inhibition of PTI by preventing host defense elicitation. Genome architecture analysis revealed the one-speed architecture of the G. boninense genome and the lack of preferential association of CEP genes to transposable elements. The findings obtained from this study aid in the characterization of pathogenicity determinants and molecular biomarkers of BSR disease.

Abstract Background Basal stem rot (BSR) caused by hemibiotroph Ganoderma boninense is a devastating disease resulting in a major loss to the oil palm industry. Since there is no physical symptom in oil palm at the early stage of G. boninense infection, characterisation of molecular defense responses in oil palm during early interaction with the fungus is of the utmost importance. Oil palm (Elaeis guineensis) seedlings were artificially infected with G. boninense inoculums and root samples were obtained following a time-course of 0, 3, 7, and 11 days-post-inoculation (d.p.i) for RNA sequencing (RNA-seq) and identification of differentially expressed genes (DEGs). Results The host counter-attack was evidenced based on fungal hyphae and Ganoderma DNA observed at 3 d.p.i which became significantly reduced at 7 and 11 d.p.i. DEGs revealed upregulation of multifaceted defense related genes such as PR-protein (EgPR-1), protease inhibitor (EgBGIA), PRR protein (EgLYK3) chitinase (EgCht) and expansin (EgEXPB18) at 3 d.p.i and 7 d.p.i which dropped at 11 d.p.i. Later stage involved highly expressed transcription factors EgERF113 and EgMYC2 as potential regulators of necrotrophic defense at 11 d.p.i. The reactive oxygen species (ROS) elicitor: peroxidase (EgPER) and NADPH oxidase (EgRBOH) were upregulated and maintained throughout the treatment period. Growth and nutrient distribution were probably compromised through suppression of auxin signalling and iron uptake genes. Conclusions Based on the analysis of oil palm gene expression, it was deduced that the biotrophic phase of Ganoderma had possibly occurred at the early phase (3 until 7 d.p.i) before being challenged by the fungus via switching its lifestyle into the necrotrophic phase at later stage (11 d.p.i) and finally succumbed the host. Together, the findings suggest the dynamic defense process in oil palm and potential candidates that can serve as phase-specific biomarkers at the early stages of oil palm-G. boninense interaction.

The rapid expansion of oil palm (OP) has led to its emergence as a commodity of strategic global importance. Palm oil is used extensively in food and as a precursor for biodiesel. The oil generates export earnings and bolsters the economy of many countries, particularly Indonesia and Malaysia. However, oil palms are prone to basal stem rot (BSR) caused by Ganoderma boninense which is the most threatening disease of OP. The current control measures for BSR management including cultural practices, mechanical and chemical treatment have not proved satisfactory. Alternative control measures to overcome the G. boninense problem are focused on the use of biological control agents and many potential bioagents were identified with little proven practical application. Planting OP varieties resistant to G. boninense could provide the ideal long-term solution to basal stem rot. The total resistance of palms to G. boninense has not yet been reported, and few examples of partial resistances have been observed. Importantly, basidiospores are now recognized as the method by which the disease is spread, and control methods require to be revaluated because of this phenomenon. Many methods developed to prevent the spread of the disease effectively are only tested at nursery levels and are only reported in national journals inhibiting the development of useful techniques globally. The initial procedures employed by the fungus to infect the OP require consideration in terms of the physiology of the growth of the fungus and its possible control. This review assesses critically the progress that has been made in BSR development and management in OP. [ABSTRACT FROM AUTHOR]