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Background   Brachypodium distachyon  ( Brachypodium ) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in a model, such as a small genome size, short stature, self-pollinating habit, and short generation cycle. To maximize the utility of  Brachypodiu m as a model for basic and applied research it is necessary to develop genomic resources for it. A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence.    Results  A total of 67,151  Brachypodium  BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the  Brachypodium  genome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing that  Brachypodium  and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of  Brachypodium  contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum.  Brachypodium  contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to  Brachypodium -Triticeae comparative genomics.    Conclusion  The construction of the  Brachypodium  physical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion of  Brachypodium  genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at   .

A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat