Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes

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dc.authorid0000-0003-3798-5977
dc.authorid0000-0003-1794-1651
dc.authorid0000-0001-9773-522X
dc.authorid0000-0003-0553-4880
dc.contributor.authorHenkel, Jan.
dc.contributor.authorSaif, Rashid.
dc.contributor.authorJagannathan, Vidhya.
dc.contributor.authorSchmocker, Corinne.
dc.contributor.authorZeindler, Flurina.
dc.contributor.authorBangerter, Erika.
dc.contributor.authorHerren, Ursula.
dc.contributor.authorPosantzis, Dimitris.
dc.contributor.authorBulut, Zafer.
dc.contributor.authorAmmann, Philippe.
dc.contributor.authorDrögemüller, Cord.
dc.contributor.authorFlury, Christine.
dc.contributor.authorLeeb, Tosso.
dc.date.accessioned2020-03-26T20:19:16Z
dc.date.available2020-03-26T20:19:16Z
dc.date.issued2019
dc.departmentSelçuk Üniversitesi, Veteriner Fakültesi, Temel Bilimler Bölümüen_US
dc.description.abstractDomestication and human selection have formed diverse goat breeds with characteristic phenotypes. This process correlated with the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity, so called selection signatures or selective sweeps. Using whole genome sequencing of DNA pools (pool-seq) from 20 genetically diverse modern goat breeds and bezoars, we identified 2,239 putative selection signatures. In two Pakistani goat breeds, Pak Angora and Barbari, we found selection signatures in a region harboring KIT, a gene involved in melanoblast development, migration, and survival. The search for candidate causative variants responsible for these selective sweeps revealed two different copy number variants (CNVs) downstream of KIT that were exclusively present in white Pak Angora and white-spotted Barbari goats. Several Swiss goat breeds selected for specific coat colors showed selection signatures at the ASIP locus encoding the agouti signaling protein. Analysis of these selective sweeps revealed four different CNVs associated with the white or tan (A(Wt)), Swiss markings (A(sm)), badger-face (A(b)), and the newly proposed peacock (A(pc)) allele. RNA-seq analyses on skin samples from goats with the different CNV alleles suggest that the identified structural variants lead to an altered expression of ASIP between eumelanistic and pheomelanistic body areas. Our study yields novel insights into the genetic control of pigmentation by identifying six functionally relevant CNVs. It illustrates how structural changes of the genome have contributed to phenotypic evolution in domestic goats.en_US
dc.description.sponsorshipSwiss National Science FoundationSwiss National Science Foundation (SNSF) [31003A_172964]; Swiss Government Excellence Scholarship; Hans Sigrist Foundationen_US
dc.description.sponsorshipThis study was funded by a grant from the Swiss National Science Foundation (31003A_172964). R.S. was supported by a Swiss Government Excellence Scholarship and a supplementary grant from the Hans Sigrist Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en_US
dc.identifier.citationHenkel, J., Saif, R., Jagannathan, V., Schmocker, C., Zeindler, F., Bangerter, E., Herren, U., Posantzis, D., Bulut, Z., Ammann, P., Drögemüller, C., Flury, C., Leeb, T. (2019). Selection Signatures in Goats Reveal Copy Number Variants Underlying Breed-Defining Coat Color Phenotypes. PLoS Genetics, 15(12), e1008536.
dc.identifier.doi10.1371/journal.pgen.1008536en_US
dc.identifier.issn1553-7404en_US
dc.identifier.issue12en_US
dc.identifier.pmid31841508en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://dx.doi.org/10.1371/journal.pgen.1008536
dc.identifier.urihttps://hdl.handle.net/20.500.12395/38182
dc.identifier.volume15en_US
dc.identifier.wosWOS:000512336600034en_US
dc.identifier.wosqualityQ1en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.institutionauthorBulut, Zafer.
dc.language.isoenen_US
dc.publisherPUBLIC LIBRARY SCIENCEen_US
dc.relation.ispartofPLOS GENETICSen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.selcuk20240510_oaigen_US
dc.subjectgoats
dc.subjectbreed-defining coat color
dc.subjectSelection signatures
dc.subjectphenotypes
dc.titleSelection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypesen_US
dc.typeArticleen_US

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