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Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array
Author(s) -
Kader Adiljan,
Liu Xuexue,
Dong Kunzhe,
Song Shen,
Pan Jianfei,
Yang Min,
Chen Xiaofei,
He Xiaohong,
Jiang Lin,
Ma Yuehui
Publication year - 2016
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12451
Subject(s) - biology , genetics , copy number variation , genotyping , single nucleotide polymorphism , snp genotyping , genome , gene , genotype
Summary 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 CNV s in 96 horses from three diverse Chinese breeds: Debao pony ( DB ), Mongolian horse ( MG ) and Yili horse ( YL ). A total of 287 CNV s were determined and merged into 122 CNV regions ( CNVR s) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVR s were integrated with seven existing reports to generate a composite genome‐wide dataset of 1558 equine CNVR s, revealing 69 (56.6%) novel CNVR s. The majority (69.7%) of the 122 CNVR s overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVR s, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed‐specific s s were identified in DB , MG and YL respectively. Among these genes, FGF 11 , SPEM 1 , PPARG , CIDEB , HIVEP 1 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 CNVR s in the future.