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Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE28239: Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (expression array) GSE28276: Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (CGH ZV81M) GSE28278: Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (CGH ZV81M 2) GSE33962: Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis (CGH) Refer to individual Series

ORGANISM(S): Danio rerio

SUBMITTER: Charles Lee

PROVIDER: E-GEOD-28328 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis (CGH)

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Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (expression array)

Project description:Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information. We developed a zebrafish CNV map using 80 zebrafish genomes from laboratory strains (AB, Tubingen, and WIK) and one native population, identifying 6,080 CNV elements. Overlapping or adjacent CNVs account for 14.6% of the genome, representing four times the CNV levels from other vertebrates including humans. Highest intra-specific CNV levels were observed for Tubingen, a common laboratory strain due to high fecundity. Tubingen variation likely represents higher initial population size and composite population founders initiating the laboratory strain. Extensive zebrafish CNVs, along with associated phenotypic impacts, advocates for increased usage of isogenic strains for genetic studies intended for human disease translation. 7 full sib adult hybrid fish used for expression Quantatitive Trait Loci (eQLT) analysis to support CNV affects on gene expresion in zebrafish.

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