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Background  Physical maps employing libraries of bacterial artificial chromosome (BAC) clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat ( Triticum aestivum ),  Aegilops tauschii , is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the  Triticeae  and  T. aestivum  since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and  Brachypodium distachyon  to  Ae. tauschii  or barley, and then to wheat.    Results  We report the use of  Ae. tauschii  for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of  Ae. tauschii  with 85 EST on the  Ae. tauschii  and barley genetic maps. The 24 contigs were aligned to the rice and  B. distachyon  genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in  B. distachyon  and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the  Ae. tauschii -rice and  Ae. tauschii - Brachypodium  syntenies were identical. We observed chromosomal rearrangements between  Ae. tauschii  and barley. The comparison of  Ae. tauschii  physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs.    Conclusions  The physical map reported here is the first physical map using fingerprinting of a complete  Triticeae  genome. This study demonstrates that global fingerprinting of the large plant genomes is a viable strategy for generating physical maps. Physical maps allow the description of the co-linearity between wheat and grass genomes and provide a powerful tool for positional cloning of new genes.

bmc genomics

Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS