Ganoderma In Oil Palm Research Articles

Validation of Early Infection Markers for Ganoderma in Oil Palm at Three Endemic Ganoderma Locations

A serious disease that affects the viability of the oil palm industry is basal stem rot, which is caused by Ganoderma. The current level of disease can be viewed as unmanageable, given that the palms were growing in an unfavorable or unsuitable climate. Today, there are numerous approaches to diagnose diseases early, and one of them using molecular methods. Seven genes for early infection markers were effectively generated by a reference's transcriptome study, including LEUCO, ETHYLENE, CHALCONE, ANTHOCYANIDIN, ETHYLENE, MANNOSE, and SENESCENCE. The purpose of this study is to validate and confirm the presence of Ganoderma infections in three endemic oil palm field in Indonesia i.e. Cisalak Baru, Rejosari, and Bekri plantation. This study conducted real time qPCR of RNA from oil palm roots with four different severities of infection. Manual processing of RNA isolation and cDNA synthesis were carried out, to provide quantification expression level. In addition, gene ontology (GO) analysis was also performed in order to explain the roles of each gene tested. The results revealed that CHALCONE is the only marker that consistently elucidate the Ganoderma's early infection appear in three locations. The drawbacks of the analysis results are tightly correlating to the age of oil palm as well as endemic location. GO results declare that seven genes function related to the response of infection. This work was successful in confirming early infection in three places, elucidating the variables influencing the efficacy and sensitivity of molecular detection, and revealing the function and importance of particular genes for detection.

Metabolomics approach in identifying biomarkers from pathogenic Ganoderma boninense involved in early interactions with oil palm host

This study attempts to identify key biomarkers that may be involved in the early interactions of oil palm and Ganoderma boninense. To achieve this, the oil palm extract medium (OPEM) was adopted as a model to simulate oil palm-Ganoderma interactions in planta with biomarkers identified using the LC-MS-based metabolomics approach. The metabolic profiles of ethyl acetate crude extracts of OPEM and G. boninense-inoculated OPEM (OPEM + Gb, incubated for 1, 3, 7, 14, 21 and 28 days) were compared using liquid chromatography quadrupole/time-of-flight-mass spectrometry (LC-Q/TOF-MS) coupled with multivariate data analysis using the platform MetaboAnalyst. Results revealed that the OPEM constituents such as kakuol, kanokoside A, abruquinone B and robinetin 3-rutinoside are naturally occurring plant metabolites and may be involved in defense mechanisms against G. boninense. By contrast, aspulvinone H and methylisocitric acid were produced by G. boninense and may be precursors for the synthesis of other compounds that contribute to successful disease infection. Additionally, the metabolomics analyses further ranked 15 important secondary metabolites according to their variable importance in projection (VIP) scores. These compounds comprise one ketone, two fatty acids, two flavonoids and, one isomer and nine unknowns that are suggestive of early plant-pathogen interactions. These 15 compounds were further analysed using a heatmap revealing decreased concentrations of plant-derived metabolites kakuol, kanokoside A and 5,7,4ʹ-trihydroxy-3,6,8,3ʹ,5ʹ-pentamethoxyflavone and increased concentrations of plant-derived fatty acids 9-hydroxy-hexadecan-1,16-dioic acid and 11-hydroperoxy-12,13-epoxy-9-octadecenoic acid in the presence of G. boninense. Changes in the concentrations of these compounds suggest the presence of G. boninense, thereby indicating early infections in the oil palm. These biomarkers may be further developed as a rapid and non-invasive diagnostic for early detection of Ganoderma infection in oil palm.

Expression of genes related to hydrogen peroxide generation and phytohormones in Ganoderma-inoculated oil palm seedlings pretreated with phytohormones and their inhibitors

Hydrogen peroxide, salicylic acid (SA) and jasmonic acid (JA) are reported to play important role in plant defense responses against pathogens. In this study, we analyzed the transcript abundance of oil palm respiratory burst oxidase B (EgRbohB1) and H (EgRbohH), Coronatine Insensitive 1 (EgCOI1), OPR5 (EgOPR5), hypersensitive induced response 1 (EgHIR1) and Nonexpressor of pathogenesis-related (EgNPR1) in Ganoderma boninense-inoculated oil palm roots that were pretreated with SA, JA and their inhibitors, paclobutrazol (PAC) and diethyldithiocarbamate (DIECA), respectively. We showed that EgNPR1 was down-regulated by G. boninense infection in SA-pretreated oil palm roots while EgHIR1 was up-regulated by G. boninense in PAC-pretreated oil palm roots. G. boninense inoculation did not change the gene expression levels of EgOPR5 in JA- and DIECA-treated oil palm roots significantly, compared to the uninoculated oil palms roots that were treated similarly. EgCOI1 was up-regulated by G. boninense in JA- and DIECA-pretreated oil palm roots, respectively. G. boninense up-regulated EgRbohB1 in SA-pretreated oil palm roots but down-regulated it in PAC-pretreated oil palm roots. EgRbohH was also down-regulated by G. boninense in PAC-pretreated oil palm roots. These findings facilitate the understanding of phytohormone effects on oil palm-Ganoderma interaction.

Plant Defense Inducers and Antioxidant Metabolites Produced During Oil Palm-Ganoderma boninense Interaction In Vitro

Plant Defense Inducers and Antioxidant Metabolites Produced During Oil Palm-Ganoderma boninense Interaction In Vitro

Metabolite fingerprinting of oil palm (Elaeis guineensis Jacq.) root for the identification of altered metabolic pathways associated with basal stem rot (BSR) disease

Basal stem rot (BSR) disease caused by Ganoderma boninense has remained as one of the major obstacles in oil palm (Elaeis guineensis Jacq.) plantation. BSR is a destructive disease, which contributes to significant yield losses and impacts to the oil palm industry. However, to date, there is still no effective control of the disease. Metabolite fingerprinting is an established non-targeted screening approach to classify samples based on metabolite patterns that change in response to G. boninense infection in oil palm. This study aimed to compare the metabolic profiles of natural Ganoderma-infected and healthy control oil palm root samples using liquid chromatography-quadrupole/time-of-flight-mass spectrometry (LC-Q/TOF-MS) combined with multivariate data analysis (MVDA) and to identify potential metabolic pathway(s) involved in response to BSR. MVDA revealed differential metabolites from oil palm root associated with natural Ganoderma-infected vs. healthy oil palms. A systematic metabolic pathway analysis of differential metabolites discovered the significant involvement of amino acid metabolism, carbohydrate metabolism and biosynthesis of other secondary metabolites in response to BSR disease. Unravelling the metabolic mechanisms involved during pathogen attack provides new knowledge and fill gaps in the information related to the oil palm-Ganoderma pathosystem.

Electronic nose for early detection of basal stem rot caused by Ganoderma in oil palm

The successful control of basal rot disease (BSR) determined by early detection of infection because when the symptoms already appear, generally plants are difficult to save. The earlier the Ganoderma infection is known, the easier the control will be and the losses can be minimized. Therefore, early detection of Ganoderma infection is very necessary, which in this study was carried out by detecting volatile compounds using electronic nose (E-nose). E-nose detection has been carried out to analyze the compounds formed in pure Ganoderma culture. Detection of plants in the field carried out at 4 levels of infection, i.e. healthy, early, moderate and severe infection. The results concluded that Ganoderma mycelium when compared with other fungi (Trichoderma, Aspergillus and Omphalina) showed significant differences when analyzed using an unsupervised PCA chemometric system. The E-nose data processed using machine learning Support Vector Machine (SVM) was able to distinguish the aroma between Ganoderma boninense CSB, G. boninense ‘Rejosari’, and G. lucidum with an accuracy rate of 99.64%. E nose was able to differentiate with high accuracy (90.95%) of each infection level even though there was still a slice between in root sample.

Ganoderma infection of oil palm – a persistent problem in Papua New Guinea and Solomon Islands

Basal stem rot (BSR) disease caused by Ganoderma boninense Pat. is a major limiting factor to palm oil producing countries in South East Asia, which produce 90% of the world’s palm oil demand. BSR has been known for over 100 years and to date continues to be a disease of increasing economic importance. Once considered a disease of senescing palms, BSR has persisted through successive replants, infecting younger plantings and shortening the economic life span of each cropping cycle. Many approaches have been applied to control BSR of oil palm with varying levels of success. To date, there is still no single approach that has been demonstrated to be effective in BSR management. The long-term strategy would be to breed genotypes resistant or tolerant to BSR. However, this is dependent on a multi-disciplinary approach to understanding oil palm-Ganoderma interactions that can reveal the mechanisms involved with infectivity and pathogenicity of Ganoderma, and susceptibility, resistance or tolerance of oil palm. This review aims to highlight the knowledge gaps that need addressing to improve the control and management of BSR.

Molecular performances of oil palm (Elaeis guineensis) tolerance to Ganoderma sp.

Oil palm plantations in Asia, particularly in Indonesia and Malaysia face the threat of basal stem root diseases caused by Ganoderma sp. Various methods and approaches have been made to select the oil palm tolerant to Ganoderma, among others with genes selection. The purpose of this research is to analyze the molecular performance of some oil palm that tolerant to Ganoderma based specific SSR markers. The plant material used in this trial is two cross-series of genetic material belonging to PT Socfindo, which has been known the level of resistance to Ganoderma, first is cross-series of 15-year-old oil palm in the field, and secondly is a new cross-series for early detection in the nursery stage. The results showed all target genes are presented in all samples. There are differences in predicted gene expression between tolerant and susceptible palm in the healthy mature plant leave tissue. The five molecular markers (EgMT, EgIFR, Rgen_Pto, Eg002, and Eg003) in healthy palm leaf tissue can be considered as potential molecular markers for oil palm Ganoderma tolerant screening.

Application of Proteomics Technologies in Oil Palm Research.

Proteomics technologies were first applied in the oil palm research back in 2008. Since proteins are the gene products that are directly correspond to phenotypic traits, proteomic tools hold a strong advantage above other molecular tools to comprehend the biological and molecular mechanisms in the oil palm system. These emerging technologies have been used as non-overlapping tools to link genome-wide transcriptomics and metabolomics-based studies to enhance the oil palm yield and quality through sustainable plant breeding. Many efforts have also been made using the proteomics technologies to address the oil palm's Ganoderma disease; the cause and management. At present, the high-throughput screening technologies are being applied to identify potential biomarkers involved in metabolism and cellular development through determination of protein expression changes that correlate with oil production and disease. This review highlights key elements in proteomics pipeline, challenges and some examples of their implementations in plant studies in the context of oil palm in particular. We foresee that the proteomics technologies will play more significant role to address diverse issues related to the oil palm in the effort to improve the oil crop.

A Rapid Inoculation Method for Infection of Ganoderma in Oil Palm

Basal stem rot (BSR) is a major disease of oil palm plantation caused by pathogenic fungus Ganoderma boninense. To overcome the disease, development of resistant or tolerantoil palms is crucial for susta inable production of palm oil. Thus a reliable and rapid method to assess resistance of oil palm to BSR is important. Here we report an inoculation technique designated as mycelium inoculation technique. This method is faster and simpler compared to the traditional technique using rubber wood block. The technique that we developed results in consistency of infection and disease can be evaluated as early as two weeks after inoculation with G. boninense. Furthermore, this method is also able to differentially assess resistant and susceptible palm seedlings to BSR. The results show that this new inoculation technique can be used as a routine method to infect oil palm seedlings and can be utilised for development of resistant cultivar of oil palm to G. boninense.

