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Wong WC, Tung HJ, Nurul Fadhilah M, Midot F, Lau SYL, Melling L, Astari S, Hadziabdic Đ, Trigiano RN, Goh YK, Goh KJ. Evidence for high gene flow, nonrandom mating, and genetic bottlenecks of Ganoderma boninense infecting oil palm ( Elaeis guineensis Jacq.) plantations in Malaysia and Indonesia. Mycologia 2022; 114:947-963. [PMID: 36239960 DOI: 10.1080/00275514.2022.2118512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Ganoderma boninense, the causal agent of basal stem rot (BSR) disease, has been recognized as a major economic threat to commercial plantings of oil palm (Elaeis guineensis Jacq.) in Southeast Asia, which supplies 86% of the world's palm oil. High genetic diversity and gene flow among regional populations of 417 G. boninense isolates collected from Sabah, Sarawak, and Peninsular Malaysia (Malaysia) and Sumatra (Indonesia) were demonstrated using 16 microsatellite loci. Three genetic clusters and different admixed populations of G. boninense across regions were detected, and they appeared to follow the spread of the fungus from the oldest (Peninsular Malaysia and Sumatra) to younger generations of oil palm plantings (Sabah and Sarawak). Low spatial genetic differentiation of G. boninense (FST = 0.05) among the sampling regions revealed geographically nonrestricted gene dispersal, but isolation by distance was still evident. Analysis of molecular variance (AMOVA) confirmed the little to no genetic differentiation among the pathogen populations and the three genetic clusters defined by STRUCTURE and minimum spanning network. Despite G. boninense being highly outcrossing and spread by sexual spores, linkage disequilibrium was detected in 7 of the 14 populations. Linkage disequilibrium indicated that the reproduction of the fungus was not entirely by random mating and genetic drift could be an important structuring factor. Furthermore, evidence of population bottleneck was indicated in the oldest oil palm plantations as detected in genetic clusters 2 and 3, which consisted mainly of Peninsular Malaysia and Sumatra isolates. The population bottleneck or founding event could have arisen from either new planting or replanting after the removal of large number of palm hosts. The present study also demonstrated that migration and nonrandom mating of G. boninense could be important for survival and adaptation to new palm hosts.
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Affiliation(s)
- W C Wong
- Biotechnology Section, Advanced Agriecological Research Sendirian Berhad, AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - H J Tung
- Biotechnology Section, Advanced Agriecological Research Sendirian Berhad, AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - M Nurul Fadhilah
- Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - F Midot
- Molecular and Microbiology Division, Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - S Y L Lau
- Molecular and Microbiology Division, Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - L Melling
- Molecular and Microbiology Division, Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - S Astari
- Pest and Disease Section, Perseroan Terbatas Applied Agricultural Resources Indonesia, KLK Plantation Crop Research Centre, Jalan Harapan Utama No. 10, Rukun Tetangga 001 / Rukun Warga 001, Kelurahan Delima, Kecamatan Binawidya, Pekanbaru 28295, Riau, Indonesia
| | - Đ Hadziabdic
- Department of Entomology and Plant Pathology, The University of Tennessee, 370 Plant Biotechnology Building, 2505 E.J. Chapman Drive, Knoxville, Tennessee 37996
| | - R N Trigiano
- Department of Entomology and Plant Pathology, The University of Tennessee, 370 Plant Biotechnology Building, 2505 E.J. Chapman Drive, Knoxville, Tennessee 37996
| | - Y K Goh
- Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - K J Goh
- Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
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Grinn-Gofroń A, Bogawski P, Bosiacka B, Nowosad J, Camacho I, Sadyś M, Skjøth CA, Pashley CH, Rodinkova V, Çeter T, Traidl-Hoffmann C, Damialis A. Abundance of Ganoderma sp. in Europe and SW Asia: modelling the pathogen infection levels in local trees using the proxy of airborne fungal spore concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148509. [PMID: 34175598 DOI: 10.1016/j.scitotenv.2021.148509] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/09/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Ganoderma comprises a common bracket fungal genus that causes basal stem rot in deciduous and coniferous trees and palms, thus having a large economic impact on forestry production. We estimated pathogen abundance using long-term, daily spore concentration data collected in five biogeographic regions in Europe and SW Asia. We hypothesized that pathogen abundance in the air depends on the density of potential hosts (trees) in the surrounding area, and that its spores originate locally. We tested this hypothesis by (1) calculating tree cover density, (2) assessing the impact of local meteorological variables on spore concentration, (3) computing back trajectories, (4) developing random forest models predicting daily spore concentration. The area covered by trees was calculated based on Tree Density Datasets within a 30 km radius from sampling sites. Variations in daily and seasonal spore concentrations were cross-examined between sites using a selection of statistical tools including HYSPLIT and random forest models. Our results showed that spore concentrations were higher in Northern and Central Europe than in South Europe and SW Asia. High and unusually high spore concentrations (> 90th and > 98th percentile, respectively) were partially associated with long distance transported spores: at least 33% of Ganoderma spores recorded in Madeira during days with high concentrations originated from the Iberian Peninsula located >900 km away. Random forest models developed on local meteorological data performed better in sites where the contribution of long distance transported spores was lower. We found that high concentrations were recorded in sites with low host density (Leicester, Worcester), and low concentrations in Kastamonu with high host density. This suggests that south European and SW Asian forests may be less severely affected by Ganoderma. This study highlights the effectiveness of monitoring airborne Ganoderma spore concentrations as a tool for assessing local Ganoderma pathogen infection levels.
