Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7

Bacterial artificial chromosome (BAC) contigs have been genetically mapped to the 10 linkage groups of Brassica rapa by BAC end sequences (BES). To integrate the genetic, physical, and cytogenetic maps, fluorescence in situ hybridization (FISH) was used to anchor the assembly of BAC contigs onto Brassica chromosomes using representative BACs. This BAC-FISH approach can be used to identify chromosome arms on separate mitotic metaphase chromosomes or to map multiple BACs to single long pachytene chromosomes. As part of an international consortium that is sequencing the B. rapa genome, we integrated the linkage and physical maps with the B. rapa cytogenetic map for chromosome A7 by hybridizing BACs to mitotic chromosomes and along the length of pachytene chromosome spreads. A total of 31 BACs that were putatively located on A7 were used as probes for FISH analyses; however, only 19 BACs mapped unambiguously to A7 while the remaining BACs either mapped to other chromosomes or hybridized to multiple locations. We then created a multicolor FISH cocktail of 16 BAC probes to simultaneously hybridize the entire length of the A7 chromosome. We successfully applied the 16 A7 BAC probe mix to B. rapa, B. oleracea, and domesticated and resynthesized genotypes of B. napus to demonstrate that this approach can facilitate studies of genome evolution by integrating the genetic, physical, and cytogenetic maps among closely related species of Brassica.