Physical mapping of chromosome 1BS was conducted within the framework of the European consortium TriticeaeGenome designed to develop physical maps of wheat and barley group 1 and 3 chromosomes. Contig assembly of HICF fingerprinted BAC clones from 1BS specific BAC library was conducted using LTC program with liberal cutoff 10-25 of Sulston score. First assembly included 33,912 clones in 385 contigs (6-846 clones, each) covering 283 Mb (90% of 1BS). Then, contigs verified by parallel clone overlaps were assembled, using even more liberal cutoff 10-15, into 52 long supercontigs of ~1.2-22.3 Mb (average 5.1 Mb) that cover about 85% (267 Mb) of 1BS. Additional verification steps were conducted using markers produced from BAC-end-sequences (BES) and by anchoring of the supercontigs to 1BS deletion bin map and group 1 Genome Zipper, based on synteny with Brachypodium, rice and sorghum model genomes. In total, 62 in silico markers, based on BESs and 79 PCR markers developed based on genes and ESTs, were used for anchoring of the supercontigs. Furthermore, high-throughput transcriptomic approach (~40,000 wheat unigenes, NimbleGen 135K chip, hybridized with 1BS MTP BAC 3D pools) resulted in the identification of 228 wheat unigenes that show synteny with group 1S genome Zipper. In summary, 48 of 52 supercontigs (90% of clones arranged in contigs) were anchored to group 1 Genome Zipper and 1BS deletion bins, 7 contigs and supercontigs (3% of clones from contigs) were anchored to 1BS deletion bin map, 38 SSR and EST-based markers were used to anchor 1BS supercontigs to 1BS genetic map.
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