Development of Single-Copy Gene FISH for Wheat and its Application in Studying Chromosomal Rearrangements in Wild Relatives and Mapping of the Wheat Genome

Wheat, Triticum aestivum L., is an allohexaploid species (2n=6x=42, AABBDD) with one of the largest plant genomes (17 Gb), containing about 90% repetitive sequences. The genic regions are highly conserved and homoeologous genomes of wheat are collinear, i.e. composed of homoeologous genes at equivalent positions along the chromosomes. We have developed a fast and robust method for single-copy gene fluorescence in situ hybridization (FISH) for wheat, which also will be applicable for other crop plants. The long (>3 kb), full-length (FL) cDNAs were selected from the Triticeae FLcDNA database. The chromosomal locations of selected cDNAs were detected by BLAST against expressed sequence tags (ESTs) mapped to the deletion bins of wheat chromosomes and verified by BLAST against the barley, rice, and Brachypodium genomes. Most probes produced FISH signals at the expected chromosomal positions in all three wheat genomes. We developed a single-copy gene FISH karyotype with at least one proximal, interstitial, and distal FISH marker for each of fourteen homoeologous chromosome arms. The set of probes was used to study chromosome rearrangements in wheat relatives and this methodology can also be useful for the physical mapping and anchoring BAC contigs.