Evaluation of nematode DNA extraction methods for species identification of root rice nematode (Hirschmanniella spp.)

Abstract

The species-level identification of rice root nematode (Hirschmanniella spp.) is an important effort in pest management. Meanwhile, the selection of DNA extraction methods is the first important step in the molecular identification. Thereby, this study aimed to obtain the DNA extraction method and optimal quantity in the identification of Hirschmanniella spp. to the species level. The DNA extraction methods used were Cetyltrimethylammonium bromide (CTAB) and Commercial Kit (Geneaid; Genomic DNA Mini Kit Tissue), with variations in the number of nematodes: 1, 5, 10, 15 and 20 nematodes. There were no significant differences on DNA concentration and purity between CTAB and commercial kit method, but the DNA extraction of Hirschmaniella spp. with the CTAB method reached the highest DNA concentration of 189.57 ng/µL. DNA purity level in the ratio (A260/A280) ranging from 1.80 to 1.99. The PCR test obtained the amplification of the extracted DNA at ∼766 bp.

Keywords:

• DNA extraction
• Hirschmanniella spp
• nematode
• molecular
• CTAB
• KIT

Acknowledgements

The authors would like to thank Universitas Gadjah Mada for research funded by RTA (Rekognisi Tugas Akhir-Student Final Project Recognition) with Contract No. 3550/UN1.P.III/Dit-Lit/PT.01.05/2022.

Disclosure statement

The authors confirm that they have no known financial or interpersonal conflicts that would have appeared to have an impact on the research presented in this paper.