W431 Optimizing the construction of robust physical map in wheat

Date: Saturday, January 14, 2012
Time: 3:50 PM
Room: Town and Country
Romain Philippe , INRA GDEC, Clermont-Ferrand, France
Etienne Paux , INRA GDEC, Clermont-Ferrand, France
Pierre Sourdille , INRA GDEC, Clermont-Ferrand, France
Isabelle Bertin , INRA GDEC, Clermont-Ferrand, France
Frederic Choulet , INRA GDEC, Clermont-Ferrand, France
Abraham Korol , University of Haifa, Haifa, Israel
Helene Berges , INRA-CNRGV, Castanet Tolosan, France
Sonia Vautrin , INRA-CNRGV, Castanet Tolosan, France
Jan van Oeveren , KeyGene, Wageningen, Netherlands
Keith Stormo, PhD. , Amplicon Express, Pullman, WA
Simone Scalabrin , Instituto di Genomica Applicata, Udine, Italy
Federica Cattonaro , Instituto di Genomica Applicata, Udine, Italy
Hana Simkova , Institute of Experimental Botany, Olomouc, Czech Republic
Edwin van der Vossen , KeyGene, Wageningen, Netherlands
Jaroslav Dolezel , Institute of Experimental Botany, Olomouc, Czech Republic
Catherine Feuillet , INRA GDEC, Clermont-Ferrand, France
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.