Comparison of DNA extraction and detection of ganoderma, causal of basal stem rot disease in oil palm using loop-mediated isothermal amplification

A. Z. Madihah, M. Maizatul-Suriza, A. S. Idris, M. F.A. Bakar, S. Kamaruddin, Izwan Bharudin, Farah Diba Abu Bakar, Abdul Munir Abd. Murad

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Ganoderma boninense, a phytopathogenic fungus in the causal of the basal stem rot (BSR) disease of oil palm in Malaysia. Current detection method requires longer time and subjected to cross-reactivity with other fungi. The aim of this study is to develop fast and reliable method for detecting Ganoderma using loop-mediated isothermal amplification (LAMP). Several protocols of DNA extraction were compared to produce good quality of genomic DNA for LAMP detection. The highest concentration was achieved at 2197.8 ng µL-1 when using polyvinylpyrrolidone and sodium dodecyl sulphate method. Several genes from transcriptomic data were selected for LAMP detection such as mating genes (STE3 and STE12), regulatory genes (MnSOD and lac) and G. boninense novel genes (BUG1, BUG2, BUG3 and BUG4). Sensitivity test revealed the ability of LAMP detection at DNA concentration of 0.002 ng µL-1 in less than 40 min at 65ºC; whereas a minimum of 0.02 ng µL-1 was required to detect Ganoderma using polymerase chain reaction (PCR). Out of eight set of LAMP primers designed, only bug1A primer combination was able to distinguish between Ganoderma pathogenic strains (G. boninense, G. zonatum and G. miniatocinctum) and Ganoderma non-pathogenic strain (G. tornatum) and other actinomycetes/basidiomycetes fungi. Result was confirmed by conventional PCR indicating that LAMP is more sensitive and better potential in detecting Ganoderma pathogenic to oil palm.

Original languageEnglish
Pages (from-to)119-127
Number of pages9
JournalMalaysian Applied Biology
Volume47
Issue number5
Publication statusPublished - 1 Nov 2018

Fingerprint

Ganoderma
stem rot
Elaeis guineensis
Oils
DNA
Fungi
polymerase chain reaction
Genes
Povidone
Polymerase Chain Reaction
Basidiomycota
fungi
genes
avirulent strains
Actinobacteria
Malaysia
plant pathogenic fungi
sodium dodecyl sulfate
Regulator Genes
regulator genes

Keywords

  • Basal stem rot
  • Ganoderma
  • LAMP
  • Loop-mediated isothermal amplification
  • Oil palm

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Comparison of DNA extraction and detection of ganoderma, causal of basal stem rot disease in oil palm using loop-mediated isothermal amplification. / Madihah, A. Z.; Maizatul-Suriza, M.; Idris, A. S.; Bakar, M. F.A.; Kamaruddin, S.; Bharudin, Izwan; Abu Bakar, Farah Diba; Abd. Murad, Abdul Munir.

In: Malaysian Applied Biology, Vol. 47, No. 5, 01.11.2018, p. 119-127.

Research output: Contribution to journalArticle

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