Structural variation in beets (BeetSV)

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.