Physical Mapping Resources for Bread Wheat Chromosome 5A: Radiation Hybrids and an Integrated Physical Map

High-quality integrated physical maps for both arms of bread wheat chromosome 5A were developed within the frame of the International Wheat Genome Sequence Consortium. Overall, 75,995 fingerprinted BACs were assembled into contigs independently by FingerPrinted Contig and Linear Topological Contig tools, and two partially overlapping versions of Minimal Tiling Paths were established for short (5AS) and long arm (5AL). Combined anchoring approaches based on polymerase chain reaction marker screening, microarray, and sequence homology searches applied to several genomic tools (genetic maps, deletion bin map, neighbor maps, BAC end sequences, genome zipper, and chromosome survey sequences) allowed the development of a high-quality physical map with an anchored physical coverage of 75% for 5AS and 53% for 5AL with high portions (64 and 48%, respectively) of contigs ordered along the chromosome. However, due to the lack of recombination in certain regions of the chromosome, genetic mapping, which uses recombination frequency to map marker loci, alone was not likely to result in a saturated marker scaffold for a sequence ready physical map. Therefore, a Radiation hybrid (RH) mapping technique, which uses radiation induced chromosomal breaks to map gene-based markers and BAC contigs has been undertaken. A RH panel was developed for the chromosome 5A in order to complement available data from genetic and physical mapping. This RH panel together with the generated physical map represent invaluable resources for developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and map-based cloning of agronomically relevant traits.