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Extensive Genetic Diversity and Substructuring Among Zebrafish Strains Revealed Through Copy Number Variant Analysis
PNS (2012)
  • Kim H. Brown, Brigham and Women's Hospital
  • Kimberly P. Dobrinski, Brigham and Women's Hospital
  • Arthur S. Lee, Brigham and Women's Hospital
  • Omer Gokcumen, Brigham and Women's Hospital
  • Ryan E. Mills, Brigham and Women's Hospital
  • Xinghua Shi, Brigham and Women's Hospital
  • Wilson W. S. Chong, Brigham and Women's Hospital
  • Jin Yun Helen Chen, Brigham and Women's Hospital
  • Paulo Yoo, Brigham and Women's Hospital
  • Sthuthi David, Brigham and Women's Hospital
  • Samuel M. Peterson, Purdue University
  • Towfique Raj, Harvard Medical School
  • Kwong Wai Choy, Chinese University of Hong Kong
  • Barbara E. Stranger, Harvard Medical School
  • Robin E. Williamson, Harvard Medical School
  • Leonard I. Zon, Harvard Medical School
  • Jennifer L. Freeman, Brigham and Women's Hospital
  • Charles Lee, Brigham and Women's Hospital
Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population, we constructed a genome-wide, high-resolution CNV map for the zebrafish comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. This amount of copy number variation is four times that previously observed in other vertebrates, including humans. Moreover, 69% of the CNV elements exhibited strain specificity, with the highest number observed for Tubingen. This variation likely arose, in part, from Tubingen's large founding size and composite population origin. Additional population genetic studies also provided important insight into the origins and substructure of these commonly used laboratory strains. This extensive variation among and within zebrafish strains may have functional effects that impact phenotype and, if not properly addressed, such extensive levels of germ-line variation and population substructure in this commonly used model organism can potentially confound studies intended for translation to human diseases.
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Citation Information
Brown KH, Dobrinski KP*, Lee AS, Gokcumen O, Mills RE, Shi X, Chong WWS, Chen, JYH, Yoo P, David S, Peterson SM, Raj T, Choy KW, Stranger B, Williamson RE, Zon LI, Freeman JL, Lee C. Extensive genetic diversity and strain sub-structuring among zebrafish strains revealed through copy number variant analysis. Proc Natl Acad Sci U S A 2012; 109, 529-534.