Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences

Authors: GALEWSKI, PAUL - Michigan State University; McGrath, Jon

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/3/2020
Publication Date: 3/2/2020
Citation: Galewski, P.J., McGrath, J.M. 2020. Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences. BMC Genomics. 21:189. https://doi.org/10.1186/s12864-020-6451-1.
DOI: https://doi.org/10.1186/s12864-020-6451-1

Interpretive Summary: Beets are a familiar crop, used as vegetables (table beet and chard), animal feed (fodder beet), and sucrose extraction (sugar beet). These crops diversified over hundreds to thousands of years and often are treated separately despite their being completely interfertile. This paper examines the genetic constitution of each of the beet types and demonstrates that each type has undergone specific changes likely due to selection for crop ideotype, but the changes are small in comparison to the total genetic variation within the crop type complex. Knowing which genes and gene regions contribute to crop type diversification will help direct genetic improvement and breeding and facilitate moving desirable traits between crop types and from crop wild relatives.

Technical Abstract: Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet), as well as other crop species. Often, crop improvement and management activities are segregated by crop type, thus preserving unique genome diversity and differentiation, with occasional introgressions between diverged lineages for specific traits where needed. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including the familiar table, leaf (chard), fodder, and sugar beet crop types. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between populations based on identity-by-state and shared genetic variation among lineages. Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history inferences for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages. A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between the table and chard groups, perhaps the result of less intensive selection for their end use.