Skip to main content

Oat CHRomosome Evolution and drivers enabling widespread terminal intergenomic translocations in polyploid species

Periodic Reporting for period 1 - OCHRE (Oat CHRomosome Evolution and drivers enabling widespread terminal intergenomic translocations in polyploid species)

Reporting period: 2019-07-01 to 2021-06-30

Polyploidy and whole genome duplication have been recognized as major evolutionary processes in plants. There is evidence for a strong association between duplication, genomic instability and large-scale chromosomal rearrangements. Genome or chromosome changes resulting from polyploidization include elimination of whole chromosomes or whole genomes, as well as intra- and inter-genomic chromosome translocations. Comparative genetic analysis of grasses, one of the most widely distributed plant families and including the three most important human foods, has demonstrated that different groups differ in the evolutionary presence of intergenomic chromosome translocations in polyploid species. The overall goal of the project OCHRE was to define the nature and mechanism of distal and intercalary (terminal or subterminal) intergenomic translocations in different species, hybrids and amphiploids of oats (genus Avena) where these are frequent, which allowed us to model their contribution to cereal genome evolution. For comparative analyses, we used different grass species which do not show multiple intergenomic translocations, such as those belonging to the Triticeae tribe (Aegilops, Secale, Triticum, Triticale) and tropical forage grasses (including Cenchrus and Urochloa/Brachiaria). We concluded that the presence of terminal, mostly non-reciprocal translocations in the Avena group makes oat chromosomes particularly rearranged. Our research suggests that intergenomic translocations were the main mechanisms of divergence in the evolution of oat species, and a new pattern of translocations was established in synthetic hybrids and amphiploids. Changes in copy number of repetitive DNA sequences are speculated to happen as a result of polyploidization events together with increase and decrease in DNA methylation of this major fraction of grass genomes. The knowledge generated from our research will assist in developing better crops for sustainable agriculture.
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.
Allopolyploid plants are of huge evolutionary significance, often exhibiting novel physiological and morphological traits compared to their diploid progenitors, due to their hybrid vigour, buffering of deleterious mutations and increased heterozygosity. Our research revealed aspects of the complex evolutionary processes leading to the formation of new species (speciation). In the current project, we brought to the topic a vision and unique ability to integrate different methods, exploiting genome-wide bioinformatic approaches, molecular cytogenetics on mitotic chromosomes and epigenetics to understand chromosomes, genome composition and evolution of oat species. The project applies powerful tools and give a unique approach to develop evolutionary models of grass genomes, with implications for fundamental biology and exploitation of biodiversity in germplasm for breeding. Our approaches developed a general model of genomic changes that led to the evolutionary success of allopolyploid plants. Our research developed the broader knowledge on the ploidy, genome composition and genome interactions in polyploids and hybrids, necessary to understand and manage the environmental and societal impact of crops and forages and to build more productive food systems for humans and farm animals. The results obtained during project duration will be of direct relevance to plant breeders and germplasm collections. The generated knowledge is of practical importance because it enables expansion of the gene pool of cultivated forages through the transfer of alien genetic material from wild species. Understanding polyploid nature and the processes that occur soon after polyploid formation when different genomes are joined together in the hybrid plants will help address key concerns of sustainable development, food security, health and environmental response to climate change, and plant conservation.
Intergenomic chromosome translocations in Avena sativa.