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Development and application of microsatellite DNA molecular markers for the laboratory red crucian carp (Carassius auratus) strain C1HD

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Abstract

The genetic backgrounds of crucian carp (Carassius auratus) and goldfish are highly similar, and these fish are often considered a single variety. It is therefore difficult to distinguish crucian carp using traditional genetic and molecular methods. In this study, we developed microsatellite markers for the laboratory red crucian carp (C1HD strain) by analyzing its genome sequence using a Perl script. We investigated the polymorphism of these potential markers in the C1HD strain, two other crucian carp lineages (DLCC strain and red crucian carp-like fish, RCC-L), and two other cyprinid species (Ryukin and koi carp, Cyprinus carpio haematopterus, KOC). Among nine screened loci, two loci (SSR-4, SSR-21) showed specific genotypes to C1HD, SSR-4, and SSR-21 observed in C1HD with 209/238 and 214/238, respectively. Additionally, one locus (SSR-763) presented one private allele in C1HD (389) and other locus (SSR-228) detected with one private allele in C1HD (135). Across the five strains, a total of 42 alleles were identified in the nine microsatellite markers. Nei’s unbiased genetic distances revealed a close relationship between the C1HD strain and the red crucian carp-like fish. The laboratory red crucian carp was recovered on an independent branch in the evolutionary tree drawn based on genetic distance. Our microsatellite makers clearly distinguish the laboratory crucian carp for RCC-L, DLCC, and Ryukin lineages.

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Data availability

All the datasets used and/or analyzed throughout the present study are available from the corresponding author on reasonable request.

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Acknowledgements

We sincerely appreciate the many researchers who helped us to complete this manuscript. We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript.

Funding

This work was supported by the National Science and Technology Support Plan of the 12th Five-Year Plan (2015BAIO9BO5), Key Project of Science and Technology Plan of Hunan Provincial Department of Science and Technology (2014TT1002), Outstanding Youth Program of Hunan Education Department (20B343) and the National Key Research and Development Program of China (2020YFD0900104).

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Author notes

  1. Yude Wang, Kejie Chen and Duansheng Wu contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People’s Republic of China

    Yude Wang, Dishan Hong & Duansheng Wu

  2. Department of Laboratory Animal Science, University of South China, Hengyang, 421001, China

    Kejie Chen & Duansheng Wu

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  1. Yude Wang
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  2. Kejie Chen
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  3. Dishan Hong
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  4. Duansheng Wu
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Contributions

This study was conceived and designed by D.S.W. and Y.D.W. Y.D.W. and K.J.C performed the experimental work, most of the statistical analyses, and the manuscript writing. D.S.H. performed much of the English proofreading. All authors read and approved the final manuscript.

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Correspondence to Duansheng Wu.

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The authors declare no competing interests.

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Wang, Y., Chen, K., Hong, D. et al. Development and application of microsatellite DNA molecular markers for the laboratory red crucian carp (Carassius auratus) strain C1HD. Aquacult Int 30, 87–97 (2022). https://doi.org/10.1007/s10499-021-00786-3

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  • DOI: https://doi.org/10.1007/s10499-021-00786-3

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