Integrated analysis of ATAC-seq and transcriptomic reveals the ScDof3-ScproC molecular module regulating the cold acclimation capacity of potato

Low temperature severely affects the geographical distribution and production of potato, which may incur cold damage in early spring or winter. Cultivated potatoes, mainly derived from Solanum tuberosum, are sensitive to freezing stress, but wild species of potato such as S. commersonii exhibit both constitutive freezing tolerance and/or cold acclimation tolerance. Hence, such wild species could assist in cold hardiness breeding. Yet the key transcription factors and their downstream functional genes that confer freezing tolerance are far from clear, hindering the breeding process. Here, we used ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) alongside RNA-seq to investigate the variation in chromatin accessibility and patterns of gene expression in freezing-tolerant CMM5 (S. commersonii), before and after its cold treatment. Our results suggest that after exposure to cold, transcription factors including Dof3, ABF2, PIF4, and MYB4 were predicted to further control the genes active in the synthetic/metabolic pathways of plant hormones, namely abscisic acid, polyamine, and reductive glutathione (among others). This suggests these transcription factors could regulate freezing tolerance of CMM5 leaves. In particular, ScDof3 was proven to regulate the expression of ScproC (pyrroline-5-carboxylate reductase, P5CR) according to dual-LUC assays. Overexpressing ScDof3 in Nicotiana benthamiana leaves led to an increase in both the proline content and expression level of NbproC (homolog of ScproC). These results demonstrate the ScDof3-ScproC module regulates the proline content and thus promotes freezing tolerance in potato. Our research provides valuable genetic resources to further study the molecular mechanisms underpinning cold tolerance in potato.

Drought priming at seedling stage improves photosynthetic performance and yield of potato exposed to a short-term drought stress

Potato (Solanum tuberosum L.) is an important food and vegetable crop worldwide. In recent years, the arid environment resulting from climate change has caused a sharp decline in potato yield. To clarify the effect of drought priming at the seedling stage on the tolerance of potato plants to drought stress during tuber expansion, we conducted a pot experiment to investigate the physiological response of the plants generated from seed potatoes of the variety 'Favorita' to varied water supply conditions: normal water supply at the seedling stage (control), normal water supply at the seedling stage and drought stress at the mid-tuber-expansion stage (non-primed), and drought priming at the seedling stage plus drought stress at the mid-tuber-expansion stage (primed). Drought priming resulted in an increase in the number of small vascular bundles in potato plants compared to non-primed plants. It also altered the shape and density of stomata, enhancing water use efficiency and reducing whole-plant transpiration. The primed plants maintained the basal stem cambium for a longer time under drought stress, which gained an extended differentiation ability to generate a greater number of small vascular bundles compared to non-primed plants. Drought priming increased the amount and rate of dry matter translocation, and so reduced the adverse effects on tubers of potato under drought stress. Therefore, drought priming at the seedling stage improved the photosynthetic performance and yield, and probably enhanced the drought tolerance of potato.

Transcriptomics Analysis Reveals a More Refined Regulation Mechanism of Methylation in a Drought-Tolerant Variety of Potato

Whether DNA methylation modification affects the gene transcription and expression of potatoes under drought stress is still unknown. In this study, we used comparative transcriptomics to explore the expression pattern of related genes of the drought-tolerant variety Qingshu 9 (Q) and the drought-sensitive variety Atlantic (A) under drought stress and DNA methylation inhibitor treatment. The results showed that there was a significant difference in the number of DEGs between the two varieties' responses to mannitol and 5-azad C, especially when they were co-treated with two reagents, and the gene expression of Q was more sensitive to mannitol after two hours. Furthermore, we found that these differentially expressed genes (DEGs) were significantly enriched in DNA replication, transcription, translation, carbohydrate metabolism, photosynthesis, signal transduction, and glutathione metabolism. These results indicate that the difference in the background of methylation leads to the difference in drought resistance of the two varieties. The complexity of the DNA methylation of variety Q might be higher than that of variety A, and the method of methylation regulation is more refined. This study systematically expands the understanding of the molecular mechanism wherein DNA methylation regulates the response to drought stress.

Physiological response and yield components under greenhouse drought stress conditions in potato

Due to the effects of climate change, conditions tend to be increasingly extreme, with water availability being one of the main limiting factors in potato production. The objective of this study was to analyze the differential response of physiological and yield components in six potato varieties under water deficit conditions. For this purpose, a greenhouse trial was carried out with the varieties Agata, Agria, Kennebec, Monalisa, Sante and Zorba. The drought stress was applied in stressed plants 36 days after planting (DAP) by withholding water for 25 days. All measurements were taken at four different times: before stress (T0), 17 days (T1) and 24 days (T2) after stress and five days after re-watering. The physiological parameters evaluated were chlorophyll content and fluorescence, relative leaf water content, stomatal conductance, electrolytic leakage and water potential. After the drought period, the aerial part of half of the plants was cut to evaluate the produced biomass. At the end of the cycle yield components were determined. Stomatal conductance and water potential were the parameters that showed the highest differences between the two hydric conditions, and Monalisa was the variety with the best response in tuber production under stress conditions. Indirect selection based on parameters associated with water stress can be a useful tool in potato breeding programs for the identification of more tolerant varieties.

Construction of drought stress regulation networks in potato based on SMRT and RNA sequencing data

BACKGROUND

Potato (Solanum tuberosum) is the fourth most important food crop in the world and plays an important role in food security. Drought stress has a significantly negative impact on potato growth and production. There are several publications involved drought stress in potato, this research contributes to enrich the knowledge.

RESULTS

In this study, next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing technology were used to study the transcription profiles in potato in response to 20%PEG6000 simulates drought stress. The leaves of the variety "Désirée" from in vitro plantlets after drought stress at six time points from 0 to 48 hours were used to perform NGS and SMRT sequencing. According to the sequencing data, a total of 12,798 differentially expressed genes (DEGs) were identified in six time points. The real-time (RT)-PCR results are significantly correlated with the sequencing data, confirming the accuracy of the sequencing data. Gene ontology and KEGG analysis show that these DEGs participate in response to drought stress through galactose metabolism, fatty acid metabolism, plant-pathogen interaction, glutathione metabolism and other pathways. Through the analysis of alternative splicing of 66,888 transcripts, the functional pathways of these transcripts were enriched, and 51,098 transcripts were newly discovered from alternative splicing events and 47,994 transcripts were functionally annotated. Moreover, 3445 lncRNAs were predicted and enrichment analysis of corresponding target genes was also performed. Additionally, Alternative polyadenylation was analyzed by TADIS, and 26,153 poly (A) sites from 13,010 genes were detected in the Iso-Seq data.

CONCLUSION

Our research greatly enhanced potato drought-induced gene annotations and provides transcriptome-wide insights into the molecular basis of potato drought resistance.

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

BACKGROUND

Potato (Solanum tuberosum L.) is one of the world's most important crops, the cultivated potato is frost-sensitive, and low-temperature severely influences potato production. However, the mechanism by which potato responds to low-temperature stress is unclear. In this research, we apply a combination of second-generation sequencing and third-generation sequencing technologies to sequence full-length transcriptomes in low-temperature-sensitive cultivars to identify the important genes and main pathways related to low-temperature resistance.

RESULTS

In this study, we obtained 41,016 high-quality transcripts, which included 15,189 putative new transcripts. Amongst them, we identified 11,665 open reading frames, 6085 simple sequence repeats out of the potato dataset. We used public available genomic contigs to analyze the gene features, simple sequence repeat, and alternative splicing event of 24,658 non-redundant transcript sequences, predicted the coding sequence and identified the alternative polyadenylation. We performed cluster analysis, GO, and KEGG functional analysis of 4518 genes that were differentially expressed between the different low-temperature treatments. We examined 36 transcription factor families and identified 542 transcription factors in the differentially expressed genes, and 64 transcription factors were found in the AP2 transcription factor family which was the most. We measured the malondialdehyde, soluble sugar, and proline contents and the expression genes changed associated with low temperature resistance in the low-temperature treated leaves. We also tentatively speculate that StLPIN10369.5 and StCDPK16 may play a central coordinating role in the response of potatoes to low temperature stress.

CONCLUSIONS

Overall, this study provided the first large-scale full-length transcriptome sequencing of potato and will facilitate structure-function genetic and comparative genomics studies of this important crop.

BBX21 reduces abscisic acid sensitivity, mesophyll conductance and chloroplast electron transport capacity to increase photosynthesis and water use efficiency in potato plants cultivated under moderated drought

The B-box (BBX) proteins are zinc-finger transcription factors with a key role in growth and developmental regulatory networks mediated by light. AtBBX21 overexpressing (BBX21-OE) potato (Solanum tuberosum) plants, cultivated in optimal water conditions, have a higher photosynthesis rate and stomatal conductance without penalty in water use efficiency (WUE) and with a higher tuber yield. In this work, we cultivated potato plants in two water regimes: 100 and 35% field capacity of water restriction that imposed leaf water potentials between -0.3 and -1.2 MPa for vegetative and tuber growth during 14 or 28 days, respectively. We found that 42-day-old plants of BBX21-OE were more tolerant to water restriction with higher levels of chlorophylls and tuber yield than wild-type spunta (WT) plants. In addition, the BBX21-OE lines showed higher photosynthesis rates and WUE under water restriction during the morning. Mechanistically, we found that BBX21-OE lines were more tolerant to moderated drought by enhancing mesophyll conductance (g_m ) and maximum capacity of electron transport (J_max ), and by reducing abscisic acid (ABA) sensitivity in plant tissues. By RNA-seq analysis, we found 204 genes whose expression decreased by drought in WT plants and expressed independently of the water condition in BBX21-OE lines as SAP12, MYB73, EGYP1, TIP2-1 and DREB2A, and expressions were confirmed by quantitative polymerase chain reaction. These results suggest that BBX21 interplays with the ABA and growth signaling networks, improving the photosynthetic behavior in suboptimal water conditions with an increase in potato tuber yield.

Sensing stress responses in potato with whole-plant redox imaging

Environmental stresses are among the major factors that limit crop productivity and plant growth. Various nondestructive approaches for monitoring plant stress states have been developed. However, early sensing of the initial biochemical events during stress responses remains a significant challenge. In this work, we established whole-plant redox imaging using potato (Solanum tuberosum) plants expressing a chloroplast-targeted redox-sensitive green fluorescence protein 2 (roGFP2), which reports the glutathione redox potential (EGSH). Ratiometric imaging analysis demonstrated the probe response to redox perturbations induced by H2O2, DTT, or a GSH biosynthesis inhibitor. We mapped alterations in the chloroplast EGSH under several stress conditions including, high-light (HL), cold, and drought. An extremely high increase in chloroplast EGSH was observed under the combination of HL and low temperatures, conditions that specifically induce PSI photoinhibition. Intriguingly, we noted a higher reduced state in newly developed compared with mature leaves under steady-state and stress conditions, suggesting a graded stress sensitivity as part of the plant strategies for coping with stress. The presented observations suggest that whole-plant redox imaging can serve as a powerful tool for the basic understanding of plant stress responses and applied agricultural research, such as toward improving phenotyping capabilities in breeding programs and early detection of stress responses in the field.

Characterization of C-26 aminotransferase, indispensable for steroidal glycoalkaloid biosynthesis

Steroidal glycoalkaloids (SGAs) are toxic specialized metabolites found in members of the Solanaceae, such as Solanum tuberosum (potato) and Solanum lycopersicum (tomato). The major potato SGAs are α-solanine and α-chaconine, which are biosynthesized from cholesterol. Previously, we have characterized two cytochrome P450 monooxygenases and a 2-oxoglutarate-dependent dioxygenase that function in hydroxylation at the C-22, C-26 and C-16α positions, but the aminotransferase responsible for the introduction of a nitrogen moiety into the steroidal skeleton remains uncharacterized. Here, we show that PGA4 encoding a putative γ-aminobutyrate aminotransferase is involved in SGA biosynthesis in potatoes. The PGA4 transcript was expressed at high levels in tuber sprouts, in which SGAs are abundant. Silencing the PGA4 gene decreased potato SGA levels and instead caused the accumulation of furostanol saponins. Analysis of the tomato PGA4 ortholog, GAME12, essentially provided the same results. Recombinant PGA4 protein exhibited catalysis of transamination at the C-26 position of 22-hydroxy-26-oxocholesterol using γ-aminobutyric acid as an amino donor. Solanum stipuloideum (PI 498120), a tuber-bearing wild potato species lacking SGA, was found to have a defective PGA4 gene expressing the truncated transcripts, and transformation of PI 498120 with functional PGA4 resulted in the complementation of SGA production. These findings indicate that PGA4 is a key enzyme for transamination in SGA biosynthesis. The disruption of PGA4 function by genome editing will be a viable approach for accumulating valuable steroidal saponins in SGA-free potatoes.

Genome-wide identification, evolution, and transcript profiling of Aldehyde dehydrogenase superfamily in potato during development stages and stress conditions

The Aldehyde dehydrogenase (ALDH) superfamily comprises a group of enzymes involved in the scavenging of toxic aldehyde molecules by converting them into their corresponding non-toxic carboxylic acids. A genome-wide study in potato identified a total of 22 ALDH genes grouped into ten families that are presented unevenly throughout all the 12 chromosomes. Based on the evolutionary analysis of ALDH proteins from different plant species, ALDH2 and ALDH3 were found to be the most abundant families in the plant, while ALDH18 was found to be the most distantly related one. Gene expression analysis revealed that the expression of StALDH genes is highly tissue-specific and divergent in various abiotic, biotic, and hormonal treatments. Structural modelling and functional analysis of selected StALDH members revealed conservancy in their secondary structures and cofactor binding sites. Taken together, our findings provide comprehensive information on the ALDH gene family in potato that will help in developing a framework for further functional studies.

HD2-type histone deacetylases: unique regulators of plant development and stress responses

Plants have developed sophisticated and complex epigenetic regulation-based mechanisms to maintain stable growth and development under diverse environmental conditions. Histone deacetylases (HDACs) are important epigenetic regulators in eukaryotes that are involved in the deacetylation of lysine residues of histone H3 and H4 proteins. Plants have developed a unique HDAC family, HD2, in addition to the RPD3 and Sir2 families, which are also present in other eukaryotes. HD2s are well conserved plant-specific HDACs, which were first identified as nucleolar phosphoproteins in maize. The HD2 family plays important roles not only in fundamental developmental processes, including seed germination, root and leaf development, floral transition, and seed development but also in regulating plant responses to biotic and abiotic stresses. Some of the HD2 members coordinate with each other to function. The HD2 family proteins also show functional association with RPD3-type HDACs and other transcription factors as a part of repression complexes in gene regulatory networks involved in environmental stress responses. This review aims to analyse and summarise recent research progress in the HD2 family, and to describe their role in plant growth and development and in response to different environmental stresses.

Transcriptional regulation of wound suberin deposition in potato cultivars with differential wound healing capacity

Wounding during mechanical harvesting and post-harvest handling results in tuber desiccation and provides an entry point for pathogens resulting in substantial post​-harvest crop losses. Poor wound healing is a major culprit of these losses. Wound tissue in potato (Solanum tuberosum) tubers, and all higher plants, is composed of a large proportion of suberin that is deposited in a specialized tissue called the wound periderm. However, the genetic regulatory pathway controlling wound-induced suberization remains unknown. Here, we implicate two potato transcription factors, StMYB102 (PGSC0003DMG400011250) and StMYB74 (PGSC0003DMG400022399), as regulators of wound suberin biosynthesis and deposition. Using targeted metabolomics and transcript profiling from the wound healing tissues of two commercial potato cultivars, as well as heterologous expression, we provide evidence for the molecular-genetic basis of the differential wound suberization capacities of different potato cultivars. Our results suggest that (i) the export of suberin from the cytosol to the apoplast and ligno-suberin deposition may be limiting factors for wound suberization, (ii) StMYB74 and StMYB102 are important regulators of the wound suberization process in tubers, and (iii) polymorphisms in StMYB102 may influence cultivar-specific wound suberization capacity. These results represent an important step in understanding the regulated biosynthesis and deposition of wound suberin and provide a practical foundation for targeted breeding approaches aimed at improving potato tuber storage life.

Genome-Wide Approach to Identify Quantitative Trait Loci for Drought Tolerance in Tetraploid Potato (Solanum tuberosum L.)

Drought represents a major abiotic stress factor negatively affecting growth, yield and tuber quality of potatoes. Quantitative trait locus (QTL) analyses were performed in cultivated potatoes for drought tolerance index DRYM (deviation of relative starch yield from the experimental median), tuber starch content, tuber starch yield, tuber fresh weight, selected transcripts and metabolites under control and drought stress conditions. Eight genomic regions of major interest for drought tolerance were identified, three representing standalone DRYM QTL. Candidate genes, e.g., from signaling pathways for ethylene, abscisic acid and brassinosteroids, and genes encoding cell wall remodeling enzymes were identified within DRYM QTL. Co-localizations of DRYM QTL and QTL for tuber starch content, tuber starch yield and tuber fresh weight with underlying genes of the carbohydrate metabolism were observed. Overlaps of DRYM QTL with metabolite QTL for ribitol or galactinol may indicate trade-offs between starch and compatible solute biosynthesis. Expression QTL confirmed the drought stress relevance of selected transcripts by overlaps with DRYM QTL. Bulked segregant analyses combined with next-generation sequencing (BSAseq) were used to identify mutations in genes under the DRYM QTL on linkage group 3. Future analyses of identified genes for drought tolerance will give a better insight into drought tolerance in potatoes.

Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait

BACKGROUND

Scientific literature carries a wealth of information crucial for research, but only a fraction of it is present as structured information in databases and therefore can be analyzed using traditional data analysis tools. Natural language processing (NLP) is often and successfully employed to support humans by distilling relevant information from large corpora of free text and structuring it in a way that lends itself to further computational analyses. For this pilot, we developed a pipeline that uses NLP on biological literature to produce knowledge networks. We focused on the flesh color of potato, a well-studied trait with known associations, and we investigated whether these knowledge networks can assist us in formulating new hypotheses on the underlying biological processes.

RESULTS

We trained an NLP model based on a manually annotated corpus of 34 full-text potato articles, to recognize relevant biological entities and relationships between them in text (genes, proteins, metabolites and traits). This model detected the number of biological entities with a precision of 97.65% and a recall of 88.91% on the training set. We conducted a time series analysis on 4023 PubMed abstract of plant genetics-based articles which focus on 4 major Solanaceous crops (tomato, potato, eggplant and capsicum), to determine that the networks contained both previously known and contemporaneously unknown leads to subsequently discovered biological phenomena relating to flesh color. A novel time-based analysis of these networks indicates a connection between our trait and a candidate gene (zeaxanthin epoxidase) already two years prior to explicit statements of that connection in the literature.

CONCLUSIONS

Our time-based analysis indicates that network-assisted hypothesis generation shows promise for knowledge discovery, data integration and hypothesis generation in scientific research.

Apparent inhibition of induced plant volatiles by a fungal pathogen prevents airborne communication between potato plants

Plant communication in response to insect herbivory has been increasingly studied, whereas that involving pathogen attack has received much less attention. We tested for communication between potato (Solanum tuberosum) plants in response to leaf infection by the fungal pathogen Sclerotinia sclerotiorum. To this end, we measured the total amount and composition of volatile organic compounds (VOCs) produced by control and infected emitter plants, as well as tested for induced resistance of receiver plants exposed to VOCs from emitters. We further tested for changes in the expression of defensive genes due to pathogen infection. Fungal infection did not significantly affect the total amount or composition of VOCs produced by emitter plants. Correspondingly, we found no evidence of higher resistance to the pathogen in receiver plants exposed to VOCs from infected emitters relative to control emitters. Molecular analyses indicated that pathogen infection drove a down-regulation of genes coding for VOC precursors, potentially explaining the absence of pathogen effects on VOC emissions and thus of communication. Overall, these results indicate no evidence of airborne communication between potato plants in response to fungal infection and point at pathogen inhibition of VOC emissions as a likely explanation for this result.

Mitogen-activated protein kinase 11 (MAPK11) maintains growth and photosynthesis of potato plant under drought condition

KEY MESSAGE

StMAPK11 overexpression promotes potato growth, physiological activities and photosynthesis under drought conditions. Mitogen-activated protein kinases (MAPKs) are import regulators of MAPK pathway in plants under drought condition. However, the critical role in potato (Solanum tuberosum L.) drought resistance is not fully understood. In this study, we aimed to explore the role of StMAPK11 under drought stress. The result of RT-qPCR for assay of StMAPKs expression demonstrated that 15 StMAPKs were differentially expressed in leaves, flowers, petioles, stamens, pistils, stems, stolons, roots, tubers and tuber peels of potato. StMAPKs was dynamically modulated by abiotic stresses and plant hormone treatments, and StMAPK11 was apparently up-regulated under drought conditions. Therefore, the vectors pCPB-StMAPK11 and pCPBI121-miRmapk11 for over-expression and down-regulation of StMAPK11 were constructed, respectively, and introduced into potato cultivar Atlantic. The result showed that StMAPK11 promoted potato growth under drought conditions, as well as the physiological activities evidenced by changes in SOD, CAT and POD activity and H2O2, proline and MDA content. StMAPK11 up-regulation intensified drought resistance of potato plant by elevating antioxidant activities and photosynthesis. Moreover, we consolidated the protective role of StMAPK11 in tobacco and Arabidopsis against drought stress. The result could provide new insights into the function of StMAPK11 in drought response and its possible mechanisms.

Modelling the physiological relevance of sucrose export repression by an Flowering Time homolog in the long-distance phloem of potato

Yield of harvestable plant organs depends on photosynthetic assimilate production in source leaves, long-distance sucrose transport and sink-strength. While photosynthesis optimization has received considerable interest for optimizing plant yield, the potential for improving long-distance sucrose transport has received far less attention. Interestingly, a recent potato study demonstrates that the tuberigen StSP6A binds to and reduces activity of the StSWEET11 sucrose exporter. While the study suggested that reducing phloem sucrose efflux may enhance tuber yield, the precise mechanism and physiological relevance of this effect remained an open question. Here, we develop the first mechanistic model for sucrose transport, parameterized for potato plants. The model incorporates SWEET-mediated sucrose export, SUT-mediated sucrose retrieval from the apoplast and StSP6A-StSWEET11 interactions. Using this model, we were able to substantiate the physiological relevance of the StSP6A-StSWEET11 interaction in the long-distance phloem for potato tuber yield, as well as to show the non-linear nature of this effect.

Potato CYCLING DOF FACTOR 1 and its lncRNA counterpart StFLORE link tuber development and drought response

Plants regulate their reproductive cycles under the influence of environmental cues, such as day length, temperature and water availability. In Solanum tuberosum (potato), vegetative reproduction via tuberization is known to be regulated by photoperiod, in a very similar way to flowering. The central clock output transcription factor CYCLING DOF FACTOR 1 (StCDF1) was shown to regulate tuberization. We now show that StCDF1, together with a long non-coding RNA (lncRNA) counterpart, named StFLORE, also regulates water loss through affecting stomatal growth and diurnal opening. Both natural and CRISPR-Cas9 mutations in the StFLORE transcript produce plants with increased sensitivity to water-limiting conditions. Conversely, elevated expression of StFLORE, both by the overexpression of StFLORE or by the downregulation of StCDF1, results in an increased tolerance to drought through reducing water loss. Although StFLORE appears to act as a natural antisense transcript, it is in turn regulated by the StCDF1 transcription factor. We further show that StCDF1 is a non-redundant regulator of tuberization that affects the expression of two other members of the potato StCDF gene family, as well as StCO genes, through binding to a canonical sequence motif. Taken together, we demonstrate that the StCDF1-StFLORE locus is important for vegetative reproduction and water homeostasis, both of which are important traits for potato plant breeding.

Response of spring wheat and potato to foliar application of Zn, Mn and EDTA fertilizers on 137Cs uptake

The impact of foliar fertilization with zinc (ZnSO₄) and manganese (MnSO₄ on ¹³⁷Cs uptake by spring wheat and potato was studied. The experiments were conducted during 3 years (2014-2016) in a¹³⁷Cs-contaminated area, Zhytomyr region of Ukraine. The fertilization was carried out on podzolic loamy sand soil, poor in most of the microelements. Both crops were fertilized at four successive stages of growth. Foliar application of fertilizers caused higher yield of wheat grain/straw and potato tubers yield in 2014-2015 years but had no effect in 2016. Thus, the overall effect of fertilization between 2014 and 2016 was less pronounced and generally insignificant. Application of Zn, Mn and EDTA reduced ¹³⁷Cs uptake by wheat grain and potato tubers, when fertilized at earlier stages of growth and development in years 2014 and 2015 by factor 1.5-2.0, while in 2016 the effect was generally statistically insignificant. It is suggested, that reduction of ¹³⁷Cs uptake by spring wheat and potato, at least partly, was caused by an effect of radionuclide dilution due to the higher biomass of the plants. A foliar spray of EDTA at earlier stages of plant growth and development may be considered as a potential countermeasure aiming reducing ¹³⁷Cs uptake from soil to plants, even if such effect appeared to be conditional.

Genome-wide analysis of the NRAMP gene family in potato (Solanum tuberosum): Identification, expression analysis and response to five heavy metals stress

NRAMP family genes participate in the absorption and transport of heavy metals such as cadmium (Cd), zinc (Zn), copper (Cu), lead (Pb), iron (Fe) and manganese (Mn) and play an important role in the response to heavy metal stress. There is an abundance of research on these genes in bacteria, plants and fungi, although not in S. tuberosum. A total of 48 members(potato(5), Arabidopsis(7), Tomato(9), pepper(9), rice(12) and tobacco(6)) were identified from 6 species (potato (Solanum tuberosum), Arabidopsis thaliana, Tomato (Solanum lycopersicum), pepper (Capsicum annuum), rice (Oryza sativa) and tobacco (Nicotiana attenuate)) and were classified into four subgroups. Across NRAMP gene family members, there are 15 highly conserved motifs that have similar genetic structures and characteristics. In addition, a total of 16 pairs of colinear genes were found in eight species. Analysis of cis-elements indicated that, in response to abiotic stress, NRAMPs are mainly regulated by phytohormones and transcription factors. In addition, analysis of expression profiles indicated that StNRAMP4 is mainly expressed in the roots. According to a qRT-PCR-based analysis of the StNRAMP family, with the exception of Pb²⁺ stress, StNRAMPs positively responded to stress from Cu²⁺, Cd²⁺, Zn²⁺ and Ni²⁺ and The expression patterns is similar of StNRAMP2, under Pb²⁺, and Cu²⁺ treatment, the relative expression peaked at 24 h. the relative expression peaked at 12 h and was upregulated 428-fold in the roots under Ni²⁺ stress. Under Cd²⁺ stress, StNRAMP3 was upregulated 28-fold in the leaves. StNRAMP1, StNRAMP4 and StNRAMP5 showed significant upregulation under Cu²⁺, Cd²⁺ and Zn²⁺ stress, respectively. Expression of StNRAMPs could be specifically induced by heavy metals, implying their possible role in the transport and absorption of heavy metals. This research explains the colinear characteristics of NRAMPs in several food crop species, which is useful for providing important genetic resources for cultivating food crop that accumulate low amounts of heavy metals and for explaining the biological functions of NRAMPs in plants.

24-Epibrassinolide alleviates the toxic effects of NaCl on photosynthetic processes in potato plants

Brassinosteroids are promising agents for alleviating the negative effects of salinity on plants, but the mechanism of their protective action is far from being understood. We investigated the effect of pretreatment with 24-epibrassinolide (24-EBL) on the photosynthetic and physiological parameters of potato plants under progressive salinity stress caused by root application of 100 mM NaCl. Salinity clearly inhibited primary photosynthetic processes in potato plants by reducing the contents of photosynthetic pigments, photosynthetic electron transport and photosystem II (PSII) maximal and effective quantum yields. These negative effects of salinity on primary photosynthetic processes were mainly due to toxic ionic effects on the plant's ability to oxidize the plastoquinone pool. Pretreatment with 24-EBL alleviated this stress effect and allowed the maintenance of plastoquinone pool oxidation and the efficiency of photosystem II photochemistry to be at the same levels as those in unstressed plants; however, the pretreatment did not affect the photosynthetic pigment content. 24-EBL pretreatment clearly alleviated the decrease in leaf osmotic potential under salinity stress. The stress-induced increases in lipid peroxidation and proline contents were not changed under brassinosteroid pretreatment. However, 24-EBL pretreatment increased the peroxidase activity and improved the K⁺/Na⁺ ratio in potato leaves, which were likely responsible for the protective 24-EBL action under salt stress.

Assessment of physiological age and antioxidant status of new somatic hybrid potato seeds during extended cold storage

Yield components of potato are largely affected by the physiology age of the tuber seeds at planting. The current study focuses on monitoring seed tuber aging in two CN1 and CN2 somatic hybrid lines and Spunta (Sp) variety during 270 days of storage at 4 °C. Aging rate was monitored based on sprouting, emergence and tissue oxidation rates. Investigation of sprouting parameters such as physiological age index (PAI) considering physiological and chronological age and the incubation period (IP) indicated lower physiological age in hybrids than in Sp during the storage. Moreover, these analyses showed that off-seasonal growing conditions increased the aging, more clearly, in Sp tubers than in hybrid ones. However, dormancy periods (endodormancy and after storage dormancy) were equivalent in the different tuber lots. PAI and IP data when combined with those from emergence parameters (duration until emergence and stem number) seem more efficient for the characterization of the different potato lines. However, emergence indicators, when considered separately, were not able to distinguish clearly between seasonal and off-seasonal tubers. Data suggest that hybrid seeds exhibited high performances since they produced higher stem number per plant than Sp. The high aging rate in Sp tubers seems to be associated with the few developed stems. Biochemical analyses supported in part morphophysiological differences between hybrids and Sp seeds although these indicators seem more sensitive to aging. Indeed data showed that the dormancy break, and then, the development were associated with some level of tissue oxidation. Antioxidants such as superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX) and carotenoids seem more enhanced after the release of dormancy. However, induction of these activities started earlier in off-seasonal tubers than in seasonal ones, this was consistent with their advanced aging level revealed by PAI and IP data. Activation of these antioxidants appears to respond effectively to the increase of ROS suggesting a better control of postharvest development and tissue deterioration especially in CN2 off-seasonal tubers. This study suggests that CN2 followed by CN1 exhibited the best performance compared to Sp variety.

Morphological and metabolic profiling of a tropical-adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor

Potato (Solanum tuberosum L.) is one of the world's most important crops, but it is facing major challenges due to climatic changes. To investigate the effects of intermittent drought on the natural variability of plant morphology and tuber metabolism in a novel potato association panel comprising 258 varieties we performed an augmented block design field study under normal irrigation and under water-deficit and recovery conditions in Ica, Peru. All potato genotypes were profiled for 45 morphological traits and 42 central metabolites via nuclear magnetic resonance. Statistical tests and norm of reaction analysis revealed that the observed variations were trait specific, that is, genotypic versus environmental. Principal component analysis showed a separation of samples as a result of conditional changes. To explore the relational ties between morphological traits and metabolites, correlation-based network analysis was employed, constructing one network for normal irrigation and one network for water-recovery samples. Community detection and difference network analysis highlighted the differences between the two networks, revealing a significant correlational link between fumarate and plant vigor. A genome-wide association study was performed for each metabolic trait. Eleven single nucleotide polymorphism (SNP) markers were associated with fumarate. Gene Ontology analysis of quantitative trait loci regions associated with fumarate revealed an enrichment of genes regulating metabolic processes. Three of the 11 SNPs were located within genes, coding for a protein of unknown function, a RING domain protein and a zinc finger protein ZAT2. Our findings have important implications for future potato breeding regimes, especially in countries suffering from climate change.

Modifying Plant Photosynthesis and Growth via Simultaneous Chloroplast Transformation of Rubisco Large and Small Subunits

Engineering improved Rubisco for the enhancement of photosynthesis is challenged by the alternate locations of the chloroplast rbcL gene and nuclear RbcS genes. Here we develop an RNAi-RbcS tobacco (Nicotiana tabacum) master-line, tobRrΔS, for producing homogenous plant Rubisco by rbcL-rbcS operon chloroplast transformation. Four genotypes encoding alternative rbcS genes and adjoining 5'-intergenic sequences revealed that Rubisco production was highest (50% of the wild type) in the lines incorporating a rbcS gene whose codon use and 5' untranslated-region matched rbcL Additional tobacco genotypes produced here incorporated differing potato (Solanum tuberosum) rbcL-rbcS operons that either encoded one of three mesophyll small subunits (pS1, pS2, and pS3) or the potato trichome pST-subunit. The pS3-subunit caused impairment of potato Rubisco production by ∼15% relative to the lines producing pS1, pS2, or pST However, the βA-βB loop Asn-55-His and Lys-57-Ser substitutions in the pS3-subunit improved carboxylation rates by 13% and carboxylation efficiency (CE) by 17%, relative to potato Rubisco incorporating pS1 or pS2-subunits. Tobacco photosynthesis and growth were most impaired in lines producing potato Rubisco incorporating the pST-subunit, which reduced CE and CO2/O2 specificity 40% and 15%, respectively. Returning the rbcS gene to the plant plastome provides an effective bioengineering chassis for introduction and evaluation of novel homogeneous Rubisco complexes in a whole plant context.

Aldehyde dehydrogenase plays crucial roles in response to lower temperature stress in Solanum tuberosum and Nicotiana benthamiana

The aim of this study is to elucidate the role of ALDH2B7a during the response to lower temperature in Solanum tuberosum. This gene was found to have altered intragenic DNA methylation status in our previous reports. A total of 18 orthologs of StALDH2B7a were identified in the S. tuberosum genome, which were then divided into 8 aldehyde dehydrogenase (ALDH) subfamilies. The methylation statuses of four intragenic cytosine sites in intron 5 and exon 6 of genomic StALDH2B7a were altered by lower temperature stress, resulting in changes in the expression of StALDH2B7a. Silencing of NbALDH2C4, a homolog of StALDH2B7a in Nicotiana benthamiana, resulted in plants which were sensitive to lower temperature and accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA). These data suggested that the expression of StALDH2B7a was upregulated by alteration of its intragenic cytosine methylation status during lower temperature stress, and additional StALDH2B7a enzymes scavenged excess aldehydes resulting from ROS in a response to cold stress in potato. Our study expands the understanding of the mechanisms involved in plant responses to lower temperature, and provides a new gene source to improve potato tolerance to cold stress in northern China, where lower temperature is one of the key limiting factors for crop production.