Characterization of Streptomyces spp. isolated from the rhizosphere of oil palm and evaluation of their ability to suppress basal stem rot disease in oil palm seedlings when applied as powder formulations in a glasshouse trial.

Ganoderma boninense, the main causal agent of oil palm (Elaeis guineensis) basal stem rot (BSR), severely reduces oil palm yields around the world. To reduce reliance on fungicide applications to control BSR, we are investigating the efficacy of alternative control methods, such as the application of biological control agents. In this study, we used four Streptomyces-like actinomycetes (isolates AGA43, AGA48, AGA347 and AGA506) that had been isolated from the oil palm rhizosphere and screened for antagonism towards G. boninense in a previous study. The aim of this study was to characterize these four isolates and then to assess their ability to suppress BSR in oil palm seedlings when applied individually to the soil in a vermiculite powder formulation. Analysis of partial 16S rRNA gene sequences (512bp) revealed that the isolates exhibited a very high level of sequence similarity (> 98%) with GenBank reference sequences. Isolates AGA347 and AGA506 showed 99% similarity with Streptomyces hygroscopicus subsp. hygroscopicus and Streptomyces ahygroscopicus, respectively. Isolates AGA43 and AGA48 also belonged to the Streptomyces genus. The most effective formulation, AGA347, reduced BSR in seedlings by 73.1%. Formulations using the known antifungal producer Streptomyces noursei, AGA043, AGA048 or AGA506 reduced BSR by 47.4, 30.1, 54.8 and 44.1%, respectively. This glasshouse trial indicates that these Streptomyces spp. show promise as potential biological control agents against Ganoderma in oil palm. Further investigations are needed to determine the mechanism of antagonism and to increase the shelf life of Streptomyces formulations.

Comparative proteomic analysis of Ganoderma species during in vitro interaction with oil palm root

Basal stem rot disease caused by Ganoderma spp. is still considered a large threat to oil palm production in many countries, especially in Malaysia, which contributes to approximately 45% of the world's palm oil exports. In the last 10 years, studies on the oil palm-Ganoderma interaction have mainly focused on the response of the plant towards the fungus. In this study, a comparative proteomic analysis was conducted to investigate the change in protein expression of two Ganoderma spp., namely Ganoderma boninense, which is known as the most aggressive species and Ganoderma tornatum, previously reported as non-pathogenic. Our results showed that both species colonize and penetrate the oil palm root after only 72 h of inoculation. In addition, proteins were expressed differentially in both species that have either direct or indirect links to virulence and pathogenicity. Other proteins related to fungal growth, metabolism and stress from both species were also discussed in this study.

Comparative proteomic analysis of Ganoderma species during in vitro interaction with oil palm root

Basal stem rot disease caused by Ganoderma spp. is still considered a large threat to oil palm production in many countries, especially in Malaysia, which contributes to approximately 45% of the world's palm oil exports. In the last 10 years, studies on the oil palm-Ganoderma interaction have mainly focused on the response of the plant towards the fungus. In this study, a comparative proteomic analysis was conducted to investigate the change in protein expression of two Ganoderma spp., namely Ganoderma boninense, which is known as the most aggressive species and Ganoderma tornatum, previously reported as non-pathogenic. Our results showed that both species colonize and penetrate the oil palm root after only 72 h of inoculation. In addition, proteins were expressed differentially in both species that have either direct or indirect links to virulence and pathogenicity. Other proteins related to fungal growth, metabolism and stress from both species were also discussed in this study.

