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  • Perspective
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A fish is not a mouse: understanding differences in background genetics is critical for reproducibility

Lab Animal volume 50, pages 19–25 (2021)Cite this article

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Abstract

Poorly controlled background genetics in animal models contributes to the lack of reproducibility that is increasingly recognized in biomedical research. The laboratory zebrafish, Danio rerio, has been an important model organism for decades in many research areas, yet inbred strains and traditionally managed outbred stocks are not available for this species. Sometimes incorrectly referred to as ‘inbred strains’ or ‘strains’, zebrafish wild-type lines possess background genetics that are often not well characterized, and breeding practices for these lines have not been consistent over time or among institutions. In this Perspective, we trace key milestones in the history of one of the most widely used genetic backgrounds, the AB line, to illustrate the dynamic complexity within an example background that is largely invisible when reading the scientific literature. Failure to adequately control for genetic background compromises the validity of experimental outcomes. We therefore propose that authors provide as much specific detail about the origin and genetic makeup of zebrafish lines as is reasonable and possible, and that the terms used to describe background genetics be applied in a way that is consistent with other fish and mammalian model organisms. We strongly encourage the adoption of genetic monitoring for the characterization of existing zebrafish lines, to help detect genetic contamination in breeding colonies and to verify the level of genetic heterogeneity in breeding colonies over time. Careful attention to background genetics will improve transparency and reproducibility, therefore improving the utility of the zebrafish as a model organism.

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Fig. 1: Tracing the origin and distribution of a subset of AB zebrafish.

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References

  1. Franklin, C. L. & Ericsson, A. C. Microbiota and reproducibility of rodent models. Lab Anim. (NY) 46, 114–122 (2017).

    Google Scholar 

  2. Chan, J. C., Houghton, A. B. & Bale, T. L. Strained in planning your mouse background? Using the HPA stress axis as a biological readout for backcrossing strategies. Neuropsychopharmacology 42, 1749–1751 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Carter, T. et al. Standardized nomenclature for inbred strains of mice: prepared by the Committee on Standardized Nomenclature for Inbred Strains of Mice. Cancer Res. 12, 602–613 (1952).

    Google Scholar 

  4. Green, M. C. in Handbook of Genetics Vol. 4 (ed. King, R. C.) 203–241 (Plenum Press, 1975).

  5. Whary, M. T., Baumgarth, N., Fox, J. G. & Barthold, S. W. in Laboratory Animal Medicine 3rd edn (eds Fox, J. G. et al.) 43–149 (Academic Press, 2015).

  6. Eppig, J. T. in The Mouse in Biomedical Research 2nd edn, Vol. 1 (eds Fox, J. G. et al.) 79–98 (Elsevier, 2007).

  7. Festing, M. F. W. in Encyclopedia of Immunology 2nd edn, Vol. 3 (eds Delves, P. J. & Roitt, I. M.) 1369–1372 (Academic Press, 1998).

  8. Franěk, R. et al. Isogenic lines in fish–a critical review. Rev. Aquac. 12, 1412–1434 (2020).

    Google Scholar 

  9. Sundberg, J. P. & Schofield, P. N. Commentary: mouse genetic nomenclature. Standardization of strain, gene, and protein symbols. Vet. Pathol. 47, 1100–1104 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Mandillo, S. et al. Reliability, robustness, and reproducibility in mouse behavioral phenotyping: a cross-laboratory study. Physiol. Genomics 34, 243–255 (2008).

    PubMed  PubMed Central  Google Scholar 

  11. Montkowski, A., Poettig, M., Mederer, A. & Holsboer, F. Behavioural performance in three substrains of mouse strain 129. Brain Res. 762, 12–18 (1997).

    CAS  PubMed  Google Scholar 

  12. Simon, M. M. et al. A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains. Genome Biol. 14, R82 (2013).

    PubMed  PubMed Central  Google Scholar 

  13. Spivakov, M. et al. Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish. G3 (Bethesda) 4, 433–445 (2014).

    Google Scholar 

  14. Kirchmaier, S., Naruse, K., Wittbrodt, J. & Loosli, F. The genomic and genetic toolbox of the teleost medaka (Oryzias latipes). Genetics 199, 905–918 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Hyodo-Taguchi, Y. Inbred strains of the medaka, Oryzias latipes. Fish Biol. J. MEDAKA 8, 11–14 (1996).

    Google Scholar 

  16. Angus, R. A. & Schultz, J. Clonal diversity in the unisexual fish Poeciliopsis monacha-lucida: a tissue graft analysis. Evolution 33, 27–40 (1979).

    PubMed  Google Scholar 

  17. Schultz, M. E. & Schultz, R. J. Differences in response to a chemical carcinogen within species and clones of the livebearing fish, Poeciliopsis. Carcinogenesis 9, 1029–1032 (1988).

    CAS  PubMed  Google Scholar 

  18. Vrijenhoek, R. C., Angus, R. A. & Schultz, R. J. Variation and heterozygosity in sexually vs. clonally reproducing populations of Poeciliopsis. Evolution 31, 767–781 (1977).

