Open Access Research article

Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication

Julia Metzger1, Raul Tonda2, Sergi Beltran2, Lídia Águeda2, Marta Gut2 and Ottmar Distl1*

Author Affiliations

1 Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany

2 Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, Barcelona 08028, Spain

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BMC Genomics 2014, 15:562  doi:10.1186/1471-2164-15-562

Published: 4 July 2014



Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces.


Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses.


Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses.