Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci

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dc.contributor.authorBrandt, Monikaen
dc.contributor.authorAhsan, Muhammaden
dc.contributor.authorHonaker, Christa F.en
dc.contributor.authorSiegel, Paul B.en
dc.contributor.authorCarlborg, Örjanen
dc.contributor.departmentAnimal and Poultry Sciencesen
dc.date.accessioned2019-12-23T17:29:14Zen
dc.date.available2019-12-23T17:29:14Zen
dc.date.issued2017-01en
dc.description.abstractThe Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high-and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F-2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.en
dc.description.notesWe thank Leif Andersson for initiating the AIL experiment with P.B.S. and sharing the data from the F2 intercross. Per Wahlberg and Francois Besnier are acknowledged for their valuable contributions during preparation and quality control work of the genotype and phenotype data from the AIL. Genotyping was performed by the SNP&SEQ Technology Platform in Uppsala, which is part of Science for Life Laboratory at Uppsala University and is supported as a national infrastructure by the Swedish Research Council (VR-RFI). Formas (grant 221-2013-450 to O.C.) and the Swedish Research Council (grant 621-2012-4634 to O.C.) are acknowledged for financial support.en
dc.description.sponsorshipFormasSwedish Research Council Formas [221-2013-450]; Swedish Research CouncilSwedish Research Council [621-2012-4634]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1534/g3.116.036012en
dc.identifier.eissn2160-1836en
dc.identifier.issue1en
dc.identifier.pmid27799342en
dc.identifier.urihttp://hdl.handle.net/10919/96205en
dc.identifier.volume7en
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.subjectimputation-based associationen
dc.subjectadvanced intercross body weight lineen
dc.subjectVirginia chicken linesen
dc.subjectQTL fine-mappingen
dc.titleImputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Locien
dc.title.serialG3-Genes Genomes Geneticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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