Skip to main content
SpringerLink
Log in

Genetic diversity and population structure of wild Macrobrachium nipponense populations across China: Implication for population management

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

  • 1 Altmetric

Abstract

Background

Macrobrachium nipponense, is an important economic indigenous prawn and is widely distributed in China. However, most these genetic structure analysis researches were focused on a certain water area, systematic comparative studies on genetic structure of M. nipponense across China are not yet available.

Methods and results

In this study, D-loop region sequences was used to investigate the genetic diversity and population structure of 22 wild populations of M. nipponense through China, containing the major rivers and lakes of China. Totally 473 valid D-loop sequences with a length of 1110 bp were obtained, and 348 variation sites and 221 haplotypes were detected. The haplotype diversity (h) was ranged from 0.1630 (Bayannur) ~ 1.0000 (Amur River) and the nucleotide diversity π value ranged from 0.001164 (Min River) ~ 0.037168 (Nen River). The pairwise genetic differentiation index (FST) ranged from 0.00344 to 0.91243 and most pair-wised FST was significant (P < 0.05). The lowest FST was displayed in Min River and Jialing River populations and the highest was between Nandu River and Nen River populations. The phylogenetic tree of genetic distance showed that all populations were divided into two branches. The Dianchi Lake, Nandu River, Jialing River and Min River populations were clustered into one branch. The neutral test and mismatch distribution results showed that M. nipponense populations were not experienced expanding and kept a steady increase.

Conclusions

Taken together, a joint resources protection and management strategy for M. nipponense have been suggested based on the results of this study for its sustainable use.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Cai Y, Shokita S (2006) Report on a collection of freshwater shrimps (Crustacea: Decapoda: Caridea) from the Philippines, with descriptions of four new species. Raffles Bullet Zool 54(2):245–270

    Google Scholar 

  2. Fu HT, Gong YS, Wu Y, Xu P, Wu CJ (2004) Artificial interspecific hybridization between Macrobrachium species. Aquaculture 232:215–223

    Article  CAS  Google Scholar 

  3. Fu HT, Jiang SF, Xiong YW (2012) Current status and prospects of farming the giant river prawn (Macrobrachium rosenbergii) and the oriental river prawn (Macrobrachium nipponense) in China. Aquac Res 43(7):993–998. https://doi.org/10.1111/j.1365-2109.2011.03085.x

    Article  Google Scholar 

  4. Zhang W, Jiang SF, Salumy KR, Xuan Z, Xiong Y, Jin SB, Fu HT (2022) Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences. Aquaculture Reports 23:10108. https://doi.org/10.1016/j.aqrep.2022.10108

    Article  Google Scholar 

  5. Fu, H.T., Jin, S.B., (2018). Culture of the oriental river prawn (Macrobrachium nipponense). Aquaculture in China: Success stories and modern trends. 218–225.

  6. Ge, J., Xu, Z., Huang, Y., Lu, Q., Pan, J., Yang, J., (2011). Genetic Variation in Wild and Cultured Populations of the Freshwater Prawn, Macrobrachium nipponense, in China. Journal of the World Aquaculture Society, 42(4), 504–511.https://doi.org/10.1111/j.1749-7345.2011.00492.x

  7. Ma KY, Feng JB, Li JL (2012) Genetic variation based on microsatellite analysis of the oriental river prawn, Macrobrachium nipponense from Qiandao Lake in China. Genet Mol Res 11(4):4235–4244. https://doi.org/10.3724/SP.J.1141.2011.04363

    Article  CAS  PubMed  Google Scholar 

  8. Qiao, H., Lv, D., Jiang, S.F., Sun, S.M., Gong, Y.S., Xiong, Y.W., Fu, H.T., (2013). Genetic diversity analysis of oriental river prawn, Macrobrachium nipponense, in Yellow River using microsatellite marker. Genetics and Molecular Research, 12(4), 5694–5703.https://doi.org/10.4238/2013.November.18.18

  9. Chen, P.C., Shih, C.H., Chu, T.J., Lee, Y.C., Tzeng, T.D., (2017). Phylogeography and genetic structure of the oriental river prawn Macrobrachium nipponense (Crustacea: Decapoda: Palaemonidae) in East Asia. PloS one, 12(3), e0173490. https://doi.org/10.1371/journal.pone.0173490

  10. Cui F, Yu Y, Bao F, Wang S, Xiao MS (2018) Genetic diversity analysis of the oriental river prawn (Macrobrachium nipponense) in Huaihe River. Mitochondrial DNA Part A 29(5):737–744. https://doi.org/10.1080/24701394.2017.1350953

