title: Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array.
abstract: Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome-wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome-wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed-specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed-specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.|Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 83000, China.
authors.forename: Adiljan
authors.initials: A
authors.lastname: Kader
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
authors.forename: Xuexue
authors.initials: X
authors.lastname: Liu
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.|United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA.
authors.forename: Kunzhe
authors.initials: K
authors.lastname: Dong
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.|Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China.
authors.forename: Shen
authors.initials: S
authors.lastname: Song
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
authors.forename: Jianfei
authors.initials: J
authors.lastname: Pan
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
authors.forename: Min
authors.initials: M
authors.lastname: Yang
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Chen
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: He
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China. jianglin@caas.cn.
authors.forename: Lin
authors.initials: L
authors.lastname: Jiang
authors.affiliation: The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China. mayuehui@caas.cn.
authors.forename: Yuehui
authors.initials: Y
authors.lastname: Ma
mesh_terms: D000818:Animals; D001947:Breeding; D002681:China; D056915:DNA Copy Number Variations; D005838:Genotype; D006736:Horses / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary; D020641:Polymorphism, Single Nucleotide
keywords: Debao pony; copy number variation region; growth; single nucleotide polymorphism array