Abstract
The genus Beta encompasses important crops like sugar, table, fodder, and leaf beets. These cultivated beets are believed to have originated from wild progenitors of sea beet (Beta vulgaris subsp. maritima). Sugar beet has been selectively bred over the past 200 years to enhance root yield and sucrose content, making it economically significant. To investigate genetic diversity, a Beta diversity panel comprising wild and cultivated beet accessions was assembled. Whole-genome sequencing identified 10.3 million single nucleotide polymorphisms (SNPs) and revealed four genetic clusters: table beet, sugar beet, Mediterranean sea beet, and Atlantic sea beet. Phylogenetic analysis indicated that cultivated beets, especially those with storage roots, are genetically closer to Mediterranean sea beet, suggesting a shared ancestor. Regions with reduced nucleotide diversity in cultivated beets highlighted areas of selection during domestication. Candidate genes in these regions are linked to key traits such as root development, flowering time regulation, and sucrose metabolism. A novel sucrose transporter on chromosome 6 exhibited reduced nucleotide diversity in sugar beet, indicating its role in sucrose storage. Further analysis revealed high nucleotide diversity among accessions with contrasting root phenotypes, highlighting two genes encoding auxin response factors critical for root development and thickening. Genome-wide association studies (GWAS) identified marker-trait associations for nine phenotypic traits, clarifying the genetic control of important characteristics. Notably, the identification of the M locus controlling monogermity—a desirable trait that facilitates efficient planting—was a major finding. The strongest association for monogermity was found at the end of chromosome 4, marking a breakthrough for developing uniform monogerm sugar beet varieties. The study also investigated the genetic basis for pigmentation in table and leaf beets. Accumulation of betalain pigments, responsible for red and yellow colors, was associated with regions near two key genes: Cytochrome P450 and a MYB-like transcription factor, both vital for betalain biosynthesis. Moreover, significant genetic associations for resistance to Cercospora leaf spot, a damaging fungal disease in beets, were identified on chromosomes 1, 2, 7, and 9, corresponding to genes encoding leucine-rich repeat (LRR) and nucleotide-binding site (NBS) proteins involved in plant defense. This analysis of genetic and phenotypic diversity within Beta clarifies the evolutionary history and domestication of these crops and provides valuable genetic resources for breeding programs aimed at enhancing sucrose content, root development, disease resistance, and pigmentation. The identification of key genes related to traits like monogermity and betalain biosynthesis marks significant advances in understanding beet genetics, benefiting both commercial cultivation and scientific research.