Comparative genomics is a powerful means for establishing relationships between gene function and location in a range of organisms. Moreover it allows insight into large-scale genomic rearrangements, conservation of functional elements and tracing of evolutionary phylogenies through the examination of both closely and distantly related species. The completion of the chicken (Gallus gallus, GGA) genome  and its associated resources provide the basis for the rapid development of detailed genomic information, potentially in all other birds. The most powerful strategies combine in-silico and experimental approaches, e.g. sequence comparison, cross-species fluorescent in-situ hybridization (zoo-FISH) [2, 3] and, more recently, the use of whole-genome tiling path microarrays for cross-species array comparative genomic hybridization (array CGH) [4–8]. Such a combination of modalities provides information on gross genomic rearrangements, gene gains/losses, copy number variation and gene order.
Following the completion of the chicken genome sequence assembly , one of the most obvious targets for comparative genomics in birds is the turkey (Meleagris gallopavo, MGA). Turkey is an agriculturally important species accounting for over 4.5 million tonnes of meat consumed per year worldwide, with the obvious cultural associations such as Christmas and Thanksgiving. Genetic mapping efforts in the turkey have focused on linkage mapping [9–13] and the physical information available is very limited. With 2n = 78 in the chicken and 2n = 80 in the turkey, about 10 pairs of macro- and 28–30 pairs of microchromosomes in both species, the karyotypes of chicken and turkey are quite similar to the hypothetical ancestral Galliform karyotype . Chromosome banding and zoo-FISH with chromosome paints for chicken chromosomes GGA1–9 and Z in a range of Galliform species have suggested that chicken and turkey karyotypes are distinguished by at least two interchromosomal rearrangements [15, 16]. That is, the orthologues of chicken chromosomes GGA2 and 4 are represented by turkey chromosomes MGA3 & 6, and 4 & 9 respectively . Comparisons of a series of other Galliformes suggest that GGA2 is the ancestral form (the acrocentric MGA3 and MGA6 suggesting a breakpoint in the short arm just above the centromere). By contrast, the most parsimonious explanation for the formation of the sub-metacentric GGA4 suggests a fusion of an ancestral acrocentric chromosome 4 with a smaller chromosome . This fusion model is supported by sequence evidence which suggests that GGA4p retains the properties (e.g. high gene density, high recombination frequency) of the smaller chromosome it once was . The chromosomal break- and fusion points involved in these rearrangements however have not been characterized in detail, nor has gene order on macrochromosomes; moreover no molecular evidence has yet been generated regarding synteny between microchromosomes though simple chromosome counts suggest extensive conservation.
To the best of our knowledge, no study has examined inter-specific differences in copy number variants (CNVs) between birds. CNVs are defined as copy number changes involving DNA fragments that are ~1 kb or larger , with the exception of insertions or deletions of transposable elements . Recent high-resolution, high-throughput techniques for genomic analysis such as array CGH and quantitative (real-time) PCR as well as in-silico approaches have revealed a significant contribution of CNVs to human genetic variation [18, 19], and studies in humans and other primates have suggested an important role for CNVs in disease-related as well as normal phenotypic variation [18, 19] and in evolutionary adaptation [4–6, 20–22]. However, the paucity of data and the almost exclusive focus on primates preclude any general conclusions about the significance of CNVs in phenotypic variation and evolution; data from other species is therefore essential.
In this paper, by examination of chicken and turkey genomes for chromosomal and CNV differences we test the hypothesis that Galliform genomes have remained relatively stable during ~28 million years of evolution compared to an equivalent period in mammals. To date, this information has been limited to zoo-FISH of chicken chromosome paints on other species and partial karyotypes but these early studies do suggest relative stability of the avian genome compared to the mammalian one. We thus present a detailed comparative cytogenetic map of the turkey based on reciprocal zoo-FISH with chicken and turkey macrochromosome paints, zoo-FISH with chicken microchromosome paints and single/dual color FISH mapping of more than 300 chicken BACs to turkey metaphases. In addition, we provide a molecular characterization of inter- and intra-chromosomal rearrangements by FISH mapping of BACs to chicken metaphase chromosomes, painting of chicken lampbrush chromosomes with turkey chromosome paints and hybridization of turkey chromosome paints onto a chicken whole genome tiling array. Finally, we present comparative data on CNVs in chicken and turkey, which constitute the first array CGH-based data set on inter-specific differences of CNVs in birds.