Development of wheat cDNA FISH markers for detecting homoeology within the Triticeae and application as chromosome specific molecular markers

To transfer agronomically important genes from wild relatives to bread wheat (Triticum aestivum L., 2n=6x=42, AABBDD) by induced homoeologous recombination, it is important to know the chromosomal relationships of the species involved. Fluorescence in situ hybridization (FISH) can be used to study chromosome structure, rearrangements and evolution. The genomes of allohexaploid wheat and other species from the Triticeae tribe are colinear to some extent, i.e., composed of homoeoloci located at similar positions along the chromosomes, with genic regions being highly conserved. To develop cytogenetic markers specific for genic regions of wheat homoeologs, we selected more than 60 full-length wheat cDNAs by BLAST against mapped expressed sequence tags and used them as FISH probes. Most probes produced signals on all three wheat homoeologs at the expected positions. We developed a wheat physical map with several cDNA markers located on each of the 14 homoeologous chromosome arms. The FISH markers confirmed chromosome rearrangements within wheat genomes and were successfully used to map genes and define chromosome rearrangements and homoeology in wheat closest diploid and tetraploid relatives and more distant Triticeae species Aegilops umbellulata, Ae. caudata and Thinopyrum intermedium. Chromosome arm 7S#3L of Th. intermedium was found to be colinear to the long arm of group-7 wheat chromosomes. The cDNA FISH markers were converted into molecular markers for screening wheat- Th. intermedium recombinant chromosomes.