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Plant Metabolism in Crops: A Systems Biology Perspective
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Plant Metabolism in Crops: A Systems Biology Perspective

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 November 2018) | Viewed by 76170

Special Issue Editor

Dr. Vicent Arbona

E-Mail Website
Guest Editor
Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
Interests: abiotic stress; Arabidopsis; biochemistry; citrus; drought; flooding; metabolomics; plant physiology; tomato
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metabolism integrates both the influence of external stimuli and the actual endogenous status of an organism. The extraordinary plasticity of plant metabolism has allowed these organisms to adapt and colonize different environments, and to rapidly induce changes to cope with adverse conditions. Metabolism can be divided into primary and secondary metabolism. Primary metabolites are usually found in high concentrations in plant tissues and also exhibit a cross-species nature, whereas secondary metabolites are present in trace amounts and are highly specific of species, genera, or families. Nevertheless, although considered and (often) analyzed separately, primary and secondary metabolism are intertwined and variations in primary metabolites are usually mirrored by secondary metabolites. For these reasons, it is important to analyze plant metabolites in a non-targeted and unbiased fashion using exhaustive and comprehensive techniques, collectively known as plant metabolomics.

Plant metabolomics has moved from being an emerging field, arising from the combination of analytical chemistry and bioinformatics, to becoming an essential aspect in almost every study in plant biology. The untargeted and unbiased analysis of small molecular weight metabolite fractions in plants provides insights into molecular mechanisms underlying abiotic stress responses, the elicitation of plant defense mechanisms, the production of signaling compounds and the effects of selection or genetic manipulation on plant biochemistry and the differential accumulation of metabolites in fruits and other edible parts of plants.

This Special Issue will focus on the untargeted and integrated study of the plant metabolism to enhance our understanding of physiology and biochemistry of non-model crops in response to abiotic or biotic challenges, developmental processes, selection or genetic manipulation. In this respect, the analysis of endogenous and/or secreted metabolites (including the volatile fraction) will be considered as valid approaches, as long as they provide relevant insight into physiological/biochemical mechanisms. Especially, manuscripts describing the metabolism of xenobiotics with relevance to plant biology or agriculture may be accepted.

Dr. Vicent Arbona
Guest Editor

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Keywords

  • biochemistry
  • crops
  • tomato
  • development
  • genetic modification
  • integration with other omics
  • metabolomics
  • signaling
  • stress

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Published Papers (13 papers)