    Article  CAS  Google Scholar 

  11. Li Y, Fan W, Huang Y, Huang Y, Du X, Liu Z, Zhao Y (2021) Comparison of morphology and genetic diversity between broodstock and hybrid offspring of oriental river prawn, Macrobrachium nipponense based on morphological analysis and SNP markers. Anim Genet 52(4):461–471. https://doi.org/10.1111/age.13081

    Article  PubMed  Google Scholar 

  12. Gallagher J, Finarelli JA, Jonasson JP, Carlsson J (2019) Mitochondrial D-loop DNA analyses of Norway lobster (Nephrops norvegicus) reveals genetic isolation between Atlantic and East Mediterranean populations. J Mar Biol Assoc UK 99(4):933–940. https://doi.org/10.1017/S0025315418000929

    Article  CAS  Google Scholar 

  13. Song CY, Sun ZC, Gao TX, Song N (2020) Structure analysis of mitochondrial DNA control region sequences and its applications for the study of population genetic diversity of Acanthogobius ommaturus. Russ J Mar Biol 46(4):292–301. https://doi.org/10.1134/S1063074020040082

    Article  CAS  Google Scholar 

  14. Rendón-Hernández JF, Pérez-Rostro CI, González-Trujillo R, Arcos-Ortega GF, Jiménez-Badillo MDL, Galindo-Cortes G (2021) Genetic diversity of the blue land crab Cardisoma guanhumi (Latreille 1825) in the Alvarado Lagoon System in Veracruz, gulf coast of Mexico. Lat Am J Aquat Res 49(1):136–147. https://doi.org/10.3856/vol49-issue1-fulltext-2478

    Article  Google Scholar 

  15. Pan Z, Zhao H, Zhu C, Chen H, Zhao P, Cheng Y (2021) Genetic diversity analysis of crucian carp (Carassius auratus) based on cyt b and D-loop-containing region around Hongze Lake. Environ Biol Fishes 1–20:10. https://doi.org/10.1007/s10641-021-01175-8

    Article  Google Scholar 

  16. Peng M, Zhu W, Yang C, Yao J, Chen H, Jiang W, Chen X (2021) Genetic diversity of mitochondrial D-LOOP sequences in the spotted scat (Scatophagus argus) from different geographical populations along the northern coast of the South China Sea. J Appl Ichthyol 37(1):73–82. https://doi.org/10.1111/jai.14121

    Article  Google Scholar 

  17. Englund, T., Stromstedt, L., Johansson, A., (2014). Relatedness and diversity of nine Swedish local chicken breeds as indicated by the mtDNA D-loop. Hereditas 151 (6), 229e233. https://doi.org/10.1111/hrd2.00064

  18. Zhang, J., Jiao, T., Zhao, S., (2016). Genetic diversity in the mitochondrial DNA D-loop region of global swine (Sus scrofa) populations. Biochem. Biophys. Res. Commun. 473 (4), 814e820. https://doi.org/10.1016/j.bbrc.2016.03.125

  19. Jiang B, Fu J, Dong Z, Fang M, Zhu W, Wang L (2019) Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations. PeerJ. https://doi.org/10.7717/peerj.7007

    Article  PubMed  PubMed Central  Google Scholar 

  20. Hall TA (1999) BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nuclc Acids Symposium Series 41:95–98. https://doi.org/10.1093/oxfordjournals.molbev.a004062

    Article  CAS  Google Scholar 

  21. Excoffier, L., Lischer, H.E., (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular ecology resources, 10(3), 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x

  22. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Spielman D, Brook BW, Frankham R (2004) Most species are not driven to extinction before genetic factors impact them. Proc Natl Acad Sci 101(42):15261–15264. https://doi.org/10.1093/jhered/esab078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Beati L, Nava S, Burkman, E.J., (2013). Amblyomma cajennense (Fabricius, 1787) (Acari: Ixodidae), the Cayenne tick: phylogeography and evidence for allopatric speciation. Bmc Evolutionary Biology, 2013, 13(1): 267–267. https://doi.org/10.1186/1471-2148-13-267

  25. Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablanca FX, Wilson AC (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci 86(16):6196–6200. https://doi.org/10.1676/13-054.1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Wilson K (2001) Phylogeography and systematics of the mud turtle, kinosternon baurii. Copeia 2001(3):797–801. https://doi.org/10.1643/0045-8511(2001)001[0797:PASOTM]2.0.CO;2

    Article  Google Scholar 

  27. Wang YJ, Lu JH, Liu Z, Zhang JP (2021) Genetic diversity of Gymnocypris chilianensis (Cypriniformes, Cyprinidae) unveiled by the mitochondrial DNA D-loop region. Mitochondrial DNA Part B 6(4):1292–1297. https://doi.org/10.1080/23802359.2021.1906172

    Article  PubMed  PubMed Central  Google Scholar 

  28. Grant WAS, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89(5):415–426. https://doi.org/10.1093/jhered/89.5.415

    Article  Google Scholar 

  29. Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science 236(4803):787–792. https://doi.org/10.1016/0198-0254(87)90895-8

    Article  CAS  PubMed  Google Scholar 

  30. Sun N, Zhu DM, Li Q, Wang GY, Chen J, Zheng F, Sun YH (2021) Genetic diversity analysis of Topmouth Culter (Culter alburnus) based on microsatellites and D-loop sequences. Environ Biol Fishes 104(3):213–228. https://doi.org/10.1007/s10641-021-01062-2

    Article  Google Scholar 

  31. Gao W, Zeng Y, Zhao D, Wu B, Ren Z (2020) Land cover changes and drivers in the water source area of the Middle Route of the South-to-North Water Diversion Project in China from 2000 to 2015. Chin Geogra Sci 30(1):115–126. https://doi.org/10.1007/s11769-020-1099-y

    Article  Google Scholar 

  32. Walker K, Yang H (1999) Fish and fisheries in western China. Fish Fish Higher Altitudes: Asia 385:304

    Google Scholar 

  33. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147(2):915–925. https://doi.org/10.1093/genetics/147.2.915

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. De Oliveira-Neto JF, Pie MR, Chammas MA, Ostrensky A, Boeger WA (2008) Phylogeography of the blue land crab, Cardisoma guanhumi (Decapoda Gecarcinidae) along the Brazilian coast. J Mar Biol Ass United Kingdom 88(7):1417–1423

    Article  Google Scholar 

  35. Neraas LP, Spruell P (2001) Fragmentation of riverine systems: the genetic effects of dams on bull trout (Salvelinus confluentus) in the Clark Fork River system. Mol Ecol 10(5):1153–1164. https://doi.org/10.1046/j.1365-294X.2001.01269.x

    Article  CAS  PubMed  Google Scholar 

  36. Cook DR, Sullivan SMP (2018) Associations between riffle development and aquatic biota following lowhead dam removal. Environ Monit Assess 190(6):1–14. https://doi.org/10.1007/s1061-081-6716-1

    Article  CAS  Google Scholar 

Download references

Funding

This research was supported by grants from Central Public-interest Scientific Institution Basal Research Fund CAFS (2020TD36); Jiangsu Agricultural Industry Technology System; the National Key R&D Program of China (2018YFD0901303); the earmarked fund for CARS-48; the New cultivar breeding Major Project of Jiangsu province (PZCZ201745). The seed industry revitalization project of Jiangsu province (JBGS [2021] 118). Thanks for the Jiangsu Province Platform for the Conservation and Utilization of Agricultural Germplasm.

Author information

Author notes

  1. Sufei Jiang, Yiwei Xiong, Lijuan Zhang have contributed equally to this work and should be considered co-first authors.

Authors and Affiliations

  1. Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of China

    Sufei Jiang, Yiwei Xiong, Wenyi Zhang, Shubo Jin, Yongsheng Gong, Yan Wu, Hui Qiao & Hongtuo Fu

  2. Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, People’s Republic of China

    Lijuan Zhang, Yalu Zheng, Jisheng Wang, Hui Qiao & Hongtuo Fu

Authors
  1. Sufei Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yiwei Xiong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lijuan Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Wenyi Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yalu Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jisheng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Shubo Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yongsheng Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yan Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Hui Qiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Hongtuo Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Hongtuo Fu and Hui Qiao designed the research; Sufei Jiang, Yiwei, Xiong collect samples and performed the study; Lijuan Zhang and Wenyi Zhang analyzed the data;, Jisheng Wang, Yalu Zheng, Shubo Jin, Yongsheng Gong and Yan Wu contributed reagents, materials and tools; Sufei Jiang and Hui Qiao drafted the manuscript; Hongtuo Fu revised the manuscript; all authors approved the final version.

Corresponding authors

Correspondence to Hui Qiao or Hongtuo Fu.

Ethics declarations

Competing interests

The authors declare no conflicts of interest.

Ethical approval

No endangered or protected species were involved in this study and all experimental protocols, methods were approved in July 2021 (Authorization NO. 20211105001) by the Animal Care and Use Ethics Committee in the Freshwater Fisheries Research Center (Wuxi, China).

Consent to participate

Informed consent was obtained from all individual participants included in the study.

Consent to publish

The authors affirm that human research participants provided informed consent for publication of the images in Figure(s) 1, 2,3 and 4.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 230 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jiang, S., Xiong, Y., Zhang, L. et al. Genetic diversity and population structure of wild Macrobrachium nipponense populations across China: Implication for population management. Mol Biol Rep 50, 5069–5080 (2023). https://doi.org/10.1007/s11033-023-08402-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-023-08402-8

Keywords

Search

Navigation