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Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): Conserved synteny but gene order rearrangements on the avian Z chromosome
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Molecular evolution)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Molecular Evolution)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.ORCID iD: 0000-0002-1178-4053
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2006 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 174, no 1, 377-386 p.Article in journal (Refereed) Published
Abstract [en]

Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher-one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only similar to 50% that of chicken, challenging the widely held view that birds generally have high recombination rates.

Place, publisher, year, edition, pages
2006. Vol. 174, no 1, 377-386 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-97940DOI: 10.1534/genetics.106.058917ISI: 000241134400033OAI: oai:DiVA.org:uu-97940DiVA: diva2:173066
Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2015-11-24Bibliographically approved
In thesis
1. Gene Mapping in Ficedula Flycatchers
Open this publication in new window or tab >>Gene Mapping in Ficedula Flycatchers
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.

Place, publisher, year, edition, pages
Uppsala: Universitetsbiblioteket, 2009. 82 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 587Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 587
Keyword
collared flycatcher, SNP, linkage disequilibrium, genetic map, pedigree
Identifiers
urn:nbn:se:uu:diva-9513 (URN)978-91-554-7380-8 (ISBN)
Public defence
2009-01-16, Zootissalen, EBC, Villavägen 9, Uppsala, 09:00
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Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2011-02-24Bibliographically approved

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Backström, NiclasBrandström, MikaelGustafsson, LarsQvarnström, AnnaEllegren, Hans

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