Repetitive DNA elements are rapidly evolving major components of plant genomes, thus becoming important tools for studying the large-scale organization and evolution of plant genomes. In the current project, we used a focused series of complementary molecular cytogenetic, bioinformatic, and epigenetic studies on grass genomes to characterize the physical genome rearrangement process. We developed specific probes using bioinformatics and tested them on mitotic chromosomes of polyploid grass species, hybrids and amphiploids using fluorescence in situ hyridization (FISH) to better understand the evolutionary divergence of the genomes. A comprehensive model illustrating the potential mechanisms involved in terminal intergenomic translocations was elucidated by the simultaneous hybridization with the use of genome-specific probes and retrotransposon sequences, and immunostaining of histones and 5-methylcytosine in mitotic cells. FISH with the use of repetitive DNA motifs to chromosomes enabled identification of intergenomic translocations. Our studies indicated that the chromosomes of A, B, C and D genomes differ significantly in their involvement in translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes, and at least some of the translocations in oat polyploids were non-reciprocal. Our developed model of translocations in oats indicated that three types of intergenomic translocations should be distinguished: common or group-specific, species-specific, and cultivar- or accession-specific, and at least some of them contributed to the evolution of oat genomes. DNA methylation has been tracked by immunostaining of 5-methylcytosine in mitotic cells simultaneously with labelling of individual genomes. Diploid species of Avena and Secale showed uniformly distributed whole-genome methylation patterns along their chromosomes, while diploid wheats and Aegilops showed unmethylated telomeres. Polyploid oat and wheat species showed different methylation patterns from those observed in diploids: chromosomes had less uniformly distributed DNA methylation signals. Methylation patterns in oats changed after treatment with zebularine and 5-azacitidine. New cytogenetic abnormalities were induced, and these data are consistent with the analysis performed on Triticale.
Although the commercialization of research findings were not expected during the project duration, the results and developed protocols are of direct relevance to scientists, plant breeders and germplasm collections, and can be exploited or commercialized. The new knowledge generated by our research was disseminated to different scientific and public audiences. We took measures to disseminate and exploit our results through international peer-reviewed scientific journals, international scientific conferences and invited talks during interactive online workshops, seminars and laboratory meetings. DNA sequencing data, repetitive DNA database and designed probes generated during project duration, were made accessible to the public, and can be used by other researchers.