Abstract
BackgroundCopy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Most surveys of CNV in livestock have been conducted in the cattle genome, and often utilise only a single approach for the detection of copy number differences. Here we performed a study of CNV in sheep, using multiple methods to identify and characterise copy number changes. Comprehensive information from small pedigrees (trios) was collected using multiple platforms (array CGH, SNP chip and whole genome sequence data), with these data then analysed via multiple approaches to identify and verify CNVs.ResultsIn total, 3,488 autosomal CNV regions (CNVRs) were identified in this study, which substantially builds on an initial survey of the sheep genome that identified 135 CNVRs. The average length of the identified CNVRs was 19 kb (range of 1 kb to 3.6 Mb), with shorter CNVRs being more frequent than longer CNVRs. The total length of all CNVRs was 67.6Mbps, which equates to 2.7 % of the sheep autosomes. For individuals this value ranged from 0.24 to 0.55 %, and the majority of CNVRs were identified in single animals. Rather than being uniformly distributed throughout the genome, CNVRs tended to be clustered. Application of three independent approaches for CNVR detection facilitated a comparison of validation rates. CNVs identified on the Roche-NimbleGen 2.1M CGH array generally had low validation rates with lower density arrays, while whole genome sequence data had the highest validation rate (>60 %).ConclusionsThis study represents the first comprehensive survey of the distribution, prevalence and characteristics of CNVR in sheep. Multiple approaches were used to detect CNV regions and it appears that the best method for verifying CNVR on a large scale involves using a combination of detection methodologies. The characteristics of the 3,488 autosomal CNV regions identified in this study are comparable to other CNV regions reported in the literature and provide a valuable and sizeable addition to the small subset of published sheep CNVs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2754-7) contains supplementary material, which is available to authorized users.
Highlights
Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock
The array was used to assay a total of 36 sheep genomes, consisting of 30 individuals drawn from the International Mapping Flock [45] and a further six from a Reference Panel of International Sheep Genomics Consortium (ISGC) sheep (Additional file 1: Table S1)
These criteria are often selected using the results from a self-self hybridisation experiment, whereby self-self calls are used to indicate false positive calls, and rely on the assumption that the self-self hybridisation CNV calls cover the range of characteristics of false positive calls
Summary
Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Comprehensive information from small pedigrees (trios) was collected using multiple platforms (array CGH, SNP chip and whole genome sequence data), with these data analysed via multiple approaches to identify and verify CNVs. Copy number variants (CNVs) are a type of genomic polymorphism that potentially underlie a significant fraction of phenotypic variation [1]. There are many examples, in humans, of CNVs influencing traits These include multiple examples of CNVs associated with cancer susceptibility [10,11,12], the association of the FCGR3B gene copy number variant with systemic lupus erythematosus (SLE) [13], and CCL3L1 gene copy number, which has been linked to HIV susceptibility [14]. Not an association analysis, Chen et al [17] identified one CNV that had previously been associated with skin colour in pigs [18]
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