Analysis of the wheat genome by BAC-FISH

Fluorescence in situ hybridization (FISH) has been widely used in the physical mapping of genes and chromosome landmarks in plants and animals. Bacterial artificial chromosomes (BACs) contain large inserts making them amenable for FISH mapping. We used BAC-FISH to study the genome organization and evolution in hexaploid wheat and its related species. The objectives of this study were to develop the BAC-FISH technique in bread wheat and to physically map BAC clones to metaphase chromosomes. We tested 56 BAC clones from the libraries of Triticum monococcum and Aegilops tauschii, which are the A- and D-genome donors of wheat, respectively. Different types of repetitive sequences have been identified using BAC-FISH. Two BAC clones gave FISH patterns similar to that of the repetitive DNA family pSc119; one BAC gave a FISH pattern similar to that of the repetitive DNA family pAs1; one BAC hybridized to all subtelomeric chromosomes regions in wheat, rye, barley and oat; one BAC hybridized to the centromeric regions of wheat and other cereal species, except rice; and four BAC clones hybridized only to a proximal region in the long arm of chromosome 4A of hexaploid wheat. These repeats can be used as chromosome landmarks or cytogenetic markers for chromosome identification. In addition, one BAC contains a localized tandem repeat and hybridized to five D-genome chromosome pairs in wheat, one BAC (676D4) contains A-genome-specific dispersed repeats, and two BAC clones contain D-genome-specific dispersed repeats, which are useful in identifying intergenomic translocations in wheat. The dispersed repeat present in BAC clone 676D4 hybridized to the D-genome parental species Ae. tauschii, but not to the D-genome chromosomes in the derived synthetic wheat indicating that this sequence was eliminated during the polyploidization process. This genome-specific hybridization pattern was also observed in Ae. cylindrica, Ae. juvenalis , and Ae. vavilovii, which suggests that sequence elimination is a more general phenomenon and is present not only in T. turgidum and T. aestivum but also in other polyploid Aegilops species. Sequencing results show that all of these repeats are transposable elements (TEs), indicating the important role of TEs, especially retrotransposons, in genome evolution of wheat.