Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

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dc.contributor.authorLillie, Metteen
dc.contributor.authorHonaker, Christa F.en
dc.contributor.authorSiegel, Paul B.en
dc.contributor.authorCarlborg, Örjanen
dc.contributor.departmentAnimal and Poultry Sciencesen
dc.date.accessioned2019-12-20T18:33:29Zen
dc.date.available2019-12-20T18:33:29Zen
dc.date.issued2019-04en
dc.description.abstractExperimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of divergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions. Here, we report more detailed analyses of these data exploring the regions displaying within- and between-line genomic signatures of the bidirectional selection applied in these lines. Despite the strict selection regime for opposite extremes in body weight, this did not result in opposite genomic signatures between the lines. The lines often displayed a duality of the sweep signatures, where an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consisted of short, distinct haploblocks of variable between-line divergence, likely the results of a complex demographic history involving bottlenecks, introgressions and moderate inbreeding. We demonstrate this using the example of complex haplotype mosaicism in the growth1 QTL. These mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.en
dc.description.notesFor help with genome sequencing, we thank Uppsala University SNP&SEQ Technology Platform (Science for Life Laboratory), a national infrastructure supported by the Swedish Research Council (VR-RFI) and the Knut and Alice Wallenberg Foundation. For computational resources, we thank the Uppsala Multidisciplinary Center for Advanced Computational Science and the associated Next generation sequencing Cluster and Storage (UPPNEX) project, funded by the Knut and Alice Wallenberg Foundation and the Swedish National Infrastructure for Computing (SNIC; project id: b2015010). This work was supported by the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (DNR 221-2013-450 to oC) and various sources at Virginia Tech. Lastly, individuals at Virginia Tech for a range of roles in producing and maintaining the chickens across more than half a century.en
dc.description.sponsorshipSwedish Research Council (VR-RFI)Swedish Research Council; Knut and Alice Wallenberg FoundationKnut & Alice Wallenberg Foundation; Swedish National Infrastructure for Computing (SNIC) [b2015010]; Swedish Research Council for Environment, Agricultural Sciences and Spatial PlanningSwedish Research Council Formas [DNR 221-2013-450]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1534/g3.119.400038en
dc.identifier.eissn2160-1836en
dc.identifier.issue4en
dc.identifier.pmid30737239en
dc.identifier.urihttp://hdl.handle.net/10919/96170en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherGenetics Society of Americaen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectChickenen
dc.subjectWhite Plymouth Rocken
dc.subjectselective sweepsen
dc.subjectbody weighten
dc.subjectquantitative traiten
dc.titleBidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Modelen
dc.title.serialG3-Genes Genomes Geneticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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