The chicken genome: from maps to sequence

The chicken has long served as a model organism with which to study principles of genetics, virology, development, immunology, and other basic biological processes. The chicken is also a prime model species in which to study complex quantitative trait loci. The chicken genome provides an intermediate comparison to human between those of mouse and fugu. Although avian genomes are only about 40% the size of those of mammals, and despite a separation of about 300 million years from their last common ancestor, local gene order and arrangement can be surprisingly well-conserved between the chicken and human genomes. The chicken genetic map is about 4000 cM, with 2000+ molecular markers mapped using three major reference families. Both bacterial artificial chromosome (BAC) and small insert sequencing libraries have been constructed from DNA of a single female inbred Red Jungle Fowl, the nearest wild relative of domestic chickens. BAC fingerprint analyses and alignments of BACs to the pre-existing linkage map have generated a BAC contig physical map of the genome. This is the platform on which the Washington University Genome Sequencing Center has assembled a 6.6X draft sequence of the chicken. We have contributed to the assembly process by mapping markers/genes to BACs and contigs using overgo hybridization. We've assigned over 6000 BACs to over 600 markers across almost all chicken chromosomes and linkage groups. Overgo hybridization provides a cost-effective, high throughput method for integration of physical maps, sequences and linkage maps for many species, including other avians. Supported, in part, by the USDA/CSREES (Project numbers: 99-35205-8566 and 2001-52100-11225)