The Whole Genome ProfilingTM for Physical Mapping of Wheat Chromosome 6A

Under the framework of the international wheat genome sequencing consortium (IWGSC; http://www.wheatgenome.org), a sequence-based physical map of wheat chromosomes 6A has been constructed. The physical map was formed utilizing the recently developed Whole Genome Profiling^TM (WGP^TM) approach (Keygene, http://keygene.com). A total number of 24,576 (6AS) and 22,656 (6AL) BACs served as input for WGP^TM. Two different tools including the Finger Printed Contigs (FPC) tool and its alternative called Linear Topological Contig (LTC) were employed for contig formation. The resulting assemblies of the two tools were compared and visually inspected. This visual investigation revealed a highly robust assembly made by LTC compared to FPC. Thus, the BAC contigs built by LTC that contained at least 5 BCAs per contig were selected. These assemblies contained 331 contigs for 6AS (L₅₀ of 1.86 Mb) and 594 contigs for 6AL (L₅₀ of 1.04 Mb). In order to facilitate an in-silico anchoring approach, the WGP tags underlying the BAC contigs were extended by publicly available wheat sequence information. This resulted in an increase of the cumulative sequence information per physical contigs from 2144 nt to 11,067 nt. The extended sequence data were used for the in-silico anchoring against wheat and barley genetic markers with known sequences by which almost 79% of the physical map could be anchored. This robustly assembled and genetically anchored physical map will serve as the framework for sequencing of chromosome 6A and is of immediate use for map based isolation of agronomically important genes/ QTLs located on this wheat chromosome.