Globular garden beet represents a distinct lineage in the domestication of Beta vulgaris

A single plant species can give rise to multiple crop types, but the mechanisms underlying this diversification remain unclear. Clarifying the evolutionary relationships among these crops is a crucial first step in addressing this question. Cultivated beet (Beta vulgaris ssp. vulgaris) provides a good example, as it includes several distinct crop types, both vegetable and industrial, which are classified into cultivar groups. Among these are the swollen-rooted types, including the garden beet group and the sugar beet group. While the garden beet has traditionally been considered the ancestor of sugar beet, molecular genomic data indicated that the two are actually distantly related within this subspecies. We hypothesized that the genetic diversity of garden beet has been insufficiently characterized to clarify its evolutionary role within cultivated beets. One of our expectations was the discovery of an unrecognized lineage within garden beet genetic resources. We measured 15 taproot traits in 622 plants from 74 garden beet and 7 sugar beet accessions. Hierarchical clustering and principal component analysis of these phenotypic data revealed that the garden beet accessions can be divided into two groups. Visual inspection of the taproot images revealed that the accessions with conical taproots were grouped together with sugar beet, while accessions with globular (as well as other shapes such as cylindrical) taproots formed a separate group. Genomic DNA polymorphism analysis supported this grouping, a noticeable correlation with root morphology. Reanalysis of previous studies revealed that the globular group exhibits reduced mitochondrial polymorphism compared to the conical group. Moreover, garden beet accessions with genomic patterns showing unique demographic separation also displayed globular taproots, pointing to a possible genetic bottleneck during the evolution of this group. These findings indicate that the garden beet group with globular taproots is likely a distinct lineage in the evolution of cultivated beet. We favor the hypothesis that different cultivar groups, such as the (globular) garden beet group and the sugar beet group, originated from a genetically heterogenous population that served as the common ancestor of root-type beet.