A rapid and efficient DNA extraction protocol for Ganoderma zonatum a basal and upper stem rot pathogen of oil palm in Malaysia

Chin Chiew Foan, . and Faizun Kadri, . and May Sean T., . and Idris Abu Seman, . and Jayanthi Nagappan, . and Low Eng Ti Leslie, . and Cooper Richard M., . A rapid and efficient DNA extraction protocol for Ganoderma zonatum a basal and upper stem rot pathogen of oil palm in Malaysia. pp. 12-20. ISSN 1511-2780

Ganoderma zonatum is associated with both the basal and upper stem rot diseases in oil palm. Despite the severity of these diseases there is only limited information on the molecular characteristics of this oil palm pathogen. Most of the studies on G. zonatum related to oil palm are focused on the epidemiology and genetic diversity of the organism. In other palm species G. zonatum has also been identifed as the causal agent of bud rot disease. To further characterise the organism using molecular techniques the ability to isolate good quality DNA samples is important. In this study seven DNA extraction protocols were evaluated and the best protocol Boehm protocol had the highest yield of good quality DNA. The protocol was able to yield 208.95 4.52 g DNA per gram of sample with purities above 1.80 for A‚‚‚‚�„‚‚‚‚ and 2.0 for A‚‚‚‚/‚‚‚‚. This extraction protocol is a rapid and efficient protocol that employs cetyl trimethylammonium bromide (CTAB) sodium dodecyl sulphate (SDS) -mercaptoethanol and proteinase K in the lysis bufer. The Boehm protocol was further tested on three other Ganoderma species found in the oil palm plantations and a medicinal fungus G. lucidum. It was noted that the protocol was efficient with high yields for G. zonatum when compared to the other four species. This is probably due to the fact that extraction protocols for each organism requires specific optimisation to obtain optimal yield and purity. In conclusion the Boehm protocol was best suited for genomic DNA extraction of G. zonatum and found suitable for downstream application such as PacBio sequencing.

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Abstract

Ganoderma zonatum is associated with both the basal and upper stem rot diseases in oil palm. Despite the severity of these diseases there is only limited information on the molecular characteristics of this oil palm pathogen. Most of the studies on G. zonatum related to oil palm are focused on the epidemiology and genetic diversity of the organism. In other palm species G. zonatum has also been identifed as the causal agent of bud rot disease. To further characterise the organism using molecular techniques the ability to isolate good quality DNA samples is important. In this study seven DNA extraction protocols were evaluated and the best protocol Boehm protocol had the highest yield of good quality DNA. The protocol was able to yield 208.95 4.52 g DNA per gram of sample with purities above 1.80 for A‚‚‚‚�„‚‚‚‚ and 2.0 for A‚‚‚‚/‚‚‚‚. This extraction protocol is a rapid and efficient protocol that employs cetyl trimethylammonium bromide (CTAB) sodium dodecyl sulphate (SDS) -mercaptoethanol and proteinase K in the lysis bufer. The Boehm protocol was further tested on three other Ganoderma species found in the oil palm plantations and a medicinal fungus G. lucidum. It was noted that the protocol was efficient with high yields for G. zonatum when compared to the other four species. This is probably due to the fact that extraction protocols for each organism requires specific optimisation to obtain optimal yield and purity. In conclusion the Boehm protocol was best suited for genomic DNA extraction of G. zonatum and found suitable for downstream application such as PacBio sequencing.

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Item Type:	Article
AGROVOC Term:	Oil palm
AGROVOC Term:	Pathogens
AGROVOC Term:	Diseases
AGROVOC Term:	Sampling
AGROVOC Term:	Statistical analysis
AGROVOC Term:	Gel electrophoresis
AGROVOC Term:	Polymerase chain reaction
AGROVOC Term:	DNA
AGROVOC Term:	Mycelium
Depositing User:	Mr. AFANDI ABDUL MALEK
Last Modified:	24 Apr 2025 00:55
URI:	http://webagris.upm.edu.my/id/eprint/9807

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