Abstract
BackgroundCopy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus) using Illumina short-read sequencing data, by comparing our lab data for 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) to public data for 26 individuals from three other breeds (two Moroccan and one Chinese) and 21samples from Bezoar ibexes.ResultsWe obtained a total of 2394 CNV regions (CNVRs) by merging 208,649 high-confidence CNVs, which spanned ~ 267 Mb of total length and accounted for 10.80% of the goat autosomal genome. Functional analyses showed that 2322 genes overlapping with the CNVRs were significantly enriched in 57 functional GO terms and KEGG pathways, most related to the nervous system, metabolic process, and reproduction system. Clustering patterns of all 85 samples generated separately from duplications and deletions were generally consistent with the results from SNPs, agreeing with the geographical origins of these goats. Based on genome-wide FST at each CNV locus, some genes overlapping with the highly divergent CNVs between domestic and wild goats were mainly enriched for several immunity-related pathways, whereas the genes overlapping with the highly differentiated CNVs between highland and lowland goats were mainly related to vitamin and lipid metabolism. Remarkably, a 507-bp deletion at ~ 14 kb downstream of FGF5 on chromosome 6 showed highly divergent (FST = 0.973) between the highland and lowland goats. Together with an enhancer activity of this sequence shown previously, the function of this duplication in regulating fiber growth deserved to be further investigated in detail.ConclusionWe generated a comprehensive map of CNVs in goats. Many genetically differentiated CNVs among various goat populations might be associated with the population characteristics of domestic goat breeds.
Highlights
Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments
CNVs distribute ubiquitously in the goat genome Based on the short-read sequencing data for 85 goats with the coverage depth of 5.25× ~ 15.90× (Additional file 1), we identified a total of 208,649 CNVs, including 17,876 duplications and 190,773 deletions across all autosomes (Additional file 2)
It is noted that the number of identified CNVs in each goat appeared to increase with sequence depth in general
Summary
Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. As a major class of structural variations (SVs) that complement to single nucleotide variations (SNVs), copy number variations (CNVs) refer to duplications, deletions, and insertions of DNA sequences ≥50 bp in size between individuals within a species [1]. A growing body of work demonstrates important effects of CNVs on phenotypic variations of Mendelian and quantitative traits in domestic animals by various molecular mechanisms, such as gene dosage, gene disruption, and gene fusion. An inverted duplication and junction of two distinct regions of the chicken genome disrupt long-range cis-regulatory elements of EDN3 and thereby result in the Silkie phenotype (i.e., dermal hyperpigmentation) [3]. A genome-wide association study and wholegenome sequencing identified a significant correlation between the degree of white spotting and a 1 Mb copy number region harboring EDNRA in Boer goats [4]. There are few studies concerning genome-wide characteristics of CNVs in goats so far [7, 8]
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