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Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
2008 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 4, 964-980 p.Article in journal (Refereed) Published
Abstract [en]

Although there is growing interest to take genomics into the complex realms of natural populations, there is a general shortage of genomic resources and tools available for wild species. This applies not at least to birds, for which genomic approaches should be helpful to questions such as adaptation, speciation and population genetics. In this study, we describe a genome-wide reference set of conserved avian gene markers, broadly applicable across birds. By aligning protein-coding sequences from the recently assembled chicken genome with orthologous sequences in zebra finch, we identified particularly conserved exonic regions flanking introns of suitable size for subsequent amplification and sequencing. Primers were designed for 242 gene markers evenly distributed across the chicken genome, with a mean inter-marker interval of 4.2 Mb. Between 78% and 93% of the markers amplified a specific product in five species tested (chicken, peregrine falcon, collared flycatcher, great reed warbler and blue tit). Two hundred markers were sequenced in collared flycatcher, yielding a total of 122.41 kb of genomic DNA sequence (12096 bp coding sequence and 110 314 bp noncoding). Intron size of collared flycatcher and chicken was highly correlated, as was GC content. A polymorphism screening using these markers in a panel of 10 unrelated collared flycatchers identified 871 single nucleotide polymorphisms (pi = 0.0029) and 33 indels (mainly very short). Avian genome characteristics such as uniform genome size and low rate of syntenic rearrangements suggest that this marker set will find broad utility as a genome-wide reference resource for molecular ecological and population genomic analysis of birds. We envision that it will be particularly useful for obtaining large-scale orthologous targets in different species--important in, for instance, phylogenetics--and for large-scale identification of evenly distributed single nucleotide polymorphisms needed in linkage mapping or in studies of gene flow and hybridization.

Place, publisher, year, edition, pages
2008. Vol. 17, no 4, 964-980 p.
Keyword [en]
chicken, collared flycatcher, comparative anchored tagged sequences, linkage mapping, QTL analysis, single nucleotide polymorphism
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-97941DOI: 10.1111/j.1365-294X.2007.03551.xISI: 000252900200003PubMedID: 17927703OAI: oai:DiVA.org:uu-97941DiVA: diva2:173067
Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2016-04-25
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
Opponent
Supervisors
Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2011-02-24Bibliographically approved

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Backström, NiclasEllegren, Hans

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