Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet

Abstract

AbstractMost crop plants, including sugar beet (Beta vulgarissubsp.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 genes undergo reorganisation after the polyploidisation event. Through neo-and subfunctionalisation, novel functions emerge, which enable plants to cope with changing environments and extreme/harsh conditions. Particularly in the face of climate change, specific stress and pathogen resistances or tolerances gain importance. To introduce such traits into breeding material, CWRs have already been identified as an important source for sustainable breeding. The identification of genes underlying traits of interest is crucial for crop improvement.For beets, the sectionCorollinaecontains the tetraploid speciesBeta corolliflora(2n=4x=36) that harbours salt and frost tolerances as well as a wealth of pathogen resistances. The number of beneficial traits ofB. corolliflorais increased compared to those of the known diploids in this section (all 2n=2x=18). Nevertheless, neither the parental relationships ofB. corolliflorahave 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 a comprehensive pangenome dataset includingB. corolliflora,Beta lomatogona, andBeta macrorhiza, as well as a more distant wild beetPatellifolia procumbens(2n=2x=18). Joined analyses with publicly available genome sequences of two additional wild beets allowed the identification of genomic regions absent from cultivated beet, providing a sequence database harbouring traits relevant for future breeding endeavours. In addition, we present strong evidence for the parental relationship of theB. corolliflorawild beet as an autotetraploid emerging fromB. macrorhiza.