Optimizing the construction of robust physical map in wheat

The SNaPshot technology, based on comparison of restriction fragments, was used recently to build the first physical map of wheat chromosome 3B. We explored the potential of a new technology for physical mapping, Whole Genome Profiling, which is based on the comparison of BAC-derived sequence tags. A subset of the wheat 3B chromosome BAC library covering 230 Mb was used to compare WGP and SNaPshot physical maps. We showed that the WGP map covers the same length than the SNaPshot map but with 30% less contigs and with 3.5 times less mis-assembled BACs. We evaluated the benefit of integrating WGP tags in different sequence assemblies obtained after Roche/454 sequencing of BAC pools. We showed that while WGP tag integration improves low quality assemblies (unpaired reads and/or low coverage), it does not significantly improve sequence assemblies performed at high coverage (25x) with paired-end reads.

Concomitantly, we initiated the construction of the 1BL physical map. BACs from a 15x coverage BAC library were fingerprinted with SNaPhot and assembled in parallel with FPC and LTC, to compare the efficiency of these two software. LTC greatly improved the robustness (linearity) of the map and produced significantly longer contigs than FPC. The LTC physical map was anchored with 5538 markers. In parallel, a 1BL neighbor genetic map containing 478 markers was developed using 6 genetic maps. To date, 229 LTC contigs covering 264 Mb and 82 contigs covering 94 Mb have been assigned to a deletion bin and on the 1BL neighbor genetic map, respectively.