Investigating potato late blight physiological differences across potato cultivars with spectroscopy and machine learning

Understanding plant disease resistance is important in the integrated management of Phytophthora infestans, causal agent of potato late blight. Advanced field-based methods of disease detection that can identify infection before the onset of visual symptoms would improve management by greatly reducing disease potential and spread as well as improve both the financial and environmental sustainability of potato farms. In-vivo foliar spectroscopy offers the capacity to rapidly and non-destructively characterize plant physiological status, which can be used to detect the effects of necrotizing pathogens on plant condition prior to the appearance of visual symptoms. Here, we tested differences in spectral response of four potato cultivars, including two cultivars with a shared genotypic background except for a single copy of a resistance gene, to inoculation with Phytophthora infestans clonal lineage US-23 using three statistical approaches: random forest discrimination (RF), partial least squares discrimination analysis (PLS-DA), and normalized difference spectral index (NDSI). We find that cultivar, or plant genotype, has a significant impact on spectral reflectance of plants undergoing P. infestans infection. The spectral response of four potato cultivars to infection by Phytophthora infestans clonal lineage US-23 was highly variable, yet with important shared characteristics that facilitated discrimination. Early disease physiology was found to be variable across cultivars as well using non-destructively derived PLS-regression trait models. This work lays the foundation to better understand host-pathogen interactions across a variety of genotypic backgrounds, and establishes that host genotype has a significant impact on spectral reflectance, and hence on biochemical and physiological traits, of plants undergoing pathogen infection.

Influence of variation in the volumetric moisture content of the substrate on irrigation efficiency in early potato varieties

Potato is a plant with high water requirements. This factor affects not only the weight of potato tubers but also their quality parameters. In order to achieve quantity and quality goal, it is helpful if we apply the principles of precision agriculture, which also contributes to sustainable management of environmental resources. Accurate identification of the water requirements of crops is the basis for determining optimal irrigation doses and dates. After their application, it is possible to assess the effectiveness of irrigation treatments and their impact on the air-water conditions in soil with a root system. The aim of the presented study was to analyse the influence of volumetric soil moisture diversity on the vegetation of early potato varieties. Two potato varieties were subject to investigation: Denar and Julinka. Pot experiments were carried out at the Department of Horticulture of Wroclaw University of Environmental and Life Sciences. Three variants were analysed: one with a low water content in the soil (pF 2.7), one with the optimal water content (pF 2.5) and one with a high water content (pF 2.2). The basis for the selection of the frequency and application rate of water doses was soil moisture measured with an SM150-Kit set. Volumetric moisture was measured with a TDR apparatus. It was found that the water requirements of both potato varieties differ and increase along with the development of the aboveground and underground parts. Moreover, it was shown that the irrigation requirements of cv. Julinka are higher than those of Denar (31.4–33.0% higher), depending on the adopted variant. The research also showed that the most effective method of potato cultivation is to maintain soil moisture at a lower level. This should be taken into account in regions where the cultivation of this species uses supplementation of the water requirements by irrigation.

Reactive oxygen species scavenging mechanisms associated with polyethylene glycol mediated osmotic stress tolerance in Chinese potato

Influence of polyethylene glycol (PEG) mediated osmotic stress on reactive oxygen species (ROS) scavenging machinery of Chinese potato (Solenostemon rotundifolius (Poir.) J. K. Morton) was investigated. Five genotypes of Chinese potato were raised in Murashige and Skoog (MS) basal medium containing 6-benzylaminopurine (BAP, 1 mg L-1) along with various concentrations of PEG-6000 mediated stress conditions (0, -0.2 and -0.5 MPa) and evaluated for osmotic stress tolerance in vitro. The medium containing PEG-6000 had a detrimental effect on plantlet growth and development while compared with the control. Accumulation of H2O2 was lower in Sreedhara and Subala and higher in Nidhi under PEG stress, which was evident by in situ detection in leaves. Lipid peroxidation product such as malondialdehyde (MDA) content was increased due to PEG stress which was more in susceptible genotype than that in tolerant ones. An enhanced ROS-scavenging antioxidant enzyme was observed under stress with respect to the control. The enzymes of ascorbate-glutathione cycle showed an important role in scavenging ROS. The imposition of PEG stress also increased the non-enzymatic antioxidants viz., the ascorbate and reduced glutathione content which was prominent in tolerant genotypes in comparison to susceptible. The present study indicated that, Sreedhara and Subala showed more tolerance to osmotic stress with better ROS scavenging machineries which would be the lines of interest for augmenting future breeding strategies in this climate resilient minor tuber crop.

Reactive oxygen species induce cyanide-resistant respiration in potato infected by Erwinia carotovora subsp. Carotovora

Studies have shown that pathogenic bacteria infections induce the overproduction of reactive oxygen species (ROS) in plants. Cyanide-resistant respiration, an energy-dissipating pathway in plants, has also been induced by a pathogenic bacteria infection. However, it is unknown whether the induction of cyanide-resistant respiration under the pathogenic bacteria infection was caused by ROS. In this study, two pathogenic Erwinia strains were used to infect potato tuber, and membrane lipid peroxidation levels and the cyanide-resistant respiration capacity were determined. In addition, StAOX expression and regulation by ROS in potato tuber were analyzed. Moreover, the role of the Ca²⁺ pathway in regulating cyanide-resistant respiration was determined. The results showed that ROS induced cyanide-resistant respiration in potato tuber infected by Erwinia. Cyanide-resistant respiration inhibited the production of H₂O₂. Intracellular Ca²⁺ regulated the expression of calcium-dependent protein kinase (StCDPK1, StCDPK4, and StCDPK5) in potato, which indirectly controlled intracellular ROS levels. These results indicate that Ca²⁺ metabolism is involved in ROS-induced cyanide-resistant respiration.

An integrative overview of physiological and proteomic changes of cytokinin-induced potato (Solanum tuberosum L.) tuber development in vitro

Potato tuberization is a complicated biological process regulated by multiple phytohormones, in particular cytokinins (CKs). The information available on the molecular mechanisms regulating tuber development by CKs remains largely unclear. Physiological results initially indicated that low 6-benzylaminopurine (BAP) concentration (3 mg l^-1 ) advanced the tuberization beginning time and promoted tuber formation. A comparative proteomics approach was applied to investigate the proteome change of tuber development by two-dimensional gel electrophoresis in vitro, subjected to exogenous BAP treatments (0, 3, 6 and 13 mg l^-1 ). Quantitative image analysis showed a total of 83 protein spots with significantly altered abundance (>2.5-fold, P < 0.05), and 55 differentially abundant proteins were identified by MALDI-TOF/TOF MS. Among these proteins, 22 proteins exhibited up-regulation with the increase of exogenous BAP concentration, and 31 proteins were upregulated at 3 mg l^-1 BAP whereas being downregulated at higher BAP concentrations. These proteins were involved in metabolism and bioenergy, storage, redox homeostasis, cell defense and rescue, transcription and translation, chaperones, signaling and transport. The favorable effects of low BAP concentrations on tuber development were found in various cellular processes, mainly including the stimulation of starch and storage protein accumulation, the enhancement of the glycolysis pathway and ATP synthesis, the cellular homeostasis maintenance, the activation of pathogen defense, the higher efficiency of transcription and translation, as well as the enhanced metabolite transport. However, higher BAP concentration, especially 13 mg l^-1 , showed disadvantageous effects. The proposed hypothetical model would explain the interaction of these proteins associated with CK-induced tuber development in vitro.

Morphological and physiological responses of the potato stem transport tissues to dehydration stress

Adaptation of the xylem under dehydration to smaller sized vessels and the increase in xylem density per stem area facilitate water transport during water-limiting conditions, and this has implications for assimilate transport during drought. The potato stem is the communication and transport channel between the assimilate-exporting source leaves and the terminal sink tissues of the plant. During environmental stress conditions like water scarcity, which adversely affect the performance (canopy growth and tuber yield) of the potato plant, the response of stem tissues is essential, however, still understudied. In this study, we investigated the response of the stem tissues of cultivated potato grown in the greenhouse to dehydration using a multidisciplinary approach including physiological, biochemical, morphological, microscopic, and magnetic resonance imaging techniques. We observed the most significant effects of water limitation in the lower stem regions of plants. The light microscopy analysis of the potato stem sections revealed that plants exposed to this particular dehydration stress have higher total xylem density per unit area than control plants. This increase in the total xylem density was accompanied by an increase in the number of narrow-diameter xylem vessels and a decrease in the number of large-diameter xylem vessels. Our MRI approach revealed a diurnal rhythm of xylem flux between day and night, with a reduction in xylem flux that is linked to dehydration sensitivity. We also observed that sink strength was the main driver of assimilate transport through the stem in our data set. These findings may present potential breeding targets for drought tolerance in potato.

RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure

Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other Solanaceae plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based on RNA sequencing (RNA-seq) and bioinformatics analysis, the global gene expression profiles of potato variety Helan 15 (Favorita) was investigated at four-time points during light exposure. The data was further verified by using quantitative Real-time PCR (qRT-PCR). When compared to the control group, 1288, 1592, 1737, and 1870 differentially expressed genes (DEGs) were detected at 6 h, 24 h, 48 h, and 8 d, respectively. The results of both RNAseq and qRT-PCR showed that SGA biosynthetic genes were up-regulated in the potato tuber under light exposure. Functional enrichment analysis revealed that genes related to PS light reaction and Protein degradation were significantly enriched in most time points of light exposure. Additionally, enriched Bins included Receptor kinases, Secondary metabolic process in flavonoids, Abiotic stress, and Biotic stress in the early stage of light exposure, but PS Calvin cycle, RNA regulation of transcription, and UDP glucosyl and glucoronyl transferases in the later stage. Most of the DEGs involved in PS light reaction and Abiotic stress were up-regulated at all four time points, whereas DEGs that participated in biotic stresses were mainly up-regulated at the later stage (48 h and 8 d). Cis-element prediction and co-expression assay were used to confirm the expressional correlation between genes that are responsible for SGA biosynthesis and disease resistance. In conclusion, the expressions of genes involved in PS light reaction, Abiotic stress, and Biotic stress were obviously aroused during the accumulation of SGAs induced by light exposure. Moreover, an increased defense response might contribute to the potato resistance to the infection by phytopathogenic microorganisms.

LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions

Copia/Ale is the youngest lineage in both Solanum tuberosum and S. commersonii. Within it, we identified nightshade, a new LTR element active in the cultivated potato. From an evolutionary perspective, long-terminal repeat retrotransposons (LTR-RT) activity during stress may be viewed as a mean by which organisms can keep up rates of genetic adaptation to changing conditions. Potato is one of the most important crop consumed worldwide, but studies on LTR-RT characterization are still lacking. Here, we assessed the abundance, insertion time and activity of LTR-RTs in both cultivated Solanum tuberosum and its cold-tolerant wild relative S. commersonii genomes. Gypsy elements were more abundant than Copia ones, suggesting that the former was somehow more successful in colonizing potato genomes. However, Copia elements, and in particular, the Ale lineage, are younger than Gypsy ones, since their insertion time was in average ~ 2 Mya. Due to the ability of LTR-RTs to be circularized by the host DNA repair mechanisms, we identified via mobilome-seq a Copia/Ale element (called nightshade, informal name used for potato family) active in S. tuberosum genome. Our analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in potato.

Identification of TIMING OF CAB EXPRESSION 1 as a temperature-sensitive negative regulator of tuberization in potato

For many potato cultivars, tuber yield is optimal at average daytime temperatures in the range 14-22 °C. Above this range, tuber yield is reduced for most cultivars. We previously reported that moderately elevated temperature increases steady-state expression of the core circadian clock gene TIMING OF CAB EXPRESSION 1 (StTOC1) in developing tubers, whereas expression of the StSP6A tuberization signal is reduced, along with tuber yield. In this study we provide evidence that StTOC1 links environmental signalling with potato tuberization by suppressing StSP6A autoactivation in the stolons. We show that transgenic lines silenced in StTOC1 expression exhibit enhanced StSP6A transcript levels and changes in gene expression in developing tubers that are indicative of an elevated sink strength. Nodal cuttings of StTOC1 antisense lines displayed increased tuber yields at moderately elevated temperatures, whereas tuber yield and StSP6A expression were reduced in StTOC1 overexpressor lines. Here we identify a number of StTOC1 binding partners and demonstrate that suppression of StSP6A expression is independent of StTOC1 complex formation with the potato homolog StPIF3. Down-regulation of StTOC1 thus provides a strategy to mitigate the effects of elevated temperature on tuber yield.

BEL1-like protein (StBEL5) regulates CYCLING DOF FACTOR1 (StCDF1) through tandem TGAC core motifs in potato

Tuberization in potato is governed by many intrinsic and extrinsic factors. Various molecular signals, such as red light photoreceptor (StPHYB), BEL1-like transcription factor (StBEL5), CYCLING DOF FACTOR1 (StCDF1), StCO1/2 (CONSTANS1/2) and StSP6A (Flowering Locus T orthologue), function as crucial regulators during the photoperiod-dependent tuberization pathway. StCDF1 induces tuberization by increasing StSP6A levels via StCO1/2 suppression. Although the circadian clock proteins, GIGANTEA (StGI) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (StFKF1), are reported as StCDF1 interactors, how the StCDF1 gene is regulated in potato is unknown. The BEL-KNOX heterodimer regulates key tuberization genes through tandem TGAC core motifs in their promoters. A recent study reported the presence of six tandem TGAC core motifs in the StCDF1 promoter, suggesting possible regulation of StCDF1 by StBEL5. In our study, we observed a positive correlation between StBEL5 and StCDF1 expression, whereas StCDF1 and its known repressor, StFKF1, showed a negative correlation for the tested tissue types. To investigate the StBEL5-StCDF1 interaction, we generated transgenic potato promoter lines containing a wild-type or mutated (deletion of six tandem TGAC sites) StCDF1 promoter fused to GUS. Wild-type promoter transgenic lines exhibited widespread GUS activity, whereas this activity was absent in the mutated promoter transgenic lines. Moreover, StBEL5 and StCDF1 transcript levels were significantly higher in the stolon-to-tuber stages under short-day conditions compared to long-day conditions. Using wild-type and mutated prStCDF1 as baits in Y1H assays, we further demonstrated that StBEL5 interacts with the StCDF1 promoter through tandem TGAC motifs, indicating direct regulation of StCDF1 by StBEL5 in potato.

Coincidence of potato CONSTANS (StCOL1) expression and light cannot explain night-break repression of tuberization

In the obligate short-day potato Solanum tuberosum group Andigena (Solanum andigena), short days, or actually long nights, induce tuberization. Applying a night break in the middle of this long night represses tuberization. However, it is not yet understood how this repression takes place. We suggest a coincidence model, similar to the model explaining photoperiodic flowering in Arabidopsis. We hypothesize that potato CONSTANS (StCOL1), expressed in the night of a short day, is stabilized by the light of the night break. This allows for StCOL1 to repress tuberization through induction of StSP5G, which represses the tuberization signal StSP6A. We grew S. andigena plants in short days, with night breaks applied at different time points during the dark period, either coinciding with StCOL1 expression or not. StCOL1 protein presence, StCOL1 expression and expression of downstream targets StSP5G and StSP6A were measured during a 24-h time course. Our results show that a night break applied during peak StCOL1 expression is unable to delay tuberization, while coincidence with low or no StCOL1 expression leads to severely repressed tuberization. These results imply that coincidence between StCOL1 expression and light does not explain why a night break represses tuberization in short days. Furthermore, stable StCOL1 did not always induce StSP5G, and upregulated StSP5G did not always lead to fully repressed StSP6A. Our findings suggest there is a yet unknown level of control between StCOL1, StSP5G and StSP6A expression, which determines whether a plant tuberizes.

Improving salt tolerance in potato through overexpression of AtHKT1 gene

BACKGROUND

Survival of plants in response to salinity stress is typically related to Na⁺ toxicity, but little is known about how heterologous high-affinity potassium transporter (HKT) may help alleviate salt-induced damages in potato (Solanum tuberosum L.).

RESULTS

In this study, we used the Arabidopsis thaliana high-affinity potassium transporter gene (AtHKT1) to enhance the capacity of potato plants to tolerate salinity stress by decreasing Na⁺ content and improving K⁺/Na⁺ ratio in plant leaves, while maintaining osmotic balance. Seven AtHKT1 transformed potato lines (namely T1, T2, T3, T5, T11, T13 and T15) were compared with non-transgenic control plant at molecule and whole-plant levels. The lines T3 and T13 had the highest AtHKT1 expression with the tolerance index (an quantitative assessment) being 6.8 times that of the control. At 30 days under 100 and 150 mmol L^- 1 NaCl stress treatments, the T3 and T13 lines had least reductions in net photosynthetic rate, stomatal conductance and transpiration rate among the seven lines, leading to the increased water use efficiency and decreased yield loss.

CONCLUSIONS

We conclude that the constitutive overexpression of AtHKT1 reduces Na⁺ accumulation in potato leaves and promotes the K⁺/Na⁺ homeostasis that minimizes osmotic imbalance, maintains photosynthesis and stomatal conductance, and increases plant productivity.

