Genetic Structure and Genetic Diversity of Leuciscus waleckii in the Luohe River System
1. Henan Academy of Fishery Sciences, Zhengzhou 450044, China
2. College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450056, China
| Abstract: | Leuciscus waleckii, an endemic fish species in the Yellow River Basin, holds significant ecological and germplasm value. However, its wild populations have declined sharply due to habitat destruction, overfishing, and environmental pollution, now surviving only in localized waters such as the upper Yellow River and the Luohe River system. To elucidate its germplasm characteristics and adaptive evolutionary mechanisms, we employed whole-genome resequencing to analyze 15 samples: 5 L. waleckii from the Luohe River system (LH group), 5 L. waleckii from the Wusuli River (WS group), and 5 L. waleckii from Dalai Lake in Inner Mongolia (ALK group, data downloaded from NCBI SRA database with accession number PRJNAXXXXXX). Analyses included SNP/InDel detection, genetic differentiation index (Fst), nucleotide polymorphism (θπ), and GO/KEGG enrichment. Results showed that the LH group exhibited the highest nucleotide polymorphism (θπ = 0.000998656), indicating optimal genetic diversity. Overall genetic differentiation among the three populations was low: Fst values between LH and WS, and between LH and ALK were 0.0402803 and 0.0370886, respectively (indicating minimal differentiation), while ALK and WS showed moderate differentiation (Fst = 0.0970577). UPGMA phylogenetic tree analysis confirmed that the Luohe River system L. waleckii forms an independent clade, distinct from the other two populations, verifying it as a separate species. This study provides insights into the adaptive evolution and germplasm potential of L. waleckii, offering a scientific basis for developing conservation strategies and sustainable utilization of this endangered species. |
| Keywords: | Leuciscus waleckii; Whole-genome Resequencing; Genetic Structure; Genetic Diversity; Adaptive Evolution |
| DOI: | 10.57237/j.life.2026.01.001 |
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收稿日期: 2026-02-27
接受日期: 2026-03-23
在线出版日期: 2026-03-24
参考文献
| [1] | Cai WX. Ichthyological Atlas of the Yellow River Basin. Xi'an: Northwest A&F University Press, 2013. |
| [2] | Yan HC, Gao L, Fu CL, et al. Advances in Molecular Methods for Studying Fish Genetic Diversity and Their Applications. Fisheries Science, 2004, (12): 44-48. https://doi.org/CNKI:SUN:CHAN.0.2004-12-014 |
| [3] | Manel S, Guerin PE, Mouillot D, et al. Global determinants of freshwater and marine fish genetic diversity. Nat Commun, 2020, 11(1): 692. https://doi.org/10.1038/s41467-020-14409-7 |
| [4] | Cheung KH, Osier MV, Kidd JR, et al. ALFRED: an allele frequency database for diverse populations and DNA polymorphisms. Nucleic Acids Res, 2000, 28(1): 361-363. https://doi.org/10.1093/nar/28.1.361 |
| [5] | Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature, 2011, 475(7357): 493-496. https://doi.org/10.1038/nature10231 |
| [6] | Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution, 1984, 38(6): 1358-1370. https://doi.org/10.1111/j.1558-5646.1984.tb05657.x |
| [7] | Biscarini F, Nicolazzi EL, Stella A, et al. Challenges and opportunities in genetic improvement of local livestock breeds. Front Genet, 2015, 6: 33. https://doi.org/10.3389/fgene.2015.00033 |
| [8] | Sasazaki S, Tomita K, Nomura Y, et al. FGF5 and EPAS1 gene polymorphisms are associated with high-altitude adaptation in Nepalese goat breeds. Animal Science Journal, 2021, 92(1): e13640. https://doi.org/10.1111/asj.13640 |
