Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization

Abstract

BackgroundCopy number variants contribute to genetic variation in birds. Analyses of copy number variants in chicken breeds had focused primarily on those from commercial varieties with nothing known about the occurrence and diversity of copy number variants in locally raised Chinese chicken breeds. To address this deficiency, we characterized copy number variants in 11 chicken breeds and compared the variation among these breeds.ResultsWe presented a detailed analysis of the copy number variants in locally raised Chinese chicken breeds identified using a customized comparative genomic hybridization array. We identified 833 copy number variants contained within 308 copy number variant regions. The median and mean sizes of the copy number variant regions were 14.6 kb and 35.1 kb, respectively. Of the copy number variant regions, 138 (45%) involved gain of DNA, 159 (52%) involved loss of DNA, and 11 (3%) involved both gain and loss of DNA. Principal component analysis and agglomerative hierarchical clustering revealed the close relatedness of the four locally raised chicken breeds, Shek-Ki, Langshan, Qingyuan partridge, and Wenchang. Biological process enrichment analysis of the copy number variant regions confirmed the greater variation among the four aforementioned varieties than among the seven other breeds studied.ConclusionOur description of the distribution of the copy number variants and comparison of the differences among the copy number variant regions of the 11 chicken breeds supplemented the information available concerning the copy number variants of other Chinese chicken breeds. In addition to its relevance for functional analysis, our results provided the first insight into how chicken breeds can be clustered on the basis of their genomic copy number variation.

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

“…Moreover, these enriched GO terms were mainly involved in cellular regulation and structure, various binding functions as well as stress and immune responses, which are consistent with several previous studies [9,[32][33][34], suggesting that the copy number variable genes may influence the responses to external stimuli and provide the mutational flexibility to adapt rapidly to changing selective pressures due to evolutionary adaption [59]. Most CNVRs also spanned some QTL regions, which indicated that these CNVRs may exert significant effects on traits of economic interest in chickens.…”

“…The NGS technology and RD method employed in our work has advantages in both technology platform and genetic diversity compared with the eight previous reports [9,[32][33][34]36,[39][40][41]. Because a significant fraction of CNVs falls into genomic regions not well-covered by microarrays, especially for SD regions lacking sufficient probes [16,23], CNV as a major source of genetic variation is complementary to SNP and could account for a substantial part of missing heritability [14].…”

“…These unique CNVRs may be recent events in evolution and contribute to breed-specific phenotype and performance [44]. Compared with the eight previous chicken CNV studies [9,[32][33][34]36,[39][40][41], far more CNVRs both on average and in total were found. A total of 6,478 (86.0%) autosomal CNVRs with slightly smaller average size (10.6 kb) were novel, likely due to the higher resolution and sensitivity of NGS method than aCGH and SNP array.…”

“…However, some previous CNV studies in chickens based on aCGH and SNP platforms mainly suffered from low resolution and sensitivity [9,[32][33][34][35]. A latest study exhibited the detection of four main types of genetic variation from whole genome sequencing data using two chickens [36], suggesting the efficiency of CNV detection via deep sequencing.…”

A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens

“…The causative mutation should be located in this 18.9 kb region, and no structural change in this region was identified in the present study via Sanger sequencing or in our previous study using array CGH [25]. The sequence of the assembly gap in this region (GenBank KC166241) contained 83.5% G and C with numerous poly G, poly C and CpG sites.…”