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


CONCLUSIONS
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.
Skinner
Benjamin M
BM
Department of Biosciences, University of Kent, Canterbury CT2 7NJ, UK.
Robertson
Lindsay B W
LB
Tempest
Helen G
HG
Langley
Elizabeth J
EJ
Ioannou
Dimitris
D
Fowler
Katie E
KE
Crooijmans
Richard P M A
RP
Hall
Anthony D
AD
Griffin
Darren K
DK
Völker
Martin
M
D000818:Animals; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D055028:Comparative Genomic Hybridization; D004372:Ducks / Q000235:genetics*; D019143:Evolution, Molecular; D018628:Gene Dosage; D023281:Genomics / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA; D026801:Synteny