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Open Access Highly Accessed Research article

Analysis of structural diversity in wolf-like canids reveals post-domestication variants

Oscar Ramirez1, Iñigo Olalde1, Jonas Berglund2, Belen Lorente-Galdos1, Jessica Hernandez-Rodriguez1, Javier Quilez1, Matthew T Webster2, Robert K Wayne3, Carles Lalueza-Fox1, Carles Vilà4 and Tomas Marques-Bonet156*

Author Affiliations

1 Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC), Ciències Experimentals i de la Salut, Barcelona 08003, Spain

2 Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden

3 UCLA, Department of Ecology and Evolutionary Biology, Los Angeles 90095, CA, USA

4 Estación Biológica de Doñana EBD-CSIC, Conservation and Evolutionary Genetics Group, Sevilla 41092, Spain

5 Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

6 Centro Nacional de Análisi Genómico (CNAG), Barcelona 08028, Spain

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BMC Genomics 2014, 15:465  doi:10.1186/1471-2164-15-465

Published: 12 June 2014

Abstract

Background

Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication.

Results

In this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB).

Conclusions

Our results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process.

Keywords:
Domestication; CNV; Candidate genes; Dog and wolf