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dc.contributor.authorZhang, Liangzhi
dc.contributor.authorJia, Shangang
dc.contributor.authorYang, Mingjuan
dc.contributor.authorXu, Yao
dc.contributor.authorLi, Congjun
dc.contributor.authorSun, Jiajie
dc.contributor.authorHuang, Yongzhen
dc.contributor.authorLan, Xianyong
dc.contributor.authorLei, Chuzhao
dc.contributor.authorZhou, Yang
dc.contributor.authorZhang, Chunlei
dc.contributor.authorZhao, Xin
dc.contributor.authorChen, Hong
dc.date.accessioned2014-08-27T09:42:03Z
dc.date.available2014-08-27T09:42:03Z
dc.date.issued2014-06-17
dc.identifier.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.
dc.identifier.issn14712164
dc.identifier.pmid24935859
dc.identifier.doi10.1186/1471-2164-15-480
dc.identifier.urihttp://hdl.handle.net/10754/325244
dc.description.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.
dc.language.isoen
dc.publisherSpringer Nature
dc.rightsThis article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.subjectBos grunniens
dc.subjectBos taurus
dc.subjectBubalus bubalis
dc.subjectCopy number variations
dc.subjectGene expression
dc.subjectmitochondrial DNA
dc.subjectbull (mammal)
dc.subjectChinese
dc.subjectCNVR22 gene
dc.subjectCNVR310 gene
dc.subjectcomparative genomic hybridization
dc.subjectcopy number variation
dc.subjectdomestic animal
dc.subjectEDA gene
dc.subjectgene
dc.subjectgene expression
dc.subjectgene function
dc.subjectgene locus
dc.subjectgene loss
dc.subjectgenetic variability
dc.subjectgenome analysis
dc.subjectgrowth inhibition
dc.subjectnucleotide sequence
dc.subjectPLA2G2D gene
dc.subjectquantitative trait locus
dc.subjectSLC4A2 gene
dc.subjectwater buffalo
dc.subjectyak
dc.titleDetection of copy number variations and their effects in Chinese bulls
dc.typeArticle
dc.contributor.departmentRed Sea Research Center (RSRC)
dc.identifier.journalBMC Genomics
dc.identifier.pmcidPMC4073501
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionCollege of Animal Science and Technology, Northwest A and F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
dc.contributor.institutionUnited States Department of Agriculture-Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, United States
dc.contributor.institutionInstitutes of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personJia, Shangang
refterms.dateFOA2018-06-13T14:35:59Z


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