| [9] | Amills M, Capote J, Tosser-Klopp G. Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces. Animal genetics, 2017, 48(6): 631-644. https://doi.org/10.1111/age.12598 |
| [10] | Xiao WH, Zhang YP. Mitochondrial DNA Genetics and Evolution in Fishes. Acta Hydrobiologica Sinica, 2000, (4): 384-391. https://doi.org/10.3321/j.issn:1000-3207.2000.04.014 |
| [11] | Anan K, Puangsomlee WP, Pornpimol J. Genetic variations and population structure in three populations of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) inferred from mitochondrial cytochrome b sequences. Mitochondrial DNA Part A, 2018, 29(1): 82-90. https://doi.org/10.1080/24701394.2016.1242581 |
| [12] | Zhao WH, Yi SK, Su JX, et al. Study on Genetic Diversity of Triplophysa yarqantensis in the Tarim River, Xinjiang. Acta Hydrobiologica Sinica, 2022, 46(03): 364-374. https://doi.org/10.7541/2022.2021.006 |
| [13] | RL, VCR. Analysis of genetic diversity in CYTB and control region sequences of Melanochelys trijuga (Schweigger, 1812) from Karnataka. Journal of Asia-Pacific Biodiversity, 2018, 11(3): 346-352. https://doi.org/10.1016/j.japb.2018.05.001 |
| [14] | Dou XJ, Chang YM, Tang R, et al. Genetic Diversity Analysis of Varicorhinus waleckii Population Based on CO I Sequence. Acta Agriculturae Boreali-Occidentalis Sinica, 2014, 29(S1): 29-34. https://doi.org/10.7668/hbnxb.2014.S1.007 |
| [15] | Hu W. Genetic Diversity Analysis of the Yellow River Turtle (Mauremys reevesii) Population at Wuwang Ferry. Shanxi University, 2021. |
| [16] | Hamada H, Petrino MG, Kakunaga T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci U S A, 1982, 79(21): 6465-6469. https://doi.org/10.1073/pnas.79.21.6465 |
| [17] | Tautz D, Renz M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res, 1984, 12(10): 4127-4138. https://doi.org/10.1093/nar/12.10.4127 |
| [18] | Goldstein DB, Roemer GW, Smith DA, et al. The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics, 1999, 151(2): 797-801. https://doi.org/10.3389/fpls.2025.1651814 |
| [19] | Hosoya S, Kikuchi K, Nagashima H, et al. Assessment of genetic diversity in Coho salmon (Oncorhynchus kisutch) populations with no family records using ddRAD-seq. BMC Res Notes, 2018, 11: 548. https://doi.org/10.1186/s13104-018-3663-4 |
| [20] | Larson WA, Seeb JE, Pascal CE, et al. Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Can J Fish Aquat Sci, 2014, 71: 698-708. https://doi.org/10.1139/cjfas-2013-0502 |
| [21] | Yang HN, Peng GX, Yan YC, et al. Application of DNA Molecular Marker Technology in Ecological Research. Research on Life Sciences, 2004, (S1): 96-101. https://doi.org/CNKI:SUN:SMKY.0.2004-S1-019 |
| [22] | Nei M. Molecular population genetics and evolution. North-Holland Publishing Company, 1975. |
| [23] | Ding R, Yu D, Yang K, et al. Chromosome-Level Genome Assembly and Whole-Genome Resequencing Revealed Contrasting Population Genetic Differentiation of Black Bream (Megalobrama skolkovii) (Teleostei: Cyprinidae) Allopatric and Sympatric to Its Kin Species. Ecol Evol, 2025, 15(1): e70874. https://doi.org/10.1002/ece3.70874 |
| [24] | Dalvit C, Demarchi M, Cassandro M. Genetic traceability of livestock products: A review. Meat Science, 2007, 77(4): 437-49. https://doi.org/10.1016/j.meatsci.2007.05.027 |
| [25] | Nazareno AG, Bemmels JB, Dick CW, et al. Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Molecular Ecology Resources, 2017, 17(6): 1136-1147. https://doi.org/10.1111/1755-0998.12654 |
| [26] | Chi BJ, Chang YM, Yan XC, et al. Analysis of Genetic Diversity and Genetic Structure between the Dalai Lake Population and the Ussuri River Population of Leuciscus waleckii. Journal of Fishery Sciences of China, 2010, 17(02): 228-235. https://doi.org/CNKI:SUN:ZSCK.0.2010-02-007 |
