Decoding the autotetraploid origin of the stress-tolerant wild beet Beta corolliflora

Most crop plants, including sugar beet (Beta vulgaris subsp. vulgaris), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, crop wild relatives (CWRs) harbour useful traits relevant for crop improvement, including enhanced adaptation to biotic and abiotic stresses. Especially polyploids are interesting from an evolutionary perspective as the genome undergoes reorganisation after the polyploidisation event. Through neo- and subfunctionalisation, novel gene functions emerge, which enable plants to cope with changing environments and extreme/harsh conditions. To introduce such resilience traits into breeding material, CWRs have already been identified as an important source for sustainable breeding. For beets, the section Corollinae contains the tetraploid species Beta corolliflora (2n = 4x = 36) that is believed to harbour salt and frost tolerances as well as a wealth of pathogen resistances. The number of beneficial traits of B. corolliflora is increased compared to those of the known diploids in this section (all 2n = 2x = 18). Nevertheless, neither the parental relationships of B. corolliflora have been resolved, nor are genomic resources available to steer sustainable, genomics-informed breeding.

To benefit from the resources offered by (polyploid) beet wild relatives, we generated and evaluated genome resources and assemblies for four different sugar beet wild relatives - Beta corolliflora (tetraploid), Beta lomatogona (diploid), Beta macrorhiza (diploid), and as an outgroup Patellifolia procumbens (diploid). We combined cytogenetic, k-mer-, and gene-based approaches that present strong evidence for the parental relationship of the B. corolliflora wild beet as an autotetraploid emerging from B. macrorhiza. Together with the publicly available genome sequences of two additional wild beets, we identified genomic regions absent from the cultivated beet, providing a sequence database harbouring traits relevant for future breeding endeavours.

The provided evidence for the evolutionary history of wild beets, especially Beta corolliflora`s derivation from the diploid B. macrorhiza, resolves long-standing questions and highlights how genomic data can clarify crop evolution and support breeding.