Alignment of the linkage map, physical map, and sequence of the chicken genome

Four BAC libraries constructed at Texas A&M University and at the Children's Hospital of Oakland Research Institute providing altogether ~28X coverage of the chicken genome have been screened with most of the suitable genes and markers that are found on the chicken genetic linkage map (Schmid et al., 2000). This has provided the means to align the chicken BAC contig physical map (Ren et al., 2003) with the linkage map and assign most contigs to their appropriate location on a chicken chromosome. It also has aided in assembly of the first draft sequence of the chicken genome. Our screening approach of choice is overgo hybridization, using four-dimensional pooling (36 probes at a time, one degree of redundancy), chosen from a matrix of 216 probes per screen. All BACs assigned to chicken genes and markers have been incorporated into a database available online (https://www.msu.edu/~dodgson/resources/resources.htm#bacdata). As of October 2003, the database includes nearly 5000 BAC assignments for 577 markers across almost all chicken chromosomes and linkage groups. On-going overgo hybridization is being used to do fine structure comparative mapping between the human and chicken genomes and to close gaps detected in the first round chicken sequence assembly. Overgo hybridization provides a cost-effective, high throughput method for integration of physical maps and linkage maps for domestic animal (and plant) species. Supported by the USDA/CSREES (Project numbers: 99-35205-8566 and 2001-52100-11225).