Open Access Open Badges Methodology article

Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

Hindrik HD Kerstens1, Richard PMA Crooijmans1, Bert W Dibbits1, Addie Vereijken2, Ron Okimoto3 and Martien AM Groenen1*

Author Affiliations

1 Animal Breeding and Genomics Center, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, the Netherlands

2 Research and Technology Centre, Hendrix Genetics, P.O. Box 30, 5830 AE, Boxmeer, The Netherlands

3 Cobb-Vantress Inc, P.O. Box 1030, Siloam Springs, AR 72761, USA

For all author emails, please log on.

BMC Genomics 2011, 12:94  doi:10.1186/1471-2164-12-94

Published: 3 February 2011



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.


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.


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.