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Genetic and Genomic Studies in Chicken: Assigning Function to Vertebrate Genes
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

A major challenge in the post-genomic era is to understand how genome sequence variants (genotype) give rise to the enormous diversity observed in terms of morphology, physiology and behavior (phenotype) among living organisms. Domestic animals—with their tremendous phenotypic variation—are excellent model organisms for determining the relationships between genotype and phenotype. In this thesis, I describe the utilization of the chicken, in combination with modern genetic and genomic approaches, in developing our understanding of the genetic mechanisms underlying phenotypic variation. These studies provide novel information on the genetics behind variation in carotenoid- and melanin-based pigmentation—observed in many organisms—and also cast light on the genetic basis of chicken domestication.

In paper I, we report that the yellow skin phenotype—observed in most commercial chickens—is caused by one or several tissue-specific mutations altering the expression of beta-carotene oxygenase 2 (BCO2 or BCDO2) in skin. In addition, we present the first conclusive evidence of a hybrid origin of the domestic chicken, since the allele causing yellow skin most likely originates from the grey jungle fowl (Gallus sonneratii) and not from the previously described sole ancestor, the red jungle fowl (Gallus gallus).

In paper II, we detect a number of loci that were likely important during the domestication process of chicken and the later specialization into meat (broiler) and egg (layer) producing lines. One of the major findings was that worldwide, almost all domestic chickens carry a missense mutation in TSHR (thyroid stimulating hormone receptor) in a position that is completely conserved amongst vertebrates. We speculate that this “domestication-mutation” has played an important role in the transformation of the wild red jungle fowl ancestor into the modern domestic chicken.

In paper III, we demonstrate that the dilution of red (pheomelanin) pigmentation—observed in the plumage of the Inhibitor of Gold chicken—is caused by a frame-shift mutation in the catechol-O-methyltransferase domain containing 1 (COMTD1) gene. The production and regulation of pheomelanin is poorly understood and this discovery advances our current knowledge of this pathway.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2012. , 56 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 732
Keyword [en]
Chicken, BCO2, TSHR, COMTD1, Phenotypic variation, Domestication, Selective sweeps, Pigmentation
National Category
Medical and Health Sciences
Research subject
Molecular Genetics
Identifiers
URN: urn:nbn:se:uu:diva-162597ISBN: 978-91-554-8246-6 (print)OAI: oai:DiVA.org:uu-162597DiVA: diva2:464538
Public defence
2012-02-03, B42, BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2012-01-13 Created: 2011-12-01 Last updated: 2012-01-16Bibliographically approved
List of papers
1. Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken
Open this publication in new window or tab >>Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken
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2008 (English)In: PLoS Genetics, ISSN 1553-7390, Vol. 4, no 2, e1000010- p.Article in journal (Refereed) Published
Abstract [en]

Yellow skin is an abundant phenotype among domestic chickens and is caused by a recessive allele (W*Y) that allows deposition of yellow carotenoids in the skin. Here we show that yellow skin is caused by one or more cis-acting and tissue-specific regulatory mutation(s) that inhibit expression of BCDO2 (beta-carotene dioxygenase 2) in skin. Our data imply that carotenoids are taken up from the circulation in both genotypes but are degraded by BCDO2 in skin from animals carrying the white skin allele (W*W). Surprisingly, our results demonstrate that yellow skin does not originate from the red junglefowl (Gallus gallus), the presumed sole wild ancestor of the domestic chicken, but most likely from the closely related grey junglefowl (Gallus sonneratii). This is the first conclusive evidence for a hybrid origin of the domestic chicken, and it has important implications for our views of the domestication process.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-98252 (URN)10.1371/journal.pgen.1000010 (DOI)000255386100011 ()18454198 (PubMedID)
Available from: 2009-02-18 Created: 2009-02-18 Last updated: 2012-01-16Bibliographically approved
2. Whole genome resequencing reveals loci under selection during chicken domestication
Open this publication in new window or tab >>Whole genome resequencing reveals loci under selection during chicken domestication
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2010 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 464, no 7288, 587-591 p.Article in journal (Refereed) Published
Abstract [en]

Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.

National Category
Genetics
Research subject
Genetics
Identifiers
urn:nbn:se:uu:diva-108259 (URN)10.1038/nature08832 (DOI)000275974200047 ()20220755 (PubMedID)
Available from: 2009-09-10 Created: 2009-09-10 Last updated: 2017-12-13
3. A frameshift mutation in COMTD1 specifically dilutes pheomelanin pigmentation in chicken
Open this publication in new window or tab >>A frameshift mutation in COMTD1 specifically dilutes pheomelanin pigmentation in chicken
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(English)Manuscript (preprint) (Other academic)
National Category
Genetics
Research subject
Molecular Genetics
Identifiers
urn:nbn:se:uu:diva-162593 (URN)
Available from: 2011-12-12 Created: 2011-12-01 Last updated: 2012-01-16

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