Comprehensive transcriptome profiling and phenotyping of rootstock and scion in a tomato/potato heterografting system

Tomato/potato heterografting-triggered phenotypic variations are well documented, yet the molecular mechanisms underlying grafting-induced phenotypic processes remain unknown. To investigate the phenotypic and transcriptomic responses of grafting parents in heterografting in comparison with self-grafting, tomato (Sl) was grafted onto potato rootstocks (St), and comparative phenotyping and transcriptome profiling were performed. Phenotypic analysis showed that Sl/St heterografting induced few phenotypic changes in the tomato scion. A total of 209 upregulated genes were identified in the tomato scion, some of which appear to be involved in starch and sucrose biosynthesis. Sl/St heterografting induced several modifications in the potato rootstocks (St-R), stolon number, stolon length and tuber number decreased significantly, together with an increase in GA₃ content of stolon and tuber, compared with self-grafted potato (St-WT). These results indicate that the tomato scion is less effective at producing substances or signals to induce tuberization but promotes stolon development into aerial stems and sprouting. RNA-Seq data analysis showed that 1529 genes were upregulated and 1329 downregulated between St-WT and St-R; some of these genes are involved in plant hormone signal transduction, with GID1-like gibberellin receptor (StGID1) and DELLA protein (StDELLA) being upregulated. Several genes in auxin, abscisic acid and ethylene pathways were differentially expressed as well. Various hormone signals engage in crosstalk to regulate diverse phenotypic events after grafting. This work provides abundant transcriptome profile data and lays a foundation for further research on the molecular mechanisms underlying RNA-based interactions between rootstocks and scions after tomato/potato heterografting.

Comparative proteomics illustrates the complexity of Fe, Mn and Zn deficiency-responsive mechanisms of potato (Solanum tuberosum L.) plants in vitro

The present study is the first to integrate physiological and proteomic data providing information on Fe, Mn and Zn deficiency-responsive mechanisms of potato plants in vitro. Micronutrient deficiency is an important limiting factor for potato production that causes substantial tuber yield and quality losses. To under the underlying molecular mechanisms of potato in response to Fe, Mn and Zn deficiency, a comparative proteomic approach was applied. Leaf proteome change of in vitro-propagated potato plantlets subjected to a range of Fe-deficiency treatments (20, 10 and 0 μM Na-Fe-EDTA), Mn-deficiency treatments (1 and 0 μM MnCl₂·4H₂O) and Zn-deficiency treatment (0 μM ZnCl₂) using two-dimensional gel electrophoresis was analyzed. Quantitative image analysis showed a total of 146, 55 and 42 protein spots under Fe, Mn and Zn deficiency with their abundance significantly altered (P < 0.05) more than twofold, respectively. By MALDI-TOF/TOF MS analyses, the differentially abundant proteins were found mainly involved in bioenergy and metabolism, photosynthesis, defence, redox homeostasis and protein biosynthesis/degradation under the metal deficiencies. Signaling, transport, cellular structure and transcription-related proteins were also identified. The hierarchical clustering results revealed that these proteins were involved in a dynamic network in response to Fe, Mn and Zn deficiency. All these metal deficiencies caused cellular metabolic remodeling to improve metal acquisition and distribution in potato plants. The reduced photosynthetic efficiency occurred under each metal deficiency, yet Fe-deficient plants showed a more severe damage of photosynthesis. More defence mechanisms were induced by Fe deficiency than Mn and Zn deficiency, and the antioxidant systems showed different responses to each metal deficiency. Reprogramming of protein biosynthesis/degradation and assembly was more strongly required for acclimation to Fe deficiency. The signaling cascades involving auxin and NDPKs might also play roles in micronutrient stress signaling and pinpoint interesting candidates for future studies. Our results first provide an insight into the complex functional and regulatory networks in potato plants under Fe, Mn and Zn deficiency.

Silencing of α-amylase StAmy23 in potato tuber leads to delayed sprouting

Potato tuber dormancy is critical for the postharvest quality. The supply of carbohydrates is considered as one of the important factors controlling the rate of potato tuber sprouting. Starch is the major carbohydrate reserve in potato tuber, but very little is known about the specific starch degrading enzymes responsible for controlling tuber dormancy and sprouting. In this study, we demonstrate that an α-amylase gene StAmy23 is involved in starch breakdown and regulation of tuber dormancy. Silencing of StAmy23 delayed tuber sprouting by one to two weeks compared with the control. This phenotype is accompanied by reduced levels of reducing sugars and elevated levels of malto-oligosaccharides in tuber cortex and pith tissue below the bud eye of StAmy23-deficient potato tubers. Changes in soluble sugars is accompanied by a slight variation of phytoglycogen structure and starch granule size. Our results suggest that StAmy23 may stimulate sprouting by hydrolyzing soluble phytoglycogen to ensure supply of sugars during tuber dormancy.

Accumulation of glycine betaine in transplastomic potato plants expressing choline oxidase confers improved drought tolerance

Plastid genome engineering is an effective method to generate drought-resistant potato plants accumulating glycine betaine in plastids. Glycine betaine (GB) plays an important role under abiotic stress, and its accumulation in chloroplasts is more effective on stress tolerance than that in cytosol of transgenic plants. Here, we report that the codA gene from Arthrobacter globiformis, which encoded choline oxidase to catalyze the conversion of choline to GB, was successfully introduced into potato (Solanum tuberosum) plastid genome by plastid genetic engineering. Two independent plastid-transformed lines were isolated and confirmed as homoplasmic via Southern-blot analysis, in which the mRNA level of codA was much higher in leaves than in tubers. GB accumulated in similar levels in both leaves and tubers of codA-transplastomic potato plants (referred to as PC plants). The GB content was moderately increased in PC plants, and compartmentation of GB in plastids conferred considerably higher tolerance to drought stress compared to wild-type (WT) plants. Higher levels of relative water content and chlorophyll content under drought stress were detected in the leaves of PC plants compared to WT plants. Moreover, PC plants presented a significantly higher photosynthetic performance as well as antioxidant enzyme activities during drought stress. These results suggested that biosynthesis of GB by chloroplast engineering was an effective method to increase drought tolerance.

Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data

BACKGROUND

Our study is the first to provide RNA-Seq data analysis related to transcriptomic responses towards drought across different crops. The aim was to identify and map which genes play a key role in drought response on leaves across different crops. Forty-two RNA-seq samples were analyzed from 9 published studies in 7 plant species (Arabidopsis thaliana, Solanum lycopersicum, Zea mays, Vitis vinifera, Malus X domestica, Solanum tuberosum, Triticum aestivum).

RESULTS

Twenty-seven (16 up-regulated and 11 down-regulated) drought-regulated genes were commonly present in at least 7 of 9 studies, while 351 (147 up-regulated and 204 down-regulated) were commonly drought-regulated in 6 of 9 studies. Across all kind of leaves, the drought repressed gene-ontologies were related to the cell wall and membrane re-structuring such as wax biosynthesis, cell wall organization, fatty acid biosynthesis. On the other hand, drought-up-regulated biological processes were related to responses to osmotic stress, abscisic acid, water deprivation, abscisic-activated signalling pathway, salt stress, hydrogen peroxide treatment. A common metabolic feature linked to drought response in leaves is the repression of terpenoid pathways. There was an induction of AL1 (alfin-like), UGKYAH (trihelix), WRKY20, homeobox genes and members of the SET domain family in 6 of 9 studies. Several genes involved in detoxifying and antioxidant reactions, signalling pathways and cell protection were commonly modulated by drought across the 7 species. The chromosome (Chr) mapping of these key abiotic stress genes highlighted that Chr 4 in Arabidopsis thaliana, Chr 1 in Zea mays, Chr 2 and Chr 5 in Triticum aestivum contained a higher presence of drought-related genes compared to the other remaining chromosomes. In seedling studies, it is worth notice the up-regulation of ERF4 and ESE3 (ethylene), HVA22 (abscisic acid), TIR1 (auxin) and some transcription factors (MYB3, MYB94, MYB1, WRKY53 and WRKY20). In mature leaves, ERF1 and Alfin-like 1 were induced by drought while other transcription factors (YABBY5, ARR2, TRFL2) and genes involved phospholipid biosynthesis were repressed.

CONCLUSIONS

The identified and mapped genes might be potential targets of molecular breeding activities to develop cultivars with enhanced drought resistance and tolerance across different crops.

Regeneration of Solanum tuberosum Plants from Protoplasts Induces Widespread Genome Instability

Nontransgenic genome editing in regenerable protoplasts, plant cells free of their cell wall, could revolutionize crop improvement because it reduces regulatory and technical complexity. However, plant tissue culture is known to engender frequent unwanted variation, termed somaclonal variation. To evaluate the contribution of large-scale genome instability to this phenomenon, we analyzed potatoes (Solanum tuberosum) regenerated from either protoplasts or stem explants for copy number changes by comparison of Illumina read depth. Whereas a control set of eight plants that had been propagated by cuttings displayed no changes, all 15 protoplast regenerants tested were affected by aneuploidy or structural chromosomal changes. Certain chromosomes displayed segmental deletions and duplications ranging from one to many. Resampling different leaves of the same plant found differences in three regenerants, indicating frequent persistence of instability. By comparison, 33 regenerants from stem explants used for Agrobacterium-mediated transformation displayed less frequent but still considerable (18%) large-scale copy number changes. Repetition of certain instability patterns suggested greater susceptibility in specific genomic sites. These results indicate that tissue culture, depending on the protocol used, can induce genomic instability resulting in large-scale changes likely to compromise final plant phenotype.

Tolerance of Potato Plants to Chloride Salinity Is Regulated by Selective Light

Potato plant tolerance to chloride salinity rose after short-term exposure to blue light, which has been first shown in this study. The protective effect of blue light was based on its ability to stimulate the accumulation of low-molecular weight organic compounds with antioxidant activity.

Mycorrhiza-Induced Resistance in Potato Involves Priming of Defense Responses Against Cabbage Looper (Noctuidae: Lepidoptera)

Most plants form mutualistic associations with arbuscular mycorrhizal (AM) fungi that are ubiquitous in soils. Through this symbiosis, plants can withstand abiotic and biotic stresses. The underlying molecular mechanisms involved in mediating mycorrhiza-induced resistance against insects needs further research, and this is particularly true for potato (Solanum tuberosum L. (Solanales: Solanaceae)), which is the fourth most important crop worldwide. In this study, the tripartite interaction between potato, the AM fungus Rhizophagus irregularis (Glomerales: Glomeraceae), and cabbage looper (Trichoplusia ni Hübner) (Lepidoptera: Noctuidae) was examined to determine whether potato exhibits mycorrhiza-induced resistance against this insect. Plant growth, insect fitness, AM fungal colonization of roots, and transcript levels of defense-related genes were measured in shoots and roots after 5 and 8 d of herbivory on mycorrhizal and nonmycorrhizal plants. AM fungal colonization of roots did not have an effect on potato growth, but root colonization levels increased by herbivory. Larval weight gain was reduced after 8 d of feeding on mycorrhizal plants compared with nonmycorrhizal plants. Systemic upregulation of Allene Oxide Synthase 1 (AOS1), 12-Oxo-Phytodienoate Reductase 3 (OPR3) (jasmonic acid pathway), Protease Inhibitor Type I (PI-I) (anti-herbivore defense), and Phenylalanine Ammonia Lyase (PAL) transcripts (phenylpropanoid pathway) was found during the tripartite interaction. Together, these findings suggest that potato may exhibit mycorrhiza-induced resistance to cabbage looper by priming anti-herbivore defenses aboveground. This study illustrates how mycorrhizal potato responds to herbivory by a generalist-chewing insect and serves as the basis for future studies involving tripartite interactions with other pests.

Phytochrome F plays critical roles in potato photoperiodic tuberization

The transition to tuberization contributes greatly to the adaptability of potato to a wide range of environments. Phytochromes are important light receptors for the growth and development of plants, but the detailed functions of phytochromes remain unclear in potato. In this study, we first confirmed that phytochrome F (StPHYF) played essential roles in photoperiodic tuberization in potato. By suppressing the StPHYF gene, the strict short-day potato genotype exhibited normal tuber formation under long-day (LD) conditions, together with the degradation of the CONSTANTS protein StCOL1 and modulation of two FLOWERING LOCUS T (FT) paralogs, as demonstrated by the repression of StSP5G and by the activation of StSP6A during the light period. The function of StPHYF was further confirmed through grafting the scion of StPHYF-silenced lines, which induced the tuberization of untransformed stock under LDs, suggesting that StPHYF was involved in the production of mobile signals for tuberization in potato. We also identified that StPHYF exhibited substantial interaction with StPHYB both in vitro and in vivo. Therefore, our results indicate that StPHYF plays a role in potato photoperiodic tuberization, possibly by forming a heterodimer with StPHYB.

Transient heat stress during tuber development alters post-harvest carbohydrate composition and decreases processing quality of chipping potatoes

BACKGROUND

Adverse air and soil temperatures are abiotic stresses that occur frequently and vary widely in duration and magnitude. Heat stress limits productivity of cool-weather crops such as potato (Solanum tuberosum) and may degrade crop quality. Stem-end chip defect is a localized discoloration of potato chips that adversely affects finished chip quality. The causes of stem-end chip defects are poorly understood.

RESULTS

Chipping potatoes were grown under controlled environmental conditions to test the hypothesis that stem-end chip defect is caused by transient heat stress during the growing season. Heat stress periods with 35 °C days and 29 °C nights were imposed approximately 3 months after planting and lasted for 3, 7 or 14 days. At harvest and after 1, 2 and 3 months of storage at 13 °C, potato tubers were evaluated for glucose, fructose, sucrose and dry matter contents at the basal and apical ends. Chips were fried and rated for defects at the same sampling times. Differences in responses to heat stress were observed among four varieties of chipping potatoes. Heat stress periods of 7 and 14 days increased reducing sugar content in the tuber basal and apical ends, decreased dry matter content, and increased the severity of stem-end chip defects.

CONCLUSION

Transient heat stress during the growing season decreased post-harvest chipping potato quality. Tuber reducing sugars and stem-end chip defects increased while dry matter content decreased. Planting varieties with tolerance to transient heat stress may be an effective way to mitigate these detrimental effects on chipping potato quality. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Transcriptome Profiling Reveals Effects of Drought Stress on Gene Expression in Diploid Potato Genotype P3-198

Potato (Solanum tuberosum L.) is one of the three most important food crops worldwide; however, it is strongly affected by drought stress. The precise molecular mechanisms of drought stress response in potato are not very well understood. The diploid potato genotype P3-198 has been verified to be highly resistant to drought stress. Here, a time-course experiment was performed to identify drought resistance response genes in P3-198 under polyethylene glycol (PEG)-induced stress using RNA-sequencing. A total of 1665 differentially expressed genes (DEGs) were specifically identified, and based on gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the transcription factor activity, protein kinase activity, and the plant hormone signal transduction process were significantly enriched. Annotation revealed that these DEGs mainly encode transcription factors, protein kinases, and proteins related to redox regulation, carbohydrate metabolism, and osmotic adjustment. In particular, genes encoding abscisic acid (ABA)-dependent signaling molecules were significantly differentially expressed, which revealed the important roles of the ABA-dependent signaling pathway in the early response of P3-198 to drought stress. Quantitative real-time PCR experimental verification confirmed the differential expression of genes in the drought resistance signaling pathway. Our results provide valuable information for understanding potato drought-resistance mechanisms, and also enrich the gene resources available for drought-resistant potato breeding.

Application of essential oils as a natural and alternate method for inhibiting and inducing the sprouting of potato tubers

Use of harmful chemicals and expensive maintenance of cold-storage conditions for controlling sprouting are among the major problems in potato storage. Here, 20 essential oils (EOs) were tested for their sprouting-inhibiting and sprouting-inducing activities. Overall, treatments of lemon grass (LG) and clove (CL) oils could induce sprouting whereas palmarosa (PR) and ajwain (AZ) oils could inhibit sprouting of potato tubers at normal-room-temperature (25 ± 2 °C) storage. Selected-EOs treatments affected sprouting by modulation of accumulation of reducing sugars, ethylene, and expression of genes involved in tuber-sprouting such as ARF, ARP, AIP and ERF. Surprisingly, 7-days AZ-treatments could inhibit sprouting for 30-days which was mediated via damaging apical meristem. However, LG- and CL-treated tubers could produce enhanced potato yield as well. Present work clearly demonstrates that selected-EOs can be used as a promising eco-friendly approach for inducing/inhibiting sprouting of potato tubers during potato storage and those enhancing sprouting can be used for enhancing productivity.

Endophytic bacterial communities in peels and pulp of five root vegetables

Plants contain endophytic bacteria, whose communities both influence plant growth and can be an important source of probiotics. Here we used deep sequencing of a 16S rRNA gene fragment and bacterial cultivation to independently characterize the microbiomes of five plant species from divergent taxonomic orders—potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), neep (Brassica napus spp. napobrassica), and topinambur (Helianthus tuberosus). We found that both species richness and diversity tend to be higher in the peel, where Alphaproteobacteria and Actinobacteria dominate, while Gammaproteobacteria and Firmicutes dominate in the pulp. A statistical analysis revealed that the main characteristic features of the microbiomes of plant species originate from the peel microbiomes. Topinambur pulp displayed an interesting characteristic feature: it contained up to 10⁸ CFUs of lactic acid bacteria, suggesting its use as a source of probiotic bacteria. We also detected Listeria sp., in topinambur pulps, however, the 16S rRNA gene fragment is unable to distinguish between pathogenic versus non-pathogenic species, so the evaluation of this potential health risk is left to a future study.