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

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Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorInstituto de Zootecnia (IZ)-
Autor(es): dc.contributorEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)-
Autor(es): dc.contributorNational Council for Scientific and Technological Development (CNPq)-
Autor(es): dc.creatorPeripolli, Elisa-
Autor(es): dc.creatorStafuzza, Nedenia Bonvino-
Autor(es): dc.creatorMachado, Marco Antonio-
Autor(es): dc.creatordo Carmo Panetto, João Cláudio-
Autor(es): dc.creatordo Egito, Andréa Alves-
Autor(es): dc.creatorBaldi, Fernando-
Autor(es): dc.creatorda Silva, Marcos Vinícius Gualberto Barbosa-
Data de aceite: dc.date.accessioned2025-08-21T17:33:40Z-
Data de disponibilização: dc.date.available2025-08-21T17:33:40Z-
Data de envio: dc.date.issued2023-07-29-
Data de envio: dc.date.issued2023-07-29-
Data de envio: dc.date.issued2023-06-01-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1111/age.13298-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/246777-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/246777-
Descrição: dc.descriptionFurther 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.-
Descrição: dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)-
Descrição: dc.descriptionConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)-
Descrição: dc.descriptionFundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)-
Descrição: dc.descriptionEmpresa Brasileira de Pesquisa Agropecuária-
Descrição: dc.descriptionSchool of Agricultural and Veterinarian Sciences São Paulo State University (Unesp)-
Descrição: dc.descriptionCentro de Pesquisa em Bovinos de Corte Instituto de Zootecnia (IZ)-
Descrição: dc.descriptionEmbrapa Dairy Cattle-
Descrição: dc.descriptionEmbrapa Beef Cattle-
Descrição: dc.descriptionNational Council for Scientific and Technological Development (CNPq)-
Descrição: dc.descriptionSchool of Agricultural and Veterinarian Sciences São Paulo State University (Unesp)-
Descrição: dc.descriptionFAPESP: 2016/24084-7-
Descrição: dc.descriptionCNPq: 310199/2015-8-
Descrição: dc.descriptionFAPEMIG: CVZ PPM 00606/16-
Descrição: dc.descriptionEmpresa Brasileira de Pesquisa Agropecuária: SEG 02.13.05.011.00.00-
Formato: dc.format254-270-
Idioma: dc.languageen-
Relação: dc.relationAnimal Genetics-
???dc.source???: dc.sourceScopus-
Palavras-chave: dc.subjectBos primigenius taurus-
Palavras-chave: dc.subjectCNV-
Palavras-chave: dc.subjectcreole breeds-
Palavras-chave: dc.subjectnext-generation sequencing-
Palavras-chave: dc.subjectstructural variants-
Título: dc.titleAssessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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