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

Alma, Nikkie Ratya and Indarti, Siwi and Hartono, Sedyo and Soffan, Alan (2023) Evaluation of nematode DNA extraction methods for species identification of root rice nematode (Hirschmanniella spp.). Archives of Phytopathology and Plant Protection, 56 (2). pp. 127-136. ISSN 03235408

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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.

Item Type: Article
Additional Information: Cited by: 0
Subjects: S Agriculture > S Agriculture (General)
Depositing User: Laili Hidayah Hidayah
Date Deposited: 23 Aug 2024 08:58
Last Modified: 23 Aug 2024 08:58
URI: https://ir.lib.ugm.ac.id/id/eprint/3152

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