Phylogenetic relationships among wild and cultivated species of the genus Beta and genome wide association mapping of agronomically important traits

Beta vulgaris ssp. vulgaris includes sugar, table, leaf, and fodder beets, essential in sugar production, food, medicine, and livestock feed. Cultivated beets originate from wild sea beet (B. vulgaris subsp. maritima). Sugar beet, domesticated about 200 years ago for high sucrose content, resulting in a narrow genetic base. However, the full impact of domestication on the beet genome remains unclear due to limited genomic tools. A Beta mini-core collection of 290 wild and cultivated accessions was assembled. Whole-genome sequencing identified ~11 million genetic variants, revealing four genetic clusters: table beet, sugar beet, Mediterranean and Atlantic sea beet. Cultivated beets were genetically closer to Mediterranean sea beets. Phylogenetic analysis showed that beets with thickened storage roots share a common ancestor. Cultivated beets showed reduced nucleotide diversity, with selective sweeps in genes linked to root development, lateral root suppression, flowering time, and sucrose metabolism. This study is the first large-scale effort to identify genetic associations for Cercospora Leaf Spot resistance, monogermity, and red pigmentation in beets. A novel candidate gene in the M locus on chromosome 4 was identified, with the most significant association at 64,590,348 bp. A non-synonymous mutation in the Zinc-Finger domain of WIP2 co-segregated with mono- and multigermity. Significant associations for CLS resistance were found on chromosomes 1, 2, 7, and 9, in regions linked to plant defense, disease resistance, and actin depolymerization. The strongest associations for red pigmentation were at R and Y loci, near CYP76AD1 and BvMYB1, which control beet pigmentation. These findings establish a genetic framework for functional gene validation and breeding strategies to enhance desirable traits in beets.