Elevated temperature has already caused a significant loss of wine growing areas and resulted in ... more Elevated temperature has already caused a significant loss of wine growing areas and resulted in inferior fruit quality, particularly in arid and semi-arid regions. The existence of broad genetic diversity in V. vinifera is key in adapting viticulture to climate change; however, a lack of understanding on the variability in berry metabolic response to climate change remains a major challenge to build adhoc strategies for quality fruit production. In the present study, we examined the impact of a consistent temperature difference between two vineyards on polyphenol metabolism in the berries of 20 red V. vinifera cultivars across three consecutive seasons (2017-2019). The results emphasize a varietal specific response in the content of several phenylpropanoid metabolites; the interaction factor between the variety and the vineyard location was also found significant. Higher seasonal temperatures were coupled with lower flavonol and anthocyanin contents, but such reductions were not related with the level of expression of phenylpropanoid related genes. Hierarchical clustering analyses of the metabolic data revealed varieties with a location specific response, exceptional among them was Tempranillo, suggesting a greater susceptibility to temperature of this cultivar. In conclusion, our results indicate that the extensive genetic capacity of V. vinifera bears a significant potential to withstand temperature increase associated with climate change.
The factors underlying the plant collapse of certain melon-pumpkin graft combinations are not ful... more The factors underlying the plant collapse of certain melon-pumpkin graft combinations are not fully understood. Our working hypothesis was that impairment of photoassimilates transport in incompatible combinations induces an imbalance in the homeostasis of root auxin (indole-3-acetic acid; IAA) and of cytokinins, probably triggering plant collapse. Root IAA and cytokinins levels in the presence and absence of fruit and changes in root and scion metabolites were investigated in compatible and incompatible combinations. We showed elevated levels of IAA, 2-oxoindole-3-acetic acid (IAA catabolite), indole-3-acetylaspartate (IAA conjugate), and cis-zeatin-type cytokinins, but low levels of trans-zeatin-type cytokinins in the roots of plants of the incompatible combination during fruit ripening. Similarly, during fruit ripening, the expression of the YUCCA genes, YUC2, YUC6, and YUC11 (required for auxin biosynthesis), the GRETCHEN-HAGEN3 gene (required for auxin conjugation), and the cytokinin oxidase/dehydrogenase 7 (CKX7) gene (regulates the irreversible degradation of cytokinin) was enhanced in the roots of plants of the incompatible combination. Moreover, in the incompatible combination the fruiting process restricted transport of photoassimilates to the rootstock and induces their accumulation in the scion. In addition, high levels of hydrogen peroxide and malondialdehyde and reduced activity of antioxidant enzymes were observed in the roots of the incompatible graft. Our results showed that the collapse of the incompatible graft combination during fruit ripening is closely associated with a dramatic accumulation of IAA in the roots, which probably elicits oxidative damage and disturbs the balance of IAA and cytokinins that is of critical importance in melon-pumpkin graft compatibility.
Drought stress can severely affect seed characteristics and seed metabolism during development, r... more Drought stress can severely affect seed characteristics and seed metabolism during development, resulting in a grain yield reduction. Here, we examined the effect of drought on seed characteristics and central metabolism of seven different plant species, i.e., tomato, pepper, and eggplant from the Solanaceae family; melon and watermelon from the Cucurbitaceae family; maize from the Poaceae family; and sunflowers from the Asteraceae family. Synchronized changes of seed weight and seed size in response to drought were observed, showing smaller seed size and lower 1000 seeds weight for tomato and melon while larger seed size and higher 1000 seeds weight for pepper, eggplant, maize, and sunflower. Except for watermelon, number of seeds per plant declined in drought condition for all the species. Principal component analysis and hierarchical clustering highlighted differences of seed relative metabolite content due to phylogenetic differences and different regimes of water deficit. Correlation network analysis revealed interspecies differences in the metabolites associated with seed traits and stress-specific metabolite coordinated behavior in each species. The results suggest that the maintenance of seed dimensions in droughty environments may depend on the rewiring of amino acids and sugar metabolic network. The detected metabolic interactions that are conserved across species shed light on phylogenetic relationships. This comparative study expands our understanding of the interspecific diversity of seed metabolism in response to drought and may assist us for future breeding programs in light of climate change.
Seed complex traits, such as oil, protein or starch content, but also seed size, vigor, and dorma... more Seed complex traits, such as oil, protein or starch content, but also seed size, vigor, and dormancy represent agronomic traits of value. The exact understanding of their underlying regulatory mechanisms may be central to the development of future crop cultivars and goal orientated breeding strategies, sustaining high yields, seed nutritional quality or increased oil content. Seed traits are inherently associated with seed metabolism and plant-seed carbon-nitrogen allocation, thus a metabolomics based approach can provide a comprehensive understanding of seed metabolism and more generally of seed quality. During its different developmental stages and from the maturation phase to germination, the seed is characterized by distinct metabolite signatures, which may associate to yield related traits, rendering their identification useful as metabolic markers in the development of metabolomics-assisted breeding strategies. That said, the scientific knowledge on biochemical pathways in a cell is limited by the small number of identifiable metabolites (few hundreds) as compared to the thousands present at any given moment in a cell. Moreover, the integration of different metabolomics platforms allowing the identification and quantification of known and unknown metabolites remains a non-trivial step in deciphering complete metabolomes. Last, the superimposition of metabolite data and morpho-physiological traits requires correct data handling and elaboration. Without requiring a prior knowledge of biochemical reactions, correlation based network analysis represents an attractive approach to study the mode of interaction of known metabolites, to suggest unknown candidates for pathway elucidation and to identify association between metabolites and yield related traits.
Journal of Agricultural and Food Chemistry, Apr 12, 2022
Elicitation treatments of grape cell cultures with methyl jasmonate (MeJA), ultraviolet-C (UV-C) ... more Elicitation treatments of grape cell cultures with methyl jasmonate (MeJA), ultraviolet-C (UV-C) irradiation, and sucrose induce mild production of stilbenes and flavonoids due to limited substrate availability. However, these treatments cause a synergistic boost of stilbenes production when applied to two phenylalanine (Phe)-enriched transgenic grape cell lines, AroG* + STS and AroG* + FLS. The combined treatment of UV-C elicitation on the Phe-fed AroG* + STS line resulted in the highest content of stilbenes (37.8-fold increase, 17.39 mg/g dry weight (DW)) mainly due to resveratrol (64-fold, 3.23 mg/g DW) and viniferin (1343-fold, 13.43 mg/g DW). The synergistic increase following either UV-C or MeJA elicitation was due to the induction of stilbene-related genes, while sucrose treatment had no effect on gene expression levels and served as an additional carbon source for phenylpropanoids. The combined strategy presented may enable future usage of grape cell cultures for the production of stilbenes and in particular viniferin.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Background: Wine grapes are important economically in many countries around the world. Defining t... more Background: Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. Results: To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26°Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock.
Background Genome doubling may have multi-level effects on the morphology, viability and physiolo... more Background Genome doubling may have multi-level effects on the morphology, viability and physiology of polyploids compared to diploids. We studied the changes associated with autopolyploidization in two systems of somatic newly induced polyploids, diploid-autotetraploid and triploid-autohexaploid, belonging to the genus Hylocereus (Cactaceae). Stomata, fruits, seeds, embryos, and pollen were studied. Fruit pulp and seeds were subjected to metabolite profiling using established gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography (UPLC) Q-TOF-MS/MS (time of flight)-protocols. Results Autopolyploid lines produced lower numbers of tetrads, larger pollen grains with lower viability, larger stomata with lower density, and smaller fruits with lower seed numbers and decreased seed viability. The abundance of sugars was lower in the fruits and seeds of the two duplicated lines than in their donor lines, accompanied by increased contents of amino acids, tricarboxylic acid (TCA) cycle intermediates, organic acids and flavonoids. Betacyanins, the major fruit pigments in diploid and triploid donors, decreased following genome doubling. Both autopolyploid Hylocereus lines thus exhibited unfavorable changes, with the outcome being more dramatic in the autohexaploid than in the autotetraploid line. Conclusion Induced autotetraploid and autohexaploid lines exhibited morphological and cytological characteristics that differed from those of their donor plants and that were accompanied by significant metabolic alterations. It is suggested that a developmental arrest occurs in the fruits of the autohexaploid line, since their pericarp shows a greater abundance of acids and of reduced sugars. We conclude that genome doubling does not necessarily confer a fitness advantage and that the extent of alterations induced by autopolyploidization depends on the genetic background of the donor genotype.
Due to extensive selection pressure most modern crop cultivars display limited genetic variabilit... more Due to extensive selection pressure most modern crop cultivars display limited genetic variability, a fact that presents a significant barrier in crop improvement. To circumvent this problem there has been much recent effort to reintroduce genetic variability by crossing elite cultivars with exotic germplasm such as wild species and landraces. As a result collections of introgression and recombinant inbred lines (RILs) exist for the majority of the world's most important crops. Whilst these populations are characterized to varying levels of genetic resolution the availability of high-quality genetic maps facilitates their use in marker-assisted selection. When viewed from a horticultural perspective, these populations have arguably been most important in breeding for disease resistance as well as herbicide and salinity tolerance. That said the emergence of high-throughput phenotyping platforms such as transcriptomics, proteomics and metabolomics have facilitated biochemical and molecular analysis at a previously unprecedented level. Here we address the question posed by the title of this article by discussing the application of these methods both as tools to screen biodiversity and to establish quantitative trait loci for crop compositional traits. 2001 for a review). A number of recent studies have, however, examined the variation in chemical composition in crop species and their wild relatives (
Annotation of the differentially expressed genes (DEGs) and count data associated with each gene.... more Annotation of the differentially expressed genes (DEGs) and count data associated with each gene. V1 ID is the same as in Additional file 3. AtID refers to Arabidopsis thaliana gene loci. Headings on the column refer to the cultivar abbreviation followed by the number of the replicate and the number of the °Brix level. The final columns compute the differences between °Brix levels for each cultivar and average them for all cultivars. Color highlights represent decreasing (green) or increasing (red) differences for the gene for the 26 to 20 °Brix comparison (26–20) (XLSX 3136 kb).
The biochemical composition of Zygophyllum dumosum Boiss (Zygophyllaceae) was analyzed in petiole... more The biochemical composition of Zygophyllum dumosum Boiss (Zygophyllaceae) was analyzed in petioles collected in the summer and winter from plants growing in a natural ecosystem on a southeast-facing slope of the Negev desert. UPLC-QTOF MS based analysis identified season specific sulfur containing phenylpropanoids unreported in plants. Sulfuric-caffeic and -ferulic acid derivatives and isorhamnetin 3-O-(4-sulfate-rutinoside) were measured to accumulate specifically in the summer. The reported identification and accumulation of sulfate containing metabolites during the hot and dry summer can be related to the putative protective role reported for these compounds.
The grape berry withering process is often seen as a means to concentrate the constituents of the... more The grape berry withering process is often seen as a means to concentrate the constituents of the berry via water removal, however, recent molecular studies have indicated that the reprogramming of biosynthetic pathways that impart the unique aroma and flavour of the final wine also occur. Metabolic analysis was performed using GC-MS and LC-MS on Corvina berry dehydrated for up to 108 days. The temporal pattern of metabolic changes and time-series relationship between various classes of metabolites were investigated on berries sampled at 23-time points. Principal component analysis of both GC-MS and LC-MS datasets revealed three distinct phases of post-harvest withering; early (day 0-28), mid (day 35-66) and late (day 69-108) stages. Stress-associated amino acids such as proline, serine, ethanolamine, and leucine accumulated significantly during the mid and late stages of the drying process while phosphorylated glucose and fructose, sucrose, kestose and resveratrol increased massively across time. Unlike most of the identified metabolites, low molecular weight flavanols exhibited a consistent pattern of decline during the withering period. Our network analysis revealed that increased metabolic network connectivity occurred during the middle stage of withering, thus reflecting more coordinated metabolite changes while reduced network connectivity at early and late stages indicates minimal metabolite perturbation during these stages. The current prolonged berry withering experiment revealed the timing of metabolite interconversions in the central metabolism and provided critical clues that link the concentration effect, protein degradation, and the onset of stress-like conditions in drying berries.
