Unravelling large, diverse crop genomes with graphical pangenomics – Faba bean as a case study

• Applicants: Professorin Agnieszka Golicz, Ph.D.; Professor Dr. Björn Usadel
• Subject Area: Plant Breeding and Plant Pathology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 497667402

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, particularly due to abiotic and biotic stress susceptibility, and breeding progress is hampered by an almost complete lack of genomic resources which could help breeders address key limitations. Faba bean exhibits enormous phenotypic diversity, with 38,000 accession entries available worldwide, however the extent and background of genetic and genomic diversity has been only poorly explored to date. To overcome this deficit, we propose to 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 represent an unprecedented 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. To analyse the faba bean pangenome we propose development of a suite of new methods for pangenome graph construction, functional annotation and visualization, providing a significant advance in the analysis of complex crop plant genomes. The project will not only develop a key resource for faba bean breeding, but also novel and widely applicable tools for crop plant pangenome analysis.

• DFG Programme: Research Grants