The interplay of DNA methyltransferases and demethylases with tuberization genes in potato (Solanum tuberosum L.) genotypes under high temperature

Potato microtuberization: its regulation and applications

Potato (Solanum tuberosum L.) is a globally consumed staple food crop grown in temperate regions. The underground storage organs (tubers) are a rich source of carbohydrates, proteins, vitamins, and minerals, contributing to food and nutritional security. Tuberization, the process by which underground stems (stolons) develop into tubers, is intricately regulated by genetic, epigenetic, and environmental factors. Studying the developmental transition from stolon to tuber in soil-based systems is challenging due to the limited visibility of below-ground stages. Microtuberization is the formation of small tubers under controlled, soil-less, and in vitro conditions, offering an effective alternative for precise monitoring of tuber development stages. Microtubers are valuable as disease-free seed propagules and essential for germplasm conservation, supporting the preservation and propagation of genetic resources. Microtuberization is influenced by both internal factors, viz., genotype and explant, and external factors, viz., photoperiod, temperature, light, plant growth regulators, sucrose, and synthetic molecules. These factors collectively regulate the transition from stolon to tuber. Microtubers exhibit strong similarities to field-grown tubers, making them a reliable model to study the environmental and molecular mechanisms of tuberization. This review examines the key factors driving microtuberization and explores potential molecular regulators involved in stolon-to-tuber transition. Furthermore, the applications of microtuberization are highlighted, including disease-free seed production, mass multiplication, germplasm evaluation and conservation, molecular farming, genetic engineering, and stress adaptation research. Additionally, microtubers serve as an experimental tool for unraveling the molecular intricacies of tuberization, paving the way for advancements in potato research and global food security strategies.

Unlocking epigenetic breeding potential in tomato and potato

Tomato (Solanum lycopersicum) and potato (Solanum tuberosum), two integral crops within the nightshade family, are crucial sources of nutrients and serve as staple foods worldwide. Molecular genetic studies have significantly advanced our understanding of their domestication, evolution, and the establishment of key agronomic traits. Recent studies have revealed that epigenetic modifications act as "molecular switches", crucially regulating phenotypic variations essential for traits such as fruit ripening in tomatoes and tuberization in potatoes. This review summarizes the latest findings on the regulatory mechanisms of epigenetic modifications in these crops and discusses the integration of biotechnology and epigenomics to enhance breeding strategies. By highlighting the role of epigenetic control in augmenting crop yield and adaptation, we underscores its potential to address the challenges posed by a growing global population as well as changing climate.

Identification of heat stress-related genomic regions by genome-wide association study in Solanum tuberosum

The climate crisis impairs yield and quality of crucial crops like potatoes. We investigated the effects of heat stress on five morpho-physiological parameters in a diverse panel of 178 potato cultivars under glasshouse conditions. Overall, heat stress increased shoot elongation and green fresh weight, but reduced tuber yield, starch content and harvest index. Genomic information was obtained from 258 tetraploid and three diploid cultivars by a genotyping-by-sequencing approach using methylation-sensitive restriction enzymes. This resulted in an enrichment of sequences in gene-rich regions. Population structure analyses using genetic distances and hierarchical clustering revealed strong kinship but weak overall population structure cultivars. A genome-wide association study (GWAS) was conducted with a subset of 20 K stringently filtered SNPs to identify quantitative trait loci (QTL) linked to heat tolerance. We identified 67 QTL and established haploblock boundaries to narrow down the number of candidate genes. Additionally, GO-enrichment analyses provided insights into gene functions. Heritability and genomic prediction were conducted to assess the usability of the collected data for selecting breeding material. The detected QTL might be exploited in marker-assisted selection to develop heat-resilient potato cultivars.

Genome-wide identification and expression analysis reveal the role of histone methyltransferase and demethylase genes in heat stress response in potato (Solanum tuberosum L.)

BACKGROUND

Potato (Solanum tuberosum L.), the third most important non-cereal crop, is sensitive to high temperature. Histone modifications have been known to regulate various abiotic stress responses. However, the role of histone methyltransferases and demethylases remain unexplored in potato under heat stress.

METHODS

Potato genome database was used for genome-wide analysis of StPRMT and StHDMA gene families, which were further characterized by analyzing gene structure, conserved motif, domain organization, sub-cellular localization, promoter region and phylogenetic relationships. Additionally, expression profiling under high-temperature stress in leaf and stolon tissue of heat contrasting potato genotypes was done to study their role in response to high temperature stress.

RESULTS

The genome-wide analysis led to identification of nine StPRMT and eleven StHDMA genes. Structural analysis, including conserved motifs, exon/intron structure and phylogenetic relationships classified StPRMT and StHDMA gene families into two classes viz. Class I and Class II. A variety of cis-regulatory elements were explored in the promoter region associated with light, developmental, hormonal and stress responses. Prediction of sub-cellular localization of StPRMT proteins revealed their occurrence in nucleus and cytoplasm, whereas StHDMA proteins were observed in different sub-cellular compartments. Furthermore, expression profiling of StPRMT and StHDMA gene family members revealed genes responding to heat stress. Heat-inducible expression of StPRMT1, StPRMT3, StPRMT4 and StPRMT5 in leaf and stolon tissues of HS and HT cultivar indicated them as probable candidates for enhancing thermotolerance in potato. However, StHDMAs responded dynamically in leaf and stolon tissue of heat contrasting genotypes under high temperature.

