Locus-specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattle

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dc.contributor.authorKhayatzadeh, N.
dc.contributor.authorMészáros, G.
dc.contributor.authorUtsunomiya, Y. T. [UNESP]
dc.contributor.authorGarcia, J. F. [UNESP]
dc.contributor.authorSchnyder, U.
dc.contributor.authorGredler, B.
dc.contributor.authorCurik, I.
dc.contributor.authorSölkner, J.
dc.contributor.institutionUniversity of Natural Resources and Life Sciences
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionQualitas AG
dc.contributor.institutionUniversity of Zagreb
dc.date.accessioned2018-12-11T17:04:19Z
dc.date.available2018-12-11T17:04:19Z
dc.date.issued2016-12-01
dc.description.abstractIdentification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post-admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3–47.3 Mb) and 18 (18.7–25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within (iHS) and between (Rsb) populations was calculated to explore additional patterns of pre- and post-admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6–24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI (Fst), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and Fst was observed. We found two regions with significant signatures of post-admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions.en
dc.description.affiliationDivision of Livestock Science Department of Sustainable Agricultural Systems University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33
dc.description.affiliationDepartamento de Medicina Veterinária Preventiva e Reprodução Animal Faculdade de Ciências Agrárias e Veterinárias UNESP – Univ Estadual Paulista
dc.description.affiliationDepartamento de Apoio Saúde e Produção Animal Faculdade de Medicina Veterinária de Araçatuba UNESP – Univ Estadual Paulista
dc.description.affiliationQualitas AG, Chamerstrasse 56
dc.description.affiliationDepartment of Animal Science Faculty of Agriculture University of Zagreb, Svetošimunska cesta 25
dc.description.affiliationUnespDepartamento de Medicina Veterinária Preventiva e Reprodução Animal Faculdade de Ciências Agrárias e Veterinárias UNESP – Univ Estadual Paulista
dc.description.affiliationUnespDepartamento de Apoio Saúde e Produção Animal Faculdade de Medicina Veterinária de Araçatuba UNESP – Univ Estadual Paulista
dc.format.extent637-646
dc.identifierhttp://dx.doi.org/10.1111/age.12470
dc.identifier.citationAnimal Genetics, v. 47, n. 6, p. 637-646, 2016.
dc.identifier.doi10.1111/age.12470
dc.identifier.issn1365-2052
dc.identifier.issn0268-9146
dc.identifier.scopus2-s2.0-84978771884
dc.identifier.urihttp://hdl.handle.net/11449/173247
dc.language.isoeng
dc.relation.ispartofAnimal Genetics
dc.relation.ispartofsjr0,830
dc.relation.ispartofsjr0,830
dc.rights.accessRightsAcesso restrito
dc.sourceScopus
dc.subjectadmixture
dc.subjectextended haplotype homozygosity
dc.subjectF st
dc.subjectiHS
dc.subjectlocal ancestry deviation
dc.subjectpermutation
dc.subjectRsb
dc.subjectselection signature
dc.subjectSNP
dc.subjectSwiss Fleckvieh
dc.titleLocus-specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattleen
dc.typeArtigo
unesp.author.orcid0000-0002-5937-0060[2]

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Artigos - Medicina Veterinária Preventiva e Reprodução Animal - FCAV
Artigos - Apoio, Produção e Saúde Animal - FMVA