A comparative proteomic study of cold responses in potato leaves

Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days

There are limited molecular data and few biomarkers available for studies of field-grown plants, especially for plants grown during extremely long days. In this study we present quantitative proteomics data from 3 years of field trials on potato, conducted in northern and southern Sweden and analyze over 3000 proteins per year of the study and complement the proteomic analysis with metabolomic and transcriptomic analyses. Small but consistent differences linked to the longer days (an average of four more hours of light per day) in northern Sweden (20 h light/day) compared to southern Sweden can be observed, with a high correlation between the mRNA determined by RNA-seq and protein abundances. The majority of the proteins with differential abundances between northern and southern Sweden could be divided into three groups: metabolic enzymes (especially GABA metabolism), proteins involved in redox metabolism, and hydrolytic enzymes. The observed differences in metabolic enzyme abundances corresponded well with untargeted metabolite data determined by GC and LC mass-spectrometry. We also analyzed differences in protein abundance between potato varieties that performed relatively well in northern Sweden in terms of yield with those that performed relatively less well. This comparison indicates that the proteins with higher abundance in the high-yield quotient group are more anabolic in their character, whereas the proteins with lower abundance are more catabolic. Our results create a base of information about potato "field-omics" for improved understanding of physiological and molecular processes in field-grown plants, and our data indicate that the potato plant is not generally stressed by extremely long days.

Overexpression of StERECTA enhances drought tolerance in Arabidopsis thaliana

Drought is a major abiotic stresses that severely hinder plant growth and agricultural productivity. The receptor-like kinase gene, ERECTA, has been proved to play important role in promoting the response to abiotic stress in crops. However, the specific molecular mechanisms underlying the drought resistance mediated by ERECTA in potato (Solanum tuberosum L.) are not well understood. In this study, sequence analysis confirmed that the StERECTA gene contains eight leucine-rich repeat (LRR) domains and an S_TKc domain, and these domains were highly conserved in Solanaceae family. Under drought stress, Arabidopsis thaliana strains overexpressing StERECTA showed increased biomass, proline (PRO) content, and antioxidant enzyme activities compared to the wild-type strains while the mutant ERECTA strain (er105) exhibited opposite phenotype. Additionally, StERECTA overexpression upregulated the expression of drought response marker genes (LEA3, DREB2A and P5CS1), improved levels of ABA and auxin, reduced stomatal density and relative expression level of stomatal development related genes (SPCH, FAMA and MUTE). Furthermore, Co-immunoprecipitation (Co-IP) assays demonstrated that StERECTA physically interacted with the YODA protein. In conclusion, our study provides new insights into the role and regulatory mechanism of StERECTA in response to drought stress. These findings may serve as a basis for genetic improvement of potato to enhance their tolerance to abiotic stress.

Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii

Solanum commersonii (2n = 2x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55 Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16 Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25 Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.

Effects of appropriate low-temperature treatment on the yield and quality of pigmented potato (Solanum tuberosum L.) tubers

Temperature is one of the important environmental factors affecting plant growth, yield and quality. Moreover, appropriately low temperature is also beneficial for tuber coloration. The red potato variety Jianchuanhong, whose tuber color is susceptible to temperature, and the purple potato variety Huaxinyangyu, whose tuber color is stable, were used as experimental materials and subjected to 20 °C (control check), 15 °C and 10 °C treatments during the whole growth period. The effects of temperature treatment on the phenotype, the expression levels of structural genes related to anthocyanins and the correlations of each indicator were analyzed. The results showed that treatment at 10 °C significantly inhibited the potato plant height, and the chlorophyll content and photosynthetic parameters in the leaves were reduced, and the enzyme activities of SOD and POD were significantly increased, all indicating that the leaves were damaged. Treatment at 10 °C also affected the tuberization of Huaxinyangyu and reduced the tuberization and coloring of Jianchuanhong, while treatment at 15 °C significantly increased the stem diameter, root-to-shoot ratio, yield and content of secondary metabolites, especially anthocyanins. Similarly, the expression of structural genes were enhanced in two pigmented potatoes under low-temperature treatment conditions. In short, proper low temperature can not only increase yield but also enhance secondary metabolites production. Previous studies have not focused on the effects of appropriate low-temperature treatment during the whole growth period of potato on the changes in metabolites during tuber growth and development, these results can provide a theoretical basis and technical guidance for the selection of pigmented potatoes with better nutritional quality planting environment and the formulation of cultivation measures.

Ubiquitylome analysis reveals the involvement of ubiquitination in the cold responses of banana seedling leaves

Low temperature is a crucial environmental factor limiting the productivity and distribution of banana. Ubiquitination (Kub) is one of the main posttranslational modifications (PTMs) involved in plant responses to abiotic stresses. However, little information is available on the effects of Kub on banana under cold stress. In this study, we used label-free quantification (LFQ) to identify changes in the protein expression and Kub levels in banana seedling leaves after chilling treatment. In total, 4156 proteins, 1089 ubiquitinated proteins and 2636 Kub sites were quantified. Western blot assays showed that Kub was abundant in leaves after low-temperature treatment. Our results show that the proteome and ubiquitylome were negatively correlated, indicating that Kub could be involved in the degradation of proteins in banana after chilling treatment. Based on bioinformatics analysis, low-temperature stress-related signals and metabolic pathways such as cold acclimation, glutathione metabolism, calcium signaling, and photosynthesis signaling were identified. In addition, we found that transcription factors and chromatin remodeling factors related to low-temperature stress were ubiquitinated. Overall, our work presents the first systematic analysis of the Kub proteome in banana under cold stress and provides support for future studies on the regulatory mechanisms of Kub during the cold stress response in plants. SIGNIFICANCE: Banana is a typical tropical fruit tree with poor low-temperature tolerance,however, the role of PTMs such as Kub in the cold response of banana remains unclear. This study highlights the fact that the effects of low-temperature on proteome and ubiquitylome in the banana seedling leaves, we discussed the correlation between transcriptome and proteome, ubiquitylome and proteome, and we analyzed the expression and the changes of ubiquitination levels of low-temperature related proteins and pathway after chilling treatment, and we found that transcription factors and chromatin remodeling factors related to low-temperature stress were ubiquitinated. This study provides new insights into the ubiquitination pathway of banana under cold stress.

Effect of different drying techniques on rose (Rosa rugosa cv. Plena) proteome based on label-free quantitative proteomics

To explore the molecular mechanisms of different processing technologies on rose tea (Rosa rugosa cv. Plena), we investigated the rose tea proteome (fresh rose tea [CS], vacuum freeze-drying rose tea [FD], and vacuum microwave rose tea [VD]) using label-free quantification proteomics (LFQ). A total of 2187 proteins were identified, with 1864, 1905, and 1660 proteins identified in CS, FD, and VD, respectively. Of those, 1500 proteins were quantified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and enrichment analysis of differential expression proteins (DEPs) in VD vs. CS, FD vs. CS, and FD vs. VD showed that these pathways were associated with energy metabolism, the metabolic breakdown of energy substances and protein biosynthesis, such as oxidative phosphorylation, citrate cycle, carbon metabolism pathways, and ribosome and protein processing in endoplasmic reticulum. FD could ensure the synthesis of protein translation and energy metabolism, thereby maintaining the high quality of rose tea.

Measuring the impact of climate change on potato production in Bangladesh using Bayesian Hierarchical Spatial-temporal modeling

BACKGROUND

Potato is a staple food and a main crop of Bangladesh. Climate plays an important role in different crop production all over the world. Potato production is influenced by climate change, which is occurring at a rapid pace according to time and space.

OBJECTIVE

The main objective of this research is to observe the variation in potato production based on the discrepancy of the variability in the spatial and temporal domains. The research is based on secondary data on potato production from different parts of Bangladesh and five major climate variables for the last 17 years ending with 2020.

METHODS

Bayesian Spatial-temporal modelling for linear, analysis of variance (ANOVA), and auto-Regressive models were used to find the best-fitted model compared with the independent Error Bayesian model. The Watanabe-Akaike information criterion (WAIC) and Deviance Information Criterion (DIC) were used as the model choice criteria and the Markov Chain Monte Carlo (MCMC) method was implemented to generate information about the prior and posterior realizations.

RESULTS

Findings revealed that the ANOVA model under the Spatial-temporal framework was the best model for all model choice and validation criteria. Results depict that there is a significant impact of spatial and temporal variation on potato yield rate. Besides, the windspeed does not show any influence on potato production, however, temperature, humidity, rainfall, and sunshine are important components of potato yield rate in Bangladesh.

CONCLUSION

It is evident that there is a potential impact of climate change on potato production in Bangladesh. Therefore, the authors believed that the findings will be helpful to the policymakers or farmers in developing potato varieties that are resilient to climate change to ensure the United Nations Sustainable Development Goal of zero hunger.

Germplasm, Breeding, and Genomics in Potato Improvement of Biotic and Abiotic Stresses Tolerance

Potato is one of the most important food crops in the world. Late blight, viruses, soil and tuber-borne diseases, insect-pests mainly aphids, whiteflies, and potato tuber moths are the major biotic stresses affecting potato production. Potato is an irrigated and highly fertilizer-responsive crop, and therefore, heat, drought, and nutrient stresses are the key abiotic stresses. The genus Solanum is a reservoir of genetic diversity, however, a little fraction of total diversity has been utilized in potato breeding. The conventional breeding has contributed significantly to the development of potato varieties. In recent years, a tremendous progress has been achieved in the sequencing technologies from short-reads to long-reads sequence data, genomes of Solanum species (i.e., pan-genomics), bioinformatics and multi-omics platforms such as genomics, transcriptomics, proteomics, metabolomics, ionomics, and phenomics. As such, genome editing has been extensively explored as a next-generation breeding tool. With the available high-throughput genotyping facilities and tetraploid allele calling softwares, genomic selection would be a reality in potato in the near future. This mini-review covers an update on germplasm, breeding, and genomics in potato improvement for biotic and abiotic stress tolerance.

Psychrophilic Bacterial Phosphate-Biofertilizers: A Novel Extremophile for Sustainable Crop Production under Cold Environment

Abiotic stresses, including low-temperature environments, adversely affect the structure, composition, and physiological activities of soil microbiomes. Also, low temperatures disturb physiological and metabolic processes, leading to major crop losses worldwide. Extreme cold temperature habitats are, however, an interesting source of psychrophilic and psychrotolerant phosphate solubilizing bacteria (PSB) that can ameliorate the low-temperature conditions while maintaining their physiological activities. The production of antifreeze proteins and expression of stress-induced genes at low temperatures favors the survival of such organisms during cold stress. The ability to facilitate plant growth by supplying a major plant nutrient, phosphorus, in P-deficient soil is one of the novel functional properties of cold-tolerant PSB. By contrast, plants growing under stress conditions require cold-tolerant rhizosphere bacteria to enhance their performance. To this end, the use of psychrophilic PSB formulations has been found effective in yield optimization under temperature-stressed conditions. Most of the research has been done on microbial P biofertilizers impacting plant growth under normal cultivation practices but little attention has been paid to the plant growth-promoting activities of cold-tolerant PSB on crops growing in low-temperature environments. This scientific gap formed the basis of the present manuscript and explains the rationale for the introduction of cold-tolerant PSB in competitive agronomic practices, including the mechanism of solubilization/mineralization, release of biosensor active biomolecules, molecular engineering of PSB for increasing both P solubilizing/mineralizing efficiency, and host range. The impact of extreme cold on the physiological activities of plants and how plants overcome such stresses is discussed briefly. It is time to enlarge the prospects of psychrophilic/psychrotolerant phosphate biofertilizers and take advantage of their precious, fundamental, and economical but enormous plant growth augmenting potential to ameliorate stress and facilitate crop production to satisfy the food demands of frighteningly growing human populations. The production and application of cold-tolerant P-biofertilizers will recuperate sustainable agriculture in cold adaptive agrosystems.