Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics

dc.contributor.authorPeripolli, Elisa [UNESP]
dc.contributor.authorMetzger, Julia
dc.contributor.authorDe Lemos, Marcos Vinícius Antunes [UNESP]
dc.contributor.authorStafuzza, Nedenia Bonvino [UNESP]
dc.contributor.authorKluska, Sabrina [UNESP]
dc.contributor.authorOlivieri, Bianca Ferreira [UNESP]
dc.contributor.authorFeitosa, Fabieli Louise Braga [UNESP]
dc.contributor.authorBerton, Mariana Piatto [UNESP]
dc.contributor.authorLopes, Fernando Brito [UNESP]
dc.contributor.authorMunari, Danísio Prado [UNESP]
dc.contributor.authorLôbo, Raysildo Barbosa
dc.contributor.authorMagnabosco, Cláudio De Ulhoa
dc.contributor.authorDi Croce, Fernando
dc.contributor.authorOsterstock, Jason
dc.contributor.authorDenise, Sue
dc.contributor.authorPereira, Angélica Simone Cravo
dc.contributor.authorBaldi, Fernando [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionUniversity of Veterinary Medicine Hannover
dc.contributor.institutionAssociação Nacional de Criadores e Pesquisadores (ANCP)
dc.contributor.institutionEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
dc.contributor.institutionZoetis
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.date.accessioned2018-12-11T17:22:48Z
dc.date.available2018-12-11T17:22:48Z
dc.date.issued2018-09-17
dc.description.abstractBackground: The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results: The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (- 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (- 0.01 to - 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (- 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions: Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle.en
dc.description.affiliationDepartamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita Filho
dc.description.affiliationInstitute for Animal Breeding and Genetics University of Veterinary Medicine Hannover
dc.description.affiliationDepartamento de Ciências Exatas Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita Filho
dc.description.affiliationAssociação Nacional de Criadores e Pesquisadores (ANCP)
dc.description.affiliationEmbrapa Cerrados
dc.description.affiliationZoetis
dc.description.affiliationUniversidade de São Paulo Departamento de Nutrição e Produção Animal
dc.description.affiliationUnespDepartamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita Filho
dc.description.affiliationUnespDepartamento de Ciências Exatas Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita Filho
dc.identifierhttp://dx.doi.org/10.1186/s12864-018-5060-8
dc.identifier.citationBMC Genomics, v. 19, n. 1, 2018.
dc.identifier.doi10.1186/s12864-018-5060-8
dc.identifier.file2-s2.0-85053561955.pdf
dc.identifier.issn1471-2164
dc.identifier.scopus2-s2.0-85053561955
dc.identifier.urihttp://hdl.handle.net/11449/176858
dc.language.isoeng
dc.relation.ispartofBMC Genomics
dc.relation.ispartofsjr2,110
dc.rights.accessRightsAcesso aberto
dc.sourceScopus
dc.subjectBos indicus
dc.subjectGene ontology
dc.subjectGenomic inbreeding
dc.subjectIndicine
dc.titleAutozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Geneticsen
dc.typeArtigo
unesp.author.orcid0000-0002-0962-6603[1]

Arquivos

Pacote Original
Agora exibindo 1 - 1 de 1
Carregando...
Imagem de Miniatura
Nome:
2-s2.0-85053561955.pdf
Tamanho:
1.67 MB
Formato:
Adobe Portable Document Format
Descrição: