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Feralisation targets different genomic loci to domestication in the chicken.
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0003-1262-4585
Department of Zoology, Michigan University, Michigan, USA.
Department of Biology, University of Victoria, Victoria, British Columbia, Canada.
UCL Genetics Institute, University College London, London, UK.
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2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, 12950Article in journal (Refereed) Published
Abstract [en]

Feralisation occurs when a domestic population recolonizes the wild, escaping its previous restricted environment, and has been considered as the reverse of domestication. We have previously shown that Kauai Island's feral chickens are a highly variable and admixed population. Here we map selective sweeps in feral Kauai chickens using whole-genome sequencing. The detected sweeps were mostly unique to feralisation and distinct to those selected for during domestication. To ascribe potential phenotypic functions to these genes we utilize a laboratory-controlled equivalent to the Kauai population-an advanced intercross between Red Junglefowl and domestic layer birds that has been used previously for both QTL and expression QTL studies. Certain sweep genes exhibit significant correlations with comb mass, maternal brooding behaviour and fecundity. Our analyses indicate that adaptations to feral and domestic environments involve different genomic regions and feral chickens show some evidence of adaptation at genes associated with sexual selection and reproduction.

Place, publisher, year, edition, pages
London: Nature Publishing Group, 2016. Vol. 7, 12950
National Category
Genetics
Identifiers
URN: urn:nbn:se:liu:diva-122279DOI: 10.1038/ncomms12950ISI: 000385444300002PubMedID: 27686863OAI: oai:DiVA.org:liu-122279DiVA: diva2:865191
Note

The prevous status of this article was Manuscript and the title was The genomic signals of feralisation: Not just domestication in reverse?

Funding agencies: We thank Tony Lydgate and the Steelgrass Institute for invaluable assistance and accommodation on Kauai. The research was carried out within the framework of the Linkoping University Neuro-network. WGS was performed by the Uppsala Genome Center as part of NGI Sweden. Computations were performed at UPPMAX as part of SNIC Sweden. The project was supported by grants from the Swedish Research Council (VR), the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS), the Carl Trygers Stiftelse and by the National Science Foundation under Cooperative Agreement No. DBI-0939454. S.L. is supported by BBSRC (grant number BB/L009382/1). L.V.D. is supported by CoMPLEX via EPSRC (grant number EP/F500351/1). G.H. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 098386/Z/12/Z) and supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Available from: 2015-10-27 Created: 2015-10-27 Last updated: 2017-05-10Bibliographically approved
In thesis
1. Genomics of chicken domestication and feralisation
Open this publication in new window or tab >>Genomics of chicken domestication and feralisation
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Domestication can serve as a study system of rapid evolutionary change with wide-ranging effects on traits in animals. The chicken was domesticated from the Red Junglefowl and has diverged in behaviour, morphology and life history traits. Conversely, feralisation is a more recent process when domestic animals are again exposed and respond to an environment outside of human husbandry. Linkage-based quantitative trait locus (QTL) mapping has been used to localise genetic variants that affect domestication traits in the chicken genome. Because of the limited resolution of linkage mapping, the QTL regions associated with domestication traits are often broad and contain many genes. One approach to help sort out potential causative genes is to measure gene expression as an intermediary molecular phenotype. In this dissertation, expression quantitative trait locus (eQTL) mapping of gene expression traits is used to search for potential causative genes for domestication traits in the chicken. Expression quantitative trait loci were mapped across the whole genome in bone and hypothalamus samples, and targeted at QTL regions in the base of the comb. These studies have resulted in candidate quantitative trait genes, supported by genetic and gene expression evidence, for relative comb mass, bone allocation, egg production and fearful behaviour as measured in an open field test. Secondly, a population genomics approach was used to study the molecular basis of feralisation in a free-range feral chicken population from the Pacific island of Kauai. Mitochondrial DNA sequences and phenotypic observations establish the hybrid origin of this population as a mixture of wild and domestic chickens. Genome-wide mapping of pooled heterozygosity highlight regions that may be involved in adaptation to the feral environment. The expression QTL results bring us closer to knowledge about the molecular basis of domestication traits in the chicken, suggesting plausible candidate genes and opening up for functional studies of individual loci. The population genomic study shows that feralisation has a mostly different genomic architecture than domestication, and suggests phenotypic effects, based on overlap with domestication QTL regions, for some of the identified regions.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2015. 28 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1708
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-122280 (URN)10.3384/diss.diva-122280 (DOI)978-91-7685-932-2 (ISBN)
Public defence
2015-12-18, Planck, Fysikhuset, Campus Valla, Linköping, 10:15 (English)
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Supervisors
Available from: 2015-11-02 Created: 2015-10-27 Last updated: 2017-01-03Bibliographically approved

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