Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data

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dc.contributor.authorPeripolli, Elisa [UNESP]
dc.contributor.authorStafuzza, Nedenia Bonvino
dc.contributor.authorMachado, Marco Antonio
dc.contributor.authordo Carmo Panetto, João Cláudio
dc.contributor.authordo Egito, Andréa Alves
dc.contributor.authorBaldi, Fernando [UNESP]
dc.contributor.authorda Silva, Marcos Vinícius Gualberto Barbosa
dc.contributor.institutionUniversidade Estadual Paulista (UNESP)
dc.contributor.institutionInstituto de Zootecnia (IZ)
dc.contributor.institutionEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
dc.contributor.institutionNational Council for Scientific and Technological Development (CNPq)
dc.date.accessioned2023-07-29T12:50:12Z
dc.date.available2023-07-29T12:50:12Z
dc.date.issued2023-06-01
dc.description.abstractFurther characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome-wide assessment of copy number variations (CNVs) based on whole-genome re-sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS-UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75–2.07-fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA-DQB, BOLA-DQA5, CD1A, β-defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over-represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy-related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.en
dc.description.affiliationSchool of Agricultural and Veterinarian Sciences São Paulo State University (Unesp)
dc.description.affiliationCentro de Pesquisa em Bovinos de Corte Instituto de Zootecnia (IZ)
dc.description.affiliationEmbrapa Dairy Cattle
dc.description.affiliationEmbrapa Beef Cattle
dc.description.affiliationNational Council for Scientific and Technological Development (CNPq)
dc.description.affiliationUnespSchool of Agricultural and Veterinarian Sciences São Paulo State University (Unesp)
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.sponsorshipFundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)
dc.description.sponsorshipEmpresa Brasileira de Pesquisa Agropecuária
dc.description.sponsorshipIdFAPESP: 2016/24084-7
dc.description.sponsorshipIdCNPq: 310199/2015-8
dc.description.sponsorshipIdFAPEMIG: CVZ PPM 00606/16
dc.description.sponsorshipIdEmpresa Brasileira de Pesquisa Agropecuária: SEG 02.13.05.011.00.00
dc.format.extent254-270
dc.identifierhttp://dx.doi.org/10.1111/age.13298
dc.identifier.citationAnimal Genetics, v. 54, n. 3, p. 254-270, 2023.
dc.identifier.doi10.1111/age.13298
dc.identifier.issn1365-2052
dc.identifier.issn0268-9146
dc.identifier.scopus2-s2.0-85147532818
dc.identifier.urihttp://hdl.handle.net/11449/246777
dc.language.isoeng
dc.relation.ispartofAnimal Genetics
dc.sourceScopus
dc.subjectBos primigenius taurus
dc.subjectCNV
dc.subjectcreole breeds
dc.subjectnext-generation sequencing
dc.subjectstructural variants
dc.titleAssessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing dataen
dc.typeArtigo
unesp.author.orcid0000-0002-0962-6603[1]
unesp.author.orcid0000-0001-6432-2330[2]

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