Physical Map and Sequence of the Wheat Chromosome Arm 7DS

Bread wheat (Triticum aestivum) is one of the most important crops worldwide. Mapping and sequencing of the wheat genome are hampered by high genome complexity, polyploidy and prevalence of repetitive sequences. To overcome these obstacles, BAC-by-BAC sequencing strategy based on chromosome-derived physical maps has been adopted by the International Wheat Genome Sequencing Consortium as the key strategy towards obtaining a reference genome sequence.

In the framework of this effort, we focus on mapping and sequencing of the 7DS chromosome arm. Clones from a 7DS-specific BAC library were fingerprinted and assembled into contigs using FPC. Integration of the 7DS physical map with that of Aegilops tauschii (D genome progenitor) provided a clue for further merging and landing the contigs on the chromosome. The assembly has been verified by LTC software. Hitherto, 64% of the physical map has been anchored to genetic and radiation hybrid maps through markers comprised in contigs. The BAC sequencing strategy involves sequencing pools of four non-ovelapping clones using the Illumina HiSeq. The resulting pair-end reads are assembled using a custom assembler Sassy. This approach results in 1-20 contigs per clone. Deconvolution of the pools, scaffolding of the contigs and assembly validation is performed using BAC-end and mate-pair sequences of the MTP clones. Moreover, a BioNano genome map has been constructed for the 7DS and used to validate the physical map, anchor and orient BAC contigs, size gaps, deconvolute pools and support sequence assembling and scaffolding.