OpenSSL SSL_connect: Connection reset by peer in connection to v2.sherpa.ac.uk:443 PuSH - Publication Server of Helmholtz Zentrum München: Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage.

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Jansen, S.* ; Aigner, B.* ; Pausch, H.* ; Wysocki, M.* ; Eck, S. ; Benet-Pagès, A. ; Graf, E. ; Wieland, T. ; Strom, T.M. ; Meitinger, T. ; Fries, R.*

Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage.

BMC Genomics 14:446 (2013)
Publ. Version/Full Text Volltext DOI PMC
Open Access Gold
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Background: Genome- and population-wide re-sequencing would allow for most efficient detection of causal trait variants. However, despite a strong decrease of costs for next-generation sequencing in the last few years, re-sequencing of large numbers of individuals is not yet affordable. We therefore resorted to re-sequencing of a limited number of bovine animals selected to explain a major proportion of the population's genomic variation, so called key animals, in order to provide a catalogue of functional variants and a substrate for population-and genome-wide imputation of variable sites. Results: Forty-three animals accounting for about 69 percent of the genetic diversity of the Fleckvieh population, a cattle breed of Southern Germany and Austria, were sequenced with coverages ranging from 4.17 to 24.98 and averaging 7.46. After alignment to the reference genome (UMD3.1) and multi-sample variant calling, more than 17 million variant positions were identified, about 90 percent biallelic single nucleotide variants (SNVs) and 10 percent short insertions and deletions (InDels). The comparison with high-density chip data revealed a sensitivity of at least 92 percent and a specificity of 81 percent for sequencing based genotyping, and 97 percent and 93 percent when a imputation step was included. There are 91,733 variants in coding regions of 18,444 genes, 46 percent being non-synonymous exchanges, of which 575 variants are predicted to cause premature stop codons. Three variants are listed in the OMIA database as causal for specific phenotypes. Conclusions: Low- to medium-coverage re-sequencing of individuals explaining a major fraction of a population's genomic variation allows for the efficient and reliable detection of most variants. Imputation strongly improves genotype quality of lowly covered samples and thus enables maximum density genotyping by sequencing. The functional annotation of variants provides the basis for exhaustive genotype imputation in the population, e.g., for highest-resolution genome-wide association studies.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Next-generation Sequencing ; Low-coverage ; Genotyping By Sequencing ; Variant Annotation; Quantitative Trait Locus ; Growth-hormone Receptor ; Milk-yield ; Bos-taurus ; Missense Mutation ; Holstein Cattle ; Complex Traits ; Dairy-cattle ; Gene ; Discovery
ISSN (print) / ISBN 1471-2164
e-ISSN 1471-2164
Journal BMC Genomics
Quellenangaben Volume: 14, Issue: 1, Pages: , Article Number: 446 Supplement: ,
Publisher BioMed Central
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Human Genetics (IHG)