title: Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra.
abstract: The mottled skate, Beringraja pulchra is one of the commercially important fishes in the market today. However, B. pulchra identification methods have not been well developed. The current study reports a novel real-time PCR method based on TaqMan technology developed for the genetic identification of B. pulchra. The mitochondrial cytochrome oxidase subunit 1 (COI) nucleotide sequences of 29 B. pulchra, 157 skates and rays reported in GenBank DNA database were comparatively analyzed and the COI sequences specific to B. pulchra was identified. Based on this information, a system of specific primers and Minor Groove Binding (MGB) TaqMan probe were designed. The assay successfully discriminated in 29 specimens of B. pulchra and 27 commercial samples with unknown species identity. For B. pulchra DNA, an average Threshold Cycle (Ct) value of 19.1±0.1 was obtained. Among 27 commercial samples, two samples showed average Ct values 19.1±0.0 and 26.7±0.1, respectively and were confirmed to be B. pulchra based on sequencing. The other samples tested showed undetectable or extremely weak signals for the target fragment, which was also consistent with the sequencing results. These results reveal that the method developed is a rapid and efficient tool to identify B. pulchra and might prevent fraud or mislabeling during the distribution of B. pulchra products.
authors.affiliation: DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul, South Korea. Electronic address: inkai@korea.kr.
authors.forename: In Kwan
authors.initials: IK
authors.lastname: Hwang
authors.affiliation: DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul, South Korea.
authors.forename: Hae Young
authors.initials: HY
authors.lastname: Lee
authors.affiliation: Forensic DNA Division, National Forensic Service, Wonju, South Korea.
authors.forename: Min-Hee
authors.initials: MH
authors.lastname: Kim
authors.affiliation: Fisheries Researchs and Environment Division, West Sea Fisheries Research Institute, Incheon, South Korea.
authors.forename: Hyun-Su
authors.initials: HS
authors.lastname: Jo
authors.affiliation: DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul, South Korea.
authors.forename: Dong-Ho
authors.initials: DH
authors.lastname: Choi
authors.affiliation: DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul, South Korea.
authors.forename: Pil-Won
authors.initials: PW
authors.lastname: Kang
authors.affiliation: Forensic DNA Division, National Forensic Service, Wonju, South Korea.
authors.forename: Yang-Han
authors.initials: YH
authors.lastname: Lee
authors.affiliation: Forensic DNA Division, National Forensic Service, Wonju, South Korea.
authors.forename: Nam-Soo
authors.initials: NS
authors.lastname: Cho
authors.affiliation: Forensic DNA Division, National Forensic Service, Wonju, South Korea.
authors.forename: Ki-Won
authors.initials: KW
authors.lastname: Park
authors.affiliation: School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea.
authors.forename: Ho Zoon
authors.initials: HZ
authors.lastname: Chae
mesh_terms: D000818:Animals; D017931:DNA Primers; D015342:DNA Probes; D004272:DNA, Mitochondrial / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012860:Skates, Fish / Q000235:genetics*; D013045:Species Specificity; D019914:Taq Polymerase
chemical_list: D017931:DNA Primers; D015342:DNA Probes; D004272:DNA, Mitochondrial; D003576:Electron Transport Complex IV; D019914:Taq Polymerase
keywords: COI; Fish; Food; Mitochondrial DNA; Ray; Species identification