A genome-wide scan for copy number variations using high-density single nucleotide polymorphism array in Simmental cattle.
Copy number variations (CNVs) have recently been identified as promising sources of genetic variation, complementary to single nucleotide polymorphisms (SNPs). As a result, detection of CNVs has attracted a great deal of attention. In this study, we performed genome-wide CNV detection using Illumina Bovine HD BeadChip (770k) data on 792 Simmental cattle. A total of 263 CNV regions (CNVRs) were identified, which included 137 losses, 102 gains and 24 regions classified as both loss and gain, covering 35.48 Mb (1.41%) of the bovine genome. The length of these CNVRs ranged from 10.18 kb to 1.76 Mb, with an average length of 134.78 kb and a median length of 61.95 kb. In 136 of these regions, a total of 313 genes were identified related to biological functions such as transmembrane activity and olfactory transduction activity. To validate the results, we performed quantitative PCR to detect nine randomly selected CNVRs and successfully confirmed seven (77.6%) of them. Our results present a map of cattle CNVs derived from high-density SNP data, which expands the current CNV map of the cattle genome and provides useful information for investigation of genomic structural variation in cattle.
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.
Yang
Y
Wu
Huizhong
H
Fan
Shengyun
S
Jing
Jiangwei
J
Xia
Yan
Y
Chen
Lupei
L
Zhang
Xue
X
Gao
Junya
J
Li
Huijiang
H
Gao
Hongyan
H
Ren
D000818:Animals; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology; D056915:DNA Copy Number Variations; D005838:Genotype; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary; D016133:Polymerase Chain Reaction / Q000662:veterinary; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012984:Software
Illumina Bovine HD BeadChip; bovine genome; quantitative PCR; single nucleotide polymorphism