Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

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Autor(es): dc.contributorCSIRO Agriculture and Food-
Autor(es): dc.contributorUniversidade Estadual Paulista (Unesp)-
Autor(es): dc.contributorUniversity of Queensland-
Autor(es): dc.contributorCentre for AgriBioscience-
Autor(es): dc.contributorLa Trobe University-
Autor(es): dc.contributorUniversity of Guelph-
Autor(es): dc.creatorNaval-Sánchez, Marina-
Autor(es): dc.creatorPorto-Neto, Laercio R.-
Autor(es): dc.creatorCardoso, Diercles F. [UNESP]-
Autor(es): dc.creatorHayes, Ben J.-
Autor(es): dc.creatorDaetwyler, Hans D.-
Autor(es): dc.creatorKijas, James-
Autor(es): dc.creatorReverter, Antonio-
Data de aceite: dc.date.accessioned2022-02-22T00:25:50Z-
Data de disponibilização: dc.date.available2022-02-22T00:25:50Z-
Data de envio: dc.date.issued2020-12-11-
Data de envio: dc.date.issued2020-12-11-
Data de envio: dc.date.issued2020-05-27-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1186/s12711-020-00546-6-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/198894-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/198894-
Descrição: dc.descriptionBackground: Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. Results: We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N'Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region. Conclusions: Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.-
Descrição: dc.descriptionCSIRO Agriculture and Food, 306 Carmody Rd.-
Descrição: dc.descriptionDepartment of Animal Science School of Agricultural and Veterinarian Sciences Sao Paulo State University (UNESP)-
Descrição: dc.descriptionQueensland Alliance for Agriculture and Food Innovation University of Queensland-
Descrição: dc.descriptionAgriculture Victoria AgriBio Centre for AgriBioscience-
Descrição: dc.descriptionSchool of Applied Systems Biology La Trobe University-
Descrição: dc.descriptionInstitute of Molecular Biosciences University of Queensland, 306 Carmody Road-
Descrição: dc.descriptionCentre for Genetic Improvement of Livestock University of Guelph, 50 Stone Road East-
Descrição: dc.descriptionDepartment of Animal Science School of Agricultural and Veterinarian Sciences Sao Paulo State University (UNESP)-
Idioma: dc.languageen-
Relação: dc.relationGenetics Selection Evolution-
???dc.source???: dc.sourceScopus-
Título: dc.titleSelection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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