PUBLICATION
The laboratory domestication of zebrafish: from diverse populations to inbred substrains
- Authors
- Suurväli, J., Whiteley, A.R., Zheng, Y., Gharbi, K., Leptin, M., Wiehe, T.
- ID
- ZDB-PUB-191207-5
- Date
- 2019
- Source
- Molecular Biology and Evolution 37(4): 1056-1069 (Journal)
- Registered Authors
- Leptin, Maria
- Keywords
- RAD-seq, genetic differentiation, genetic diversity, inbreeding, laboratory strains, wild populations, zebrafish
- MeSH Terms
-
- Animals
- Animals, Inbred Strains
- Animals, Wild/genetics*
- Domestication*
- Gene Frequency
- Genetic Variation*
- Genome*
- Zebrafish/genetics*
- PubMed
- 31808937 Full text @ Mol Bio Evol
Citation
Suurväli, J., Whiteley, A.R., Zheng, Y., Gharbi, K., Leptin, M., Wiehe, T. (2019) The laboratory domestication of zebrafish: from diverse populations to inbred substrains. Molecular Biology and Evolution. 37(4):1056-1069.
Abstract
We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of 'personalized medicine'. Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behaviour and physiology, for modelling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species. Here we use Restriction site-Associated DNA sequencing (RAD-seq) to genetically characterize wild populations of zebrafish from India, Nepal and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic and evolutionary studies in Danio rerio.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping