Identification of proteins of altered abundance in oil palm infected with Ganoderma boninense

Traditional to technological advancements in Ganoderma detection methods in oil palm

Ganoderma sp., the fungal agent causing basal stem rot (BSR), poses a severe threat to global oil palm production. Alarming increases in BSR occurrences within oil palm growing zones are attributed to varying effectiveness in its current management strategies. Asymptomatic progression of the disease and the continuous monoculture of oil palm pose challenges for prompt and effective management. Therefore, the development of precise, early, and timely detection techniques is crucial for successful BSR management. Conventional methods such as visual assessments, culture-based assays, and biochemical and physiological approaches prove time-consuming and lack specificity. Serological-based diagnostic methods, unsuitable for fungal diagnostics due to low sensitivity, assay affinity, cross-contamination which further underscores the need for improved techniques. Molecular PCR-based assays, utilizing universal, genus-specific, and species-specific primers, along with functional primers, can overcome the limitations of conventional and serological methods in fungal diagnostics. Recent advancements, including real-time PCR, biosensors, and isothermal amplification methods, facilitate accurate, specific, and sensitive Ganoderma detection. Comparative whole genomic analysis enables high-resolution discrimination of Ganoderma at the strain level. Additionally, omics tools such as transcriptomics, proteomics, and metabolomics can identify potential biomarkers for early detection of Ganoderma infection. Innovative on-field diagnostic techniques, including remote methods like volatile organic compounds profiling, tomography, hyperspectral and multispectral imaging, terrestrial laser scanning, and Red-Green-Blue cameras, contribute to a comprehensive diagnostic approach. Ultimately, the development of point-of-care, early, and cost-effective diagnostic techniques accessible to farmers is vital for the timely management of BSR in oil palm plantations.

An In-Depth Study of Phytopathogenic Ganoderma: Pathogenicity, Advanced Detection Techniques, Control Strategies, and Sustainable Management

Phytopathogenic Ganoderma species pose a significant threat to global plant health, resulting in estimated annual economic losses exceeding USD (US Dollars) 68 billion in the agriculture and forestry sectors worldwide. To combat this pervasive menace effectively, a comprehensive understanding of the biology, ecology, and plant infection mechanisms of these pathogens is imperative. This comprehensive review critically examines various aspects of Ganoderma spp., including their intricate life cycle, their disease mechanisms, and the multifaceted environmental factors influencing their spread. Recent studies have quantified the economic impact of Ganoderma infections, revealing staggering yield losses ranging from 20% to 80% across various crops. In particular, oil palm plantations suffer devastating losses, with an estimated annual reduction in yield exceeding 50 million metric tons. Moreover, this review elucidates the dynamic interactions between Ganoderma and host plants, delineating the pathogen's colonization strategies and its elicitation of intricate plant defense responses. This comprehensive analysis underscores the imperative for adopting an integrated approach to Ganoderma disease management. By synergistically harnessing cultural practices, biological control, and chemical treatments and by deploying resistant plant varieties, substantial strides can be made in mitigating Ganoderma infestations. Furthermore, a collaborative effort involving scientists, breeders, and growers is paramount in the development and implementation of sustainable strategies against this pernicious plant pathogen. Through rigorous scientific inquiry and evidence-based practices, we can strive towards safeguarding global plant health and mitigating the dire economic consequences inflicted by Ganoderma infections.

Basal Stem Rot of Oil Palm: The Pathogen, Disease Incidence, and Control Methods

Basal stem rot of oil palm caused by Ganoderma boninense is the most serious disease of oil palm in Malaysia, Indonesia, and other oil-palm-producing countries. Economic losses caused by the disease can be up to USD500 million a year. For many years, basal stem rot was found to infect older palm trees of more than 25 to 30 years in age. Only in the 1950s, the disease began to appear in much younger palm trees, 10 to 15 years old, and, in the last decade or so, palm trees as young as 1 year were infected by the disease. The highest incidence occurs in coastal areas of Southeast Asia but the disease has now infected oil palm in inland areas, mainly oil palm planted in peat soils. Disease incidence is also high in areas previously growing coconut or forest. Basal stem rot infection and spread occur through root-to-root contact, and basidiospores that colonize the roots also play a role. In the early stages of infection by G. boninense, the pathogen behaves as a biotroph and later as a necrotroph, secreting cell-wall-degrading enzymes and triggering host defense responses. Genes, gene products, and metabolic pathways involved in oil palm defense mechanisms against G. boninense have been identified and these metabolites have the potential to be used as markers for early detection of the disease. Integrated disease management used to control basal stem rot includes cultural practices, chemical control, and application of biocontrol agents or fertilizers. Early detection tools have also been developed that could assist in management of basal stem rot infections. Development of resistant or tolerant oil palm is still at an early stage; therefore, the existing integrated disease management practices remain the most appropriate methods for managing basal stem rot of oil palm.

