Research

Beets are important crop plants in Europe and beyond encompassing sugar beet, fodder beet, table beet (also called red beet) and chard. The closest relatives of the crop are wild beet species that are native to the sea shores of the Northern Atlantic coast in Europe and in the Mediterranean area. All these beets can crossbreed, allowing traits to be transferred from wild beets to cultivated ones. Considering that crop plants represent just a small fraction of the original genetic diversity of the species, characterisation of their wild relatives is an important area of research. When comparing two genomes there can be differences that affect just one or a few neighboring base pairs in the genome, and such alterations are easy to identify and analyse. More complex differences between genomes that can involve thousands or even millions of base pairs are called structural variants (SVs). The focus of the BeetSV project is the analysis of SVs in the genomes of wild and cultivated beets. SVs in plant genomes are not well understood even though they might influence important traits like flowering and disease resistance. In order to comprehensively study SVs in beets a data set comprising more than 1100 wild and cultivated beets will be used. The DNA sequence of their genomes is available, and modern methods such as machine learning will be applied to identify and characterise SVs. In particular, it will be assessed which SVs are characteristic for certain groups of beets and which genes are affected by SVs. A particular focus will be the inspection of SVs that may promote disease resistance. Also the impact of transposons (mobile segments inside the genome) will be studied. In summary, BeetSV will enhance our understanding of the genome structure of beets, the influence of SVs on the evolution of the beet genome, and the association of SVs with important genes and disease resistances. The knowledge generated in the BeetSV project will provide essential input for breeding beet crops with improved stress tolerance. Primary researchers involved The project will be jointly led by Assoc. Prof. Dr. Juliane Dohm and Univ. Prof. Dr. Heinz Himmelbauer at the Institute of Computational Biology at BOKU.

Crop wild relatives (CWR) are wild plant species genetically related to cultivated crops. Their untapped diversity can enhance resilience to biotic and abiotic stress and the nutritional quality of modern crops. Wheat, sugar beet, and oilseed rape were selected by Pro-Wild because of their importance to food security and EU farmers and because some of their wild relatives are endemic to Europe. Moreover, these CWRs constitute a rich and under-exploited resource needed to face challenges linked to climate change and the transition to low-input agriculture. The genetic diversity and vulnerability of these CWRs must be better characterized to optimize their conservation and utilization. The objectives of Pro-Wild are to identify priorities for in-situ conservation of the selected CWR gene pools, to survey and complement CWR genebanks collections, and to increase the use of CWRs in crop improvement. Pro-Wild associates 18 partners from 11 EU and associated countries with expertise in ecology, conservation, genomics, pathology, microbiology, plant breeding, agriculture, and sociology. Pro-Wild will compile and analyse CWR occurrence maps and perform new in-situ collections. It will predict the vulnerability of several CWR species and populations to ongoing climate changes. Ex-situ collections will be complemented with endangered CWRs accessions. Pro-Wild will investigate the resilience of CWR collections for relevant biotic and abiotic stresses. The identification of CWR-derived desired traits and their transfer into elite backgrounds will be done to promote CWR use. Overall, Pro-Wild specific goals will be coordinated with input from breeders, farmers, and consumers. Pro-Wild outcomes will contribute to European Green Deal initiatives through research, education, and training. It will serve the EU biodiversity and the Farm to Fork strategies by preserving, characterizing, and utilising wild species that have unique importance for the resilience of our food systems.

Sugar beet (Beta vulgaris ssp. vulgaris) is a young crop plant that originated from wild sea beet (Beta vulgaris ssp. maritima), a coastal plant native to Western and Southern Europe. It has been shown that transposons have influence onto the genome structure and gene functionality of beets. Of the many different repeats contained in a genome, only a small subset is intact and fully functional. However, this small portion may have a huge impact on the genome and as consequence on the phenotype as well. By creating alternative splicing patterns, introduction of novel promoters, change of gene regulation or simply by inactivation of gene function. Thus, the genome is constantly in motion: Transposons get inserted into new positions in the genome; thereafter, selection and mutational processes act upon them. Repeats disrupting crucial functions will disappear quickly, while other elements which are neutral or even beneficial will stay on. By comparing different genomic sequence data of domesticated beets and their wild relatives, we assess the mutagenic events that took place in the beet genome in the recent evolutionary past and explore the role that transposons have played in the evolution of the beet genome. Advances in the repeat-related knowledge of the beet genome may discover new insights about recent transposon evolution and will provide a foundation for further improvements of beet as a crop plant.