An Integrated Approach for the Physical Mapping of Wheat Chromosome 5A

An integrated physical and genetic map represent a prerequisite for DNA sequence assembly of wheat chromosome 5A. About 95,000 BAC clones for 5A were fingerprinted using SnaPshot method and the useful fingerprints were assembled into contigs using both FPC and LTC software. Two minimal tiling paths (MTPs), were defined: FPC-MTP consisting of 4,201 for 5AS and 6,560 for 5AL overlapping BAC clones and LTC-MTP made of 5,412 for 5AS and 8,709 for 5AL overlapping BACs. Both MTPs were organized in three dimensional (3D) pools, to increase the efficiency of further anchoring, that was performed using two different strategies. The anchoring of FPC-MTP was done through screening with several classes of molecular markers mapped on four segregating populations, including SSRs (simple sequence repeat) and based on transposable element-junctions obtained either from literature or by in silico screening of 454-derived 2x coverage of 5A flow sorted DNA. To anchor the LTC-MTP an Agilent 15K specific array was produced using probes derived from the 5A Genome Zipper and all available ESTs mapped on 5A. The information deriving from both anchoring will be merged, thanks to the partial overlapping between the two MTPs. Beside this wet pipeline, an in silico anchoring procedure was undertaken, integrating the information deriving from alignment between the almost 5,000 BAC-ends belonging to the FPC-MTP, the sequences used to develop the Agilent chip, and the functional Infinium array-SNPs (Single Nucleotide Polymorphisms) genetically mapped in two segregating populations.