Korean Journal of Ecology and Environment (생태와환경)

The Korean Society of Limnology (한국수생태학회)
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Preliminary Application of Molecular Monitoring of the Pacific Herring (Clupea pallasii) Based on Real-time PCR Assay Utilization on Environmental Water Samples

  • Kim, Keun-Yong (Department of Genetic Analysis, AquaGenTech, Co., Ltd) ;
  • Heo, Jung Soo (Department of Genetic Analysis, AquaGenTech, Co., Ltd) ;
  • Moon, Seong Yong (South Sea Fisheries Research Institute, National Institute of Fisheries Science) ;
  • Kim, Keun-Sik (Fishes/Amphibians & Reptile Team, Research Center for Endangered Species, National Institute of Ecology) ;
  • Choi, Jung-Hwa (Jeju Fisheries Research Institute, National Institute of Fisheries Science) ;
  • Yoo, Joon-Taek (Cetacean Research Institute, National Institute of Fisheries Science)
  • Received : 2021.09.10
  • Accepted : 2021.09.13
  • Published : 2021.09.30
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Abstract

Pacific herring, Clupea pallasii, a keystone species with significant ecological and commercial importance, is declining globally throughout much of its range. While traditional fishing equipment methods remain limited, new sensitive and rapid detection methods should be developed to monitor fisheries resources. To monitor the presence and quantity of C. pallasii from environmental DNA (eDNA) extracted from seawater samples, a pair of primers and a TaqMan® probe specific to this fish based on mitochondrial cytochrome b (COB) sequences were designed for the real-time PCR (qPCR) assay. The combination of our molecular markers showed high specificity in the qPCR assay, which affirmed the success of presenting a positive signal only in the C. pallasii specimens. The markers also showed a high sensitivity for detecting C. pallasii genomic DNA in the range of 1 pg~100 ng rxn-1 and its DNA plasmid containing COB amplicon in the range of 1~100,000copies rxn-1, which produced linear standard calibration curves (r2=0.99). We performed a qPCR assay for environmental water samples obtained from 29 sampling stations in the southeastern coastal regions of South Korea using molecular markers. The assay successfully detected the C. pallasii eDNA from 14 stations (48.2%), with the highest mean concentration in Jinhae Bay with a value of 76.09±18.39 pg L-1 (246.20±58.58 copies L-1). Our preliminary application of molecular monitoring of C. pallasii will provide essential information for efficient ecological control and management of this valuable fisheries resource.

Keywords

Acknowledgement

We sincerely appreciate Mr. Biet Thanh Tran of Pukyong National University for his valuable comments and suggestions, which helped us to improve the quality of the article.

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