Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ~40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ~50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS. ; James Breen, Thomas Wicker, Margarita Shatalina, Zeev Frenkel, Isabelle Bertin, Romain Philippe, Wolfgang Spielmeyer, Hana Šimková, Jan Šafář, Federica Cattonaro, Simone Scalabrin, Federica Magni, Sonia Vautrin, Hélène Bergès, International Wheat Genome Sequencing Consortium, Etienne Paux, Tzion Fahima, Jaroslav Doležel, Abraham Korol, Catherine Feuillet, Beat Keller