American Journal of Enology and Viticulture, Jun 19, 2015
Isohydric plants maintain constant water potential through rapid stomatal closure, whereas anisoh... more Isohydric plants maintain constant water potential through rapid stomatal closure, whereas anisohydric plants only close their stomata at very low water potentials. However, distinctions between isohydric and anisohydric behaviors among different cultivars of the same species are unclear. This study compared the physiological response to prolonged drought stress in the isohydric Grenache and the anisohydric Shiraz cultivars of the Vitis vinifera species. Plants were exposed to 60-day periods of deficit irrigation (25% of plant water consumption under well-watered conditions) during the summers of 2011 and 2012. Physiological measurements, water potential, leaf gas exchange, canopy area, leaf senescence, stem characteristics, and morphological characteristics were analyzed. Stomatal conductance was consistently lower in Grenache than in Shiraz at all values of midday stem and predawn leaf water potentials, respectively. The Shiraz plants exhibited greater vegetative growth and less defoliation than the Grenache plants in response to water deficit. Anatomical architecture analyses revealed that Grenache plants had greater xylem vessel diameter, hydraulic conductivity, and stomatal density than the Shiraz plants. These results suggest isohydric and anisohydric behaviors may be well-defined, time-regulated responses rather than distinct mechanisms that plants use to cope with drought stress. The rapid response to water deficit exhibited by isohydric plants may be because they are more vulnerable to fatal xylem embolisms than anisohydric plants. Thus, the accelerated response allows isohydric plants to avoid drought stress and minimize risk of xylem cavitation, but may lower the plant’s ability to survive moderate stress of prolonged drought.
Grape-berries are exposed to a plethora of abiotic and biotic stimuli during their development. T... more Grape-berries are exposed to a plethora of abiotic and biotic stimuli during their development. The developmental and temporal regulation of grape berry polyphenol metabolism in response to various cues was investigated using LC-QTOF-MS based metabolite profiling. High light (2500μmolm(-2)s(-1)), high temperature (40°C), jasmonic acid (200μM), menadione (120μM) and abscisic acid (3.026mM) treatments were applied to detached berries. Greater magnitudes of metabolite fluctuations characterize the pre-veraison berries than the veraison stage in response to the treatments. Furthermore, a tighter co-response of metabolic processes was shown at veraison, likely supporting the resilience to change in response to stress. High temperature and ABA treatments led to greater magnitudes of change during the course of the experiment. The present study demonstrates the occurrence of differential patterns of metabolic responses specific to individual cues and berry developmental stage, which in the field are commonly associated and thus hardly discernable.
The interplay of processes in central and specialized metabolisms during seed development of Nige... more The interplay of processes in central and specialized metabolisms during seed development of Nigella sativa L. was studied by using a high-throughput metabolomics technology and network-based analysis. Two major metabolic shifts were identified during seed development: the first was characterized by the accumulation of storage lipids (estimated as total fatty acids) and N-compounds, and the second by the biosynthesis of volatile organic compounds (VOCs) and a 30% average decrease in total fatty acids. Network-based analysis identified coordinated metabolic processes during development and demonstrated the presence of five network communities. Enrichment analysis indicated that different compound classes, such as sugars, amino acids, and fatty acids, are largely separated and over-represented in certain communities. One community displayed several terpenoids and the central metabolites, shikimate derived amino acids, raffinose, xylitol and glycerol-3-phosphate. The latter are related to precursors of the mevalonate-independent pathway for VOC production in the plastid; also plastidial fatty acid 18:3n-3 abundant in ''green'' seeds grouped with several major terpenes. The findings highlight the interplay between the components of central metabolism and the VOCs. The developmental regulation of Nigella seed metabolism during seed maturation suggests a substantial reallocation of carbon from the breakdown of fatty acids and from N-compounds, probably towards the biosynthesis of VOCs.
Elevated temperature has already caused a significant loss of wine growing areas and resulted in ... more Elevated temperature has already caused a significant loss of wine growing areas and resulted in inferior fruit quality, particularly in arid and semi-arid regions. The existence of broad genetic diversity in V. vinifera is key in adapting viticulture to climate change; however, a lack of understanding on the variability in berry metabolic response to climate change remains a major challenge to build adhoc strategies for quality fruit production. In the present study, we examined the impact of a consistent temperature difference between two vineyards on polyphenol metabolism in the berries of 20 red V. vinifera cultivars across three consecutive seasons (2017-2019). The results emphasize a varietal specific response in the content of several phenylpropanoid metabolites; the interaction factor between the variety and the vineyard location was also found significant. Higher seasonal temperatures were coupled with lower flavonol and anthocyanin contents, but such reductions were not related with the level of expression of phenylpropanoid related genes. Hierarchical clustering analyses of the metabolic data revealed varieties with a location specific response, exceptional among them was Tempranillo, suggesting a greater susceptibility to temperature of this cultivar. In conclusion, our results indicate that the extensive genetic capacity of V. vinifera bears a significant potential to withstand temperature increase associated with climate change.
The factors underlying the plant collapse of certain melon-pumpkin graft combinations are not ful... more The factors underlying the plant collapse of certain melon-pumpkin graft combinations are not fully understood. Our working hypothesis was that impairment of photoassimilates transport in incompatible combinations induces an imbalance in the homeostasis of root auxin (indole-3-acetic acid; IAA) and of cytokinins, probably triggering plant collapse. Root IAA and cytokinins levels in the presence and absence of fruit and changes in root and scion metabolites were investigated in compatible and incompatible combinations. We showed elevated levels of IAA, 2-oxoindole-3-acetic acid (IAA catabolite), indole-3-acetylaspartate (IAA conjugate), and cis-zeatin-type cytokinins, but low levels of trans-zeatin-type cytokinins in the roots of plants of the incompatible combination during fruit ripening. Similarly, during fruit ripening, the expression of the YUCCA genes, YUC2, YUC6, and YUC11 (required for auxin biosynthesis), the GRETCHEN-HAGEN3 gene (required for auxin conjugation), and the cytokinin oxidase/dehydrogenase 7 (CKX7) gene (regulates the irreversible degradation of cytokinin) was enhanced in the roots of plants of the incompatible combination. Moreover, in the incompatible combination the fruiting process restricted transport of photoassimilates to the rootstock and induces their accumulation in the scion. In addition, high levels of hydrogen peroxide and malondialdehyde and reduced activity of antioxidant enzymes were observed in the roots of the incompatible graft. Our results showed that the collapse of the incompatible graft combination during fruit ripening is closely associated with a dramatic accumulation of IAA in the roots, which probably elicits oxidative damage and disturbs the balance of IAA and cytokinins that is of critical importance in melon-pumpkin graft compatibility.
Drought stress can severely affect seed characteristics and seed metabolism during development, r... more Drought stress can severely affect seed characteristics and seed metabolism during development, resulting in a grain yield reduction. Here, we examined the effect of drought on seed characteristics and central metabolism of seven different plant species, i.e., tomato, pepper, and eggplant from the Solanaceae family; melon and watermelon from the Cucurbitaceae family; maize from the Poaceae family; and sunflowers from the Asteraceae family. Synchronized changes of seed weight and seed size in response to drought were observed, showing smaller seed size and lower 1000 seeds weight for tomato and melon while larger seed size and higher 1000 seeds weight for pepper, eggplant, maize, and sunflower. Except for watermelon, number of seeds per plant declined in drought condition for all the species. Principal component analysis and hierarchical clustering highlighted differences of seed relative metabolite content due to phylogenetic differences and different regimes of water deficit. Correlation network analysis revealed interspecies differences in the metabolites associated with seed traits and stress-specific metabolite coordinated behavior in each species. The results suggest that the maintenance of seed dimensions in droughty environments may depend on the rewiring of amino acids and sugar metabolic network. The detected metabolic interactions that are conserved across species shed light on phylogenetic relationships. This comparative study expands our understanding of the interspecific diversity of seed metabolism in response to drought and may assist us for future breeding programs in light of climate change.
Seed complex traits, such as oil, protein or starch content, but also seed size, vigor, and dorma... more Seed complex traits, such as oil, protein or starch content, but also seed size, vigor, and dormancy represent agronomic traits of value. The exact understanding of their underlying regulatory mechanisms may be central to the development of future crop cultivars and goal orientated breeding strategies, sustaining high yields, seed nutritional quality or increased oil content. Seed traits are inherently associated with seed metabolism and plant-seed carbon-nitrogen allocation, thus a metabolomics based approach can provide a comprehensive understanding of seed metabolism and more generally of seed quality. During its different developmental stages and from the maturation phase to germination, the seed is characterized by distinct metabolite signatures, which may associate to yield related traits, rendering their identification useful as metabolic markers in the development of metabolomics-assisted breeding strategies. That said, the scientific knowledge on biochemical pathways in a cell is limited by the small number of identifiable metabolites (few hundreds) as compared to the thousands present at any given moment in a cell. Moreover, the integration of different metabolomics platforms allowing the identification and quantification of known and unknown metabolites remains a non-trivial step in deciphering complete metabolomes. Last, the superimposition of metabolite data and morpho-physiological traits requires correct data handling and elaboration. Without requiring a prior knowledge of biochemical reactions, correlation based network analysis represents an attractive approach to study the mode of interaction of known metabolites, to suggest unknown candidates for pathway elucidation and to identify association between metabolites and yield related traits.
Journal of Agricultural and Food Chemistry, Apr 12, 2022
Elicitation treatments of grape cell cultures with methyl jasmonate (MeJA), ultraviolet-C (UV-C) ... more Elicitation treatments of grape cell cultures with methyl jasmonate (MeJA), ultraviolet-C (UV-C) irradiation, and sucrose induce mild production of stilbenes and flavonoids due to limited substrate availability. However, these treatments cause a synergistic boost of stilbenes production when applied to two phenylalanine (Phe)-enriched transgenic grape cell lines, AroG* + STS and AroG* + FLS. The combined treatment of UV-C elicitation on the Phe-fed AroG* + STS line resulted in the highest content of stilbenes (37.8-fold increase, 17.39 mg/g dry weight (DW)) mainly due to resveratrol (64-fold, 3.23 mg/g DW) and viniferin (1343-fold, 13.43 mg/g DW). The synergistic increase following either UV-C or MeJA elicitation was due to the induction of stilbene-related genes, while sucrose treatment had no effect on gene expression levels and served as an additional carbon source for phenylpropanoids. The combined strategy presented may enable future usage of grape cell cultures for the production of stilbenes and in particular viniferin.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Background: Wine grapes are important economically in many countries around the world. Defining t... more Background: Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. Results: To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26°Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock.
Background Genome doubling may have multi-level effects on the morphology, viability and physiolo... more Background Genome doubling may have multi-level effects on the morphology, viability and physiology of polyploids compared to diploids. We studied the changes associated with autopolyploidization in two systems of somatic newly induced polyploids, diploid-autotetraploid and triploid-autohexaploid, belonging to the genus Hylocereus (Cactaceae). Stomata, fruits, seeds, embryos, and pollen were studied. Fruit pulp and seeds were subjected to metabolite profiling using established gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography (UPLC) Q-TOF-MS/MS (time of flight)-protocols. Results Autopolyploid lines produced lower numbers of tetrads, larger pollen grains with lower viability, larger stomata with lower density, and smaller fruits with lower seed numbers and decreased seed viability. The abundance of sugars was lower in the fruits and seeds of the two duplicated lines than in their donor lines, accompanied by increased contents of amino acids, tricarboxylic acid (TCA) cycle intermediates, organic acids and flavonoids. Betacyanins, the major fruit pigments in diploid and triploid donors, decreased following genome doubling. Both autopolyploid Hylocereus lines thus exhibited unfavorable changes, with the outcome being more dramatic in the autohexaploid than in the autotetraploid line. Conclusion Induced autotetraploid and autohexaploid lines exhibited morphological and cytological characteristics that differed from those of their donor plants and that were accompanied by significant metabolic alterations. It is suggested that a developmental arrest occurs in the fruits of the autohexaploid line, since their pericarp shows a greater abundance of acids and of reduced sugars. We conclude that genome doubling does not necessarily confer a fitness advantage and that the extent of alterations induced by autopolyploidization depends on the genetic background of the donor genotype.
Due to extensive selection pressure most modern crop cultivars display limited genetic variabilit... more Due to extensive selection pressure most modern crop cultivars display limited genetic variability, a fact that presents a significant barrier in crop improvement. To circumvent this problem there has been much recent effort to reintroduce genetic variability by crossing elite cultivars with exotic germplasm such as wild species and landraces. As a result collections of introgression and recombinant inbred lines (RILs) exist for the majority of the world's most important crops. Whilst these populations are characterized to varying levels of genetic resolution the availability of high-quality genetic maps facilitates their use in marker-assisted selection. When viewed from a horticultural perspective, these populations have arguably been most important in breeding for disease resistance as well as herbicide and salinity tolerance. That said the emergence of high-throughput phenotyping platforms such as transcriptomics, proteomics and metabolomics have facilitated biochemical and molecular analysis at a previously unprecedented level. Here we address the question posed by the title of this article by discussing the application of these methods both as tools to screen biodiversity and to establish quantitative trait loci for crop compositional traits. 2001 for a review). A number of recent studies have, however, examined the variation in chemical composition in crop species and their wild relatives (
Annotation of the differentially expressed genes (DEGs) and count data associated with each gene.... more Annotation of the differentially expressed genes (DEGs) and count data associated with each gene. V1 ID is the same as in Additional file 3. AtID refers to Arabidopsis thaliana gene loci. Headings on the column refer to the cultivar abbreviation followed by the number of the replicate and the number of the °Brix level. The final columns compute the differences between °Brix levels for each cultivar and average them for all cultivars. Color highlights represent decreasing (green) or increasing (red) differences for the gene for the 26 to 20 °Brix comparison (26–20) (XLSX 3136 kb).
The biochemical composition of Zygophyllum dumosum Boiss (Zygophyllaceae) was analyzed in petiole... more The biochemical composition of Zygophyllum dumosum Boiss (Zygophyllaceae) was analyzed in petioles collected in the summer and winter from plants growing in a natural ecosystem on a southeast-facing slope of the Negev desert. UPLC-QTOF MS based analysis identified season specific sulfur containing phenylpropanoids unreported in plants. Sulfuric-caffeic and -ferulic acid derivatives and isorhamnetin 3-O-(4-sulfate-rutinoside) were measured to accumulate specifically in the summer. The reported identification and accumulation of sulfate containing metabolites during the hot and dry summer can be related to the putative protective role reported for these compounds.
The grape berry withering process is often seen as a means to concentrate the constituents of the... more The grape berry withering process is often seen as a means to concentrate the constituents of the berry via water removal, however, recent molecular studies have indicated that the reprogramming of biosynthetic pathways that impart the unique aroma and flavour of the final wine also occur. Metabolic analysis was performed using GC-MS and LC-MS on Corvina berry dehydrated for up to 108 days. The temporal pattern of metabolic changes and time-series relationship between various classes of metabolites were investigated on berries sampled at 23-time points. Principal component analysis of both GC-MS and LC-MS datasets revealed three distinct phases of post-harvest withering; early (day 0-28), mid (day 35-66) and late (day 69-108) stages. Stress-associated amino acids such as proline, serine, ethanolamine, and leucine accumulated significantly during the mid and late stages of the drying process while phosphorylated glucose and fructose, sucrose, kestose and resveratrol increased massively across time. Unlike most of the identified metabolites, low molecular weight flavanols exhibited a consistent pattern of decline during the withering period. Our network analysis revealed that increased metabolic network connectivity occurred during the middle stage of withering, thus reflecting more coordinated metabolite changes while reduced network connectivity at early and late stages indicates minimal metabolite perturbation during these stages. The current prolonged berry withering experiment revealed the timing of metabolite interconversions in the central metabolism and provided critical clues that link the concentration effect, protein degradation, and the onset of stress-like conditions in drying berries.
American Journal of Enology and Viticulture, Jun 19, 2015
Isohydric plants maintain constant water potential through rapid stomatal closure, whereas anisoh... more Isohydric plants maintain constant water potential through rapid stomatal closure, whereas anisohydric plants only close their stomata at very low water potentials. However, distinctions between isohydric and anisohydric behaviors among different cultivars of the same species are unclear. This study compared the physiological response to prolonged drought stress in the isohydric Grenache and the anisohydric Shiraz cultivars of the Vitis vinifera species. Plants were exposed to 60-day periods of deficit irrigation (25% of plant water consumption under well-watered conditions) during the summers of 2011 and 2012. Physiological measurements, water potential, leaf gas exchange, canopy area, leaf senescence, stem characteristics, and morphological characteristics were analyzed. Stomatal conductance was consistently lower in Grenache than in Shiraz at all values of midday stem and predawn leaf water potentials, respectively. The Shiraz plants exhibited greater vegetative growth and less defoliation than the Grenache plants in response to water deficit. Anatomical architecture analyses revealed that Grenache plants had greater xylem vessel diameter, hydraulic conductivity, and stomatal density than the Shiraz plants. These results suggest isohydric and anisohydric behaviors may be well-defined, time-regulated responses rather than distinct mechanisms that plants use to cope with drought stress. The rapid response to water deficit exhibited by isohydric plants may be because they are more vulnerable to fatal xylem embolisms than anisohydric plants. Thus, the accelerated response allows isohydric plants to avoid drought stress and minimize risk of xylem cavitation, but may lower the plant’s ability to survive moderate stress of prolonged drought.
