Rapid Origin Determination of the Northern Mauxia Shrimp (Acetes chinensis) Based on Allele Specific Polymerase Chain Reaction of Partial Mitochondrial 16S rRNA Gene

  • Received : 2014.08.12
  • Accepted : 2014.09.25
  • Published : 2015.04.01


Acetes chinensis is an economically important shrimp that belongs to the Sergestidae family; following fermentation, A. chinensis' economic value, however, is low in China, and much of the catch in China is exported to Korea at a low price, thus leading to potential false labeling. For this reason, we developed a simple method to identify A. chinensis' origin using allele-specific polymerase chain reaction (PCR). Ten single nucleotide polymorphisms (SNPs) were identified from partial (i.e., 570 bp) DNA sequence analysis of the mitochondrial 16s rRNA gene in 96 Korean and 96 Chinese individual shrimp. Among 10 SNP sites, four sites were observed in populations from both countries, and two sites located in the middle with SNP sites at their 3'-ends were used to design allele-specific primers. Among the eight internal primers, the C220F primer specific to the Chinese A. chinensis population amplified a DNA fragment of 364 bp only from that population. We were able to identify the A. chinensis population origin with 100% accuracy using multiplex PCR performed with two external primers and C220F primers. These results show that the 16S rRNA gene that is generally used for the identification of species can be used for the identification of the origin within species of A. chinensis, which is an important finding for the fair trade of the species between Korea and China.


Supported by : National Fisheries Research and Development Institute(NFRDI)


  1. Anderson, E. C. and J. C. Garza. 2006. The power of singlenucleotide polymorphisms for large-scale parentage inference. Genetics 172: 2567-2582.
  2. Craig, M. T., D. J. Pondella, J. P. C. Franck, and J. C. Hafner. 2001. On the status of the serranid fish genus Epinephelus: Evidence for paraphyly based upon 16S DNA sequence. Mol. Phylogenet. Evol. 19:121-130
  3. Galtier, N., B. Nabholz, S. Glemin, and G. D. D. Hurst. 2009. Mitochondrial DNA as a marker of molecular diversity: A reappraisal. Mol. Ecol. 18:4541-4550
  4. Ivanova, N. V., T. S. Zemlak, R. H. Hanner, and P. D. Hebert. 2007. Universal primer cocktails for fish DNA barcoding. Mol. Ecol. Notes 7:544-548.
  5. Kang, J. H., K. H. Yu, J. Y. Park, C. M. An, J. C. Jun, and S. J. Lee. 2011. Allele-specific PCR genotyping of the HSP70 gene polymorphism discriminating the green and red color variants seacucumber (Apostichopus japonicus). J. Genet. Genomics 38:351-355.
  6. Kim, H. S. 1977. Illustrated Encyclopedia of Flora and Fauna of Korea, Macura. Vol. 19, Samhwa Publication Company, Seoul, Korea. 96-155.
  7. Little, S. 1997. ARMS analysis of point mutation. In: Laboratory Methods for the detection of mutations and polymorphisms in DNA (Ed. G. R. Taylor). CRC Press, Boca Raton, FL, USA. 45-51.
  8. Omori, M. 1975. The biology of pelagic shrimps in the ocean. Adv. Mar. Biol. 12:233-324.
  9. Palumbi, S. R. 1996. Nucleic acids II: the polymerase chain reaction. In: Molecular Systematics (Eds. D. M. Hillis, C. Moritz, and B. K. Mable). Sinauer & Associates Inc., Sunderland, MA, USA. 205-247.
  10. Vignal, A., D. Milan, M. San Cristobal, and A. Eggen. 2002. A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol. 34:275-305.
  11. Wang, D. W., Y. Li, and Z. Q. Li. 2011. Identification of a malespecific amplified fragment length polymorphism (AFLP) and a sequence characterized amplified region (SCAR) marker in Eucommia ulmoides Oliv. Int. J. Mol. Sci. 12:857-864.

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