Detection of copy number variations and their effects in Chinese bulls
Microsoft Excel 2007
Supplemental File 1
KAUST DepartmentRed Sea Research Center (RSRC)
MetadataShow full item record
AbstractBackground: 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. 2014 Zhang et al.; licensee BioMed Central Ltd.
CitationZhang L, Jia S, Yang M, Xu Y, Li C, et al. (2014) Detection of copy number variations and their effects in Chinese bulls. BMC Genomics 15: 480. doi:10.1186/1471-2164-15-480.
PubMed Central IDPMC4073501
- Analysis of copy number variations among diverse cattle breeds.
- Authors: Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'Aquila ME, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LC, Smith TP, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW
- Issue date: 2010 May
- Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.
- Authors: da Silva JM, Giachetto PF, da Silva LO, Cintra LC, Paiva SR, Yamagishi ME, Caetano AR
- Issue date: 2016 Jun 13
- An initial comparative map of copy number variations in the goat (Capra hircus) genome.
- Authors: Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall'Olio S, Colombo M, Casadio R, Russo V, Portolano B
- Issue date: 2010 Nov 17
- Associations of MYH3 gene copy number variations with transcriptional expression and growth traits in Chinese cattle.
- Authors: Xu Y, Shi T, Cai H, Zhou Y, Lan X, Zhang C, Lei C, Qi X, Chen H
- Issue date: 2014 Feb 10
- Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds.
- Authors: Zhang L, Jia S, Plath M, Huang Y, Li C, Lei C, Zhao X, Chen H
- Issue date: 2015 Aug 10