MBE Advance Access published online on April 13, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm071
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Research Article |
Gene Order and Recombination Rate in Homologous Chromosome Regions of the Chicken and a Passerine Bird
AVIAN COMPARATIVE GENOMICS
1 Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
2 Department of Animal Ecology, Ecology Building, Lund University, S-223 62 Lund, Sweden
3 Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
* Correspondence: Bengt Hansson, Department of Animal Ecology, Ecology Building, Lund University, S-223 62 Lund, Sweden. Phone: ++46-709-916896; Fax: ++46-46-2224716; E-mail: bengt.hansson{at}zooekol.lu.se
Received for publication August 14, 2006. Revision received December 20, 2006. Revision received April 3, 2007. Accepted for publication April 10, 2007.
Genome structure has been found to be highly conserved between distantly related birds and recent data for a limited part of the genome suggest that this is true also for gene order (synteny) within chromosomes. Here, we confirm that synteny is maintained for large chromosomal regions in chicken and a passerine bird, the great reed warbler Acrocephalus arundinaceus, with few rearrangements, but in contrast show that the recombination-based linkage map distances differ substantially between these species. We assigned a chromosomal location based on sequence similarity to the chicken genome sequence to a set of microsatellite loci mapped in a pedigree of great reed warblers. We detected homologous loci on fourteen different chromosomes corresponding to chicken chromosomes Gga1-5, 7-9, 13, 19, 20, 24, 25 and Z. It is known that two passerine macrochromosomes correspond to Gga1. Homology of two different great reed warbler linkage groups (LG13 and LG5) to Gga1 allowed us to locate the split to a position between 20.8 and 84.8 Mb on Gga1. Data from the five chromosomal regions (on Gga1, 2, 3, 5 and Z) with three or more homologous loci showed that synteny was conserved, with the exception of two large previously unreported inversions on Gga1/LG5 and Gga2/LG3, respectively. Recombination data from the nine chromosomal regions in which we identified two or more homologous loci (accounting for the inversions) showed that the linkage map distances in great reed warblers were only 6.3 and 13.3% of those in chickens for males and females, respectively. This is likely to reflect the true interspecific difference in recombination rate, since our markers were not located in potentially low-recombining regions: several linkage groups covered a substantial part of their corresponding chicken chromosomes and were not restricted to centromeres. We conclude that recombination rates may differ strongly between bird species with highly conserved genome structure and synteny, and that the chicken linkage map may not be suitable, in terms of genetic distances, as a model for all bird species.
Key Words: genome mapping • linkage • microsatellite • passerine • recombination • synteny
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