Abstract
BackgroundDiversification 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 organization. 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 accessions based on identity-by-state metrics and shared genetic variation among lineages.ResultsDistribution 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 for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages.ConclusionsA 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 table and sugar groups, perhaps the result of less intensive selection for end use.
Highlights
Diversification on the basis of utilization is a hallmark of Beta vulgaris, as well as other crop species
A total of 14,598,354 variants were detected across all accessions, and 12,411,164 (85.0%) of these were classified as a Single nucleotide polymorphism (SNP), and of these 10,215,761 (82.3%) were biallelic
After filtering for read depth (n ≥ 15), 8,461, 457 biallelic SNPs remained for computational analysis
Summary
Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet), as well as other crop species. (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. Vulgaris) These lineages, or “crop types,” include sugar beet, table beet, fodder beet, and chard. The crop types have been adapted for specific end uses and exhibit pronounced phenotypic differences. Crop type lineages breed true, indicating a genetic basis for these phenotypes. Table beet has been proposed to have been developed within Persian and Assyrian gardens [21] Whether this corresponds to the origin of the expanded root character or a restricted table beet phenotype remains unknown. Early written accounts regarding the use of root vegetables often confused beet with turnip (Brassica rapa)
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