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Background  Domestic goats ( Capra hircus ) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar ( Capra aegagrus ). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.    Results  We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which  ASIP  gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.    Conclusion  Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users.

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication