GENETIC DIVERSITY OF SPINIBARBUS DENTICULATUS POPULATIONS USING MOLECULAR MAKER

Vũ Thị Trang; Vũ Thị Huyền; Phạm Hồng Nhật; Lưu Thị Hà Giang; Cao Thị Linh Chi; Đặng Thị Lụa; Lê Văn Khôi

doi:10.34238/tnu-jst.4890

GENETIC DIVERSITY OF SPINIBARBUS DENTICULATUS POPULATIONS USING MOLECULAR MAKER

About this article

Received: 13/08/21 Revised: 20/09/21 Published: 06/10/21

Authors

1. Vu Thi Trang , Research Institute for Aquaculture No.1 (RIA1)
2. Vu Thi Huyen, Research Institute for Aquaculture No.1 (RIA1)
3. Pham Hong Nhat, Research Institute for Aquaculture No.1 (RIA1)
4. Luu Thi Ha Giang, Research Institute for Aquaculture No.1 (RIA1)
5. Cao Thi Linh Chi, Research Institute for Aquaculture No.1 (RIA1)
6. Dang Thi Lua, Research Institute for Aquaculture No.1 (RIA1); Vietnam National University of Agriculture (VNUA)
7. Le Van Khoi, Research Institute for Aquaculture No.1 (RIA1)

Abstract

Three populations of Spinibarbus denticulatus collected in Ha Giang, Tuyen Quang, and Hoa Binh were analyzed for genetic diversity based on COI gene sequence analysis. Results showed that the studied populations have relatively high haplotype diversity (Hd) and moderate nucleotide diversity (π). Eleven haplotypes were detected out of a total of 90 analyzed sequences. All haplotypes sequences were deposited in the GenBank database, with accession numbers from MW446147 to MW446157. In terms of genetic differentiation, F_ST presented that there was a large genetic difference among three populations, in which F_ST values between Ha Giang and Tuyen Quang was the largest (0.80807). Analysis of molecular variance (AMOVA) indicated that three studied fish populations were different among others because most of the genetic variation occurred between populations (64.83%). The populations had a relatively large genetic distance and a clear population structure. Analytical data revealed a lack of migration or gene flow between populations.

Keywords

COI; Genetic diversity; Spinibarbus denticulatus; Haplotype; Population

Full Text:

PDF (Tiếng Việt)

References

[1] V. H. Nguyen and S. V. Ngo, Vietnamese freshwater fish, vol. 1 - Carp family (Cyprinidae), Agriculture Publishing House, 2001, pp. 318-320.

[2] T. D. Nguyen, “National Gene Fund Program: Contributing to the development of Spinibarbus denticulatus genetic resources,” (in Vietnamese), Vietnam Journal of Science, Technology and Engineering, no. 9, pp. 30-32, 2018.

[3] L. P. Zheng, J. X. Yang, X. Y. Chen, and W. Y. Wang, “Phylogenetic relationships of the Chinese Labeoninae (Teleostei, Cypriniformes) derived from two nuclear and three mitochondrial genes,” Zoologica Scripta, vol. 39, no. 6, pp. 559-571, 2010.

[4] L. P. Zheng, J. X. Yang, and X. Y. Chen, “Molecular phylogeny and systematics of the Barbinae (Teleostei: Cyprinidae) in China inferred from mitochondrial DNA sequences,” Biochemical Systematics and Ecology, vol. 68, pp. 250-259, 2016.

[5] G. X. Tong, Y. Y. Kuang, L. W. Geng, J. S. Yin, and W. Xu, “The Complete mitochondrial genome of Spinibarbus denticulatus (Oshima),” Mitochondrial DNA, vol. 25, no. 5, pp. 363-364, 2014.

[6] P. Zhu, Y. Zhang, Q. Zhuo, D. Lu, J. Huang, X. Liu, and H. Lin, “Discovery of four estrogen receptors and their expression profiles during testis recrudescence in male Spinibarbus denticulatus,” General and Comparative Endocrinology, vol. 156, no. 2, pp. 265-276, 2008.

[7] X. Liu, H. Su, P. Zhu, Y. Zhang, J. Huang, and H. Lin, “Molecular cloning, characterization and expression pattern of androgen receptor in Spinibarbus denticulatus,” General and Comparative Endocrinology, vol. 160, no. 1, pp. 93-101, 2009.

[8] N. Hubert, R. Hanner, and E. Holm, “Identifying Canadian freshwater fishes through DNA barcodes,” PLoS one, vol. 3, no. 6, p. e2490, 2008.

[9] K. Kohlmann and P. Kersten, “Deeper insight into the origin and spread of European common carp (Cyprinus carpio carpio) based on mitochondrial D-loop sequence polymorphisms,” Aquaculture, vol. 376–379, pp. 97–104, 2013.

[10] J. Zhou, Q. Wu, Z. Wang, and Y. Ye, “Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA,” Journal of Zoological Systematics and Evolutionary Research, vol. 42, pp. 266-269, 2004.

[11] R. D. Ward, T. S. Zemlak, and B. H. Innes, “DNA barcoding Australia's fish species,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 360, no. 1462, pp. 1847-1857, 2005.

[12] J. Sambrook and D. Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2001.

[13] S. G. Kumar, G. Stecher, and K. Tamura, “MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets,” Molecular Biology and Evolution, vol. 33, no. 7, pp. 1870-1874, 2016.

[14] J. Rozas, A. Ferrer-Mata, and J. C. Sánchez-DelBarrio, “DnaSP 6: DNA sequence polymorphism analysis of large data sets,” Molecular Biology and Evolution, vol. 34, no. 12, pp. 3299-3302, 2017.

[15] L. Excoffier, G. Laval, and S. Schneider, “Arlequin ver. 3.0: An integrated software package for population genetics data analysis,” Evolutionary Bioinformatics, vol. 1, pp. 47-50, 2005.

[16] H. J. Bandelt, P. Forster, and A. Röhl, “Median-joining networks for inferring intraspecific phylogenies,” Molecular Biology and Evolution, vol. 16, pp. 37-48, 1999.

[17] M. Wang, J. X. Yang, and X. Y Chen, “Molecular phylogeny and biogeography of percocypris (Cyprinidae, Teleostei),” PloS one, vol. 8, no. 6, pp. e61827-e61827, 2013.

[18] T. T. H. Tran, T. H. Nguyen, P. T. Ngo, and N. A. H. Tran, “Genetic diversity of tra catfish populations in Vietnam using cytochrome b gene,” Scientific Journal - Vinh University, vol. 46, no. 4A, pp. 21-31, 2017.

[19] E. Bazin, S. Glémin, and N. Galtier, “Population size does not influence mitochondrial genetic diversity in animals,” Science, vol. 312, no. 5773, pp. 570-572, 2006.

[20] S. L. Boyer, J. M. Baker, G. Giribet, “Deep genetic divergences in Aoraki denticulata (arachnida, opiliones, cyphophthalmi): a widespread ‘mite harvestman' defies DNA taxonomy,” Molecular Ecology, vol. 16, pp. 4999-5016, 2007.

[21] L. Cárdenas, J. C. Castilla, and F. Viard, “A phylogeographical analysis across three biogeographical provinces of the south-eastern Pacific: the case of the marine gastropod Concholepas concholepas,” Journal of biogeography, vol. 36, pp. 969-981, 2009.

[22] J. A. Haig, R. M. Connolly, and J. M. Hughes, “Little shrimp left on the shelf: the roles that sea-level change, ocean currents and continental shelf width play in the genetic connectivity of a seagrass-associated species,” Journal of biogeography, vol. 37, pp. 1570-1583, 2010.

[23] J. P. Wares, “Natural distributions of mitochondrial sequence diversity support new null hypotheses,” Evolution, vol. 64, pp. 1136-1142, 2010.

[24] B. S. Weir and C. C Cockerham, “Estimating F-Statistics for the Analysis of Population Structure,” Evolution, vol. 38, no. 6, pp. 1358-1370, 1984.

[25] K. Tamura, M. Nei, and S. Kumar, “Prospects for inferring very large phylogenies by using the neighbor-joining method,” Proceedings of the National Academy of Sciences (USA), vol. 101, pp. 11030-11035, 2004.

[26] M. Nei, “Estimation of average heterozygosity and genetic distance from a small number of individuals,” Genetics, vol. 89, no. 3, pp. 83-90, 1978.

[27] V. S. Baisvar, M. Singh, and R. Kumar, “Population structuring of Channa striata from Indian waters using control region of mtDNA,” Mitochondrial DNA A DNA Mapp Seq Anal, vol. 30, no. 3, pp. 414-423, 2019.

[28] T. T. H. Tran, T. H. G. Luu, T. T. Vu, H. N. Pham, and T. V. Phan, “Identification and Genetic Assessment of the Pompano Based on the Molecular Markers,” Vietnam Agricultural Science Journal, vol. 17, no. 3, pp. 204-215, 2019.

[29] L. Excoffier, P. E. Smouse, and J. M. Quattro, “Analysis of molecular variance inferred from metric distances among dna haplotypes: Application to human mitochondrial dna restriction data,” Genetics, vol. 131, pp. 479-491, 1992.

DOI: https://doi.org/10.34238/tnu-jst.4890

Refbacks

There are currently no refbacks.



Remember me