Modified vegetation indices for Ganoderma disease detection in oil palm from field spectroradiometer data

High resolution field spectroradiometers are important for spectral analysis and mobile inspection of vegetation disease. The biggest challenges in using this technology for automated vegetation disease detection are in spectral signatures pre-processing, band selection and generating reflectance indices to improve the ability of hyperspectral data for early detection of disease. In this paper, new indices for oil palm Ganoderma disease detection were generated using band ratio and different band combination techniques. Unsupervised clustering method was used to cluster the values of each class resultant from each index. The wellness of band combinations was assessed by using Optimum Index Factor (OIF) while cluster validation was executed using Average Silhouette Width (ASW). 11 modified reflectance indices were generated in this study and the indices were ranked according to the values of their ASW. These modified indices were also compared to several existing and new indices. The results showed that the combination of spectral values at 610.5nm and 738nm was the best for clustering the three classes of infection levels in the determination of the best spectral index for early detection of Ganoderma disease.

Prospects for Inhibition of Lignin Degrading Enzymes to Control Ganoderma White Rot of Oil Palm

Oil palm (OP) is prone to a rot by the fungus Ganoderma which may be capable of being controlled by enzyme inhibitors. Palm oil is used in the production of vegetable oil for foods, cosmetics, pharmaceuticals and, most recently, biodiesel. However, the fundamental process of the disease as “white rot” has been ignored by researchers. White rot fungi are capable of degrading lignin ultimately to carbon dioxide and water: Celluloses become available as nutrients for the fungus. One potential control method is to inhibit the ligninolytic enzymes. There are few data on the lignin of OP and none on how it is degraded by OP Ganoderma and so specific examples on how to inhibit the enzymes of the fungus is impossible. Fortunately, there is more information on lignin and lignin model compounds degraded by other fungi. The taxonomy of Ganoderma is confused; hence drawing direct comparisons between other taxa within the genus in terms of ligninolysis is of limited utility. In general, ligninolytic enzymes can be inhibited by (a) temperature, pH and aeration, (b) high carbon and high nitrogen and (c) halides, metal chelators, heavy metals, and reducing agents. These factors require to be tested against the enzymes from Ganoderma from OPs in vitro with a view to developing control methods in the field, and this is how the area requires to be progressed. Furthermore, the procedures may be useful to control other rots of trees and wood products. In the case of OP, such compounds could be (a) injected into (b) sprayed onto and/or (c) added to the soil of the OP. In conclusion, the control of Ganoderma of OP would benefit from investigating the effect of inhibitors on the lignin degrading enzymes in vitro to enable this to be applied in plantations.

Identification of Ganoderma, the causal agent of basal stem rot disease in oil palm using a molecular method

From comparison of the alignments of the internally transcribed spacers (ITS) of ribosomal DNA from Ganoderma associated with oil palm basal stem rot (BSR) and other Ganoderma species, two specific primer pairs were selected to provide a specific DNA amplification of pathogenic Ganoderma in oil palm. Each primer pair produced a single PCR product of about 450 bp (for primer pair IT1-IT2) and 334 bp (for primer pair IT1-IT3) when oil palm Ganoderma DNA was used. No PCR amplification product was observed when other Ganoderma species DNA was used in PCR amplification with these primer pairs. Three specific restriction enzyme sites were identified in the ITS and intergenic spacer (IGS1) regions. The restriction enzymes MluI, SacI and HinfI were used to digest the ITS-PCR product and restriction enzymes TfiI, ScaI and HincII were used to digest the IGS1-PCR product. Of the three restriction enzymes used in each rDNA region, MluI specifically digested the ITS regions, and TfiI specifically digested the IGS1 region of oil palm Ganoderma. Analysis of the published ITS nucleotide sequences of 31 Ganoderma species showed that the MluI restriction site was not present in other Ganoderma species. The use of both specific primers and restriction enzyme analysis can be applied as a standard protocol to identify pathogenic Ganoderma in oil palm. In this study, the use of specific primers and PCR-RFLP analyses of the rDNA gave consistent results for the characterisation of pathogenic Ganoderma, and indicated that Ganoderma strains associated with BSR disease in oil palms belong to a single species.