    PubMed  Google Scholar 

  19. Shen, Y. et al. X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species. BMC Genomics 17, 37 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Walter, R. B., Hazlewood, L., Kazianis, S., Kallman, K. & Schartl, M. The Xiphophorus genetic stock center manual. (San Marcos, Texas State University; accessed 27 May 2020).

  21. Meyer, B. M., Froehlich, J. M., Galt, N. J. & Biga, P. R. Inbred strains of zebrafish exhibit variation in growth performance and myostatin expression following fasting. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 164, 1–9 (2013).

    CAS  PubMed  Google Scholar 

  22. Volgin, A. D. et al. Zebrafish models for personalized psychiatry: insights from individual, strain and sex differences, and modeling gene x environment interactions. J. Neurosci. Res. 97, 402–413 (2019).

    CAS  PubMed  Google Scholar 

  23. Gorissen, M. et al. Differences in inhibitory avoidance, cortisol and brain gene expression in TL and AB zebrafish. Genes Brain Behav. 14, 428–438 (2015).

    CAS  PubMed  Google Scholar 

  24. Liu, X. et al. Strain-dependent differential behavioral responses of zebrafish larvae to acute MK-801 treatment. Pharmacol. Biochem. Behav. 127, 82–89 (2014).

    CAS  PubMed  Google Scholar 

  25. Mahabir, S., Chatterjee, D. & Gerlai, R. Short exposure to low concentrations of alcohol during embryonic development has only subtle and strain-dependent effect on the levels of five amino acid neurotransmitters in zebrafish. Neurotoxicol. Teratol. 68, 91–96 (2018).

    CAS  PubMed  Google Scholar 

  26. van den Bos, R. et al. Early life exposure to cortisol in zebrafish (Danio rerio): similarities and differences in behaviour and physiology between larvae of the AB and TL strains. Behav. Pharmacol. 30, 260–271 (2019).

    PubMed  Google Scholar 

  27. Wakamatsu, Y., Ogino, K. & Hirata, H. Swimming capability of zebrafish is governed by water temperature, caudal fin length and genetic background. Sci. Rep. 9, 16307 (2019).

    PubMed  PubMed Central  Google Scholar 

  28. van den Bos, R., Flik, G. & Gorissen, M. in Behavioral and Neural Genetics of Zebrafish (ed. Gerlai, R.) 245–262 (Elsevier, 2020).

  29. Audira, G., Siregar, P., Strungaru, S. A., Huang, J. C. & Hsiao, C. D. Which zebrafish strains are more suitable to perform behavioral studies? A comprehensive comparison by phenomic approach. Biology (Basel) 9, 200 (2020).

    Google Scholar 

  30. Siregar, P. et al. Method standardization for conducting innate color preference studies in different zebrafish strains. Biomedicines 8, 271 (2020).

    PubMed Central  Google Scholar 

  31. Chapman, F. A., Fitz‐Coy, S. A., Thunberg, E. M. & Adams, C. M. United States of America trade in ornamental fish. J. World Aquac. Soc. 28, 1–10 (1997).

    Google Scholar 

  32. Freeman, A. et al. in The Biological Resources of Model Organisms: Collection, Characterization and Applications (eds Jarret, R. L. & McCluskey, K.) 108–139 (CRC Press, 2019).

  33. Solnica-Krezel, L., Schier, A. F. & Driever, W. Efficient recovery of ENU-induced mutations from the zebrafish germline. Genetics 136, 1401–1420 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Brockerhoff, S. E. et al. A behavioral screen for isolating zebrafish mutants with visual system defects. Proc. Natl Acad. Sci. USA 92, 10545–10549 (1995).

    CAS  PubMed  Google Scholar 

  35. Lawrence, C. Advances in zebrafish husbandry and management. Methods Cell Biol. 104, 429–451 (2011).

    PubMed  Google Scholar 

  36. Kimura, M. & Crow, J. F. On the maximum avoidance of inbreeding. Genet. Res. (Camb.) 4, 399–415 (1963).

    Google Scholar 

  37. Streisinger, G., Walker, C., Dower, N., Knauber, D. & Singer, F. Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 291, 293–296 (1981).

    CAS  PubMed  Google Scholar 

  38. Johnson, S. L., Africa, D., Horne, S. & Postlethwait, J. H. Half-tetrad analysis in zebrafish: mapping the ros mutation and the centromere of linkage group I. Genetics 139, 1727–1735 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Mizgirev, I. & Revskoy, S. Generation of clonal zebrafish lines and transplantable hepatic tumors. Nat. Protoc. 5, 383–394 (2010).

    CAS  PubMed  Google Scholar 

  40. Nechiporuk, A., Finney, J. E., Keating, M. T. & Johnson, S. L. Assessment of polymorphism in zebrafish mapping strains. Genome Res. 9, 1231–1238 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Shinya, M. & Sakai, N. Generation of highly homogeneous strains of zebrafish through full sib-pair mating. G3 (Bethesda) 1, 377–386 (2011).

