Development and Reproduction (한국발생생물학회지:발생과생식)

The Korean Society of Developmental Biology (한국발생생물학회)
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PCR Analysis for Genetic Distances of Two Charybdis Crab Populations

  • Yoon, Jong-Man (Department of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University)
  • Received : 2022.03.13
  • Accepted : 2022.05.21
  • Published : 2022.06.30
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Abstract

Genomic DNA (gDNA) set apart from two populations of Korean Charybdis crab (Charybdis japonica) was augmented by PCR experiments. The five oligonucleotides primers (ONT-primers) were spent to yield the number of unique loci shared to each crab population (ULSECP) and number of loci shared by the two crab populations (LSTCP). 305 fragments (FRAGs) were identified in the Charybdis crab population A (CCPA), and 344 in the Charybdis crab population B (CCPB): 44 number of ULSECP (14.43%) in the CCPA and 110 (31.98%) in the CCPB. 44 number of LSTCP, with an average of 8.8 per primer, were detected in the two crab populations. The bandsharing (BS) value between entity's no. 01 and no. 10 was the lowest (0.371) between the two CCPs. The average bandsharing (ABS) values of individuals in the CCPA (0.575±0.014) were lesser than in those originated from the CCPB (0.705±0.011) (p < 0.05). The polar hierarchical dendrogram (PHD) achieved by the five ONT-primers denotes three genetic clusters (GCs): cluster I (CHARYBCRAB 01, 04, 05, 06, and 08), cluster II (CHARYBCRAB 02, 03, 07, 09, 10, and 11) and cluster III (CHARYBCRAB 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, and 22). The shortest genetic distance (GD) displaying significant molecular difference (MD) was between individuals CHARYBCRAB no. 18 and CHARYBCRAB no. 17 (0.055).

Keywords

Acknowledgement

The author wishes to acknowledge the financial support of the Fisheries Science Institute of Kunsan National University made in the program year of 2022.

References

  1. Araneda C, Neira R, Iturra P (2005) Identification of a dominant SCAR marker associated with colour traits in coho salmon (Oncorhynchus kisutch). Aquaculture 247:67-73. https://doi.org/10.1016/j.aquaculture.2005.02.028
  2. Archak S, Gaikwad AB, Gautam D, Rao EVVB, Swamy KRM, Karihaloo JL (2003) Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India. Genome 46:362-369. https://doi.org/10.1139/g03-016
  3. Bernardet JF, Vancanneyt M, Matte-Tailliez O, Grisez L, Tailliez P, Bizet C, Nowakowski M, Kerouault B, Swings J (2005) Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals. Syst Appl Microbiol 28:640-660. https://doi.org/10.1016/j.syapm.2005.03.016
  4. Diaz-Jaimes P, Uribe-Alcocer M (2003) Allozyme and RAPD variation in the eastern Pacific yellowfin tuna (Thunnus albacares). Fish Bull 101:769-777.
  5. Dixon BA, Shinn AP, Sommerville C (2004) Genetic characterization of populations of the ectoparasitic caligid, Lepeophtheirus salmonis (Kroyer 1837) using randomly amplified polymorphic DNA. Aquac Res 35:730-741. https://doi.org/10.1111/j.1365-2109.2004.01095.x
  6. Esselman EJ, Crawford DJ, Brauner S, Stuessy TF, Anderson GJ, Silva OM (2000) RAPD marker diversity within and divergence among species of Dendroseris (Asteraceae: Lactuceae). Am J Bot 87:591-596. https://doi.org/10.2307/2656603
  7. Garcia G, Claramunt S, Lalanne AI (2004) Genetic differentiation among annual fishes of the genus Cynolebias (Cyprinodontiformes, Rivuluidae) in a biosphere reserve site from Uruguay. Environ Biol Fishes 70:247-256. https://doi.org/10.1023/B:EBFI.0000033339.55585.f6
  8. Ghatak S, Agarwal RK, Bhilegaonkar KN (2007) Species identification of clinically important Aeromonas spp. by restriction fragment length polymorphism of 16S rDNA. Lett Appl Microbiol 44:550-554. https://doi.org/10.1111/j.1472-765X.2006.02104.x
  9. Gelin A, Souty-Grosset C (2006) Species identification and ecological study of the genus Palaemonetes (Decapoda: Caridea) in the French Mediterranean. J Crustac Biol 26:124-133. https://doi.org/10.1651/C-2487.1
  10. Godhe A, McQuoid MR, Karunasagar I, Karunasagar I, Rehnstam-Holm AS (2006) Comparison of three common molecular tools for distinguishing among geographically separated clones of the diatom Skeletonema marinoi Sarno et Zingone (Bacillariophyceae). J Phycol 42:280-291. https://doi.org/10.1111/j.1529-8817.2006.00197.x
  11. Ho CT (2001) Flavor constituents in enzyme hydrolysates from shore swimming crab and spotted shrimp. J Korean Soc Food Sci Nutr 30:787-795.
  12. Heo YS, Lee BK, Huh MK (2006) Morphological variability of the Japanese swimming Charybdis japonica populations. J Life Sci 16:672-675. https://doi.org/10.5352/JLS.2006.16.4.672
  13. Huang BX, Peakall R, Hanna PJ (2000) Analysis of genetic structure of blacklip abalone (Haliotis rubra) populations using RAPD, minisatellite and microsatellite markers. Mar Biol 136:207-216. https://doi.org/10.1007/s002270050678
  14. Jo SG, Yoon JM (2021) Genetic distances between tailfin anchovy (Coilia nasus) populations analyzed by PCR. Dev Reprod 25:59-65. https://doi.org/10.12717/DR.2021.25.1.59
  15. Kim S, Kim YH, Yoon JM (2006) Genetic variation in geographic crayfish (Cambaroides similis) populations. J Fish Pathol 19:141-153.
  16. Kang SK, Yoon JM (2013) Geographic variations of three Fulvia mutica populations. Korean J Malacol 29:163-169. https://doi.org/10.9710/kjm.2013.29.3.163
  17. Kim DA, Ko KS (1987) Fishing mechanism of pots and their modification. Bull Korean Fish Soc 20:348-354.
  18. Kim JY, Park CY, Yoon JM (2004) Genetic differences and DNA polymorphism in oyster (Crassostrea spp.) analyzed by RAPD-PCR. Korean J Genet 26:123-134.
  19. Kim YS, Yoon JM (2018) Genetic distances in two Gracilaria species (Gracilariaceae, Rhodophyta) identified by PCR technique. Dev Reprod 22:393-402. https://doi.org/10.12717/DR.2018.22.4.393
  20. Koh MC, Lim CH, Chua SB, Chew ST, Phang STW (1998) Random amplified polymorphic DNA (RAPD) fingerprints for identification of red meat animal species. Meat Sci 48:275-285. https://doi.org/10.1016/S0309-1740(97)00104-6
  21. McCormack GP, Powell R, Keegan BF (2000) Comparative analysis of two populations of the brittle star Amphiura filiformis (Echinodermata: Ophiuroidea) with different life history strategies using RAPD markers. Mar Biotechnol 2:100-106. https://doi.org/10.1007/s101269900013
  22. Nagarajan M, Haniffa MA, Gopalakrishnan A, Basheer VS, Muneer A (2006) Genetic variability of Channa punctatus populations using randomly amplified polymorphic DNA. Aquac Res 37:1151-1155. https://doi.org/10.1111/j.1365-2109.2006.01539.x
  23. Oh KS (2002) The character impact compounds of odor evolved from cooked shore swimming crab flesh. Korean J Fish Aquat Sci 35:122-129. https://doi.org/10.5657/KFAS.2002.35.2.122
  24. Park IW, Kim HS, Choe KH, Choe SN, Kim JB, Lim SH (2008) Food composition of crab (Charybdis japonica) preserved in brine. J Fish Mar Sci Edu 20:95-106.
  25. Seo IS, Hong JS (2009) Food habits of the Asian paddle crab, Charybdis japonica (A. MilneEdwards) on the Jangbong tidal flat, Incheon, Korea. Korean J Environ Biol 27:297-305.
  26. Upadhyay SK, Jun W, Yong-Quan S, Shao-Xiong D, Chaturvedi S (2006) Genetic diversity of yellow grouper (Epinephelus awoara) determined by random amplified polymorphic DNA (RAPD) analysis. Fish Bull 104:638-642.
  27. Wang CH, Li SF (2004) Phylogenetic relationships of ornamental (koi) carp, Oujiang color carp and long-fin carp revealed by mitochondrial DNA COII gene sequences and RAPD analysis. Aquaculture 231:83-91. https://doi.org/10.1016/j.aquaculture.2003.10.040
  28. Wasko AP, Martins C, Oliveira C, Senhorini JA, Foresti F (2004) Genetic monitoring of the Amazonian fish matrincha (Brycon cephalus) using RAPD markers: Insights into supportive breeding and conservation programmes. J Appl Ichthyol 20:48-52. https://doi.org/10.1111/j.1439-0426.2004.00479.x
  29. Yeon IJ, Lee YS, Song MY, Park WG (2011) Seasonal timing and distribution of Charybdis japonica (Decapoda: Portunidae) larvae off Yeonpyeong-do in the Yellow Sea, Korea. Korean J Fish Aquat Sci 44:162-166. https://doi.org/10.5657/KFAS.2011.44.2.162
  30. Yoon JM, Kim YH (2003a) Wide marsh clam (Corbicula spp.) populations from three sites analysed by RAPD-PCR-AGE. Bull Electrochem 19:337-348.
  31. Yoon JM, Kim GW (2003b) Genetic differences between cultured and wild penaeid shrimp (Penaeus chinensis) populations analysed by RAPD-PCR. Korean J Genet 25:21-32.
  32. Yoon JM, Choi Y, Kim JY (2007) Genetic differences and variation in black rockfish (Sebastes schlegeli) and Hwanghae rockfish (S. koreanus) from the Yellow Sea. Korean J Genet 29:437-445.
  33. Yoon JM (2018) Genetic variations of intra- and between-razor clam Solen corneus population identified by PCR analysis. Dev Reprod 22:193-198. https://doi.org/10.12717/DR.2018.22.2.193
  34. Yoon JM (2020) Genetic differences in natural and cultured river pufferfish populations by PCR analysis. Dev Reprod 24:327-336. https://doi.org/10.12717/DR.2020.24.4.327
  35. Yoon JM (2021a) Analysis of geographical genetic differences of arkshell populations in Korea. Dev Reprod 25:105-111. https://doi.org/10.12717/DR.2021.25.2.105
  36. Yoon JM (2021b) Genetic distances for intra- and between-group of Scapharca subcrenata from Yeosu of the Korea. Dev Reprod 25:305-311. https://doi.org/10.12717/DR.2021.25.4.305