Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsWe 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.
Highlights
The goat (Capra hircus) represents one of the most important farm animal species
To identify copy number variations (CNVs) in goats, we carried out a cross-species array comparative genome hybridization (aCGH) experiment using a cattle (Bos taurus) custom tiling array including ~385,000 oligonucleotide probes and goat genomic DNA obtained from 9 goats of four different breeds (3 Saanen, 1 Camosciata delle Alpi, 3 Girgentana, and 2 Murciano-Granadina goats), chosen according to their differences in production and morphological traits, and origin (Figure 1)
The tiling arrays included 4,673 oligonucleotides designed on a portion of BTA13 derived from the University of Maryland (UMD) Bos taurus v. 2.0 assembly [75]. This additional BTA13 portion was included in the tiling arrays because the agouti signaling protein (ASIP) gene was not correctly assembled in the Btau_4.0 version of BTA13 and was reported in unassembled scaffolds only. This UMD 2.0 BTA13 region was added as an internal control because we previously demonstrated that the ASIP gene and the close S-adenosylhomocysteine hydrolase (AHCY) gene are included in a goat CNV regions (CNVRs) [22]
Summary
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. It is reared in all continents with an estimated world population of about 800 million of animals and about 560 breeds, which constitute approximately 12% of the total number of recorded domesticated mammalian livestock breeds of the world [1]. A comparative cytogenetic map of the goat genome has been developed using cattle and sheep BAC clones [3] This map has been improved adding many other physically mapped genes, as recently reviewed in a compiled list including 268 genes and 144 microsatellites, roughly including 65% of the goat chromosome bands [7].
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