Transcriptomic profiling of heat-stress response in potato periderm

Metabolic and gene-expression analyses reveal developmental dynamics of cutin deposition in pomegranate fruit grown under different environmental conditions

The chemical and transcriptional changes in the cuticle of pomegranate (Punica granatum L.) fruit grown under different environmental conditions were studied. We collected fruit from three orchards located in different regions in Israel, each with a distinct microclimate. Fruit were collected at six phenological stages, and cutin monomers in the fruit cuticle were profiled by gas chromatography-mass spectrometry (GC-MS), along with qPCR transcript-expression analyses of selected cutin-related genes. While fruit phenotypes were comparable along development in all three orchards, principal component analyses of cutin monomer profiles suggested clear separation between cuticle samples of young green fruit to those of maturing fruit. Moreover, total cutin contents in green fruit were lower in the orchard characterized by a hot and dry climate compared to orchards with moderate temperatures. The variances detected in total cutin contents between orchards corresponded well with the expression patterns of BODYGUARD, a key biosynthetic gene operating in the cutin biosynthetic pathway. Based on our extraction protocols, we found that the cutin polyester that builds the pomegranate fruit cuticle accumulates some levels of gallic acid-the precursor of punicalagin, a well-known potent antioxidant metabolite in pomegranate fruit. The gallic acid was also one of the predominant metabolites contributing to the variability between developmental stages and orchards, and its accumulation levels were opposite to the expression patterns of the UGT73AL1 gene which glycosylates gallic acid to synthesize punicalagin. To the best of our knowledge, this is the first detailed composition of the cutin polyester that forms the pomegranate fruit cuticle.

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones

Heat stress during the potato growing season reduces tuber marketable yield and quality. Tuber quality deterioration includes external (heat sprouts, chained tubers, knobs) and internal (vascular discoloration, hollow heart, internal heat necrosis) tuber defects, as well as a reduction in their specific gravity and increases in reducing sugars that result in suboptimal (darker) processed products (french fries and chips). Successfully cultivating potatoes under heat-stress conditions requires planting heat-tolerant varieties that can produce high yields of marketable tubers, few external and internal tuber defects, high specific gravity, and low reducing sugars (in the case of processing potatoes). Heat tolerance is a complex trait, and understanding its genetic basis will aid in developing heat-tolerant potato varieties. A panel of 217 diverse potato clones was evaluated for yield and quality attributes in Dalhart (2019 and 2020) and Springlake (2020 and 2021), Texas, and genotyped with the Infinium 22 K V3 Potato Array. A genome-wide association study was performed to identify genomic regions associated with heat-tolerance traits using the GWASpoly package. Quantitative trait loci were identified on chromosomes 1, 3, 4, 6, 8, and 11 for external defects and on chromosomes 1, 2, 3, 10, and 11 for internal defects. Yield-related quantitative trait loci were detected on chromosomes 1, 6, and 10 pertaining to the average tuber weight and tuber number per plant. Genomic-estimated breeding values were calculated using the StageWise package. Clones with low genomic-estimated breeding values for tuber defects were identified as donors of good traits to improve heat tolerance. The identified genomic regions associated with heat-tolerance attributes and the genomic-estimated breeding values will be helpful to develop new potato cultivars with enhanced heat tolerance in potatoes.

Epigenetic Modifications Related to Potato Skin Russeting

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

Irrigation Effect on Yield, Skin Blemishes, Phellem Formation, and Total Phenolics of Red Potatoes

Dark Red Norland is an important potato cultivar in the fresh market due to its attractive bright, red colour, and good yield. However, skin blemishes such as silver patch, surface cracking, and russeting can negatively influence the tuber skin quality and marketability. It is well known that potato is a drought-sensitive plant. This study was conducted to determine whether irrigation would affect Dark Red Norland's yield and skin quality. A three-year field trial was conducted by Peak of the Market in Manitoba, Canada. Plants were treated under both irrigation and rainfed conditions. The results show that irrigation increased the total yield by 20.6% and reduced the severity of surface cracking by 48.5%. Microscopy imaging analysis demonstrated that tubers from the rainfed trials formed higher numbers of suberized cell layers than those of the irrigated potatoes, with a difference of 0.360 to 0.652 layers in normal skins. Surface cracking and silver patch skins had more suberized cell layers than the normal skins, with ranges of 7.805 to 8.333 and 7.740 to 8.496, respectively. A significantly higher amount of total polyphenols was found in the irrigated samples with a mean of 77.30 mg gallic acid equivalents (GAE)/100 g fresh weight (fw) than that of the rainfed samples (69.80 mg GAE/100 g fw). The outcome of this study provides a better understanding of the water regime effect causing these skin blemishes, which could potentially be used to establish strategies to improve tuber skin quality and minimize market losses.

Potato Periderm Development and Tuber Skin Quality

The periderm is a corky tissue that replaces the epidermis when the latter is damaged, and is critical for preventing pathogen invasion and water loss. The periderm is formed through the meristematic activity of phellogen cells (cork cambium). The potato skin (phellem cells) composes the outer layers of the tuber periderm and is a model for studying cork development. Early in tuber development and following tuber expansion, the phellogen becomes active and produces the skin. New skin layers are continuously added by division of the phellogen cells until tuber maturation. Some physiological disorders of the potato tuber are related to abnormal development of the skin, including skinning injuries and russeting of smooth-skinned potatoes. Thus, characterizing the potato periderm contributes to modeling cork development in plants and helps to resolve critical agricultural problems. Here, we summarize the data available on potato periderm formation, highlighting tissue characteristics rather than the suberization processes.

The Combined Effect of Heat and Osmotic Stress on Suberization of Arabidopsis Roots

The simultaneous occurrence of heat stress and drought is becoming more regular as a consequence of climate change, causing extensive agricultural losses. The application of either heat or osmotic stress increase cell-wall suberization in different tissues, which may play a role in improving plant resilience. In this work, we studied how the suberization process is affected by the combination of drought and heat stress by following the expression of suberin biosynthesis genes, cell-wall suberization and the chemical composition in Arabidopsis roots. The Arabidopsis plants used in this study were at the onset of secondary root development. At this point, one can observe a developmental gradient in the main root, with primary development closer to the root tip and secondary development, confirmed by the suberized phellem, closer to the shoot. Remarkably, we found a differential response depending on the root zone. The combination of drought and heat stress increased cell wall suberization in main root segments undergoing secondary development and in lateral roots (LRs), while the main root zone, at primary development stage, was not particularly affected. We also found differences in the overall chemical composition of the cell walls in both root zones in response to combined stress. The data gathered showed that, under combined drought and heat stress, Arabidopsis roots undergo differential cell wall remodeling depending on developmental stage, with modifications in the biosynthesis and/or assembly of major cell wall components.

