TitlePopulation genetic diversity in zebrafish lines.
Publication TypeJournal Article
Year of Publication2018
AuthorsBalik-Meisner, M, Truong, L, Scholl, EH, Tanguay, RL, Reif, DM
JournalMamm Genome
Volume29
Issue1-2
Pagination90-100
Date Published2018 02
ISSN1432-1777
KeywordsAnimals, Gene Frequency, Genetic Variation, Genetics, Population, Genome, Polymorphism, Single Nucleotide, Zebrafish
Abstract

Toxicological and pharmacological researchers have seized upon the many benefits of zebrafish, including the short generation time, well-characterized development, and early maturation as clear embryos. A major difference from many model organisms is that standard husbandry practices in zebrafish are designed to maintain population diversity. While this diversity is attractive for translational applications in human and ecological health, it raises critical questions on how interindividual genetic variation might contribute to chemical exposure or disease susceptibility differences. Findings from pooled samples of zebrafish support this supposition of diversity yet cannot directly measure allele frequencies for reference versus alternate alleles. Using the Tanguay lab Tropical 5D zebrafish line (T5D), we performed whole genome sequencing on a large group (nā€‰=ā€‰276) of individual zebrafish embryos. Paired-end reads were collected on an Illumina 3000HT, then aligned to the most recent zebrafish reference genome (GRCz10). These data were used to compare observed population genetic variation across species (humans, mice, zebrafish), then across lines within zebrafish. We found more single nucleotide polymorphisms (SNPs) in T5D than have been reported in SNP databases for any of the WIK, TU, TL, or AB lines. We theorize that some subset of the novel SNPs may be shared with other zebrafish lines but have not been identified in other studies due to the limitations of capturing population diversity in pooled sequencing strategies. We establish T5D as a model that is representative of diversity levels within laboratory zebrafish lines and demonstrate that experimental design and analysis can exert major effects when characterizing genetic diversity in heterogeneous populations.

DOI10.1007/s00335-018-9735-x
Alternate JournalMamm. Genome
PubMed ID29368091
PubMed Central IDPMC5851690
Grant ListP30 ES025128 / ES / NIEHS NIH HHS / United States
835168 / / U.S. Environmental Protection Agency / International
ES007329 / ES / NIEHS NIH HHS / United States
T32 GM062758 / GM / NIGMS NIH HHS / United States
ES027294 / ES / NIEHS NIH HHS / United States
U01 ES027294 / ES / NIEHS NIH HHS / United States
T32 ES007329 / ES / NIEHS NIH HHS / United States
ES016465 / ES / NIEHS NIH HHS / United States
DGE1252376 / / National Science Foundation / International
ES019764 / ES / NIEHS NIH HHS / United States
ES025128 / ES / NIEHS NIH HHS / United States
RC4 ES019764 / ES / NIEHS NIH HHS / United States
P42 ES016465 / ES / NIEHS NIH HHS / United States
835796 / / U.S. Environmental Protection Agency / International
ES005948 / ES / NIEHS NIH HHS / United States
P42 ES005948 / ES / NIEHS NIH HHS / United States