Allelic variation at a single locus distinguishes spring and winter faba beans.

Winter faba beans exhibit significant yield advantages over spring cultivars and hold promise for enhancing local protein production and agricultural sustainability. However, the threat of winter kill limits wider cultivation, and the genetics of faba bean winter hardiness remain unresolved. Here we develop a greatly improved faba bean reference genome and combine this with resequencing and phenotyping of winter and spring accessions to identify genetic determinants of winter hardiness. Genome-wide association analysis of frost tolerance traits identifies a major winter hardiness locus, the most strongly associated variant of which explains the vast majority of phenotypic variation and accurately differentiates between winter and spring types. Furthermore, we identify additional signals within the winter faba bean gene pool that could lead to further improvement of winter hardiness. Our work provides improved genomic resources and resolves the genetics of a key agronomic trait in a global protein crop to facilitate future breeding efforts.