    Google Scholar 

  42. Trevarrow, B. & Robison, B. Genetic backgrounds, standard lines, and husbandry of zebrafish. Methods Cell Biol. 77, 599–616 (2004).

    PubMed  Google Scholar 

  43. Westerfield, M. The Zebrafish Book: A Guide for the Laboratory Use of Zebrafish Danio ("Brachydanio rerio") 5th edn (University of Oregon Press, 2007).

  44. Nasiadka, A. & Clark, M. D. Zebrafish breeding in the laboratory environment. ILAR J. 53, 161–168 (2012).

    CAS  PubMed  Google Scholar 

  45. LaFave, M. C., Varshney, G. K., Vemulapalli, M., Mullikin, J. C. & Burgess, S. M. A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1. Genetics 198, 167–170 (2014).

    PubMed  PubMed Central  Google Scholar 

  46. Balik-Meisner, M., Truong, L., Scholl, E. H., Tanguay, R. L. & Reif, D. M. Population genetic diversity in zebrafish lines. Mamm. Genome 29, 90–100 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Kent, M. L. et al. Development and maintenance of a specific pathogen-free (SPF) zebrafish research facility for Pseudoloma neurophilia. Dis. Aquat. Organ. 95, 73–79 (2011).

    PubMed  PubMed Central  Google Scholar 

  48. Almeida, J. L. et al. Interlaboratory study to validate a STR profiling method for intraspecies identification of mouse cell lines. PLoS ONE 14, e0218412 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Benavides, F. et al. Genetic quality assurance and genetic monitoring of laboratory mice and rats: FELASA Working Group Report. Lab. Anim. 54, 135–148 (2020).

    CAS  PubMed  Google Scholar 

  50. Bryda, E. C. & Riley, L. K. Multiplex microsatellite marker panels for genetic monitoring of common rat strains. J. Am. Assoc. Lab. Anim. Sci. 47, 37–41 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Guénet, J.-L. & Benavides, F. J. in Molecular Diagnostics 2nd edn (eds Patrinos, G. P. & Ansorge, W.) 461–469 (Elsevier, 2010).

  52. Fahey, J. R., Katoh, H., Malcolm, R. & Perez, A. V. The case for genetic monitoring of mice and rats used in biomedical research. Mamm. Genome 24, 89–94 (2013).

    PubMed  PubMed Central  Google Scholar 

  53. Fox, R. R., Wiles, M. V. & Petkov, P. M. in The Mouse in Biomedical Research 2nd edn, Vol. 1 (eds Fox, J. G. et al.) 135–144 (Academic Press, 2007).

  54. Butler, M. G. et al. SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. Development 142, 1542–1552 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Obholzer, N. et al. Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing. Development 139, 4280–4290 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Shimoda, N. et al. Zebrafish genetic map with 2000 microsatellite markers. Genomics 58, 219–232 (1999).

    CAS  PubMed  Google Scholar 

  57. Whiteley, A. R. et al. Population genomics of wild and laboratory zebrafish (Danio rerio). Mol. Ecol. 20, 4259–4276 (2011).

    PubMed  PubMed Central  Google Scholar 

  58. Coe, T. S. et al. Genetic variation in strains of zebrafish (Danio rerio) and the implications for ecotoxicology studies. Ecotoxicology 18, 144–150 (2009).

    CAS  PubMed  Google Scholar 

  59. Venta, P. J. et al. A 13-plex of tetra- and penta-STRs to identify zebrafish. Sci. Rep. 10, 3851 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Festing, M., Kondo, K., Loosli, R., Poiley, S. M. & Spiegel, A. International standardized nomenclature for outbred stocks of laboratory animals. Z. Versuchstierkd. 14, 215–224 (1972).

    CAS  PubMed  Google Scholar 

  61. Chia, R., Achilli, F., Festing, M. F. & Fisher, E. M. The origins and uses of mouse outbred stocks. Nat. Genet. 37, 1181–1186 (2005).

    CAS  PubMed  Google Scholar 

  62. Lohmiller, J. J., Swing, S. P. & Hanson, M. M. in The Laboratory Rat 3rd edn (eds Suckow, M. A. et al.) 157–179 (Elsevier, 2020).

  63. Percie du Sert, N. et al. The ARRIVE guidelines 2.0: updated guidelines for reporting animal research. J. Cereb. Blood Flow Metab. 40, 1769–1777 (2020).

    PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. IDEXX BioAnalytics, Columbia, MO, USA

    Marcus J. Crim

  2. Boston Children’s Hospital, Boston, MA, USA

    Christian Lawrence

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Crim, M.J., Lawrence, C. A fish is not a mouse: understanding differences in background genetics is critical for reproducibility. Lab Anim 50, 19–25 (2021). https://doi.org/10.1038/s41684-020-00683-x

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