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Affiliation(s)
| | - Paweł Bogawski
- Department of Systematic and Environmental Botany, Laboratory of Biological Spatial Information, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Beata Bosiacka
- Institute of Marine and Environmental Sciences, University of Szczecin, 70-383 Szczecin, Poland
| | - Jakub Nowosad
- Institute of Geoecology and Geoinformation, Adam Mickiewicz University, 10 Krygowskiego Street, 61-680 Poznań, Poland
| | - Irene Camacho
- Madeira University, Faculty of Life Sciences, Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Magdalena Sadyś
- Hereford & Worcester Fire and Rescue Service, Headquarters, Performance & Information, Hindlip Park, Worcester WR3 8SP, United Kingdom; University of Worcester, School of Science and the Environment, Henwick Grove, Worcester WR2 6AJ, United Kingdom
| | - Carsten Ambelas Skjøth
- University of Worcester, School of Science and the Environment, Henwick Grove, Worcester WR2 6AJ, United Kingdom
| | - Catherine Helen Pashley
- Institute for Lung Health, Department of Respiratory Sciences, University of Leicester, Leicester LE1 7RH, United Kingdom
| | | | - Talip Çeter
- Kastamonu University, Arts and Sciences Faculty, Department of Biology, 37100 Kuzeykent, Kastamonu, Turkey
| | - Claudia Traidl-Hoffmann
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany; Institute of Environmental Medicine, Helmholtz Center Munich - Research Center for Environmental Health, Augbsurg, Germany
| | - Athanasios Damialis
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany; Department of Ecology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Greece.
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Wong WC, Tung HJ, Fadhilah MN, Midot F, Lau SYL, Melling L, Astari S, Hadziabdic Đ, Trigiano RN, Goh KJ, Goh YK. Genetic diversity and gene flow amongst admixed populations of Ganoderma boninense, causal agent of basal stem rot in African oil palm ( Elaeis guineensis Jacq.) in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia). Mycologia 2021; 113:902-917. [PMID: 34161196 DOI: 10.1080/00275514.2021.1884815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In 1911 and 1917, the first commercial plantings of African oil palm (Elaeis guineensis Jacq.) were made in Indonesia and Malaysia in Southeast Asia. In less than 15 years, basal stem rot (BSR) was reported in Malaysia. It took nearly another seven decades to identify the main causal agent of BSR as the fungus, Ganoderma boninense. Since then, research efforts have focused on understanding G. boninense disease epidemiology, biology, and etiology, but limited progress was made to characterize pathogen genetic diversity, spatial structure, pathogenicity, and virulence. This study describes pathogen variability, gene flow, population differentiation, and genetic structure of G. boninense in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia) inferred by 16 highly polymorphic cDNA-SSR (simple sequence repeat) markers. Marker-inferred genotypic diversity indicated a high level of pathogen variability among individuals within a population and among different populations. This genetic variability is clearly the result of outcrossing between basidiospores to produce recombinant genotypes. Although our results indicated high gene flow among the populations, there was no significant genetic differentiation among G. boninense populations on a regional scale. It suggested that G. boninense genetic makeup is similar across a wide region. Furthermore, our results revealed the existence of three admixed genetic clusters of G. boninense associated with BSR-diseased oil palms sampled throughout Sarawak, Peninsular Malaysia, and Sumatra. We postulate that the population structure is likely a reflection of the high genetic variability of G. boninense populations. This, in turn, could be explained by highly successful outcrossing between basidiospores of G. boninense from Southeast Asia and introduced genetic sources from various regions of the world, as well as regional adaptation of various pathogen genotypes to different palm hosts. Pathogen variability and population structure could be employed to deduce the epidemiology of G. boninense, as well as the implications of plantation cultural practices on BSR disease control in different regions.
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Affiliation(s)
- W C Wong
- Applied Agricultural Resources Sdn. Bhd., AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - H J Tung
- Applied Agricultural Resources Sdn. Bhd., AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - M Nurul Fadhilah
- Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - F Midot
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - S Y L Lau
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - L Melling
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - S Astari
- PT Applied Agricultural Resources Indonesia, Kompleks Taman Anggrek Block D1, Jl Tuanku Tambusai, Pekanbaru, Riau, Indonesia, 28291
| | - Đ Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 E J Chapman Drive, Knoxville, Tennessee 37996
| | - R N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 E J Chapman Drive, Knoxville, Tennessee 37996
| | - K J Goh
- Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Y K Goh
- Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
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Mohd Bakhori N, Yusof NA, Abdullah AH, Hussein MZ. Development of a Fluorescence Resonance Energy Transfer (FRET)-Based DNA Biosensor for Detection of Synthetic Oligonucleotide of Ganoderma boninense. BIOSENSORS-BASEL 2013; 3:419-28. [PMID: 25587406 PMCID: PMC4263569 DOI: 10.3390/bios3040419] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 12/04/2022]
Abstract
An optical DNA biosensor based on fluorescence resonance energy transfer (FRET) utilizing synthesized quantum dot (QD) has been developed for the detection of specific-sequence of DNA for Ganoderma boninense, an oil palm pathogen. Modified QD that contained carboxylic groups was conjugated with a single-stranded DNA probe (ssDNA) via amide-linkage. Hybridization of the target DNA with conjugated QD-ssDNA and reporter probe labeled with Cy5 allows for the detection of related synthetic DNA sequence of Ganoderma boninense gene based on FRET signals. Detection of FRET emission before and after hybridization was confirmed through the capability of the system to produce FRET at 680 nm for hybridized sandwich with complementary target DNA. No FRET emission was observed for non-complementary system. Hybridization time, temperature and effect of different concentration of target DNA were studied in order to optimize the developed system. The developed biosensor has shown high sensitivity with detection limit of 3.55 × 10−9 M. TEM results show that the particle size of QD varies in the range between 5 to 8 nm after ligand modification and conjugation with ssDNA. This approach is capable of providing a simple, rapid and sensitive method for detection of related synthetic DNA sequence of Ganoderma boninense.
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Affiliation(s)
- Noremylia Mohd Bakhori
- Chemistry Department, Faculty Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; E-Mails: (N.M.B.); (A.H.A.); (M.Z.H.)
| | - Nor Azah Yusof
- Chemistry Department, Faculty Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; E-Mails: (N.M.B.); (A.H.A.); (M.Z.H.) ; Institute of Advanced Technology, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Abdul Halim Abdullah
- Chemistry Department, Faculty Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; E-Mails: (N.M.B.); (A.H.A.); (M.Z.H.) ; Institute of Advanced Technology, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Mohd Zobir Hussein
- Chemistry Department, Faculty Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; E-Mails: (N.M.B.); (A.H.A.); (M.Z.H.) ; Institute of Advanced Technology, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
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Hushiarian R, Yusof NA, Dutse SW. Detection and control of Ganoderma boninense: strategies and perspectives. SPRINGERPLUS 2013; 2:555. [PMID: 24255849 PMCID: PMC3824713 DOI: 10.1186/2193-1801-2-555] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/17/2013] [Indexed: 01/03/2023]
Abstract
The oil palm, an economically important tree, has been one of the world's major sources of edible oil and a significant precursor of biodiesel fuel. Unfortunately, it now faces the threat of a devastating disease. Many researchers have identified Ganoderma boninense as the major pathogen that affects the oil palm tree and eventually kills it. But identification of the pathogen is just the first step. No single method has yet been able to halt the continuing spread of the disease. This paper discusses the modes of infection and transmission of Ganoderma boninense and suggests techniques for its early detection. Additionally, the paper proposes some possible ways of controlling the disease. Such measures, if implemented, could contribute significantly to the sustainability of the palm oil industry in South East Asia.
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Affiliation(s)
- Roozbeh Hushiarian
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor 43400 UPM Malaysia
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Murphy DJ. Future prospects for oil palm in the 21st century: Biological and related challenges. EUR J LIPID SCI TECH 2007. [DOI: 10.1002/ejlt.200600229] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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