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Research

Jump to: Review

20 pages, 3538 KiB  
Article
Physiological and Metabolic Responses of Rice to Reduced Soil Moisture: Relationship of Water Stress Tolerance and Grain Production
by Jinyoung Y. Barnaby, Jai S. Rohila, Chris G. Henry, Richard C. Sicher, Vagimalla R. Reddy and Anna M. McClung
Int. J. Mol. Sci. 2019, 20(8), 1846; https://doi.org/10.3390/ijms20081846 - 15 Apr 2019
Cited by 24 | Viewed by 5136
Abstract
Access to adequate irrigation resources is critical for sustained agricultural production, and rice, a staple cereal grain for half of the world population, is one of the biggest users of irrigation. To reduce water use, several water saving irrigation systems have been developed [...] Read more.
Access to adequate irrigation resources is critical for sustained agricultural production, and rice, a staple cereal grain for half of the world population, is one of the biggest users of irrigation. To reduce water use, several water saving irrigation systems have been developed for rice production, but a reliable system to evaluate cultivars for water stress tolerance is still lacking. Here, seven rice cultivars that have diverse yield potential under water stress were evaluated in a field study using four continuous irrigation regimes varying from saturation to wilting point. To understand the relationship between water stress and yield potential, the physiological and leaf metabolic responses were investigated at the critical transition between vegetative and reproductive growth stages. Twenty-nine metabolite markers including carbohydrates, amino acids and organic acids were found to significantly differ among the seven cultivars in response to increasing water stress levels with amino acids increasing but organic acids and carbohydrates showing mixed responses. Overall, our data suggest that, in response to increasing water stress, rice cultivars that do not show a significant yield loss accumulate carbohydrates (fructose, glucose, and myo-inositol), and this is associated with a moderate reduction in stomatal conductance (gs), particularly under milder stress conditions. In contrast, cultivars that had significant yield loss due to water stress had the greatest reduction in gs, relatively lower accumulation of carbohydrates, and relatively high increases in relative chlorophyll content (SPAD) and leaf temperature (Tm). These data demonstrate the existence of genetic variation in yield under different water stress levels which results from a suite of physiological and biochemical responses to water stress. Our study, therefore, suggests that in rice there are different physiological and metabolic strategies that result in tolerance to water stress that should be considered in developing new cultivars for deficit irrigation production systems that use less water. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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19 pages, 2880 KiB  
Article
Developmental Stage- and Genotype-Dependent Regulation of Specialized Metabolite Accumulation in Fruit Tissues of Different Citrus Varieties
by Roya Nadi, Behrouz Golein, Aurelio Gómez-Cadenas and Vicent Arbona
Int. J. Mol. Sci. 2019, 20(5), 1245; https://doi.org/10.3390/ijms20051245 - 12 Mar 2019
Cited by 13 | Viewed by 4376
Abstract
Flavor traits in citrus are the result of a blend of low molecular weight metabolites including sugars, acids, flavonoids and limonoids, these latter being mainly responsible for the characteristic bitter flavor in citrus. In this work, the genotype- and developmental stage-dependent accumulation of [...] Read more.
Flavor traits in citrus are the result of a blend of low molecular weight metabolites including sugars, acids, flavonoids and limonoids, these latter being mainly responsible for the characteristic bitter flavor in citrus. In this work, the genotype- and developmental stage-dependent accumulation of flavonoids and limonoids is addressed. To fulfill this goal, three models for citrus bitterness: bitter Duncan grapefruit, bittersweet Thomson orange and sweet Wase mandarin were selected from a total of eight different varieties. Compounds were annotated from LC/ESI-QqTOF-MS non-targeted metabolite profiles from albedo and pulp tissues. Results indicated that the specific blend of compounds providing the characteristic flavor trait is genotype-specific and hence under genetic control, but it is also regulated at the developmental level. Metabolite profiles in albedo mirrored those found in pulp, the edible part of the fruit, despite differences in the concentration and accumulation/depletion rates being found. This is particularly relevant for polymethoxylated flavones and glycosylated limonoids that showed a clear partitioning towards albedo and pulp tissues, respectively. Fruit ripening was characterized by a reduction in flavonoids and the accumulation of limonoid glycosides. However, bitter grapefruit showed higher levels of limonin A-ring lactone and naringin in contrast to sweeter orange and mandarin. Data indicated that the accumulation profile was compound class-specific and conserved among the studied varieties despite differing in the respective accumulation and/or depletion rate, leading to different specialized metabolite concentration at the full ripe stage, consistent with the flavor trait output. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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32 pages, 7263 KiB  
Article
