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Genetic Diversity and Demographic History of Ganoderma boninense in Oil Palm Plantations of Sarawak, Malaysia Inferred from ITS Regions

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Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300 Kota Samarahan, Sarawak, Malaysia
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Applied Agricultural Resources Sdn. Bhd. (AAR)—University of Nottingham Malaysia Campus (UNMC) Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
*
Author to whom correspondence should be addressed.
Microorganisms 2019, 7(10), 464; https://doi.org/10.3390/microorganisms7100464
Received: 3 September 2019 / Revised: 7 October 2019 / Accepted: 14 October 2019 / Published: 16 October 2019
(This article belongs to the Section Environmental Microbiology)
Ganoderma boninense causes basal stem rot (BSR) and is responsible for substantial economic losses to Southeast Asia’s palm oil industry. Sarawak, a major producer in Malaysia, is also affected by this disease. Emergence of BSR in oil palm planted on peat throughout Sarawak is alarming as the soil type was previously regarded as non-conducive. Phylogenetic analysis indicated a single species, G. boninense as the cause of BSR in Sarawak. Information on evolutionary and demographic history for G. boninense in Sarawak inferred through informative genes is lacking. Hence, a haplotype study on single nucleotide polymorphisms in internal transcribed spacers (SNPs-ITS) of G. boninense was carried out. Sequence variations were analysed for population structure, phylogenetic and phylogeographic relationships. The internal transcribed spacers (ITS) region of 117 isolates from four populations in eight locations across Sarawak coastal areas revealed seven haplotypes. A major haplotype, designated GbHap1 (81.2%), was found throughout all sampling locations. Single nucleotide polymorphisms were observed mainly in the ITS1 region. The genetic structure was not detected, and genetic distance did not correlate with geographical distance. Haplotype network analysis suggested evidence of recent demographic expansion. Low genetic differences among populations also suggested that these isolates belong to a single G. boninense founder population adapting to oil palm as the host. View Full-Text
Keywords: Ganoderma boninense; oil palm; basal stem rot; phylogenetic; phylogeographic relationship; ITS Ganoderma boninense; oil palm; basal stem rot; phylogenetic; phylogeographic relationship; ITS
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Midot, F.; Lau, S.Y.L.; Wong, W.C.; Tung, H.J.; Yap, M.L.; Lo, M.L.; Jee, M.S.; Dom, S.P.; Melling, L. Genetic Diversity and Demographic History of Ganoderma boninense in Oil Palm Plantations of Sarawak, Malaysia Inferred from ITS Regions. Microorganisms 2019, 7, 464.

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