Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus

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dc.contributor.authorAguiar, Tamiris Sayuri [UNESP]
dc.contributor.authorPintor Torrecilha, Rafaela Beatriz [UNESP]
dc.contributor.authorMilanesi, Marco [UNESP]
dc.contributor.authorHarth Utsunomiya, Adam Taiti [UNESP]
dc.contributor.authorTrigo, Beatriz Batista [UNESP]
dc.contributor.authorTijjani, Abdulfatai
dc.contributor.authorMusa, Hassan Hussein
dc.contributor.authorLopes, Flavia Lombardi [UNESP]
dc.contributor.authorAjmone-Marsan, Paolo
dc.contributor.authorCarvalheiro, Roberto [UNESP]
dc.contributor.authorRezende Neves, Haroldo Henrique de
dc.contributor.authorCarmo, Adriana Santana do
dc.contributor.authorHanotte, Olivier
dc.contributor.authorSonstegard, Tad Stewart
dc.contributor.authorGarcia, Jose Fernando [UNESP]
dc.contributor.authorUtsunomiya, Yuri Tani [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionIAEA
dc.contributor.institutionUniv Cattolica Sacro Cuore
dc.contributor.institutionUniv Nottingham
dc.contributor.institutionUniv Khartoum
dc.contributor.institutionGenSys Consultores Associados
dc.contributor.institutionUniversidade Federal de Goiás (UFG)
dc.contributor.institutionInt Livestock Res Inst
dc.contributor.institutionRecombinetics Inc
dc.date.accessioned2019-10-04T12:33:28Z
dc.date.available2019-10-04T12:33:28Z
dc.date.issued2018-12-07
dc.description.abstractNavel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 x 10(-9)) was found on chromosome 5 spanning positions 47.9-48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a similar to 6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding.en
dc.description.affiliationSao Paulo State Univ, Dept Preventhe Vet Med & Anim Reprod, Sch Agr & Veterinarian Sci, Jaboticabal, Brazil
dc.description.affiliationIAEA, Collaborating Ctr Anim Genom & Bioinformat, Aracatuba, Brazil
dc.description.affiliationSao Paulo State Univ, Dept Support Prod & Anim Hlth, Sch Vet Med, Aracatuba, Brazil
dc.description.affiliationUniv Cattolica Sacro Cuore, Dept Anim Sci Food & Nutr, Piacenza, Italy
dc.description.affiliationUniv Cattolica Sacro Cuore, Ancient DNA Res Ctr BioDNA, Piacenza, Italy
dc.description.affiliationUniv Nottingham, Cells Organisms & Mol Genet, Sch Life Sci, Nottingham, England
dc.description.affiliationUniv Khartoum, Fac Med Lab Sci, Khartoum, Sudan
dc.description.affiliationSao Paulo State Univ, Sch Agr & Veterinarian Sci, Dept Anim Sci, Jaboticabal, Brazil
dc.description.affiliationGenSys Consultores Associados, Porto Alegre, RS, Brazil
dc.description.affiliationUniv Fed Goias, Escola Vet & Zootecnia, Goiania, Go, Brazil
dc.description.affiliationInt Livestock Res Inst, LiveGene CTLGH, Addis Ababa, Ethiopia
dc.description.affiliationRecombinetics Inc, St Paul, MN USA
dc.description.affiliationUnespSao Paulo State Univ, Dept Preventhe Vet Med & Anim Reprod, Sch Agr & Veterinarian Sci, Jaboticabal, Brazil
dc.description.affiliationUnespSao Paulo State Univ, Dept Support Prod & Anim Hlth, Sch Vet Med, Aracatuba, Brazil
dc.description.affiliationUnespSao Paulo State Univ, Sch Agr & Veterinarian Sci, Dept Anim Sci, Jaboticabal, Brazil
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
dc.description.sponsorshipIdFAPESP: 2010/52030-2
dc.description.sponsorshipIdFAPESP: 2014/01095-8
dc.description.sponsorshipIdFAPESP: 2016/07531-0
dc.description.sponsorshipIdFAPESP: 2016/05787-7
dc.description.sponsorshipIdFAPESP: 2017/08373-1
dc.description.sponsorshipIdCNPq: 560922/2010-8
dc.description.sponsorshipIdCNPq: 483590/2010-0
dc.description.sponsorshipIdCNPq: 132809/2016-8
dc.description.sponsorshipIdCNPq: 166419/2017-6
dc.format.extent11
dc.identifierhttp://dx.doi.org/10.3389/fgene.2018.00627
dc.identifier.citationFrontiers In Genetics. Lausanne: Frontiers Media Sa, v. 9, 11 p., 2018.
dc.identifier.doi10.3389/fgene.2018.00627
dc.identifier.issn1664-8021
dc.identifier.urihttp://hdl.handle.net/11449/185196
dc.identifier.wosWOS:000452653900001
dc.language.isoeng
dc.publisherFrontiers Media Sa
dc.relation.ispartofFrontiers In Genetics
dc.rights.accessRightsAcesso aberto
dc.sourceWeb of Science
dc.subjectbovine
dc.subjectSNP
dc.subjecthaplotype
dc.subjectCNV
dc.subjectHMGA2
dc.subjectPLAG1
dc.subjectIGF2
dc.titleAssociation of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicusen
dc.typeArtigo
dcterms.rightsHolderFrontiers Media Sa
unesp.author.orcid0000-0002-3173-3712[8]

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