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Background  The availability of the complete chicken ( Gallus gallus ) genome sequence as well as a large number of chicken probes for fluorescent  in-situ  hybridization (FISH) and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, we provided a comprehensive cytogenetic map for the turkey ( Meleagris gallopavo ) and the first analysis of copy number variants (CNVs) in birds. Here, we extend this approach to the Pekin duck ( Anas platyrhynchos ), an obvious target for comparative genomic studies due to its agricultural importance and resistance to avian flu.    Results  We provide a detailed molecular cytogenetic map of the duck genome through FISH assignment of 155 chicken clones. We identified one inter- and six intrachromosomal rearrangements between chicken and duck macrochromosomes and demonstrated conserved synteny among all microchromosomes analysed. Array comparative genomic hybridisation revealed 32 CNVs, of which 5 overlap previously designated "hotspot" regions between chicken and turkey.    Conclusion  Our results suggest extensive conservation of avian genomes across 90 million years of evolution in both macro- and microchromosomes. The data on CNVs between chicken and duck extends previous analyses in chicken and turkey and supports the hypotheses that avian genomes contain fewer CNVs than mammalian genomes and that genomes of evolutionarily distant species share regions of copy number variation ("CNV hotspots"). Our results will expedite duck genomics, assist marker development and highlight areas of interest for future evolutionary and functional studies.

Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis