Physical Mapping of Non-Recombining Genomic Regions in Barley Using FISH

Development of ready to sequence physical maps relies on establishment of contigs of overlapping BAC clones. The contigs are orientated and ordered along chromosomes after integration with genetic maps. Unfortunately, this approach fails in genomic regions with low recombination where genetic maps suffer from poor resolution. Mapping selected BAC clones to chromosomes using FISH is a solution, but it may not be feasible in species with excess of repetitive DNA such as barley. We demonstrate that FISH with single-copy sequences shorter than 3kb such as cDNAs is an attractive alternative. To test this option we choose 15 full length cDNAs originating from centromeric and pericentromeric regions of barley chromosome 7H. We localized five and ten cDNAs on the short and long arm of 7H, respectively. Nine cDNA clones gave FISH signals also on other chromosomes, which confirmed the presence of ancient duplications in barley. We succeeded in establishing relative order for 13 out of 15 cDNA clones and showed that non-recombining region covering the pericentromeric region represents more than 30% of barley chromosome 7H. This finding confirms the constraints of genetic mapping in anchoring physical maps of significant portions of genomes in plants with large genomes and underlines a need for alternative approaches such as FISH. This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic and the European Regional Development Fund (Operational Programme Research and Development for Innovations No. ED0007/01/01 and Internal Grant Agency of Palacky University (Grant award No. IGA PrF/2012/001).