On a Cold Night: Transcriptomics of Grapevine Flower Unveils Signal Transduction and Impacted Metabolism
by Mélodie Sawicki, Marine Rondeau, Barbara Courteaux, Fanja Rabenoelina, Gea Guerriero, Eric Gomès, Ludivine Soubigou-Taconnat, Sandrine Balzergue, Christophe Clément, Essaïd Ait Barka, Nathalie Vaillant-Gaveau and Cédric Jacquard
Int. J. Mol. Sci. 2019, 20(5), 1130; https://doi.org/10.3390/ijms20051130 - 5 Mar 2019
Cited by 8 | Viewed by 4848
Abstract
Low temperature is a critical environmental factor limiting plant productivity, especially in northern vineyards. To clarify the impact of this stress on grapevine flower, we used the Vitis array based on Roche-NimbleGen technology to investigate the gene expression of flowers submitted to a [...] Read more.
Low temperature is a critical environmental factor limiting plant productivity, especially in northern vineyards. To clarify the impact of this stress on grapevine flower, we used the Vitis array based on Roche-NimbleGen technology to investigate the gene expression of flowers submitted to a cold night. Our objectives were to identify modifications in the transcript levels after stress and during recovery. Consequently, our results confirmed some mechanisms known in grapes or other plants in response to cold stress, notably, (1) the pivotal role of calcium/calmodulin-mediated signaling; (2) the over-expression of sugar transporters and some genes involved in plant defense (especially in carbon metabolism), and (3) the down-regulation of genes encoding galactinol synthase (GOLS), pectate lyases, or polygalacturonases. We also identified some mechanisms not yet known to be involved in the response to cold stress, i.e., (1) the up-regulation of genes encoding G-type lectin S-receptor-like serine threonine-protein kinase, pathogen recognition receptor (PRR5), or heat-shock factors among others; (2) the down-regulation of Myeloblastosis (MYB)-related transcription factors and the Constans-like zinc finger family; and (3) the down-regulation of some genes encoding Pathogen-Related (PR)-proteins. Taken together, our results revealed interesting features and potentially valuable traits associated with stress responses in the grapevine flower. From a long-term perspective, our study provides useful starting points for future investigation. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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16 pages, 2097 KiB  
Article
Effects of 2,4-Dichlorophenoxyacetic Acid on Cucumber Fruit Development and Metabolism
by Chaoyang Hu, Huiyu Zhao, Jianxin Shi, Jian Li, Xiangbo Nie and Guiling Yang
Int. J. Mol. Sci. 2019, 20(5), 1126; https://doi.org/10.3390/ijms20051126 - 5 Mar 2019
Cited by 12 | Viewed by 4396
Abstract
The auxin-like compound 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used as a plant growth regulator in cucumber fruit production; however, its influence on fruit development and metabolism has not been evaluated. In this study, the phenotype of cucumber fruits in both 2,4-D treatment [...] Read more.
The auxin-like compound 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used as a plant growth regulator in cucumber fruit production; however, its influence on fruit development and metabolism has not been evaluated. In this study, the phenotype of cucumber fruits in both 2,4-D treatment and non-treatment control groups were recorded, and the metabolome of different segments of cucumber fruit at various sampling time points were profiled by a standardized non-targeted metabolomics method based on UPLC-qTOF-MS. The application of 2,4-D increased the early growth rate of the fruit length but had no significant effect on the final fruit length, and produced cucumber fruits with fresh flowers at the top. The 2,4-D treatment also affected the cucumber fruit metabolome, causing significant changes in the stylar end at 4 days after flowering (DAF). The significantly changed metabolites were mainly involved in methionine metabolism, the citric acid cycle and flavonoid metabolism pathways. At the harvest stage, 2,4–D treatment significantly decreased the levels of flavonoids and cinnamic acid derivatives while increased the levels of some of the amino acids. In summary, exogenous application of 2,4-D can greatly alter the phenotype and metabolism of cucumber fruit. These findings will assist in exploring the mechanisms of how 2,4-D treatment changes the fruit phenotype and evaluating the influence of 2,4-D treatment on the nutritional qualities of cucumber fruit. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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23 pages, 9402 KiB  
Article
Untargeted and Targeted Metabolomics and Tryptophan Decarboxylase In Vivo Characterization Provide Novel Insight on the Development of Kiwifruits (Actinidia deliciosa)
by Mauro Commisso, Stefano Negri, Martino Bianconi, Sofia Gambini, Sara Avesani, Stefania Ceoldo, Linda Avesani and Flavia Guzzo
Int. J. Mol. Sci. 2019, 20(4), 897; https://doi.org/10.3390/ijms20040897 - 19 Feb 2019
Cited by 26 | Viewed by 4690
Abstract
Kiwifruit (Actinidia deliciosa cv. Hayward) is a commercially important crop with highly nutritional green fleshy fruits. The post-harvest maturation of the fruits is well characterized, but little is known about the metabolic changes that occur during fruit development. Here we used untargeted [...] Read more.
Kiwifruit (Actinidia deliciosa cv. Hayward) is a commercially important crop with highly nutritional green fleshy fruits. The post-harvest maturation of the fruits is well characterized, but little is known about the metabolic changes that occur during fruit development. Here we used untargeted metabolomics to characterize the non-volatile metabolite profile of kiwifruits collected at different time points after anthesis, revealing profound metabolic changes before the onset of ripening including the depletion of many classes of phenolic compounds. In contrast, the phytohormone abscisic acid accumulated during development and ripening, along with two indolamines (serotonin and its precursor tryptamine), and these were monitored in greater detail by targeted metabolomics. The role of indolamines in kiwifruit development is completely unknown, so we also characterized the identity of genes encoding tryptophan decarboxylase in A. deliciosa and its close relative A. chinensis to provide insight into the corresponding biological processes. Our results indicate that abscisic acid and indolamines fulfill unrecognized functions in the development and ripening of kiwifruits. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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13 pages, 7954 KiB  
Article
Comparative Metabolic Profiling of Grape Skin Tissue along Grapevine Berry Developmental Stages Reveals Systematic Influences of Root Restriction on Skin Metabolome
by Shuyan Duan, Yusen Wu, Ruifeng Fu, Lei Wang, Yujin Chen, Wenping Xu, Caixi Zhang, Chao Ma, Jianxin Shi and Shiping Wang
Int. J. Mol. Sci. 2019, 20(3), 534; https://doi.org/10.3390/ijms20030534 - 28 Jan 2019
Cited by 18 | Viewed by 3769
Abstract
This research aimed to comparatively evaluate the influences of root restriction (RR) cultivation and traditional cultivation (RC) on grape berry skin metabolomics using a non-targeted metabolomics method. Two-hundred-and-ninety-one metabolites were annotated and the kinetics analyses showed that berry skin metabolome is stage- and [...] Read more.
This research aimed to comparatively evaluate the influences of root restriction (RR) cultivation and traditional cultivation (RC) on grape berry skin metabolomics using a non-targeted metabolomics method. Two-hundred-and-ninety-one metabolites were annotated and the kinetics analyses showed that berry skin metabolome is stage- and cultivation-dependent. Our results showed that RR influences significantly the metabolomes of berry skin tissues, particularly on secondary metabolism, and that this effect is more obvious at pre-veraison stage, which was evidenced by the early and fast metabolic shift from primary to secondary metabolism. Altogether, this study provided an insight into metabolic adaptation of berry skin to RR stress and expanded general understanding of berry development. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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21 pages, 2041 KiB  
Article
Non-Targeted Metabolomics Reveals Sorghum Rhizosphere-Associated Exudates are Influenced by the Belowground Interaction of Substrate and Sorghum Genotype
by Sarah B. Miller, Adam L. Heuberger, Corey D. Broeckling and Courtney E. Jahn
Int. J. Mol. Sci. 2019, 20(2), 431; https://doi.org/10.3390/ijms20020431 - 19 Jan 2019
Cited by 44 | Viewed by 6744
Abstract
Root exudation is an important plant process by which roots release small molecules into the rhizosphere that serve in overall plant functioning. Yet, there is a major gap in our knowledge in translating plant root exudation in artificial systems (i.e., hydroponics, sterile media) [...] Read more.
Root exudation is an important plant process by which roots release small molecules into the rhizosphere that serve in overall plant functioning. Yet, there is a major gap in our knowledge in translating plant root exudation in artificial systems (i.e., hydroponics, sterile media) to crops, specifically for soils expected in field conditions. Sorghum (Sorghum bicolor L. Moench) root exudation was determined using both ultra-performance liquid chromatography and gas chromatography mass spectrometry-based non-targeted metabolomics to evaluate variation in exudate composition of two sorghum genotypes among three substrates (sand, clay, and soil). Above and belowground plant traits were measured to determine the interaction between sorghum genotype and belowground substrate. Plant growth and quantitative exudate composition were found to vary largely by substrate. Two types of changes to rhizosphere metabolites were observed: rhizosphere-enhanced metabolites (REMs) and rhizosphere-abated metabolites (RAMs). More REMs and RAMs were detected in sand and clay substrates compared to the soil substrate. This study demonstrates that belowground substrate influences the root exudate profile in sorghum, and that two sorghum genotypes exuded metabolites at different magnitudes. However, metabolite identification remains a major bottleneck in non-targeted metabolite profiling of the rhizosphere. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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16 pages, 1931 KiB  
Article
Rootstock-Mediated Effects on Cabernet Sauvignon Performance: Vine Growth, Berry Ripening, Flavonoids, and Aromatic Profiles
by Yu Wang, Wei-Kai Chen, Xiao-Tong Gao, Lei He, Xiao-Hui Yang, Fei He, Chang-Qing Duan and Jun Wang
Int. J. Mol. Sci. 2019, 20(2), 401; https://doi.org/10.3390/ijms20020401 - 18 Jan 2019
Cited by 39 | Viewed by 4192
Abstract
Rootstocks are widely used in viticulture due to their resistance to biotic and abiotic stress. Additionally, rootstocks can affect vine growth and berry quality. This study evaluated the effects of eight rootstocks (101-14, 110R, 5A, 5BB, Ganzin 1, Harmony, Riparia Gloire, and SO4) [...] Read more.
Rootstocks are widely used in viticulture due to their resistance to biotic and abiotic stress. Additionally, rootstocks can affect vine growth and berry quality. This study evaluated the effects of eight rootstocks (101-14, 110R, 5A, 5BB, Ganzin 1, Harmony, Riparia Gloire, and SO4) on the vine growth, berry ripening, and flavonoids and aromatic profiles of Cabernet Sauvignon in two consecutive seasons (2015–2016). With few exceptions, minor differences were observed among grafted and own-rooted vines. Own-rooted vines produced the least pruning weight but the highest yield. 101-14, 5BB, and SO4 slightly reduced total soluble solids, but increased acidity, showing tendencies for retarding maturation. Ganzin 1 inhibited the accumulation of flavan-3-ols in berry skins. Furthermore, concentrations and proportions of epicatechin-3-O-galate were decreased by rootstocks, except for 110R. 5A, Harmony, and Riparia Gloire enhanced flavonol concentrations. SO4 slightly decreased most of the individual anthocyanin concentrations. With respect to volatile compounds, 110R, Riparia Gloire, and SO4 induced reductions in concentrations of total esters, whilst 101-14, Ganzin 1, 110R, and 5BB led to increases in the concentrations of C13-norisoprenoids. Therefore, with respect to the negative effects of SO4 on berry ripening and the accumulation of anthocyanin and volatile esters, SO4 is not recommended in practice. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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21 pages, 3910 KiB  
Article
Molecular Regulation of Catalpol and Acteoside Accumulation in Radial Striation and non-Radial Striation of Rehmannia glutinosa Tuberous Root
by Jingyu Zhi, Yajing Li, Zhongyi Zhang, Chaofei Yang, Xiaotong Geng, Miao Zhang, Xinrong Li, Xin Zuo, Mingjie Li, Yong Huang, Fengqing Wang and Caixia Xie
Int. J. Mol. Sci. 2018, 19(12), 3751; https://doi.org/10.3390/ijms19123751 - 26 Nov 2018
Cited by 28 | Viewed by 4241
Abstract
Rehmannia glutinosa L., a perennial plant of Scrophulariaceae, is one of the most commonly used herbs in traditional Chinese medicine (TCM) that have been widely cultivated in China. However, to date, the biosynthetic pathway of its two quality-control components, catalpol and acteoside, are [...] Read more.
Rehmannia glutinosa L., a perennial plant of Scrophulariaceae, is one of the most commonly used herbs in traditional Chinese medicine (TCM) that have been widely cultivated in China. However, to date, the biosynthetic pathway of its two quality-control components, catalpol and acteoside, are only partially elucidated and the mechanism for their tissue-specific accumulation remains unknown. To facilitate the basic understanding of the key genes and transcriptional regulators involved in the biosynthesis of catalpol and acteoside, transcriptome sequencing of radial striation (RS) and non-radial striation (nRS) from four R. glutinosa cultivars was performed. A total of 715,158,202 (~107.27 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 150,405 transcripts. Functional annotation with multiple public databases identified 155 and 223 unigenes involved in catalpol and acteoside biosynthesis, together with 325 UGTs, and important transcription factor (TF) families. Comparative analysis of the transcriptomes identified 362 unigenes, found to be differentially expressed in all RS vs. nRS comparisons, with 143 upregulated unigenes, including those encoding enzymes of the catalpol and acteoside biosynthetic pathway, such as geranyl diphosphate synthase (RgGPPS), geraniol 8-hydroxylase (RgG10H), and phenylalanine ammonia-lyase (RgPAL). Other differentially expressed unigenes predicted to be related to catalpol and acteoside biosynthesis fall into UDP-dependent glycosyltransferases (UGTs), as well as transcription factors. In addition, 16 differentially expressed genes were selectively confirmed by real-time PCR. In conclusion, a large unigene dataset of R. glutinosa generated in the current study will serve as a resource for the identification of potential candidate genes for investigation of the tuberous root development and biosynthesis of active components. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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21 pages, 6366 KiB  
Article
Metabolic Changes of Amino Acids and Flavonoids in Tea Plants in Response to Inorganic Phosphate Limitation
by Santosh KC, Meiya Liu, Qunfeng Zhang, Kai Fan, Yuanzhi Shi and Jianyun Ruan
Int. J. Mol. Sci. 2018, 19(11), 3683; https://doi.org/10.3390/ijms19113683 - 21 Nov 2018
Cited by 34 | Viewed by 13722
Abstract
The qualities of tea (Camellia sinensis) are not clearly understood in terms of integrated leading molecular regulatory network mechanisms behind inorganic phosphate (Pi) limitation. Thus, the present work aims to elucidate transcription factor-dependent responses of quality-related metabolites and the expression of [...] Read more.
The qualities of tea (Camellia sinensis) are not clearly understood in terms of integrated leading molecular regulatory network mechanisms behind inorganic phosphate (Pi) limitation. Thus, the present work aims to elucidate transcription factor-dependent responses of quality-related metabolites and the expression of genes to phosphate (P) starvation. The tea plant organs were subjected to metabolomics analysis by GC×GC-TOF/MS and UPLC-Q-TOF/MS along with transcription factors and 13 metabolic genes by qRT-PCR. We found P starvation upregulated SPX2 and the change response of Pi is highly dependent on young shoots. This led to increased change in abundance of carbohydrates (fructose and glucose), amino acids in leaves (threonine and methionine), and root (phenylalanine, alanine, tryptophan, and tyrosine). Flavonoids and their glycosides accumulated in leaves and root exposed to P limitation was consistent with the upregulated expression of anthocyanidin reductase (EC 1.3.1.77), leucoanthocyanidin dioxygenase (EC 1.4.11.19) and glycosyltransferases (UGT78D1, UGT78D2 and UGT57L12). Despite the similar kinetics and high correlation response of Pi and SPX2 in young shoots, predominating theanine and other amino acids (serine, threonine, glutamate, valine, methionine, phenylalanine) and catechin (EGC, EGCG and CG) content displayed opposite changes in response to Pi limitation between Fengqing and Longjing-43 tea cultivars. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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14 pages, 5956 KiB  
Article
Differential Accumulation of Anthocyanins in Dendrobium officinale Stems with Red and Green Peels
by Zhenming Yu, Yinyin Liao, Jaime A. Teixeira da Silva, Ziyin Yang and Jun Duan
Int. J. Mol. Sci. 2018, 19(10), 2857; https://doi.org/10.3390/ijms19102857 - 20 Sep 2018
Cited by 36 | Viewed by 4661
Abstract
Dendrobium officinale stems, including red and green stems, are widely used as a dietary supplement to develop nutraceutical beverages and food products. However, there is no detailed information on pigment composition of red and green stems. Here, we investigated the content and composition [...] Read more.
Dendrobium officinale stems, including red and green stems, are widely used as a dietary supplement to develop nutraceutical beverages and food products. However, there is no detailed information on pigment composition of red and green stems. Here, we investigated the content and composition of pigments in red and green stems by Ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry and assessed the differential accumulation of anthocyanins at the molecular level. The color of peels in red stems was caused by the presence of anthocyanins in epidermal cells unlike the peels of green stems. The glucoside derivatives delphinidin and cyanidin are responsible for the red color. Within the D. officinale anthocyanidin biosynthetic pathway, DoANS and DoUFGT, coding for anthocyanidin synthase and UDP-glucose flavonoid-3-O-glucosyltransferase, respectively, are critical regulatory genes related to the differential accumulation of anthocyanidin. These findings provide a more complete profile of pigments, especially anthocyanin, in D. officinale stems, and lay a foundation for producing functional foods. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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17 pages, 3495 KiB  
Article
Comparative Metabolic Phenotyping of Tomato (Solanum lycopersicum) for the Identification of Metabolic Signatures in Cultivars Differing in Resistance to Ralstonia solanacearum
by Dylan R. Zeiss, Msizi I. Mhlongo, Fidele Tugizimana, Paul A. Steenkamp and Ian A. Dubery
Int. J. Mol. Sci. 2018, 19(9), 2558; https://doi.org/10.3390/ijms19092558 - 29 Aug 2018
Cited by 32 | Viewed by 5769
Abstract
Tomato (Solanum lycopersicum) is an important dietary source which contains numerous bioactive phytochemicals. Active breeding programs constantly produce new cultivars possessing superior and desirable traits. However, the underlying molecular signatures that functionally describe these traits are yet to be elucidated. Thus, [...] Read more.
Tomato (Solanum lycopersicum) is an important dietary source which contains numerous bioactive phytochemicals. Active breeding programs constantly produce new cultivars possessing superior and desirable traits. However, the underlying molecular signatures that functionally describe these traits are yet to be elucidated. Thus, in this study we used an untargeted metabolomic approach to describe differential metabolic profiles of four cultivars described as having high to intermediate resistance to Ralstonia solanacearum. Metabolites were methanol-extracted from leaves, stems and root tissues and analyzed by liquid chromatography coupled with high definition mass spectrometry. Multivariate data analysis revealed cultivar-related differential metabolic phenotypes. A total of 41 metabolites were statistically selected and annotated, consisting of amino acids, organic acids, lipids, derivatives of cinnamic acid and benzoic acids, flavonoids and steroidal glycoalkaloids which were especially prominent in the two highly resistant cultivars. Interestingly, the less resistant cultivars had various fatty acid derivatives in root extracts that contributed to the differentiated metabolic signatures. Moreover, the metabolic phenotype of the STAR9008 (8SC) cultivar with intermediate resistance, was characterized by derivatives of cinnamic acids and flavonoids but at lower levels compared to the resistant cultivars. The 8SC cultivar also exhibited a lack of hydroxybenzoic acid biomarkers, which may be attributed to its lower resistance. These metabolic phenotypes provide insights into the differential metabolic signatures underlying the metabolism of these four cultivars, defining their respective phenotypic traits such as their resistance, tolerance or susceptibility to Ralstonia solanacearum. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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Review