CONCLUSION

The current study presents a detailed analysis of histone modifiers in potato and indicates their role as an important epigenetic regulators modulating heat tolerance.

GENERAL SIGNIFICANCE

Understanding epigenetic mechanisms underlying heat tolerance in potato will contribute towards breeding of thermotolerant potato varieties.

BEL transcription factors in prominent Solanaceae crops: the missing pieces of the jigsaw in plant development

MAIN CONCLUSION

Understanding BEL transcription factors roles in potato and tomato varies considerably with little overlap. The review suggests reciprocal use of gained results to proceed with the knowledge in both crops The proper development of organs that plants use for reproduction, like fruits or tubers, is crucial for the survival and competitiveness of the species and thus subject to strict regulations. Interestingly, the controls of potato (Solanum tuberosum) tuber and tomato (S. lycopersicum) fruit development use common mechanisms, including the action of the BEL transcription factors (TFs). Although more than ten BEL genes have been identified in either genome, only a few of them have been characterized. The review summarizes knowledge of BEL TFs' roles in these closely related Solanaceae species, focusing on those that are essential for tuberization in potato, namely StBEL5, StBEL11 and StBEL29, and for fruit development in tomato - SlBEL11, SlBL2 and SIBL4. Comprehension of the roles of individual BEL TFs, however, is not yet sufficient. Different levels of understanding of important characteristics are described, such as BEL transcript accumulation patterns, their mobility, BEL protein interaction with KNOX partners, subcellular localisation, and their target genes during initiation and development of the organs in question. A comparison of the knowledge on BEL TFs and their mechanisms of action in potato and tomato may provide inspiration for faster progress in the study of both models through the exchange of information and ideas. Both crops are extremely important for human nutrition. In addition, their production is likely to be threatened by the upcoming climate change, so there is a particular need for breeding using a deep knowledge of control mechanisms.

Biomod2 modeling for predicting the potential ecological distribution of three Fritillaria species under climate change

The Fritillaria species ranked as a well-known traditional medicine in China and has become rare due to excessive harvesting. To find reasonable strategy for conservation and cultivation, identification of new ecological distribution of Fritillaria species together with prediction of those responses to climate change are necessary. In terms of current occurrence records and bioclimatic variables, the suitable habitats for Fritillaria delavayi, Fritillaria taipaiensis, and Fritillaria wabuensis were predicted. In comparison with Maxent and GARP, Biomod2 obtained the best AUC, KAPPA and TSS values of larger than 0.926 and was chosen to construct model. Temperature seasonality was indicated to put the greatest influence on Fritillaria taipaiensis and Fritillaria wabuensis, while isothermality was of most importance for Fritillaria delavayi. The current suitable areas for three Fritillaria species were distributed in south-west China, accounting for approximately 17.72%, 23.06% and 20.60% of China's total area, respectively. During 2021-2100 period, the suitable habitats of F. delavayi and F. wabuensis reached the maximum under SSP585 scenario, while that of F. taipaiensis reached the maximum under SSP126 scenario. The high niche overlap among three Fritillaria species showed correlation with the chemical composition (P ≤ 0.05), while no correlation was observed between niche overlap and DNA barcodes, indicating that spatial distribution had a major influence on chemical composition in the Fritillaria species. Finally, the acquisition of species-specific habitats would contribute to decrease in habitat competition, and future conservation and cultivation of Fritillaria species.

Epigenetic Modifications Related to Potato Skin Russeting

Potato tuber skin is a protective corky tissue consisting of suberized phellem cells. Smooth-skinned varieties are characterized by a clean, shiny appearance compared to the darker hue of russeted potatoes. The rough skin of russeted cultivars is a desired, genetically inherited characteristic; however, unwanted russeting of smooth-skinned cultivars often occurs under suboptimal growth conditions. The involvement of epigenetic modifiers in regulating the smooth skin russeting disorder was tested. We used smooth-skin commercial cultivars with and without the russeting disorder and three lines from a breeding population segregating for russeting. Anatomically, the russet skin showed similar characteristics, whether the cause was environmentally triggered or genetically determined. The old outer layers of the corky phellem remain attached to the newly formed phellem layers instead of being sloughed off. Global DNA methylation analysis indicated a significant reduction in the percentage of 5-methylcytosine in mature vs. immature skin and russet vs. smooth skin. This was true for both the smooth-skin commercial cultivars and the russeted lines. The expression level of selected DNA methyltransferases was reduced in accordance. DNA demethylase expression did not change between the skin types and age. Hence, the reduced DNA methylation in mature and russet skin is more likely to be achieved through passive DNA demethylation and loss of methyltransferase activity.