Integration of chicken linkage and physical maps and sequence alignment using overgo hybridization

Research is underway to align the chicken genetic linkage map, defined primarily by segregation of DNA-based markers, with the BAC contig physical map (Ren et al., in press). This aids the assembly of BAC and genome sequence contigs and alignment of contigs with chicken chromosomes. Efforts to date have focused on the use of overgo oligonucleotide probes, ca. 40 nucleotide double-stranded DNAs, hybridized to BAC filter arrays. Four BAC libraries are now in use (BamHI, EcoRI, and HindIII insert libraries, Texas A&M, and CHORI-261, Children's Hospital of Oakland Research Institute, all using DNA from a single UCD001 inbred Jungle Fowl). A 6x6x6 matrix of 216 probes is employed, with each probe designed based on DNA sequence information for a specific mapped marker or gene. Hybridization is done with pools of 36 probes at a time, such that one probe is uniquely contained in a combination of 3 pools, each from a different dimension (row, column or plate). In our hands, a fourth, redundant dimension of six additional pools is desirable. All BACs assigned to chicken genes and markers have been incorporated into a database available online (http://poultry.mph.msu.edu/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. Overgo hybridization provides a cost-effective, high throughput method for integration of physical maps, sequences and linkage maps for domestic animal (and plant) species. Supported, in part, by the USDA/CSREES (Project numbers: 99-35205-8566 and 2001-52100-11225)