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22 pages, 1525 KiB  
Review
Analytical Methods for Detection of Plant Metabolomes Changes in Response to Biotic and Abiotic Stresses
by Anna Piasecka, Piotr Kachlicki and Maciej Stobiecki
Int. J. Mol. Sci. 2019, 20(2), 379; https://doi.org/10.3390/ijms20020379 - 17 Jan 2019
Cited by 102 | Viewed by 7881
Abstract
Abiotic and biotic stresses are the main reasons of substantial crop yield losses worldwide. Research devoted to reveal mechanisms of plant reactions during their interactions with the environment are conducted on the level of genome, transcriptome, proteome, and metabolome. Data obtained during these [...] Read more.
Abiotic and biotic stresses are the main reasons of substantial crop yield losses worldwide. Research devoted to reveal mechanisms of plant reactions during their interactions with the environment are conducted on the level of genome, transcriptome, proteome, and metabolome. Data obtained during these studies would permit to define biochemical and physiological mechanisms of plant resistance or susceptibility to affecting factors/stresses. Metabolomics based on mass spectrometric techniques is an important part of research conducted in the direction of breeding new varieties of crop plants tolerant to the affecting stresses and possessing good agronomical features. Studies of this kind are carried out on model, crop and resurrection plants. Metabolites profiling yields large sets of data and due to this fact numerous advanced statistical and bioinformatic methods permitting to obtain qualitative and quantitative evaluation of the results have been developed. Moreover, advanced integration of metabolomics data with these obtained on other omics levels: genome, transcriptome and proteome should be carried out. Such a holistic approach would bring us closer to understanding biochemical and physiological processes of the cell and whole plant interacting with the environment and further apply these observations in successful breeding of stress tolerant or resistant crop plants. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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