1H NMR metabolomics analysis of oil palm stem tissue infected by Ganoderma boninense based on field severity Indices

Basal stem rot disease (BSR) caused by G. boninense affects most oil palm plants in Southeast Asia. This disease can be fatal to palm oil production. BSR shows no signs on the tree in the early stages of infection. Therefore, it is essential to find an approach that can detect BSR disease in oil palm, especially at any level of disease severity in the field. This study aims to identify biomarkers of BSR disease in oil palm stem tissue based on various disease severity indices in the field using ¹H NMR-based metabolomics analysis. The crude extract of oil palm stem tissue with four disease severity indices was analyzed by ¹H NMR metabolomics. Approximately 90 metabolites from oil palm stem tissue were identified.Twenty of these were identified as metabolites that significantly differentiated the four disease severity indices. These metabolites include the organic acid group, the carbohydrate group, the organoheterocyclic compound group, and the benzoid group. In addition, different tentative biomarkers for different disease severity indices were also identified. These tentative biomarkers consist of groups of organic acids, carbohydrates, organoheterocyclic compounds, nitrogenous organic compounds, and benzene. There are five pathways in oil palm that are potentially affected by BSR disease.

In silico QTL mapping in an oil palm breeding program reveals a quantitative and complex genetic resistance to Ganoderma boninense

Basal stem rot caused by Ganoderma boninense is the major threat to oil palm cultivation in Southeast Asia, which accounts for 80% of palm oil production worldwide, and this disease is increasing in Africa. The use of resistant planting material as part of an integrated pest management of this disease is one sustainable solution. However, breeding for Ganoderma resistance requires long-term and costly research, which could greatly benefit from marker-assisted selection (MAS). In this study, we evaluated the effectiveness of an in silico genetic mapping approach that took advantage of extensive data recorded in an ongoing breeding program. A pedigree-based QTL mapping approach applied to more than 10 years' worth of data collected during pre-nursery tests revealed the quantitative nature of Ganoderma resistance and identified underlying loci segregating in genetic diversity that is directly relevant for the breeding program supporting the study. To assess the consistency of QTL effects between pre-nursery and field environments, information was collected on the disease status of the genitors planted in genealogical gardens and modeled with pre-nursery-based QTL genotypes. In the field, individuals were less likely to be infected with Ganoderma when they carried more favorable alleles at the pre-nursery QTL. Our results pave the way for a MAS of Ganoderma resistant and high yielding planting material, and the provided proof-of-concept of this efficient and cost-effective approach could motivate similar studies based on diverse breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01246-9.

Current strategies and perspectives in detection and control of basal stem rot of oil palm

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.

Proteomics of Sago Palm Towards Identifying Contributory Proteins in Stress-Tolerant Cultivar

Metroxylon sagu Rottb. or locally known as sago palm is a tropical starch crop grown for starch production in commercial plantations in Malaysia, especially in Sarawak, East Malaysia. This plant species accumulate the highest amount of edible starch compared to other starch-producing crops. However, the non-trunking phenomenon has been observed to be one of the major issues restricting the yield of sago palm starch. In this study, proteomics approach was utilised to discover differences between trunking and non-trunking proteomes in sago palm leaf tissues. Total protein from 16 years old trunking and non-trunking sago palm leaves from deep peat area were extracted with PEG fractionation extraction method and subjected to two-dimensional gel electrophoresis (2D PAGE). Differential protein spots were subjected to MALDI-ToF/ToF MS/MS. Proteomic analysis has identified 34 differentially expressed proteins between trunking and non-trunking sago samples. From these protein spots, all 19 proteins representing different enzymes and proteins have significantly increased in abundance in non-trunking sago plant when subjected to mass spectrometry. The identified proteins mostly function in metabolic pathways including photosynthesis, tricarboxylic acid cycle, glycolysis, carbon utilization and oxidative stress. The current study indicated that the several proteins identified through differentially expressed proteome contributed to physical differences in trunking and non-trunking sago palm.

Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis

Protein solubility is a critical prerequisite to any proteomics analysis. Combination of urea/thiourea and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) have been routinely used to enhance protein solubilization for oil palm proteomics studies in recent years. The goals of these proteomics analysis are essentially to complement the knowledge regarding the regulation networks and mechanisms of the oil palm fatty acid biosynthesis. Through omics integration, the information is able to build a regulatory model to support efforts in improving the economic value and sustainability of palm oil in the global oil and vegetable market. Our study evaluated the utilization of sodium deoxycholate as an alternative solubilization buffer/additive to urea/thiourea and CHAPS. Efficiency of urea/thiourea/CHAPS, urea/CHAPS, urea/sodium deoxycholate and sodium deoxycholate buffers in solubilizing the oil palm (Elaeis guineensis var. Tenera) mesocarp proteins were compared. Based on the protein yields and electrophoretic profile, combination of urea/thiourea/CHAPS were shown to remain a better solubilization buffer and additive, but the differences with sodium deoxycholate buffer was insignificant. A deeper mass spectrometric and statistical analyses on the identified proteins and peptides from all the evaluated solubilization buffers revealed that sodium deoxycholate had increased the number of identified proteins from oil palm mesocarps, enriched their gene ontologies and reduced the number of carbamylated lysine residues by more than 67.0%, compared to urea/thiourea/CHAPS buffer. Although only 62.0% of the total identified proteins were shared between the urea/thiourea/CHAPS and sodium deoxycholate buffers, the importance of the remaining 38.0% proteins depends on the applications. The only observed limitations to the application of sodium deoxycholate in protein solubilization were the interference with protein quantitation and but it could be easily rectified through a 4-fold dilution. All the proteomics data are available via ProteomeXchange with identifier PXD013255. In conclusion, sodium deoxycholate is applicable in the solubilization of proteins extracted from oil palm mesocarps with higher efficiency compared to urea/thiourea/CHAPS buffer. The sodium deoxycholate buffer is more favorable for proteomics analysis due to its proven advantages over urea/thiourea/CHAPS buffer.

Identification of Ganoderma Disease Resistance Loci Using Natural Field Infection of an Oil Palm Multiparental Population

Multi-parental populations are promising tools for identifying quantitative disease resistance loci. Stem rot caused by Ganoderma boninense is a major threat to palm oil production, with yield losses of up to 80% prompting premature replantation of palms. There is evidence of genetic resistance sources, but the genetic architecture of Ganoderma resistance has not yet been investigated. This study aimed to identify Ganoderma resistance loci using an oil palm multi-parental population derived from nine major founders of ongoing breeding programs. A total of 1200 palm trees of the multi-parental population was planted in plots naturally infected by Ganoderma, and their health status was assessed biannually over 25 yr. The data were treated as survival data, and modeled using the Cox regression model, including a spatial effect to take the spatial component in the spread of Ganoderma into account. Based on the genotypes of 757 palm trees out of the 1200 planted, and on pedigree information, resistance loci were identified using a random effect with identity-by-descent kinship matrices as covariance matrices in the Cox model. Four Ganoderma resistance loci were identified, two controlling the occurrence of the first Ganoderma symptoms, and two the death of palm trees, while favorable haplotypes were identified among a major gene pool for ongoing breeding programs. This study implemented an efficient and flexible QTL mapping approach, and generated unique valuable information for the selection of oil palm varieties resistant to Ganoderma disease.

Temporal regulation of proteome profile in the fruit fly, Drosophila melanogaster

Background. Diurnal rhythms of protein synthesis controlled by the biological clock underlie the rhythmic physiology in the fruit fly, Drosophila melanogaster. In this study, we conducted a proteome-wide investigation of rhythmic protein accumulation in D. melanogaster.

Materials and Methods. Total protein collected from fly samples harvested at 4 h intervals over the 24 h period were subjected to two-dimensional gel electrophoresis, trypsin digestion and MS/MS analysis. Protein spots/clusters were identified with MASCOT search engine and Swiss-Prot database. Expression of proteins was documented as percentage of volume contribution using the Image Master 2D Platinum software.

Results. A total of 124 protein spots/clusters were identified using MS/MS analysis. Significant variation in the expression of 88 proteins over the 24-h period was observed. A relatively higher number of proteins was upregulated during the night compared to the daytime. The complexity of temporal regulation of the D. melanogaster proteome was further reflected from functional annotations of the differently expressed proteins, with those that were upregulated at night being restricted to the heat shock proteins and proteins involved in metabolism, muscle activity, protein synthesis/folding/degradation and apoptosis, whilst those that were overexpressed in the daytime were apparently involved in metabolism, muscle activity, ion-channel/cellular transport, protein synthesis/folding/degradation, redox homeostasis, development and transcription.

Conclusion. Our data suggests that a wide range of proteins synthesized by the fruit fly, D. melanogaster, is under the regulation of the biological clock.