title: Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level.
abstract: BACKGROUND
  Copy number variation (CNV), a source of genetic diversity in mammals, has been shown to underlie biological functions related to production traits. Notwithstanding, there have been few studies conducted on CNVs using next generation sequencing at the population level.
  
  
  RESULTS
  Illumina NGS data was obtained for ten Holsteins, a dairy cattle, and 22 Hanwoo, a beef cattle. The sequence data for each of the 32 animals varied from 13.58-fold to almost 20-fold coverage. We detected a total of 6,811 deleted CNVs across the analyzed individuals (average length = 2732.2 bp) corresponding to 0.74% of the cattle genome (18.6 Mbp of variable sequence). By examining the overlap between CNV deletion regions and genes, we selected 30 genes with the highest deletion scores. These genes were found to be related to the nervous system, more specifically with nervous transmission, neuron motion, and neurogenesis. We regarded these genes as having been effected by the domestication process. Further analysis of the CNV genotyping information revealed 94 putative selected CNVs and 954 breed-specific CNVs.
  
  
  CONCLUSIONS
  This study provides useful information for assessing the impact of CNVs on cattle traits using NGS at the population level.
authors.forename: Dong-Hyun
authors.initials: DH
authors.lastname: Shin
authors.forename: Hyun-Jeong
authors.initials: HJ
authors.lastname: Lee
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.forename: Hyeon Jeong
authors.initials: HJ
authors.lastname: Kim
authors.forename: Jae Yeon
authors.initials: JY
authors.lastname: Hwang
authors.forename: Chang-Kyu
authors.initials: CK
authors.lastname: Lee
authors.forename: Jinyoung
authors.initials: J
authors.lastname: Jeong
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea. dhyoon@knu.ac.kr.
authors.forename: Duhak
authors.initials: D
authors.lastname: Yoon
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
mesh_terms: D000818:Animals; D002417:Cattle; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D017353:Gene Deletion; D016678:Genome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA