Genetic Diversity Among Populations of Bighead Carp (Hypophthalmichthys nobilis) Upstream and Midstream Yangtze River by Microsatellite DNA Analysis

Abstract

Bighead carp (Hypophthalmichthys nobilis) has an essential role in freshwater fisheries worldwide, especially in China, yet its germplasm resources in the upstream Yangtze River have been scarcely studied. We used nine polymorphic microsatellite markers to assess genetic diversity and differentiation in seven bighead carp populations from the upper-middle Yangtze River. In five populations from the upstream and two populations from the midstream of the Yangtze River, a total of 101 alleles were detected, with the mean value of alleles per population varying from 5.3 to 8.4. Moderate genetic diversity of seven populations was detected with the values of Ho, He and PIC ranging from 0.598 to 0.683, 0.647 to 0.703 and 0.591 to 0.639, respectively. Weak population differentiations (F_st = 0.0000-0.0478) were observed, which indicated that bighead carp populations up and down the Three Gorges Dam (TGD) could be regarded as a group. Structure and clustering analysis consistently supported that the bighead carp samples examined in this study were clustered as one group, except a population from Dongting Lake (DTL), the second largest lake of China, in the midstream of the Yangtze River. This study provided evidence of moderate genetic diversity and weak differentiation among bighead carp populations from upstream and midstream regions of the Yangtze River, suggesting that the TGD has not yet had a significant influence on population genetic structure. These results are valuable for conservation genetics and sustainable utilization of bighead carp resources in the Yangtze River.

Keywords

Bighead carp (Hypophthalmichthys nobilis) / Microsatellite / Genetic diversity / Genetic structure / The Three Gorges Reservoir

Supplementary Materials

The following supporting information can be found at: https://www.sciepublish.com/article/pii/819, Table S1: Pairwise Fst values among seven bighead carp populations after correction using FreeNA.

Acknowledgments

Authors thank Zhongjie Li, Yuxi Nian, and Deqing Tan for their technical assistance for fish sampling during field trips. Xiu Feng and Haiyang Liu are also acknowledged for their generous assistance in data analysis.

Author Contribution

J.T. conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft. L.T. and M.P. conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft. X.W. and Y.Z. prepared figures and/or tables, authored or reviewed drafts of the paper. X.Y. authored or reviewed drafts of the paper, approved the final draft.

Ethics Statement

The Committee for Animal Experiments of the Institute of Hydrobiology, the Chinese Academy of Sciences, China, approved all the experimental procedures and field study of the fish in the study (FI25-B3, 16 July 2012). The methods used in this study were carried out in accordance with the Laboratory Animal Management Principles of China.

Informed Consent Statement

Not applicable.

Data Availability Statement

All data are available upon request

Funding

This study was supported by research grants from the National Natural Science Foundation of China (31272647), State Key Laboratory of Freshwater Ecology and Biotechnology (2016FBZ05) and Scientific Research Project of China Three Gorges Corporation (CT12-08-01).

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

References

[1] Tautz D, Renz M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res. 1984, 12, 4127-4138. doi:10.1093/nar/12.10.4127.

[2] Gastier J, Pulido J, Sunden S, Brody T, Buetow K, Murray J, et al. Survey of trinucleotide repeats in the human genome: Assessment of their utility as genetic markers. Hum. Mol. Genet. 1995, 4, 1829-1836. doi:10.1093/hmg/4.10.1829.

[3] Kijas J, Thomas M, Fowler J, Roose M. Integration of trinucleotide microsatellites into a linkage map of Citrus. Theor. Appl. Genet. 1997, 94, 701-706. doi:10.1007/s001220050468.

[4] Liu Z, Cordes J. DNA marker technologies and their applications in aquaculture genetics. Aquaculture 2004, 238, 1-37. doi:10.1016/J.AQUACULTURE.2004.05.027.

[5] Manel S, Guerin P, Mouillot D, Blanchet S, Velez L, Albouy C, et al. Global determinants of freshwater and marine fish genetic diversity. Nat. Commun. 2020, 11, 692. doi:10.1038/s41467-020-14409-7.

[6] Sanz N, Nebot A, Araguas RM. Microsatellites as a good approach for detecting triploidy in brown trout hatchery stocks. Aquaculture 2020, 523, 735218. doi:10.1016/j.aquaculture.2020.735218.

[7] Lu C, Sun Z, Xu P, Na R, Lv W, Cao D, et al. Novel microsatellites reveal wild populations genetic variance in pike-perch (Sander lucioperca) in China. Aquac. Rep. 2022, 23, 101031. doi:10.1016/j.aqrep.2022.101031.

[8] Tang H, Zhang W, Tao C, Zhang C, Gui L, Xie N, et al. Estimation of genetic parameters for upper thermal tolerance and growth traits in grass carp (Ctenopharyngodon idella). Aquaculture 2025, 598, 742073. doi:10.1016/j.aquaculture.2024.742073.

[9] Wang X, Yu X, Feng J, Zhang Q, Qu C, Liu Q, et al. Estimation of the heritabilities for body Shape and body weight in Yellow River carp (Cyprinus carpio haematopterus) based on a molecular pedigree. J. Appl. Ichthyol. 2023, 2023, 1-8. doi:10.1155/2023/9326728.

[10] Pang M, Yu X, Tong J. The microsatellite analysis of genetic diversity of five silver carp populations in the Three Gorges Reservoir of the Yangtze River. Acta Hydrobiol. Sin. 2015, 39, 869-876. doi:10.7541/2015.115.

[11] Li S, Fang F. On the geographical distribution of the four kinds of pond-cultured carps in China. Acta Zool. Sin. 1990, 36, 244-249. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO_4HtmQ3GA9E4okryKWlXHXjfjluHlQ1FRyEBysix5iX_3o_vKgFiz6U6ekW0pKx74T7d5kQ47upnQj11ILUjAnLdXYIR9vl-beTkQ9DHzFRSSYMjQeE2kfMSoK06uvAUqpwhL6FOZKeOrZm3TPS1wyMddrHqY6QYxIfQGqMHRqlA==&uniplatform=NZKPT&language=CHS. (accessed on 28 November 2025).

[12] Yan J, Zhao J, Li S, Zheng D, Yang C. Genetic variation of bighead carp Aristichthys nobilis from Chinese native populations and introduced populations by AFLP. J. Fish. Sci. China 2013, 18, 283-289. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO_vDfCj7tX7nLWfOIA5in69nZXLm6fpYfFqKBCa5sKGh8GCykxvB8jT8UGzPoEMxC1R9_UAeSss5UbJgaOQsFriPGMJNtDga0E0fnWQduOhSLR6gvdUCWS0uum2AoGbl7T1dHHUDXa2rQuURqEzqOZLjeh8wJbm4b7JduxzCliunA==&uniplatform=NZKPT&language=CHS. (accessed on 28 November 2025).

[13] Zhao J, Li S. Isoenzyme analysis of population divergence of silver carp, bighead carp, grass carp and black carp in the middle and lower stream of Changjiang River. J. Fish. China 1996, 20, 104-110. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO8mYI0sgTjS5bx3XuJG6i7JTCVr6xTjJLbzx9MaSDwWtb1CdP4hlqsFswk5BWAKcObNkAseiNcscXG_LKHemq6FWLsXIdrgqvfvUEHjUzk5YLUUX2UqV1W-CtEzSVZk7gQmqU8Fj2m72GNqbWXsjoHG97O6waZA414=&uniplatform=NZKPT&language=CHS. (accessed on 28 November 2025).

[14] Chen D, Duan X, Liu S, Shi W, Wang B. On the dynamics of fishery resources of the Yangtze River and its management. Acta Hydrobiol. Sin. 2002, 26, 685-690. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO9on_dT-EtCIddaAwQ87a6WpQy5ph5aJND8mibatj8peWdu9alxJMpcVinbKl0-u8kCCW_M1niWBKHc4NmXjxr5rWGQIk58xg_AD4pSS7M4IV7O9vNPoBoBzpsjUxiPpCATl-OPi7udBNqCGSeG93E4LRflJA8a3ovj735vBNi0lg==&uniplatform=NZKPT&language=CHS. (accessed on 28 November 2025).

[15] Perera H, Li Z, De Silva S, Zhang T, Yuan J, Ye S, et al. Effect of the distance from the dam on river fish community structure and compositional trends, with reference to the Three Gorges Dam, Yangtze River, China. Acta Hydrobiol. Sin. 2014, 38, 438-445. doi:10.3724/issn1000-3207-2014-3-438-d.

[16] Baxter R. Environmental effects of dams and impoundments. Annu. Rev. Ecol. Syst. 1977, 8, 255-283. doi:10.1146/annurev.es.08.110177.001351.

[17] Cooper A, Infante D, Daniel W, Wehrly K, Wang L, Brenden T. Assessment of dam effects on streams and fish assemblages of the conterminous USA. Sci. Total Environ. 2017, 586, 879-889. doi:10.1016/j.scitotenv.2017.02.067.

[18] Zarri L, Palkovacs E, Post D, Therkildsen N, Flecker A. The evolutionary consequences of dams and other barriers for riverine fishes. BioScience 2022, 72, 431-448. doi:10.1093/biosci/biac004.

[19] Visser S, Barbarossa V, Keijzer T, Verones F, Dorber M. Characterizing dam fragmentation impacts on freshwater fish within life cycle impact assessment. Environ. Impact Assess. Rev. 2025, 114, 107929. doi:10.1016/j.eiar.2025.107929.

[20] Li S, Yang Q, Xu J, Wang C, Chapman D, Lu G. Genetic diversity and variation of mitochondrial DNA in native and introduced bighead carp. Trans. Am. Fish. Soc. 2011, 139, 937-946. doi:10.1577/T09-158.1.

[21] Zhang D, Xi Z, Dai Y, Lai Y, Yao F, Feng D, et al. Studies on genetic diversity of bighead carp (Aristichthys nobilis) in the Yangtze River. Wuhan Univ. J. 1999, 45, 857-860. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO_lpTrH9PkSyGjlPgjFqEiz2tSifdlEEdooYKzr1w-yJY9IaoFPu8G28k-j3rLGi059RI2ksRVPLO1AvztG_KLab_Lg8OazBYWswHKvl-Ei84atujiYU7q6DsrFwZc2u5bcsLSJ-usw-F1m81GqpGG0pF2QcY4S6UnYN7uhvnNGBg==&uniplatform=NZKPT&language=CHS. (accessed on 28 November 2025).

[22] Li S, Lv G, Bernatchez L. Diversity of mitochondrial DNA in the populations of silver carp, bighead carp, grass carp and black carp in the middle and lower reaches of the Yangtze River. Acta Zool. Sin. 1998, 44, 82-93. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO-RFqZyCQW8EV5WQv0jlF3EFosJrbFmkE43LkXYod3DIgP2G0-tlUVF9bDrjVjbLSn3uOx_t6YiKQc-dk2i1BTkHAZyDUzxh4cPQork2GsnHjydev2G6Oz1681WKHWj2ABU7wtC5Ao2rKN_j5SD5n2cV_g-jpbj7ms=&uniplatform=NZKPT&language=CHS. (accessed on 28 November 2025).

[23] Xia D, Yang H, Wu T, Dong Z, Jian J, Cao Y. Study on the population genetic structures of black carp, grass carp, silver carp and bighead fish in tian-e-zhou open old course of the Yangtze River. J. Fish. China 1996, 3, 11-18. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO87VJH4v6fS_HtD9XwVnTLkpbhVWdsFPE3Yxzwbv0XJw8Tg8GoAU7D4KF5OHTTRrhG34UM0w6et9v0GCB6zom1cpX2eokwJyj6olIX4tkfvgguNSkomI6WpSJ3ZwBPVErXRFSZotXL8YqFTDThONLNlZdAKfuF6Bz8=&uniplatform=NZKPT&language=CHS. (accessed on 28 November 2025).

[24] Geng B, Sun X, Liang L, Ouyang H, Tong J. Microsatellite analysis of genetic diversity of Aristichthys nobilis in China. Hereditas 2006, 28, 683-688. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO-4TrQ4Br8lSP2hAIbus0H-FML1ldTqzn4bmGn43wtEerS8xHaSo4JNmko8dmj9ZoEagA2gHNLQ9XO97OrDAGQbYpF2lzzvZEAa3IsfhSXGYC8CJ6eQZogrtVl3fvP81v_CJuHAv16e7I21jAbnixIi0Uqkp7dRkiD8SKRwzQdTUQ==&uniplatform=NZKPT&language=CHS (accessed on 28 November 2025).

[25] Sambrook J,Fritsch E, Maniatis T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory: Laurel Hollow, NY, USA, 1989.

[26] Zhang J, Wei C. Establishment a SSR-PCR system of tea plant [Camellia sinensis (L.) O. Kuntze] based on the 4300 DNA analysis system. J. Tea Sci. 2014, 34, 481-488. doi:10.13305/j.cnki.jts.2014.05.009.

[27] Yeh F, Yang R, Boyle T, Ye Z, Xiyan J. Popgene32, Microsoft Windows-Based Freeware for Population Genetic Analysis, Version 1.32; Molecular Biology and Biotechnology Centre, University of Alberta: Edmonton, AB, Canada, 2000.

[28] Park S. Trypanotolerance in West African Cattle and the Population Genetic Effects of Selection. Ph.D. Thesis, University of Dublin, Dublin, Ireland, 2001.

[29] Excoffier L, Lava G, Schneider S. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol. Bioinform. Online 2005, 1, 47-50. doi:10.1177/117693430500100003.

[30] Excoffier L, Smouse P, Quattro J. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 1992, 131, 479-491. doi:10.1093/genetics/131.2.479.

[31] Pritchard J, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155, 945-959. doi:10.1093/genetics/155.2.945.

[32] Falush D, Stephens M, Pritchard J. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 2003, 164, 1567-1587. doi:10.1093/genetics/164.4.1567.

[33] Maruyama T, Fuerst P. Population bottlenecks and nonequilibrium models in popuation genetics II. number of alleles in a small population that was formed by a recent bottleneck. Genetics 1985, 111, 675-689. doi:10.1093/genetics/111.3.675.

[34] Chapuis M, Estoup A. Microsatellite null alleles and estimation of population differentiation. Mol. Biol. Evol. 2007, 24, 621-631. doi:10.1093/molbev/msl191.

[35] Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software structure: A simulation study. Mol. Ecol. 2005, 14, 2611-2620. doi:10.1111/j.1365-294X.2005.02553.x.

[36] Nei M. Genetic distance between populations. In Molecular Evolutionary Genetics; Columbia University Press: New York, NY, USA, 1987; pp. 180-211.

[37] Zhang M, Liu K, Xu D, Duan J, Zhou Y, Fang D, et al. Analysis of genetic diversity in populations released for stock enhancement and population caught in natural water of bighead carp in the lower reaches of the Yangtze River using microsatellite markers. Acta Agric. Univ. Jiangxiensis 2013, 35, 579-586. Available online: https://kns.cnki.net/kcms2/article/abstract?v=1UNTTfPTmO-XVX8YOndUx0lrHY_ffLKkXAFioaeSDNDn6eJAWvPmCdlZLvBLptSw9hAVjQtq4HoOdhBbX6qnN9OGVuLctfSOXuYoBVNeLpOfcvt6Fu8lWcMjCIp0ctb_Xwk2ZiuE2dwKMMz-tpYOqSwtd4mtHvW8lFG35r_TBpQyMQQ3vijvqQ==&uniplatform=NZKPT&language=CHS. (accessed on 28 November 2025).

[38] Chen C, Yu Q, Hou S, Li Y, Eustice M, Skelton R, et al. Construction of a sequence-tagged high-density genetic map of papaya for comparative structural and evolutionary genomics in brassicales. Genetics 2007, 177, 2481-2491. doi:10.1534/genetics.107.081463.

[39] Li W, Yu J, Que Y, Hu X, Wang E, Liao X, et al. Population genetic investigation of Hypophthalmichthys nobilis in the Yangtze River basin based on RAD sequencing data. Biology 2024, 13, 837. doi:10.3390/biology13100837.

[40] Zhu W, Fu J, Luo M, Wang L, Wang P, Liu Q, et al. Genetic diversity and population structure of bighead carp (Hypophthalmichthys nobilis) from the middle and lower reaches of the Yangtze River revealed using microsatellite markers. Aquac. Rep. 2022, 27, 101377. doi:10.1016/j.aqrep.2022.101377.

[41] Dong F, Cheng P, Sha H, Yue H, Wan C, Zhang Y, et al. Genetic diversity and population structure analysis of blunt snout bream (Megalobrama amblycephala) in the Yangtze River Basin: Implications for conservation and utilization. Aquac. Rep. 2024, 35, 101925. doi:10.1016/j.aqrep.2024.101925.

[42] Kim K, Kwak Y, Sung M, Cho S, Bang I. Population structure and genetic diversity of the endangered fish black shinner Pseudopungtungia nigra (Cyprinidae) in Korea: A wild and restoration population. Sci. Rep. 2023, 13, 9692. doi:10.1038/s41598-023-36569-4.

[43] Weight S. Evolution and the Genetics of Population Variability within and Among Natural Population; University of Chicago Press: Chicago, IL, USA, 1978.

[44] Wang J, Lei Q, Jiang H, Liu J, Yu X, Guo X, et al. Genetic diversity among wild and cultured bighead carp (Hypophthalmichthys nobilis) in the middle Yangtze River by microsatellite markers. Genes 2025, 16, 586. doi:10.3390/genes16050586.

[45] Luo T, Fang A, Zhou F, Xu P, Peng X, Zhang Y, et al. Genetic diversity, habitat relevance and conservation strategies of the silver carp in the Yangtze River by simple sequence repeat. Front. Ecol. Evol. 2022, 10, 850183. doi:10.3389/fevo.2022.850183.

[46] Balloux F, Lugon-Moulin N. The estimation of population differentiation with microsatellite markers. Mol. Ecol. 2002, 11, 155-165. doi:10.1046/j.0962-1083.2001.01436.x.

[47] Rosenberg D, Berkes F, Bodaly R, Hecky R, Kelly C, Rudd J. Large scale impacts of hydroelectric development. Environ. Rev. 1997, 5, 27-54. doi:10.1139/er-5-1-27.

[48] Agostinho A, Pelicice F, Gomes L. Dams and the fish fauna of the neotropical region: Impacts and management related to diversity and fisheries. Braz. J. Biol. 2008, 68, 1119-1132. doi:10.1590/S1519-69842008000500019.

[49] Gao X, Zeng Y, Wang J, Liu H. Immediate impacts of the second impoundment on fish communities in the Three Gorges Reservoir. Environ. Biol. Fishes 2010, 87, 163-173. doi:10.1007/s10641-009-9577-1.

[50] Xiao M, Bao F, Cui F. Pattern of genetic variation of yellow catfish Pelteobagrus fulvidraco Richardso in Huaihe River and the Yangtze River revealed using mitochondrial DNA control region sequences. Mol. Biol. Rep. 2014, 41, 5593-5606. doi:10.1007/s11033-014-3251-1.

[51] Jiang B, Fu J, Dong Z, Fang M, Zhu W, Wang L. Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations. PeerJ 2019, 7, e7007. doi:10.7717/peerj.7007.

[52] Nei M, Maruyama T, Chakraborty R. The bottleneck effect and genetic variability in populations. Evolution 1975, 29, 1-10. doi:10.2307/2407137.

[53] Cornuet J, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 1996, 144, 2001-2014. doi:10.1093/genetics/144.4.2001.