Research

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.

Abstract Domestication and diversification are the driving forces to generate the wide variety of currently available crop plants. Diversification of cultivated beets has resulted in four cultivar groups of very different phenotypes, i.e. leaf beets (chard), fodder beet, table beet, and sugar beet. The proposed research will address the question if domestication of beet crops occurred only once or multiple times. It will be investigated how the genomes of the different beet crops are related to each other. We will aim for the identification of diversification genes in order to understand the molecular basis of the phenotypic difference of the cultivar groups. To address theses goals, we will comprehensively search for genomic regions under artificial selection in beet crops. Whole-genome sequencing data will be generated, followed by an analysis of the data using cultivar-specific reference genomes (existing or newly prepared) and statistical interpretation of population differentiation. High-resolution mapping and subsequent characterization of genes will be performed to nominate candidate genes that are crucial for the diversification of beet cultivar groups. In summary, CultiBeet will create important knowledge on the domestication history of beets and will identify the pivotal genes which are involved in beet crop diversification. The experimental setup and computational analyses may serve as a general paradigm for crop diversification studies. Primary researchers involved The project will be jointly led by Ass. Prof. Dr. Juliane Dohm and Prof. Dr. Heinz Himmelbauer.