Integration of the chicken genetic map with BAC contig-based physical maps 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 maps developed recently (Zhang et al., Texas A&M; Sekhon and McPherson, Washington U.). This aids the assembly of BAC and genome sequence contigs and is essential in elucidating the molecular basis for traits of agricultural interest (identified by linkage mapping). Efforts to date primarily have focused on the use of overgo oligonucleotide probes, ~40 nucleotide double-stranded DNAs radioactively-labeled in vitro. Pooled overgo probes are 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 required. Thus, 24 rounds of hybridization assign up to 216 probe/markers specifically to cognate BACs. We experience about a 10% failure rate in probe design and a ~20% false negative BAC-overgo assignment rate. With this approach, one can efficiently align markers in a moderately dense linkage map (about 2000 now publicly available in chicken) with BAC landmarks.