Projects & Funding

Sequence variants, cis-regulation and gene expression in a dynamic crop genome
(2020-2025) Sofja Kovalevskaja Award from the Humboldt Foundation

The past decade saw an explosion in plant genome sequencing projects, with hundreds of genomes available to date. Follow-up re-sequencing efforts generated data for thousands of diverse individuals and identified millions of genomic variants, many associated with important and agronomically relevant traits. However, the functional impact and mechanistic consequence of many of the variants remain unknown, especially since the majority fall outside of gene coding regions and do not directly alter protein sequence. A substantial proportion of the non-coding variants are expected to affect regulatory sequences controlling levels of gene expression, which in turn influence physiological, developmental and metabolic traits in plants.

Brassica napus (oilseed rape, canola), a recent allotetraploid crop plant species, is Europe’s most important oilseed crop and the second most important worldwide, with an annual production of over 70 million tonnes as the result of extensive breeding during the past five decades. The highly dynamic genome of B. napus, a model for polyploid genome evolution post hybridization, not only carries a large number of single nucleotide polymorphisms (SNPs), but also extensive structural variants caused by widespread chromosome rearrangements. This project will focus on the non-coding B. napus SNPs and structural variants aiming to improve the understanding of regulatory variants, their effect on chromatin structure and gene expression.

Defining the fine-scale recombination landscape of the oilseed rape genome
(2022-2025) Deutsche Forschungsgemeinschaft (DFG)

Crop improvement relies on reshuffling of the genetic material, which happens during meiosis, a specialized form of cell division resulting in gamete formation. A key aspect of meiosis is the exchange of genetic material between homologous chromosomes during recombination. However, the number of recombination events, as well as their distribution across chromosomes, is limited, with the majority concentrated in a small fraction of the genome. The factors affecting the recombination landscape vary across species. This project aims to integrate several strategies to build fine-scale recombination maps for the major oilseed crop Brassica napus (oilseed rape) and understand the genetic, genomic and epigenomic features driving meiotic crossover formation. This will provide researchers and plant breeders with a knowledge basis to alter the frequency and positioning of crossovers, to break existing haplotype blocks and generate new, favourable combinations of alleles.

Unravelling large, diverse crop genomes with graphical pangenomics – Faba bean as a case study
(2022-2025) Deutsche Forschungsgemeinschaft (DFG) in collaboration with Prof Björn Usadel (HHU)

Faba bean (Vicia faba) is a high-yielding cool season legume with nutrition-dense seeds that is also used as a forage and cover crop. Its ability to grow in temperate to cool environments makes it ideally suited for sustainable cropping in Germany. However, faba bean yield stability is low, in part due to abiotic and biotic stress
susceptibility, and breeding progress is hampered by a relative scarcity of genomic resources which could help breeders address key limitations. Faba bean exhibits enormous phenotypic diversity, with 38,000 accession entries available worldwide, however however little is known abour the background of its genetic and genomic diversity. In this project we will construct a faba bean pangenome using eight high quality genome assemblies of diverse faba bean accessions and further assess diversity in twenty additional genotypes. The faba bean pangenome will become a new resource for genomics-based faba bean improvement. Considering the extremely large V. faba genome size of over 13 billion base pairs, analysis of the corresponding pangenome requires development of suitable analytical approaches including construction of a pangenome graph that can be used to represent the sequence content along with corresponding functional annotation of a larger population in a single data structure. This project aims to develop a key resource for faba bean breeding and a set of novel tools for crop plant pangenome analysis.