Haplotype-resolved assembly of cultivated tetraploid potato

• Applicant: Professor Dr. Korbinian Schneeberger
• Subject Area: Plant Genetics and Genomics ; General Genetics and Functional Genome Biology ; Plant Breeding and Plant Pathology
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 514146394

Potato is one of the most important staple foods and is among the five most produced crops in the world. Globally more than 350 billion kilograms of potato are produced per year with an increasing trend particularly in developing countries in Asia. But despite this social and economic importance, our knowledge of the genomic makeup modern potato cultivars is negligibly small as the highly divergent and autotetraploid genome challenges the commonly applied genome resequencing methods. In this project, we propose to use our newly developed assembly method to generate haplotype-resolved, chromosome-scale assemblies of ten carefully chosen potatoes. For this we have selected cultivars which were introduced in the beginning of modern potato breeding and were repeatedly used in various different breeding programs. The 40 haplotypes we propose to assemble are therefore segregating in many of the contemporary potato cultivars and knowing their sequence can support functional annotation of many of these contemporary potatoes. To show how these newly generated haplotypes can actually be used in practice, we will combine the 40 haplotypes assemblies to a complex reference sequence (using genome-graph based alignment algorithms) and use them for a broad-scale genomic diversity analysis of more than 100 publicly available potato genomes (sequenced with short reads). This will allow us to showcase how the resource can be used and at the same time untangle the genomic impact of modern potato breeding. Besides these insights, the assembled haplotypes and the means how to make use of them will be an unprecedented tool for the potato community and specifically support genomic-assisted breeding efforts.

• DFG Programme: Research Grants