Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold.

BACKGROUND: DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial or perennial plants are inevitably exposed to fluctuating temperatures throughout their lifecycle and might even require such stimulus to acquire floral competence. Therefore, plants such as beets, need to fine-tune their epigenetic makeup to ensure phenotypic plasticity towards changing environmental conditions while at the same time steering essential developmental processes. Different crop species may show opposing reactions towards the same abiotic stress, or, vice versa, identical species may respond differently depending on the specific kind of stress. RESULTS: In this study, we investigated common effects of cold treatment on genome-wide DNA methylation and gene expression of two Beta vulgaris accessions via multi-omics data analysis. Cold exposure resulted in a pronounced reduction of DNA methylation levels, which particularly affected methylation in CHH context (and to a lesser extent CHG) and was accompanied by transcriptional downregulation of the chromomethyltransferase CMT2 and strong upregulation of several genes mediating active DNA demethylation. CONCLUSION: Integration of methylomic and transcriptomic data revealed that, rather than methylation having directly influenced expression, epigenetic modifications correlated with changes in expression of known players involved in DNA (de)methylation. In particular, cold triggered upregulation of genes putatively contributing to DNA demethylation via the ROS1 pathway. Our observations suggest that these transcriptional responses precede the cold-induced global DNA-hypomethylation in non-CpG, preparing beets for additional transcriptional alterations necessary for adapting to upcoming environmental changes.

Vernalization Alters Sink and Source Identities and Reverses Phloem Translocation from Taproots to Shoots in Sugar Beet.

During their first year of growth, overwintering biennial plants transport Suc through the phloem from photosynthetic source tissues to storage tissues. In their second year, they mobilize carbon from these storage tissues to fuel new growth and reproduction. However, both the mechanisms driving this shift and the link to reproductive growth remain unclear. During vegetative growth, biennial sugar beet (Beta vulgaris) maintains a steep Suc concentration gradient between the shoot (source) and the taproot (sink). To shift from vegetative to generative growth, they require a chilling phase known as vernalization. We studied sugar beet sink-source dynamics upon vernalization and showed that before flowering, the taproot underwent a reversal from a sink to a source of carbohydrates. This transition was induced by transcriptomic and functional reprogramming of sugar beet tissue, resulting in a reversal of flux direction in the phloem. In this transition, the vacuolar Suc importers and exporters TONOPLAST SUGAR TRANSPORTER2;1 and SUCROSE TRANSPORTER4 were oppositely regulated, leading to the mobilization of sugars from taproot storage vacuoles. Concomitant changes in the expression of floral regulator genes suggest that these processes are a prerequisite for bolting. Our data will help both to dissect the metabolic and developmental triggers for bolting and to identify potential targets for genome editing and breeding.

Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets.

BACKGROUND: Sugar loss due to storage rot has a substantial economic impact on the sugar industry. The gradual spread of saprophytic fungi such as Fusarium and Penicillium spp. during storage in beet clamps is an ongoing challenge for postharvest processing. Early detection of shifts in microbial communities in beet clamps is a promising approach for the initiation of targeted countermeasures during developing storage rot. In a combined approach, high-throughput sequencing of bacterial and fungal genetic markers was complemented with cultivation-dependent methods and provided detailed insights into microbial communities colonizing stored roots. These data were used to develop a multi-target qPCR technique for early detection of postharvest diseases. RESULTS: The comparison of beet microbiomes from six clamps in Austria and Germany highlighted regional differences; nevertheless, universal indicators of the health status were identified. Apart from a significant decrease in microbial diversity in decaying sugar beets (p ≤ 0.01), a distinctive shift in the taxonomic composition of the overall microbiome was found. Fungal taxa such as Candida and Penicillium together with the gram-positive Lactobacillus were the main disease indicators in the microbiome of decaying sugar beets. In contrast, the genera Plectosphaerella and Vishniacozyma as well as a higher microbial diversity in general were found to reflect the microbiome of healthy beets. Based on these findings, a qPCR-based early detection technique was developed and confirmed a twofold decrease of health indicators and an up to 10,000-fold increase of disease indicators in beet clamps. This was further verified with analyses of the sugar content in storage samples. CONCLUSION: By conducting a detailed assessment of temporal microbiome changes during the storage of sugar beets, distinct indicator species were identified that reflect progressing rot and losses in sugar content. The insights generated in this study provide a novel basis to improve current or develop next-generation postharvest management techniques by tracking disease indicators during storage.

Optimization and Scale-up of Inulin Extraction from Taraxacum kok-saghyz roots.

The optimization and scale-up of inulin extraction from Taraxacum kok-saghyz Rodin was successfully performed. Evaluating solubility investigations, the extraction temperature was fixed at 85 degrees C. The inulin stability regarding degradation or hydrolysis could be confirmed by extraction in the presence of model inulin. Confirming stability at the given conditions the isolation procedure was transferred from a 1 L- to a 1 m3-reactor. The Reynolds number was selected as the relevant dimensionless number that has to remain constant in both scales. The stirrer speed in the large scale was adjusted to 3.25 rpm regarding a 300 rpm stirrer speed in the 1 L-scale and relevant physical and process engineering parameters. Assumptions were confirmed by approximately homologous extraction kinetics in both scales. Since T. kok-saghyz is in the focus of research due to its rubber content side-product isolation from residual biomass it is of great economic interest. Inulin is one of these additional side-products that can be isolated in high quantity (- 35% of dry mass) and with a high average degree of polymerization (15.5) in large scale with a purity of 77%.