Ripening of Pomegranate Skin as Revealed by Developmental Transcriptomics

The appearance of pomegranate (Punica granatum L.) fruit is highly important for its marketing. The primary concerns are obtaining sufficient red pigment accumulation and minimal cracking of the fruit skin (the outer red layer of the peel). We analyzed the skin transcriptome of pomegranate cv. Wonderful at distinct time points of fruit development to characterize the processes that occur in the skin during fruit ripening and which may reflect on processes in the whole fruit, such as the non-climacteric nature of pomegranate. The data suggested a ripening mechanism in pomegranate skin that differs from that in strawberry—the model plant for non-climacteric fruit where abscisic acid is the growth regulator that drives ripening—involving ethylene, polyamine, and jasmonic acid pathways. The biosynthetic pathways of important metabolites in pomegranate—hydrolyzable tannins and anthocyanins—were co-upregulated at the ripening stage, in line with the visual enhancement of red coloration. Interestingly, cuticle- and cell-wall-related genes that showed differential expression between the developmental stages were mainly upregulated in the skin of early fruit, with lower expression at mid-growth and ripening stages. Nevertheless, lignification may be involved in skin hardening in the mature fruit.

The Making of Plant Armor: The Periderm

The periderm acts as armor protecting the plant's inner tissues from biotic and abiotic stress. It forms during the radial thickening of plant organs such as stems and roots and replaces the function of primary protective tissues such as the epidermis and the endodermis. A wound periderm also forms to heal and protect injured tissues. The periderm comprises a meristematic tissue called the phellogen, or cork cambium, and its derivatives: the lignosuberized phellem and the phelloderm. Research on the periderm has mainly focused on the chemical composition of the phellem due to its relevance as a raw material for industrial processes. Today, there is increasing interest in the regulatory network underlying periderm development as a novel breeding trait to improve plant resilience and to sequester CO₂. Here, we discuss our current understanding of periderm formation, focusing on aspects of periderm evolution, mechanisms of periderm ontogenesis, regulatory networks underlying phellogen initiation and cork differentiation, and future challenges of periderm research.

Translational profile of developing phellem cells in Arabidopsis thaliana roots

The phellem is a specialized boundary tissue providing the first line of defense against abiotic and biotic stresses in organs undergoing secondary growth. Phellem cells undergo several differentiation steps, which include cell wall suberization, cell expansion, and programmed cell death. Yet, the molecular players acting particularly in phellem cell differentiation remain poorly described, particularly in the widely used model plant Arabidopsis thaliana. Using specific marker lines we followed the onset and progression of phellem differentiation in A. thaliana roots and further targeted the translatome of newly developed phellem cells using translating ribosome affinity purification followed by mRNA sequencing (TRAP-SEQ). We showed that phellem suberization is initiated early after phellogen (cork cambium) division. The specific translational landscape was organized in three main domains related to energy production, synthesis and transport of cell wall components, and response to stimulus. Novel players in phellem differentiation related to suberin monomer transport and assembly as well as novel transcription regulators were identified. This strategy provided an unprecedented resolution of the translatome of developing phellem cells, giving a detailed and specific view on the molecular mechanisms acting on cell differentiation in periderm tissues of the model plant Arabidopsis.

The metabolic and proteomic repertoires of periderm tissue in skin of the reticulated Sikkim cucumber fruit

Suberized and/or lignified (i.e. lignosuberized) periderm tissue appears often on surface of fleshy fruit skin by mechanical damage caused following environmental cues or developmental programs. The mechanisms underlying lignosuberization remain largely unknown to date. Here, we combined an assortment of microscopical techniques with an integrative multi-omics approach comprising proteomics, metabolomics and lipidomics to identify novel molecular components involved in fruit skin lignosuberization. We chose to investigate the corky Sikkim cucumber (Cucumis sativus var. sikkimensis) fruit. During development, the skin of this unique species undergoes massive cracking and is coated with a thick corky layer, making it an excellent model system for revealing fundamental cellular machineries involved in fruit skin lignosuberization. The large-scale data generated provides a significant source for the field of skin periderm tissue formation in fleshy fruit and suberin metabolism.

Comparative transcriptome analyses revealed different heat stress responses in pigeonpea (Cajanus cajan) and its crop wild relatives

Comparative transcriptome analyses accompanied by biochemical assays revealed high variability in heat stress response in Cajanus species. Among the studied species, C. scarabaeoides was the most thermotolerant followed by C. cajanifolius, C. cajan, and C. acutifolius. Pigeonpea is one of the climate-resilient grain legumes. Though the optimum temperature for cultivated pigeonpea is ~ 25-35 °C, its wild relatives grow in temperatures ranging between 18 and 45 °C. To gain insight into molecular mechanisms responsible for the heat stress tolerance in pigeonpea, we conducted time-series transcriptome analysis of one pigeonpea cultivar (Cajanus cajan) and two wild relatives, Cajanus acutifolius, and Cajanus scarabaeoides subjected to heat stress at 42 ± 2 ºC for 30 min and 3 h. A total of 9521, 12,447, and 5282 identified transcripts were differentially expressed in C. cajan, C. acutifolius, and C. scarabaeoides, respectively. In this study, we observed that a significant number of genes undergo alternative splicing in a species-specific pattern during heat stress. Gene expression profiling analysis, histochemical assay, chlorophyll content, and electrolyte leakage assay showed that C. scarabaeoides has adaptive features for heat stress tolerance. The gene set enrichment analyses of differentially expressed genes in these Cajanus species during heat stress revealed that oxidoreductase activity, transcription factor activity, oxygen-evolving complex, photosystem-II, thylakoid, phenylpropanoid biosynthetic process, secondary metabolic process, and flavonoid biosynthetic process were highly affected. The histochemical assay showed more lipid peroxidation in C. acutifolius compared to other Cajanus species inferring the presence of higher quantities of polyunsaturated fatty acids in the plasma membrane which might have led to severe damage of membrane-bound organelles like chloroplast, and high electrolyte leakage during heat stress. This study paves the way for the identification of candidate genes, which can be useful for the development of thermo-tolerant pigeonpea cultivars.

Metabolic changes in pomegranate fruit skin following cold storage promote chilling injury of the peel

Pomegranate cv. ‘Wonderful’ fruit are susceptible to chilling injuries of the peel (CIp) when stored at 7 °C in modified-atmosphere bags for more than 3 months. The damage, manifested as superficial browning, is restricted to the fruit skin, i.e., the outer colored layer of the peel. To characterize possible causes of CIp development, fruit were collected at early harvest—when the premature fruit are poorly colored and susceptible to CIp development, and at late harvest—when mature fruit have fully red skin and less susceptibility to CIp. Skin samples were collected on day of harvest and at different time points during storage. Anatomical study of skin with CIp disorder showed a broken cuticle layer with underlying degenerated cells. A high total phenol content, which is associated with high antioxidant capacity, was not sufficient to prevent the development of CIp in the premature fruit. The concentration of punicalagin was the same for premature and mature skin at harvest and during storage, and therefore not associated with CIp development in the premature fruit skin. Furthermore, the expression of antioxidant-related genes CAT2, SOD and GR2 was similar for both premature and mature fruit skin. Poor pigmentation of the premature fruit skin and chilling-induced downregulation of key anthocyanin-biosynthesis genes were associated with CIp development. High total phenol concentration combined with high expression of the gene encoding PPO was also associated with CIp; however, high expression ratio of PAL to PPO was found in mature skin, and may be associated with reduced CIp disorder. The results presented suggest future possibilities for controlling the CIp phenomenon.

Gene and Metabolite Integration Analysis through Transcriptome and Metabolome Brings New Insight into Heat Stress Tolerance in Potato (Solanum tuberosum L.)

Potatoes are particularly vulnerable to elevated temperatures, with short heat stress (6 h) inducing stomatal opening and reducing membrane stability and prolonged heat stress (3-day) decreasing the photosynthetic capacity of potato leaves. The integration of transcriptomics and metabolomics methods demonstrated that 448 heat upregulated and 918 heat downregulated genes and 325 and 219 compounds in the positive and negative ionization modes, respectively, were up- or downregulated in leaves in response to short and prolonged heat stress. Differentially expressed genes enriched in photosynthesis, cell wall degradation, heat response, RNA processing, and protein degradation were highly induced during heat exposure, and differentially expressed metabolites involved in amino acid biosynthesis and secondary metabolism were mostly induced during heat exposure, suggesting a possible role of these genes and metabolites in the heat tolerance of the potato. Metabolite and transcript abundances for the upregulation of flavone and flavonol biosynthesis under prolonged heat stress were closely correlated. Heat-induced gene expression in Arabidopsisthaliana shoots and potato leaves overlapped, and heat stress-responsive genes overlapped with drought stress-related genes in potato. The transient expression of four heat-induced genes in Nicotiana benthamiana exhibited increased heat tolerance. This study provides a new transcriptome and metabolic profile of the potato’s response to heat.

Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity

To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.

Identification of Heat-Responsive Genes in Guar [Cyamopsis tetragonoloba (L.) Taub]

The threat of heat stress on crop production increased dramatically due to global warming leading to the rise on the demand of heat-tolerant crops and understanding their tolerance. The leguminous forage crop Guar [Cyamopsis tetragonoloba (L.) Taub] is a high-temperature tolerant plant with numerous works on its tolerance at morph-physiological levels but lack on molecular thermotolerance level. In the current study, the differential gene expression and the underlying metabolic pathways induced by heat treatment were investigated. An RNA-Seq study on Guar leaves was carried out to estimate gene abundance and identify genes involved in heat tolerance to better understand the response mechanisms to heat stress. The results uncovered 1551 up- and 1466 downregulated genes, from which 200 and 72 genes with unknown function could be considered as new genes specific to guar. The upregulated unigenes were associated with 158 enzymes and 102 KEGG pathways. Blast2GO, InterProScan, and Kyoto Encyclopaedia of Genes and Genomes packages were utilized to search the functional annotation, protein analysis, enzymes, and metabolic pathways and revealed hormone signal transduction were enriched during heat stress tolerance. A total of 301 protein families, 551 domains, 15 repeats, and 3 sites were upregulated and matched to those unigenes. A batch of heat-regulated transcription factor transcripts were identified using the PlantTFDB database, which may play roles in heat response in Guar. Interestingly, several heat shock protein families were expressed in response to exposure to stressful conditions for instance small HSP20, heat shock transcription factor family, heat shock protein Hsp90 family, and heat shock protein 70 family. Our results revealed the expressional changes associated with heat tolerance and identified potential key genes in the regulation of this process. These results will provide a good start to dissect the molecular behaviour of plants induced by heat stress and could identify the key genes in stress response for marker-assisted selection in Guar and reveal their roles in stress adaptation in plants.

Dynamic Transcriptome Analysis of Anther Response to Heat Stress during Anthesis in Thermotolerant Rice (Oryza sativa L.)

High temperature at anthesis is one of the most serious stress factors for rice (Oryza sativa L.) production, causing irreversible yield losses and reduces grain quality. Illustration of thermotolerance mechanism is of great importance to accelerate rice breeding aimed at thermotolerance improvement. Here, we identified a new thermotolerant germplasm, SDWG005. Microscopical analysis found that stable anther structure of SDWG005 under stress may contribute to its thermotolerance. Dynamic transcriptomic analysis totally identified 3559 differentially expressed genes (DEGs) in SDWG005 anthers at anthesis under heat treatments, including 477, 869, 2335, and 2210 for 1, 2, 6, and 12 h, respectively; however, only 131 were regulated across all four-time-points. The DEGs were divided into nine clusters according to their expressions in these heat treatments. Further analysis indicated that some main gene categories involved in heat-response of SDWG005 anthers, such as transcription factors, nucleic acid and protein metabolisms related genes, etc. Comparison with previous studies indicates that a core gene-set may exist for thermotolerance mechanism. Expression and polymorphic analysis of agmatine-coumarin-acyltransferase gene OsACT in different accessions suggested that it may involve in SDWG005 thermotolerance. This study improves our understanding of thermotolerance mechanisms in rice anthers during anthesis, and also lays foundation for breeding thermotolerant varieties via molecular breeding.

Effects of Polyhalite Fertilization on Skin Quality of Potato Tuber

The protective peel of potato tuber consists of periderm tissue, the outmost cell layers of which contain corky cell walls and are termed "skin". The skin protects the tuber from water loss and pathogen invasion, and its visual appearance is a highly important marketing factor. Physiological skin blemishes are of great concern, mainly russeting disorder and skinning injuries. We previously showed that application of calcium (Ca) reduces the rate and severity of skin russeting. Here, polyhalite fertilization was tested as an alternative source of Ca. The polyhalite mineral is a hydrated sulfate of potassium (K), Ca, and magnesium (Mg), and thus contains additional important nutrients that may contribute to skin quality. Furthermore, in view of the direct interaction of soil mineral elements with the tuber skin, we tested application of polyhalite at the end of the growth period, assuming that providing the mineral at the last stages of skin development may enhance its quality. Accordingly, polyhalite was applied at three time points: preplanting, in-season at around 3-4 weeks prior to haulm desiccation, and 2 days post-haulm desiccation. The experiments included several cultivars and locations. Data indicated that late application of polyhalite, after haulm desiccation, results in reduced concentrations of Ca and Mg and increased concentration of K in the tuber peel of fertilized plants compared to controls. Tuber appearance was improved, and the expression of FHT and CYP86A33, indicator genes for skin suberization, was significantly upregulated. Earlier applications of the polyhalite mineral did not alter mineral elements concentrations in the tuber peel compared to control plants. Overall, polyhalite fertilization positively affected tuber skin appearance and skin-related gene expression. However, the effect was moderate, and the mineral did not fully mitigate skin imperfections. The effect of polyhalite may be dependent on local conditions and cultivar type.

Functional genomic approaches to improve crop plant heat stress tolerance

Heat stress as a yield limiting issue has become a major threat for food security as global warming progresses. Being sessile, plants cannot avoid heat stress. They respond to heat stress by activating complex molecular networks, such as signal transduction, metabolite production and expressions of heat stress-associated genes. Some plants have developed an intricate signalling network to respond and adapt it. Heat stress tolerance is a polygenic trait, which is regulated by various genes, transcriptional factors, proteins and hormones. Therefore, to improve heat stress tolerance, a sound knowledge of various mechanisms involved in the response to heat stress is required. The classical breeding methods employed to enhance heat stress tolerance has had limited success. In this era of genomics, next generation sequencing techniques, availability of genome sequences and advanced biotechnological tools open several windows of opportunities to improve heat stress tolerance in crop plants. This review discusses the potential of various functional genomic approaches, such as genome wide association studies, microarray, and suppression subtractive hybridization, in the process of discovering novel genes related to heat stress, and their functional validation using both reverse and forward genetic approaches. This review also discusses how these functionally validated genes can be used to improve heat stress tolerance through plant breeding, transgenics and genome editing approaches.

The transcriptome of potato tuber phellogen reveals cellular functions of cork cambium and genes involved in periderm formation and maturation

The periderm is a protective corky tissue that is formed through the cambial activity of phellogen cells, when the outer epidermis is damaged. Timely periderm formation is critical to prevent pathogen invasion and water loss. The outer layers of the potato periderm, the tuber skin, serves as a model to study cork development. Early in tuber development the phellogen becomes active and produces the skin. During tuber maturation it becomes inactive and the skin adheres to the tuber flesh. The characterization of potato phellogen may contribute to the management of costly agricultural problems related to incomplete skin-set and the resulting skinning injuries, and provide us with new knowledge regarding cork development in planta. A transcriptome of potato tuber phellogen isolated by laser capture microdissection indicated similarity to vascular cambium and the cork from trees. Highly expressed genes and transcription factors indicated that phellogen activation involves cytokinesis and gene reprograming for the establishment of a dedifferentiation state; whereas inactivation is characterized by activity of genes that direct organ identity in meristem and cell-wall modifications. The expression of selected genes was analyzed using qPCR in native and wound periderm at distinct developmental stages. This allowed the identification of genes involved in periderm formation and maturation.

Nutritional value of potato (Solanum tuberosum) in hot climates: anthocyanins, carotenoids, and steroidal glycoalkaloids

Growth in hot climates selectively alters potato tuber secondary metabolism-such as the anthocyanins, carotenoids, and glycoalkaloids-changing its nutritive value and the composition of health-promoting components. Potato breeding for improved nutritional value focuses mainly on increasing the health-promoting carotenoids and anthocyanins, and controlling toxic steroidal glycoalkaloids (SGAs). Metabolite levels are genetically determined, but developmental, tissue-specific, and environmental cues affect their final content. Transcriptomic and metabolomic approaches were applied to monitor carotenoid, anthocyanin, and SGA metabolite levels and their biosynthetic genes' expression under heat stress. The studied cultivars differed in tuber flesh carotenoid concentration and peel anthocyanin concentration. Gene expression studies showed heat-induced downregulation of specific genes for SGA, anthocyanin, and carotenoid biosynthesis. KEGG database mapping of the heat transcriptome indicated reduced gene expression for specific metabolic pathways rather than a global heat response. Targeted metabolomics indicated reduced SGA concentration, but anthocyanin pigments concentration remained unchanged, probably due to their stabilization in the vacuole. Total carotenoid level did not change significantly in potato tuber flesh, but their composition did. Results suggest that growth in hot climates selectively alters tuber secondary metabolism, changing its nutritive value and composition of health-promoting components.

A molecular framework to study periderm formation in Arabidopsis

During secondary growth in most eudicots and gymnosperms, the periderm replaces the epidermis as the frontier tissue protecting the vasculature from biotic and abiotic stresses. Despite its importance, the mechanisms underlying periderm establishment and formation are largely unknown. The herbaceous Arabidopsis thaliana undergoes secondary growth, including periderm formation in the root and hypocotyl. Thus, we focused on these two organs to establish a framework to study periderm development in a model organism. We identified a set of characteristic developmental stages describing periderm growth from the first cell division in the pericycle to the shedding of the cortex and epidermis. We highlight that two independent mechanisms are involved in the loosening of the outer tissues as the endodermis undergoes programmed cell death, whereas the epidermis and the cortex are abscised. Moreover, the phellem of Arabidopsis, as in trees, is suberized, lignified and peels off. In addition, putative regulators from oak and potato are also expressed in the Arabidopsis periderm. Collectively, the periderm of Arabidopsis shares many characteristics/features of woody and tuberous periderms, rendering Arabidopsis thaliana an attractive model for cork biology.

Identification of candidate genes mediating apple fruit-cracking resistance following the application of gibberellic acids 4 + 7 and the cytokinin 6-benzyladenine

Calyx-end cracking in 'Pink Lady' apple is treated by a solution of gibberellic acids 4 and 7 (GA₄₊₇) and the cytokinin 6-benzyladenine (BA). Although the GA₄₊₇ and BA mixture is applied early in apple fruit development, it mitigates cracking that becomes evident in the mature fruit, implying a long-term treatment effect. The reduced incidence of peel cracking is associated with increased epidermal cell density, which is maintained until fruit maturation. Presently, the expression of genes that have been previously reported to be associated with epidermal cell patterning and cuticle formation, or cracking resistance, was monitored in the peel during fruit development and following GA₄₊₇ and BA treatment. For most of the genes whose expression is naturally upregulated during fruit development, the early GA₄₊₇ and BA treatment maintained or further increased the high expression level in the mature peel. Where the expression of a gene was downregulated during development, no change was detected in the treated mature peel. Gene-networking analysis supported the interaction between gene clusters of cell-wall synthesis, cuticle formation and GA signaling. Overall, the data suggested that the GA₄₊₇ and BA treatment did not modify developmental cues, but promoted or enhanced the innate developmental program.

Lanosterol synthase-like is involved with differential accumulation of steroidal glycoalkaloids in potato

Phytosterol homeostasis may be maintained in leaves through diversion of intermediates into glycoalkaloid biosynthesis, whereas in tuber flesh, excess intermediates are catalyzed by tuber-specific StLAS - like , resulting in low tuber glycoalkaloids. Lanosterol synthase (LAS) and cycloartenol synthase (CAS) are phylogenetically related enzymes. Cycloartenol is the accepted precursor leading to cholesterol and phytosterols, and in potato, to steroidal glycoalkaloid (SGA) biosynthesis. LAS was also shown to synthesize some plant sterols, albeit at trace amounts, questioning its role in sterol homeostasis. Presently, a potato LAS-related gene (StLAS-like) was identified and its activity verified in a yeast complementation assay. A transgenic approach with targeted gene expression and metabolic profiling of sterols and SGAs was used. Analyses of StLAS-like transcript levels and StLAS-like-promoter::GUS reporter assays indicated specific expression in tuber flesh tissue. Overexpression of Arabidopsis AtLAS in leaves where the endogenic StLAS-like is not expressed, resulted with increased SGA level and reduced phytosterol level, while in the tuber flesh SGA level was reduced. StLAS-like expression only in tuber flesh may explain the differential accumulation of SGAs in commercial cultivars-low in tubers, high in leaves. In leaves, to maintain phytosterol homeostasis, an excess of intermediates may be diverted into SGA biosynthesis, whereas in tuber flesh these intermediates are catalyzed by tuber-specific StLAS-like instead, resulting in low levels of SGA.

Identification of genes related to skin development in potato

Newly identified genes that are preferentially expressed in potato skin include genes that are associated with the secondary cell wall and stress-related activities and contribute to the skin's protective function. Microarrays were used to compare the skin and tuber-flesh transcriptomes of potato, to identify genes that contribute to the unique characteristics of the skin as a protective tissue. Functional gene analysis indicated that genes involved in developmental processes such as cell division, cell differentiation, morphogenesis and secondary cell wall formation (lignification and suberization), and stress-related activities, are more highly expressed in the skin than in the tuber flesh. Several genes that were differentially expressed in the skin (as verified by qPCR) and had not been previously identified in potato were selected for further analysis. These included the StKCS20-like, StFAR3, StCYP86A22 and StPOD72-like genes, whose sequences suggest that they may be closely related to known suberin-related genes; the StHAP3 transcription factor that directs meristem-specific expression; and the StCASP1B2-like and StCASP1-like genes, which are two orthologs of a protein family that mediates the formation of Casparian strips in the suberized endodermis of Arabidopsis roots. An examination of microtubers induced from transgenic plants carrying GUS reporter constructs of these genes indicated that these genes were expressed in the skin, with little to no expression in the tuber flesh. Some of the reporter constructs were preferentially expressed in the inner layers of the skin, the root endodermis, the vascular cambium and the epidermis of the stem. Cis-regulatory elements within the respective promoter sequences support this gene-expression pattern.

Transcriptional Profiling and Identification of Heat-Responsive Genes in Perennial Ryegrass by RNA-Sequencing

Perennial ryegrass (Lolium perenne) is one of the most widely used forage and turf grasses in the world due to its desirable agronomic qualities. However, as a cool-season perennial grass species, high temperature is a major factor limiting its performance in warmer and transition regions. In this study, a de novo transcriptome was generated using a cDNA library constructed from perennial ryegrass leaves subjected to short-term heat stress treatment. Then the expression profiling and identification of perennial ryegrass heat response genes by digital gene expression analyses was performed. The goal of this work was to produce expression profiles of high temperature stress responsive genes in perennial ryegrass leaves and further identify the potentially important candidate genes with altered levels of transcript, such as those genes involved in transcriptional regulation, antioxidant responses, plant hormones and signal transduction, and cellular metabolism. The de novo assembly of perennial ryegrass transcriptome in this study obtained more total and annotated unigenes compared to previously published ones. Many DEGs identified were genes that are known to respond to heat stress in plants, including HSFs, HSPs, and antioxidant related genes. In the meanwhile, we also identified four gene candidates mainly involved in C₄ carbon fixation, and one TOR gene. Their exact roles in plant heat stress response need to dissect further. This study would be important by providing the gene resources for improving heat stress tolerance in both perennial ryegrass and other cool-season perennial grass plants.

Potato root system development and factors that determine its architecture

The potato root system is often characterized as shallow and inefficient, with poor ability to extract water and minerals from the soil. Potato root system architecture (RSA) refers to its 3-dimensional structure as determined by adventitious root (AR) growth and branching through lateral roots (LR). Understanding how the root system develops holds potential to increase plant yield and optimize agricultural land use. Root system development was monitored in greenhouse-grown potato while a root-on-a-plate assay was developed to explore factors that affect AR and LR development. Expression study of LR-related genes was conducted. Transgenic plants carrying DR5:GFP and CycB1:GUS reporter genes were used to monitor auxin signaling and cell division during root primordia formation, respectively. Maximum root development occurred mainly during the 6-week post seed-tuber planting and slowed during the onset of tuberization. AR and LR development was coordinated - a positive correlation was found between the length of AR and LR and between LR length and number. The expression of LR-related genes was higher in LR than in AR. High nitrate levels reduced LR number and length, however ablation of root-cap by high temperature (33°C) or cutting resulted with enhanced formation of LR. Growth conditions affect AR and LR development in potato, determining the final architecture of its root system. The overall results indicate that LR formation in potato follows similar pattern as in model plants, facilitating study and manipulation of its RSA to improve soil exploitation and yield.

Silicon fertilization of potato: expression of putative transporters and tuber skin quality

A silicon transporter homolog was upregulated by Si fertilization and drought in potato roots and leaves. High Si in tuber skin resulted in anatomical and compositional changes suggesting delayed skin maturation. Silicon (Si) fertilization has beneficial effects on plant resistance to biotic and abiotic stresses. Potatoes, low Si accumulators, are susceptible to yield loss due to suboptimal growth conditions; thus Si fertilization may contribute to crop improvement. The effect of Si fertilization on transcript levels of putative transporters, Si uptake and tuber quality was studied in potatoes grown in a glasshouse and fertilized with sodium silicate, under normal and drought-stress conditions. Anatomical studies and Raman spectroscopic analyses of tuber skin were conducted. A putative transporter, StLsi1, with conserved amino acid domains for Si transport, was isolated. The StLsi1 transcript was detected in roots and leaves and its level increased twofold following Si fertilization, and about fivefold in leaves upon Si × drought interaction. Nevertheless, increased Si accumulation was detected only in tuber peel of Si-fertilized plants--probably due to passive movement of Si from the soil solution--where it modified skin cell morphology and cell-wall composition. Compared to controls, skin cell area was greater, suberin biosynthetic genes were upregulated and skin cell walls were enriched with oxidized aromatic moieties suggesting enhanced lignification and suberization. The accumulating data suggest delayed tuber skin maturation following Si fertilization. Despite StLsi1 upregulation, low accumulation of Si in roots and leaves may result from low transport activity. Study of Si metabolism in potato, a major staple food, would contribute to the improvement of other low Si crops to ensure food security under changing climate.

Microarray analysis of gene expression patterns in the leaf during potato tuberization in the potato somatic hybrid Solanum tuberosum and Solanum etuberosum

Genes involved in photoassimilate partitioning and changes in hormonal balance are important for potato tuberization. In the present study, we investigated gene expression patterns in the tuber-bearing potato somatic hybrid (E1-3) and control non-tuberous wild species Solanum etuberosum (Etb) by microarray. Plants were grown under controlled conditions and leaves were collected at eight tuber developmental stages for microarray analysis. A t-test analysis identified a total of 468 genes (94 up-regulated and 374 down-regulated) that were statistically significant (p ≤ 0.05) and differentially expressed in E1-3 and Etb. Gene Ontology (GO) characterization of the 468 genes revealed that 145 were annotated and 323 were of unknown function. Further, these 145 genes were grouped based on GO biological processes followed by molecular function and (or) PGSC description into 15 gene sets, namely (1) transport, (2) metabolic process, (3) biological process, (4) photosynthesis, (5) oxidation-reduction, (6) transcription, (7) translation, (8) binding, (9) protein phosphorylation, (10) protein folding, (11) ubiquitin-dependent protein catabolic process, (12) RNA processing, (13) negative regulation of protein, (14) methylation, and (15) mitosis. RT-PCR analysis of 10 selected highly significant genes (p ≤ 0.01) confirmed the microarray results. Overall, we show that candidate genes induced in leaves of E1-3 were implicated in tuberization processes such as transport, carbohydrate metabolism, phytohormones, and transcription/translation/binding functions. Hence, our results provide an insight into the candidate genes induced in leaf tissues during tuberization in E1-3.

Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines

BACKGROUND

Although chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm. To improve any existing cultivar, it is important to understand the genetic and physiological mechanisms underlying this tolerance.

RESULTS

In the present study, 188 recombinant inbred lines (RILs) derived from the cross ICCV 2 × JG 11 were used to assess yield and related traits in a soil with 0 mM NaCl (control) and 80 mM NaCl (salinity) over two consecutive years. Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass. A genetic map was constructed using 56 polymorphic markers (28 simple sequence repeats; SSRs and 28 single nucleotide polymorphisms; SNPs). The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07). Two major QTLs for yield in the salinity treatment (explaining 12 and 17% of the phenotypic variation) were identified within the two key genomic regions. Comparison with already published chickpea genetic maps showed that these regions conferred salinity tolerance across two other populations and the markers can be deployed for enhancing salinity tolerance in chickpea. Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome. Most of the genes were known to be involved in achieving osmoregulation under stress conditions.

CONCLUSION

Identification of putative candidate genes further strengthens the idea of using CaLG05 and CaLG07 genomic regions for marker assisted breeding (MAB). Further fine mapping of these key genomic regions may lead to novel gene identification for salinity stress tolerance in chickpea.

Anthocyanin synthesis in native and wound periderms of potato

Skin color of red potatoes is due to accumulation of anthocyanins in the tuber periderm, a protective tissue that replaces the epidermis at an early stage of tuber development. The periderm consists of external layers of suberized phellem cells making up the skin, and internal layers of parenchyma-like phelloderm cells. Red pigmentation is an important marketing factor for red-skinned potatoes. However, injuries to the tuber surface, which are common in the potato industry, result in the development of a wound periderm that is devoid of the characteristic red coloration. To study the reason for these differences in anthocyanin accumulation, the expression level of anthocyanin biosynthesis genes and regulators was monitored in native and wound periderm using microarray analysis and quantitative polymerase chain reaction. We found significantly higher expression of the anthocyanin pathway in the phelloderm cells compared with the skin and tuber-flesh samples. However, in wound periderm, the anthocyanin pathway was strongly downregulated relative to the native periderm. This was true for two developmental stages of the native periderm--'immature', when the skin is prone to skinning injuries, and 'mature', following skin set--suggesting that anthocyanin synthesis continues postharvest. Wound-induced expression of steroidal glycoalkaloid glycosyltransferases, suberin-related 3-ketoacyl-CoA synthase and actin indicated that downregulation of the anthocyanin-specific pathway does not reflect global repression of the wound-periderm transcriptome. Loss of pigmentation may result from reduced expression of the Myb-bHLH-WD40 anthocyanin regulatory complex--a possible candidate might be the bHLH transcription factor JAF13.

Identification of heat-responsive genes in carnation (Dianthus caryophyllus L.) by RNA-seq

Carnation (Dianthus caryophyllus L.) is an important flower crop, having substantial commercial value as a cut-flower due to the long vase-life and wide array of flower colors and forms. Standard carnation varieties perform well under cool climates but are very susceptible to high temperatures which adversely affect the yield and the quality of the cut-flowers. Despite several studies of carnation contributing to the number of expressed sequence tags (ESTs), transcriptomic information of this species remains very limited, particularly regarding abiotic stress-related genes. Here, transcriptome analysis was performed to generate expression profiles of heat stress (HS)-responsive genes in carnation. We sequenced a cDNA library constructed with mixed RNA from carnation leaves subjected to 42°C HS (0, 0.5, 1, and 2 h) and 46°C HS (0.5, 1, and 2 h), and obtained 45,604,882 high quality paired-end reads. After de novo assembly and quantitative assessment 99,255 contigs were generated with an average length of 1053 bp. We then obtained functional annotations by aligning contigs with public protein databases including NR, SwissProt, KEGG, and COG. Using the above carnation transcriptome as the reference, we compared the effects of high temperature treatments (42°C: duration 0.5, 2, or 12 h) delivered to aseptic carnation seedlings, relative to untreated controls, using the FPKM metric. Overall, 11,471 genes were identified which showed a significant response to one or more of the three HS treatment times. In addition, based on GO and metabolic pathway enrichment analyses, a series of candidate genes involved in thermo-tolerance responses were selected and characterized. This study represents the first expression profiling analysis of D. caryophyllus under heat stress treatments. Numerous genes were found to be induced in response to HS, the study of which may advance our understanding of heat response of carnation.

Production of phytotoxic cationic α-helical antimicrobial peptides in plant cells using inducible promoters

Synthetic linear antimicrobial peptides with cationic α-helical structures, such as BP100, have potent and specific activities against economically important plant pathogenic bacteria. They are also recognized as valuable therapeutics and preservatives. However, highly active BP100 derivatives are often phytotoxic when expressed at high levels as recombinant peptides in plants. Here we demonstrate that production of recombinant phytotoxic peptides in transgenic plants is possible by strictly limiting transgene expression to certain tissues and conditions, and specifically that minimization of this expression during transformation and regeneration of transgenic plants is essential to obtain viable plant biofactories. On the basis of whole-genome transcriptomic data available online, we identified the Os.hsp82 promoter that fulfilled this requirement and was highly induced in response to heat shock. Using this strategy, we generated transgenic rice lines producing moderate yields of severely phytotoxic BP100 derivatives on exposure to high temperature. In addition, a threshold for gene expression in selected tissues and stages was experimentally established, below which the corresponding promoters should be suitable for driving the expression of recombinant phytotoxic proteins in genetically modified plants. In view of the growing transcriptomics data available, this approach is of interest to assist promoter selection for specific purposes.

Solving the jigsaw puzzle of wound-healing potato cultivars: metabolite profiling and antioxidant activity of polar extracts

Potato (Solanum tuberosum L.) is a worldwide food staple, but substantial waste accompanies the cultivation of this crop due to wounding of the outer skin and subsequent unfavorable healing conditions. Motivated by both economic and nutritional considerations, this metabolite profiling study aims to improve understanding of closing layer and wound periderm formation and guide the development of new methods to ensure faster and more complete healing after skin breakage. The polar metabolites of wound-healing tissues from four potato cultivars with differing patterns of tuber skin russeting (Norkotah Russet, Atlantic, Chipeta, and Yukon Gold) were analyzed at three and seven days after wounding, during suberized closing layer formation and nascent wound periderm development, respectively. The polar extracts were assessed using LC-MS and NMR spectroscopic methods, including multivariate analysis and tentative identification of 22 of the 24 biomarkers that discriminate among the cultivars at a given wound-healing time point or between developmental stages. Differences among the metabolites that could be identified from NMR- and MS-derived biomarkers highlight the strengths and limitations of each method, also demonstrating the complementarity of these approaches in terms of assembling a complete molecular picture of the tissue extracts. Both methods revealed that differences among the cultivar metabolite profiles diminish as healing proceeds during the period following wounding. The biomarkers included polyphenolic amines, flavonoid glycosides, phenolic acids and glycoalkaloids. Because wound healing is associated with oxidative stress, the free radical scavenging activities of the extracts from different cultivars were measured at each wounding time point, revealing significantly higher scavenging activity of the Yukon Gold periderm especially after 7 days of wounding.

Fundamental aspects of postharvest heat treatments

Heat treatments have been investigated for use in many aspects of postharvest storage. They have been developed for insect control, prevention of fungal development and prevention of postharvest storage disorders including chilling injury. The treatment times and temperature range vary widely, from days at 35 °C to 39 °C in hot air, to up to 63 °C for less than a minute in hot water. Much of the research has been performed to develop solutions to a particular problem, and less investigation has been conducted on the responses of the commodity to the treatment. However, since the turn of the century, a number of groups have been active in examining the molecular responses and changes that occur in commodities during and after the heat treatment. This review examines the changes at the level of transcriptome, proteome and metabolome that occur in response to the different heat treatments.

Evidence of current impact of climate change on life: a walk from genes to the biosphere

We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade-offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.

Glycoalkaloid and calystegine levels in table potato cultivars subjected to wounding, light, and heat treatments

Potato tubers naturally contain a number of defense substances, some of which are of major concern for food safety. Among these substances are the glycoalkaloids and calystegines. We have here analyzed levels of glycoalkaloids (α-chaconine and α-solanine) and calystegines (A₃, B₂, and B₄) in potato tubers subjected to mechanical wounding, light exposure, or elevated temperature: stress treatments that are known or anticipated to induce glycoalkaloid levels. Basal glycoalkaloid levels in tubers varied between potato cultivars. Wounding and light exposure, but not heat, increased tuber glycoalkaloid levels, and the relative response differed among the cultivars. Also, calystegine levels varied between cultivars, with calystegine B4 showing the most marked variation. However, the total calystegine level was not affected by wounding or light exposure. The results demonstrate a strong variation among potato cultivars with regard to postharvest glycoalkaloid increases, and they suggest that the biosynthesis of glycoalkaloids and calystegines occurs independently of each other.

Perspectives on deciphering mechanisms underlying plant heat stress response and thermotolerance

Global warming is a major threat for agriculture and food safety and in many cases the negative effects are already apparent. The current challenge of basic and applied plant science is to decipher the molecular mechanisms of heat stress response (HSR) and thermotolerance in detail and use this information to identify genotypes that will withstand unfavorable environmental conditions. Nowadays X-omics approaches complement the findings of previous targeted studies and highlight the complexity of HSR mechanisms giving information for so far unrecognized genes, proteins and metabolites as potential key players of thermotolerance. Even more, roles of epigenetic mechanisms and the involvement of small RNAs in thermotolerance are currently emerging and thus open new directions of yet unexplored areas of plant HSR. In parallel it is emerging that although the whole plant is vulnerable to heat, specific organs are particularly sensitive to elevated temperatures. This has redirected research from the vegetative to generative tissues. The sexual reproduction phase is considered as the most sensitive to heat and specifically pollen exhibits the highest sensitivity and frequently an elevation of the temperature just a few degrees above the optimum during pollen development can have detrimental effects for crop production. Compared to our knowledge on HSR of vegetative tissues, the information on pollen is still scarce. Nowadays, several techniques for high-throughput X-omics approaches provide major tools to explore the principles of pollen HSR and thermotolerance mechanisms in specific genotypes. The collection of such information will provide an excellent support for improvement of breeding programs to facilitate the development of tolerant cultivars. The review aims at describing the current knowledge of thermotolerance mechanisms and the technical advances which will foster new insights into this process.

Effects of nickel, chlorpyrifos and their mixture on the Dictyostelium discoideum proteome

Mixtures of chemicals can have additive, synergistic or antagonistic interactions. We investigated the effects of the exposure to nickel, the organophosphate insecticide chlorpyrifos at effect concentrations (EC) of 25% and 50% and their binary mixture (Ec25 + EC25) on Dictyostelium discoideum amoebae based on lysosomal membrane stability (LMS). We treated D. discoideum with these compounds under controlled laboratory conditions and evaluated the changes in protein levels using a two-dimensional gel electrophoresis (2DE) proteomic approach. Nickel treatment at EC25 induced changes in 14 protein spots, 12 of which were down-regulated. Treatment with nickel at EC50 resulted in changes in 15 spots, 10 of which were down-regulated. Treatment with chlorpyrifos at EC25 induced changes in six spots, all of which were down-regulated; treatment with chlorpyrifos at EC50 induced changes in 13 spots, five of which were down-regulated. The mixture corresponding to EC25 of each compound induced changes in 19 spots, 13 of which were down-regulated. The data together reveal that a different protein expression signature exists for each treatment, and that only a few proteins are modulated in multiple different treatments. For a simple binary mixture, the proteomic response does not allow for the identification of each toxicant. The protein spots that showed significant differences were identified by mass spectrometry, which revealed modulations of proteins involved in metal detoxification, stress adaptation, the oxidative stress response and other cellular processes.

Some like it hot, some like it warm: phenotyping to explore thermotolerance diversity

Plants have evolved overlapping but distinct cellular responses to different aspects of high temperature stress. These responses include basal thermotolerance, short- and long-term acquired thermotolerance, and thermotolerance to moderately high temperatures. This 'thermotolerance diversity' means that multiple phenotypic assays are essential for fully describing the functions of genes involved in heat stress responses. A large number of genes with potential roles in heat stress responses have been identified using genetic screens and genome wide expression studies. We examine the range of phenotypic assays that have been used to characterize thermotolerance phenotypes in both Arabidopsis and crop plants. Three major variables differentiate thermotolerance assays: (1) the heat stress regime used, (2) the developmental stage of the plants being studied, and (3) the actual phenotype which is scored. Consideration of these variables will be essential for deepening our understanding of the molecular genetics of plant thermotolerance.

Transcriptomic analysis of grape (Vitis vinifera L.) leaves during and after recovery from heat stress

BACKGROUND

Grapes are a major fruit crop around the world. Heat stress can significantly reduce grape yield and quality. Changes at the molecular level in response to heat stress and subsequent recovery are poorly understood. To elucidate the effect of heat stress and subsequent recovery on expression of genes by grape leaves representing the classic heat stress response and thermotolerance mechanisms, transcript abundance of grape (Vitis vinifera L.) leaves was quantified using the Affymetrix Grape Genome oligonucleotide microarray (15,700 transcripts), followed by quantitative Real-Time PCR validation for some transcript profiles.

RESULTS

We found that about 8% of the total probe sets were responsive to heat stress and/or to subsequent recovery in grape leaves. The heat stress and recovery responses were characterized by different transcriptional changes. The number of heat stress-regulated genes was almost twice the number of recovery-regulated genes. The responsive genes identified in this study belong to a large number of important traits and biological pathways, including cell rescue (i.e., antioxidant enzymes), protein fate (i.e., HSPs), primary and secondary metabolism, transcription factors, signal transduction, and development. We have identified some common genes and heat shock factors (HSFs) that were modulated differentially by heat stress and recovery. Most HSP genes were upregulated by heat stress but were downregulated by the recovery. On the other hand, some specific HSP genes or HSFs were uniquely responsive to heat stress or recovery.

CONCLUSION

The effect of heat stress and recovery on grape appears to be associated with multiple processes and mechanisms including stress-related genes, transcription factors, and metabolism. Heat stress and recovery elicited common up- or downregulated genes as well as unique sets of responsive genes. Moreover, some genes were regulated in opposite directions by heat stress and recovery. The results indicated HSPs, especially small HSPs, antioxidant enzymes (i.e., ascorbate peroxidase), and galactinol synthase may be important to thermotolerance of grape. HSF30 may be a key regulator for heat stress and recovery, while HSF7 and HSF1 may only be specific to recovery. The identification of heat stress or recovery responsive genes in this study provides novel insights into the molecular basis for heat tolerance in grape leaves.

Induction of potato steroidal glycoalkaloid biosynthetic pathway by overexpression of cDNA encoding primary metabolism HMG-CoA reductase and squalene synthase

Potato steroidal glycoalkaloids (SGAs) are toxic secondary metabolites whose total content in tubers must be regulated. SGAs are biosynthesized by the sterol branch of the mevalonic acid/isoprenoid pathway. In a previous study, we showed a correlation between SGA levels and the abundance of transcript coding for HMG-CoA reductase 1 (HMG1) and squalene synthase 1 (SQS1) in potato tissues and potato genotypes varying in SGA content. Here, Solanum tuberosum cv. Desirée (low SGA producer) was transformed with a gene construct containing the coding region of either HMG1 or SQS1 of Solanum chacoense Bitt. clone 8380-1, a high SGA producer. SGA levels in transgenic HMG-plants were either greater than (in eight of 14 plants) or no different from untransformed controls, whereas only four of 12 SQS-transgenics had greater SGA levels than control, as determined by HPLC. Quantitative real-time PCR was used to estimate relative steady-state transcript levels of isoprenoid-, steroid-, and SGA-related genes in leaves of the transgenic plants compared to nontransgenic controls. HMG-transgenic plants exhibited increased transcript accumulation of SQS1, sterol C24-methyltransferase type1 (SMT1), and solanidine glycosyltransferase 2 (SGT2), whereas SQS-transgenic plants, had consistently lower transcript levels of HMG1 and variable SMT1 and SGT2 transcript abundance among different transgenics. HMG-transgenic plants exhibited changes in transcript accumulation for some sterol biosynthetic genes as well. Taken together, the data suggest coordinated regulation of isoprenoid metabolism and SGA secondary metabolism.

Wounding coordinately induces cell wall protein, cell cycle and pectin methyl esterase genes involved in tuber closing layer and wound periderm development

Little is known about the coordinate induction of genes that may be involved in agriculturally important wound-healing events. In this study, wound-healing events were determined together with wound-induced expression profiles of selected cell cycle, cell wall protein, and pectin methyl esterase genes using two diverse potato genotypes and two harvests (NDTX4271-5R and Russet Burbank tubers; 2008 and 2009 harvests). By 5 d after wounding, the closing layer and a nascent phellogen had formed. Phellogen cell divisions generated phellem layers until cessation of cell division at 28 d after wounding for both genotypes and harvests. Cell cycle genes encoding epidermal growth factor binding protein (StEBP), cyclin-dependent kinase B (StCDKB) and cyclin-dependent kinase regulatory subunit (StCKS1At) were induced by 1 d after wounding; these expressions coordinated with related phellogen formation and the induction and cessation of phellem cell formation. Genes encoding the structural cell wall proteins extensin (StExt1) and extensin-like (StExtlk) were dramatically up-regulated by 1-5 d after wounding, suggesting involvement with closing layer and later phellem cell layer formation. Wounding up-regulated pectin methyl esterase genes (StPME and StPrePME); StPME expression increased during closing layer and phellem cell formation, whereas maximum expression of StPrePME occurred at 5-14 d after wounding, implicating involvement in later modifications for closing layer and phellem cell formation. The coordinate induction and expression profile of StTLRP, a gene encoding a cell wall strengthening "tyrosine-and lysine-rich protein," suggested a role in the formation of the closing layer followed by phellem cell generation and maturation. Collectively, the genes monitored were wound-inducible and their expression profiles markedly coordinated with closing layer formation and the index for phellogen layer meristematic activity during wound periderm development; results were more influenced by harvest than genotype. Importantly, StTLRP was the only gene examined that may be involved in phellogen cell wall thickening after cessation of phellogen cell division.

Host-dependent suppression of RNA silencing mediated by the viral suppressor p19 in potato

p19 protein encoded by tomato bushy stunt virus (TBSV) is known as a suppressor of RNA silencing via inhibition of small RNA-guided cleavage in plants. In this study, we generated TBSVp19-expressing patatin-RNAi transgenic potatoes to identify the inhibitory mechanisms of RNA silencing mediated by TBSVp19. In TBSVp19-expressing patatin-RNAi lines, reduction of patatin-derived siRNA accumulation and complementation of patatin transcripts were detected in comparison with the non-TBSVp19-expressing patatin-RNAi line, suggesting that TBSVp19 suppresses the siRNA-mediated silencing pathway. Interestingly, no apparent effect on the accumulation of miRNA168 and other miRNAs was detected in TBSVp19-expressing lines; previous studies reported that p19 induced the accumulation of both miRNA168 and its target Argonaute 1 (AGO1) mRNA, but suppressed AGO1 translation via up-regulation of miRNA168 in Arabidopsis. In addition, the expression of Argonaute 1 (AGO1-1 and AGO1-2) and Dicer-like 1 (DCL1) was not significantly altered in p19-expressing lines. Interestingly, no translational inhibition of AGO1 mediated by p19 was detected. These results suggest that p19 suppresses siRNA-mediated silencing in potato, but may not affect miRNA-mediated silencing, possibly due to the host-dependent manner of p19 activity.

The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44

Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.

A potato skin SSH library yields new candidate genes for suberin biosynthesis and periderm formation

Potato (Solanum tuberosum) tubers are underground storage organs covered by the skin or periderm, a suberized layer that protects inner flesh from dehydration and pathogens. Understanding the molecular processes associated with periderm formation is of great importance for a better knowledge of this protective tissue and for improving the storage life of tubers. Here, to isolate new candidate genes for potato periderm, a suppression subtractive hybridization library from potato skin was performed. This library yielded a comprehensive list of 108 candidate genes that were manually sorted in functional categories according to the main cellular and metabolic processes in periderm. As expected, the list contains Suberin and wax genes, including some genes with a demonstrated role in the biosynthesis of these cell wall aliphatic compounds. Moreover, Regulation and Stress and defence genes are highly abundant in the library in general agreement with previous potato skin proteomic studies. The putative function of the genes in periderm is discussed.

Plant molecular stress responses face climate change

Environmental stress factors such as drought, elevated temperature, salinity and rising CO₂ affect plant growth and pose a growing threat to sustainable agriculture. This has become a hot issue due to concerns about the effects of climate change on plant resources, biodiversity and global food security. Plant adaptation to stress involves key changes in the '-omic' architecture. Here, we present an overview of the physiological and molecular programs in stress adaptation focusing on how genes, proteins and metabolites change after individual and multiple environmental stresses. We address the role which '-omics' research, coupled to systems biology approaches, can play in future research on plants seemingly unable to adapt as well as those which can tolerate climatic change.

Tissue-specific transcriptome profiling of the citrus fruit epidermis and subepidermis using laser capture microdissection

Most studies of the biochemical and regulatory pathways that are associated with, and control, fruit expansion and ripening are based on homogenized bulk tissues, and do not take into consideration the multiplicity of different cell types from which the analytes, be they transcripts, proteins or metabolites, are extracted. Consequently, potentially valuable spatial information is lost and the lower abundance cellular components that are expressed only in certain cell types can be diluted below the level of detection. In this study, laser microdissection (LMD) was used to isolate epidermal and subepidermal cells from green, expanding Citrus clementina fruit and their transcriptomes were compared using a 20k citrus cDNA microarray and quantitative real-time PCR. The results show striking differences in gene expression profiles between the two cell types, revealing specific metabolic pathways that can be related to their respective organelle composition and cell wall specialization. Microscopy provided additional evidence of tissue specialization that could be associated with the transcript profiles with distinct differences in organelle and metabolite accumulation. Subepidermis predominant genes are primarily involved in photosynthesis- and energy-related processes, as well as cell wall biosynthesis and restructuring. By contrast, the most epidermis predominant genes are related to the biosynthesis of the cuticle, flavonoids, and defence responses. Furthermore, the epidermis transcript profile showed a high proportion of genes with no known function, supporting the original hypothesis that analysis at the tissue/cell specific levels can promote gene discovery and lead to a better understanding of the specialized contribution of each tissue to fruit physiology.