title: Detection of copy number variations and their effects in Chinese bulls.
abstract: BACKGROUND
  Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits.
  
  
  RESULTS
  We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more "loss" events than both "gain" and "both" ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits.
  
  
  CONCLUSIONS
  The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle's evolution and breeding researches.
authors.forename: Liangzhi
authors.initials: L
authors.lastname: Zhang
authors.forename: Shangang
authors.initials: S
authors.lastname: Jia
authors.forename: Mingjuan
authors.initials: M
authors.lastname: Yang
authors.forename: Yao
authors.initials: Y
authors.lastname: Xu
authors.forename: Congjun
authors.initials: C
authors.lastname: Li
authors.forename: Jiajie
authors.initials: J
authors.lastname: Sun
authors.forename: Yongzhen
authors.initials: Y
authors.lastname: Huang
authors.forename: Xianyong
authors.initials: X
authors.lastname: Lan
authors.forename: Chuzhao
authors.initials: C
authors.lastname: Lei
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.forename: Chunlei
authors.initials: C
authors.lastname: Zhang
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: College of Animal Science and Technology, Northwest A & F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China. chenhong1212@263.net.
authors.forename: Hong
authors.initials: H
authors.lastname: Chen
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D015870:Gene Expression; D056726:Genetic Association Studies; D016678:Genome; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable