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Open Access Research article

An initial comparative map of copy number variations in the goat (Capra hircus) genome

Luca Fontanesi1*, Pier Luigi Martelli2, Francesca Beretti13, Valentina Riggio3, Stefania Dall'Olio1, Michela Colombo1, Rita Casadio2, Vincenzo Russo1 and Baldassare Portolano3

Author Affiliations

1 DIPROVAL, Sezione di Allevamenti Zootecnici, University of Bologna, Via F.lli Rosselli 107, 42123 Reggio Emilia, Italy

2 Biocomputing Group, Computational Biology Network, Dept. of Biology, University of Bologna, Via San Giacomo 9/2, 40126 Bologna, Italy

3 Dept. S.En.Fi.Mi.Zo., Sezione di Produzioni Animali, University of Palermo, Viale delle Scienze - Parco d'Orleans, 90128 Palermo, Italy

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BMC Genomics 2010, 11:639  doi:10.1186/1471-2164-11-639

Published: 17 November 2010

Abstract

Background

The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome.

Results

We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P < 0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals.

Conclusions

We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats.