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Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken

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dc.contributor.authorLi, Jingyien
dc.contributor.authorLee, Mi-Oken
dc.contributor.authorDavis, Brian W.en
dc.contributor.authorLamichhaney, Sangeeten
dc.contributor.authorDorshorst, Benjamin J.en
dc.contributor.authorSiegel, Paul B.en
dc.contributor.authorAndersson, Leifen
dc.contributor.departmentAnimal and Poultry Sciencesen
dc.date.accessioned2020-12-11T13:21:27Zen
dc.date.available2020-12-11T13:21:27Zen
dc.date.issued2020-09en
dc.description.abstractFeathered leg is a trait in domestic chickens that has undergone intense selection by fancy breeders. Previous studies have shown that two major loci controlling feathered leg are located on chromosomes 13 and 15. Here, we present genetic evidence for the identification of candidate causal mutations at these loci. This was accomplished by combining classical linkage mapping using an experimental cross segregating for feathered leg and high-resolution identical-by-descent mapping using whole-genome sequence data from 167 samples of chicken with or without feathered legs. The first predicted causal mutation is a single-base change located 25 kb upstream of the gene for the forelimb-specific transcription factor TBX5 on chromosome 15. The second is a 17.7-kb deletion located similar to 200kb upstream of the gene for the hindlimb-specific transcription factor PITX1 on chromosome 13. These mutations are predicted to activate TBX5 and repress PITX1 expression, respectively. The study reveals a remarkable convergence in the evolution of the feathered-leg phenotype in domestic chickens and domestic pigeons, as this phenotype is caused by noncoding mutations upstream of the same two genes. Furthermore, the PITX1 causal variants are large overlapping deletions, 17.7 kb in chicken and 44 kb in pigeons. The results of the present study are consistent with the previously proposed model for pigeon that feathered leg is caused by reduced PITX1 expression and ectopic expression of TBX5 in hindlimb buds resulting in a shift of limb identity from hindlimb to more forelimb-like identity.en
dc.description.notesWe thank John Thomas, Christa Honaker, Dez-Ann Sutherland, and Michelle Jambui for husbandry and sampling of the chickens, also for DNA isolation process. We thank Sandra Juarez for performing KASP assays. The National Genomics Infrastructure (NGI)/Uppsala Genome Center and UPPMAX provided service inmassive parallel sequencing and computational infrastructure. We thank researchers and breeders who provided the DNA samples used in this study (supplementary table S4, Supplementary Material online). This work was supported by Knut and Alice Wallenberg Foundation (to L.A.) and Vetenskapsradet (to L.A.). The work performed at NGI/Uppsala Genome Center has been funded by RFI/VR and Science for Life Laboratory, Sweden. The authors declare that there are no conflicts of interest.en
dc.description.sponsorshipKnut and Alice Wallenberg FoundationKnut & Alice Wallenberg Foundation; VetenskapsradetSwedish Research Council; RFI/VR; Science for Life Laboratory, Swedenen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/molbev/msaa093en
dc.identifier.eissn1537-1719en
dc.identifier.issn0737-4038en
dc.identifier.issue9en
dc.identifier.pmid32344431en
dc.identifier.urihttp://hdl.handle.net/10919/101087en
dc.identifier.volume37en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectchickenen
dc.subjectfeathered-legen
dc.subjectlinkage mappingen
dc.subjectIBD mappingen
dc.subjectTBX5en
dc.subjectPITX1en
dc.titleMutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chickenen
dc.title.serialMolecular Biology and Evolutionen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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