Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 407903
Title Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries
Author(s) Kerstens, H.H.D.; Crooijmans, R.P.M.A.; Dibbits, B.W.; Vereijken, A.; Okimoto, R.; Groenen, M.A.M.
Source BMC Genomics 12 (2011). - ISSN 1471-2164 - 16 p.
DOI https://doi.org/10.1186/1471-2164-12-94
Department(s) LR - Backoffice
Animal Breeding and Genetics
WIAS
Publication type Refereed Article in a scientific journal
Publication year 2011
Keyword(s) copy-number variation - deletion polymorphism - rearrangements - nucleotide - expression - repeats - disease - impact
Abstract Background Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken. Results We identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs) of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome. Conclusion We provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes.
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