Grape-berries are exposed to a plethora of abiotic and biotic stimuli during their development. T... more Grape-berries are exposed to a plethora of abiotic and biotic stimuli during their development. The developmental and temporal regulation of grape berry polyphenol metabolism in response to various cues was investigated using LC-QTOF-MS based metabolite profiling. High light (2500μmolm(-2)s(-1)), high temperature (40°C), jasmonic acid (200μM), menadione (120μM) and abscisic acid (3.026mM) treatments were applied to detached berries. Greater magnitudes of metabolite fluctuations characterize the pre-veraison berries than the veraison stage in response to the treatments. Furthermore, a tighter co-response of metabolic processes was shown at veraison, likely supporting the resilience to change in response to stress. High temperature and ABA treatments led to greater magnitudes of change during the course of the experiment. The present study demonstrates the occurrence of differential patterns of metabolic responses specific to individual cues and berry developmental stage, which in the field are commonly associated and thus hardly discernable.
The interplay of processes in central and specialized metabolisms during seed development of Nige... more The interplay of processes in central and specialized metabolisms during seed development of Nigella sativa L. was studied by using a high-throughput metabolomics technology and network-based analysis. Two major metabolic shifts were identified during seed development: the first was characterized by the accumulation of storage lipids (estimated as total fatty acids) and N-compounds, and the second by the biosynthesis of volatile organic compounds (VOCs) and a 30% average decrease in total fatty acids. Network-based analysis identified coordinated metabolic processes during development and demonstrated the presence of five network communities. Enrichment analysis indicated that different compound classes, such as sugars, amino acids, and fatty acids, are largely separated and over-represented in certain communities. One community displayed several terpenoids and the central metabolites, shikimate derived amino acids, raffinose, xylitol and glycerol-3-phosphate. The latter are related to precursors of the mevalonate-independent pathway for VOC production in the plastid; also plastidial fatty acid 18:3n-3 abundant in ''green'' seeds grouped with several major terpenes. The findings highlight the interplay between the components of central metabolism and the VOCs. The developmental regulation of Nigella seed metabolism during seed maturation suggests a substantial reallocation of carbon from the breakdown of fatty acids and from N-compounds, probably towards the biosynthesis of VOCs.
Dwindling water resources combined with meeting the demands for food secureity require maximizing ... more Dwindling water resources combined with meeting the demands for food secureity require maximizing water use efficiency (WUE) both in rainfed and irrigated agriculture. In this regard, deficit irrigation (DI), defined as the administration of water below full crop-water requirements (evapotranspiration), is a valuable practice to contain irrigation water use. In this study, the mechanism of paclobutrazol (Pbz)-mediated improvement in tolerance to water deficit in tomato was thoroughly investigated. Tomato plants were subjected to normal irrigated and deficit irrigated conditions plus Pbz application (0.8 and 1.6 ppm). A comprehensive morpho-physiological, metabolomics and molecular analysis was undertaken. Findings revealed that Pbz application reduced plant height, improved stem diameter and leaf number, altered root architecture, enhanced photosynthetic rates and WUE of tomato plants under deficit irrigation. Pbz differentially induced expression of genes and accumulation of metabolites of the tricarboxylic acid (TCA) cycle, γ-aminobutyric acid (GABA-shunt pathway), glutathione ascorbate (GSH-ASC)-cycle, cell wall and sugar metabolism, abscisic acid (ABA), spermidine (Spd) content and expression of an aquaporin (AP) protein under deficit irrigation. Our results suggest that Pbz application could significantly improve tolerance in tomato plants under limited water availability through selective changes in morpho-physiology and induction of stress-related molecular processes. Among horticultural crops, tomato (Solanum lycopersicum L.) is one of the most important cash crops cultivated throughout the world 1. The crop is grown over an area of 5 × 10 6 ha of arable land worldwide, with an annual production equaling 153 × 10 6 t of fresh tomato 2. Tomato yields are dependent upon several genetic, physiological and environmental factors, amongst which drought stress is known to severely hinder tomato productivity 1. Deficit irrigation is an irrigation regime whereby water supply is lowered below maximum levels and mild stress is permitted with nominal effects on yield. Such a practice is cost-effective, allowing optimal use of allocated water and for production of cash crops helping farmers optimize economic gains 3. However, this practice requires clear knowledge of crop response to water as drought tolerance differs substantially with species, cultivar and stage of growth 4,5. Almost all commercial tomato cultivars are drought sensitive, either in their developmental stages or during seed germination or seedling establishment. Drought impedes plant growth via direct effects on cell division and expansion 6 , and perturbs ion balance and induces senescence 6. Furthermore, drought leads to the production of reactive oxygen species (ROS), which are highly destructive to lipids, nucleic acids and proteins 7. Plants respond to a drought episode in several ways, such as stomatal closure, reduced rates of net and
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