Development of Species-Specific Primers for Detecting Raccoon (Procyon lotor) eDNA from Field Water

Japan Agricultural Research Quarterly
ISSN 00213551
NII recode ID (NCID) AA0068709X
Full text
In Japan, invasive alien raccoons (Procyon lotor) cause severe agricultural damage. To address this issue, it is essential to understand their distribution and ecology. Using environmental DNA (eDNA) is an efficient strategy for quickly detecting their presence and determining their distributions; however, species-specific eDNA detection methods are limited for terrestrial mammals. In this study, we developed a specific qPCR-based detection method for raccoons and tested its effectiveness through captive and field samples. Species-specific primers and probes were designed for the cytochrome c oxidase subunit I (COI) and cytochrome b (cytb) regions of mitochondrial DNA. Water samples were collected from cage water and from field ponds and rivers in a raccoon habitat. For a comparison of detection sensitivity, a metabarcoding analysis targeted to mammals was performed. In captivity, raccoon eDNA was detected in cage water that had been in contact with raccoons for a short time. In field surveys, eDNA was detected at a pond where footprints were found, as well as at other sites. Additionally, the developed qPCR assay detected raccoon eDNA at a higher frequency than the metabarcoding analysis. These results indicate that the newly developed raccoon-specific detection assay is a valuable tool for eDNA monitoring.
Date of issued
Creator Hiroyoshi KOYAMA Chinatsu KOZAKAI Hiroki MATSUMURA Hiroyuki SHIBAIKE
Subject agricultural damage by wildlife invasive alien species monitoring
Publisher Japan International Research Center for Agricultural Sciences
Received Date 2025-01-28
Accepted Date 2025-05-12
Available Online
Volume 60
Issue 1
spage 39
epage 48
DOI 10.6090/jarq.24J25
Language eng

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