Detection of copy number variations and their effects in Chinese bulls

Handle URI:
http://hdl.handle.net/10754/325244
Title:
Detection of copy number variations and their effects in Chinese bulls
Authors:
Zhang, Liangzhi; Jia, Shangang; Yang, Mingjuan; Xu, Yao; Li, Congjun; Sun, Jiajie; Huang, Yongzhen; Lan, Xianyong; Lei, Chuzhao; Zhou, Yang; Zhang, Chunlei; Zhao, Xin; Chen, Hong
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. 2014 Zhang et al.; licensee BioMed Central Ltd.
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
Zhang 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.
Publisher:
BioMed Central
Journal:
BMC Genomics
Issue Date:
17-Jun-2014
DOI:
10.1186/1471-2164-15-480
PubMed ID:
24935859
PubMed Central ID:
PMC4073501
Type:
Article
ISSN:
14712164
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorZhang, Liangzhien
dc.contributor.authorJia, Shangangen
dc.contributor.authorYang, Mingjuanen
dc.contributor.authorXu, Yaoen
dc.contributor.authorLi, Congjunen
dc.contributor.authorSun, Jiajieen
dc.contributor.authorHuang, Yongzhenen
dc.contributor.authorLan, Xianyongen
dc.contributor.authorLei, Chuzhaoen
dc.contributor.authorZhou, Yangen
dc.contributor.authorZhang, Chunleien
dc.contributor.authorZhao, Xinen
dc.contributor.authorChen, Hongen
dc.date.accessioned2014-08-27T09:42:03Z-
dc.date.available2014-08-27T09:42:03Z-
dc.date.issued2014-06-17en
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.en
dc.identifier.issn14712164en
dc.identifier.pmid24935859en
dc.identifier.doi10.1186/1471-2164-15-480en
dc.identifier.urihttp://hdl.handle.net/10754/325244en
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.en
dc.language.isoenen
dc.publisherBioMed Centralen
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.en
dc.subjectBos grunniensen
dc.subjectBos taurusen
dc.subjectBubalus bubalisen
dc.subjectCopy number variationsen
dc.subjectGene expressionen
dc.subjectmitochondrial DNAen
dc.subjectbull (mammal)en
dc.subjectChineseen
dc.subjectCNVR22 geneen
dc.subjectCNVR310 geneen
dc.subjectcomparative genomic hybridizationen
dc.subjectcopy number variationen
dc.subjectdomestic animalen
dc.subjectEDA geneen
dc.subjectgeneen
dc.subjectgene expressionen
dc.subjectgene functionen
dc.subjectgene locusen
dc.subjectgene lossen
dc.subjectgenetic variabilityen
dc.subjectgenome analysisen
dc.subjectgrowth inhibitionen
dc.subjectnucleotide sequenceen
dc.subjectPLA2G2D geneen
dc.subjectquantitative trait locusen
dc.subjectSLC4A2 geneen
dc.subjectwater buffaloen
dc.subjectyaken
dc.titleDetection of copy number variations and their effects in Chinese bullsen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalBMC Genomicsen
dc.identifier.pmcidPMC4073501en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCollege of Animal Science and Technology, Northwest A and F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, Chinaen
dc.contributor.institutionUnited States Department of Agriculture-Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, United Statesen
dc.contributor.institutionInstitutes of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, Chinaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorJia, Shangangen

Related articles on PubMed

All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.