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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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Paril JF, Balding DJ, Fournier-Level A. Optimizing sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations. Mol Ecol Resour 2021; 22:137-152. [PMID: 34192415 DOI: 10.1111/1755-0998.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/02/2021] [Accepted: 06/25/2021] [Indexed: 11/27/2022]
Abstract
Mapping the genes underlying ecologically relevant traits in natural populations is fundamental to develop a molecular understanding of species adaptation. Current sequencing technologies enable the characterization of a species' genetic diversity across the landscape or even over its whole range. The relevant capture of the genetic diversity across the landscape is critical for a successful genetic mapping of traits and there are no clear guidelines on how to achieve an optimal sampling and which sequencing strategy to implement. Here we determine, through simulation, the sampling scheme that maximizes the power to map the genetic basis of a complex trait in an outbreeding species across an idealized landscape and draw genomic predictions for the trait, comparing individual and pool sequencing strategies. Our results show that quantitative trait locus detection power and prediction accuracy are higher when more populations over the landscape are sampled and this is more cost-effectively done with pool sequencing than with individual sequencing. Additionally, we recommend sampling populations from areas of high genetic diversity. As progress in sequencing enables the integration of trait-based functional ecology into landscape genomics studies, these findings will guide study designs allowing direct measures of genetic effects in natural populations across the environment.
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Affiliation(s)
- Jefferson F Paril
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - David J Balding
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexandre Fournier-Level
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia
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