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Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development
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Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development

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

Deadline for manuscript submissions: closed (29 February 2020) | Viewed by 33199

Special Issue Editors

Dr. Maurizio Chiurazzi

E-Mail Website
Guest Editor
Consiglio Nazionale delle Ricerche, Institute of BioSciences and BioResourses, Rome, Italy
Interests: symbiotic N-fixation; nutrient transporters; signaling pathways
Special Issues, Collections and Topics in MDPI journals
Dr. Vladimir Totev Valkov

E-Mail Website
Co-Guest Editor
Consiglio Nazionale delle Ricerche, Institute of Biosciences and Bioresources, Rome, Italy
Interests: nitrate transporters; nodule organogenesis; plastid gene expression; plastid transformation; plant–bacteria interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A comprehensive understanding of plant genomes with detailed and accurate analyses of associated gene expression is of crucial importance for both fundamental research and practical applications. Transcriptomics methodologies have developed considerably in the last decade, allowing analyses of expression in plants in response to environmental changes. This information is important for the investigation of the plethora of signaling pathways involved in the control of plant development and for the elucidation of the plant resilience capacity to fluctuating growth conditions. These studies are integrated with genetic approaches, leading to the identification of functional developmental modules. In this Special Issue, entitled “Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development”, research contributions on plant gene expression profiles in different environmental conditions, as well as the functional characterization of genes involved in plant development, will be highlighted, with a particular enphasis on the mechanisms of plant responses to nutrient availability changes.

Dr. Maurizio Chiurazzi
Dr. Vladimir Totev Valkov
Guest Editors

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Keywords

  • Plant development
  • Signaling
  • Gene expression
  • Nutrient availability.

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Published Papers (7 papers)

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Research

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19 pages, 3500 KiB  
Article
Comprehensive Transcriptomic Analysis of Auxin Responses in Submerged Rice Coleoptile Growth
by Yu-Sian Wu and Chin-Ying Yang
Int. J. Mol. Sci. 2020, 21(4), 1292; https://doi.org/10.3390/ijms21041292 - 14 Feb 2020
Cited by 19 | Viewed by 3421
Abstract
Cultivating rice in wet or water direct seeding systems is simple and time and labor efficient. Rice (Oryza sativa) seeds are a unique cereal that can germinate not only when submerged, but also in anoxic conditions. Many complicated hormone signals interact [...] Read more.
Cultivating rice in wet or water direct seeding systems is simple and time and labor efficient. Rice (Oryza sativa) seeds are a unique cereal that can germinate not only when submerged, but also in anoxic conditions. Many complicated hormone signals interact in submerged seed germination. Ethylene is involved in rice coleoptile elongation, but little is known regarding the role of auxin signaling under submergence. This study demonstrated that the coleoptile is shorter and curlier when submerged with 2,3,5-triiodobenzoic acid (TIBA). In transcriptomic analysis, 3448 of the 31,860 genes were upregulated, and 4360 genes were downregulated with submergence and TIBA treatment. The Gene Ontology function classification results demonstrated that upregulated differentially expressed genes (DEGs) were mainly involved in redox, stress, and signal transduction, whereas the down-regulated DEGs were mainly involved in RNA transcription, stress, and development. Furthermore, auxin signaling involved in the carbohydrate metabolism pathway was demonstrated while using transcriptomic analysis and confirmed in a quantitative real-time polymerase chain reaction. In addition, the transcript levels of development-related genes and mitochondria-electron- transport-related genes were regulated by auxin signaling under submergence. Auxin signaling was not only involved in regulating rice coleoptile elongation and development, but also regulated secondary metabolism, carbohydrate metabolism, and mitochondria electron transport under submergence. Our results presented that auxin signaling plays an important role during rice coleoptile elongation upon the submergence condition and improving the advance of research of direct rice seeding system. Full article
(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development)
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17 pages, 3127 KiB  
Article
Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids
by Jawahar Lal Katara, Ram Lakhan Verma, Madhuchhanda Parida, Umakanta Ngangkham, Kutubuddin Ali Molla, Kalyani Makarand Barbadikar, Mitadru Mukherjee, Parameswaran C, Sanghamitra Samantaray, Nageswara Rao Ravi, Onkar Nath Singh and Trilochan Mohapatra
Int. J. Mol. Sci. 2020, 21(3), 1080; https://doi.org/10.3390/ijms21031080 - 6 Feb 2020
Cited by 12 | Viewed by 3677
Abstract
RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality [...] Read more.
RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids. Full article
(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development)
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23 pages, 5336 KiB  
Article
Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots
by Laura Ravazzolo, Sara Trevisan, Cristian Forestan, Serena Varotto, Stefania Sut, Stefano Dall’Acqua, Mario Malagoli and Silvia Quaggiotti
Int. J. Mol. Sci. 2020, 21(2), 686; https://doi.org/10.3390/ijms21020686 - 20 Jan 2020
Cited by 35 | Viewed by 5651
Abstract
Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both [...] Read more.
Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. Ammonium activates the response to stress, while nitrate acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while also reducing biomass and chlorophyll and flavonoids accumulation. Furthermore, the later physiological effects of these nutrients were evaluated through the assessment of shoot and root growth, leaf pigment content and the amino acid concentrations in root and shoot, confirming the existence of common and distinct features in response to the two nitrogen forms. Full article
(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development)
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17 pages, 3754 KiB  
Article
Transgenerational Response to Nitrogen Deprivation in Arabidopsis thaliana
by Monica Massaro, Emanuele De Paoli, Nicola Tomasi, Michele Morgante, Roberto Pinton and Laura Zanin
Int. J. Mol. Sci. 2019, 20(22), 5587; https://doi.org/10.3390/ijms20225587 - 8 Nov 2019
Cited by 8 | Viewed by 3375
Abstract
Nitrogen (N) deficiency is one of the major stresses that crops are exposed to. It is plausible to suppose that a stress condition can induce a memory in plants that might prime the following generations. Here, an experimental setup that considered four successive [...] Read more.
Nitrogen (N) deficiency is one of the major stresses that crops are exposed to. It is plausible to suppose that a stress condition can induce a memory in plants that might prime the following generations. Here, an experimental setup that considered four successive generations of N-sufficient and N-limited Arabidopsis was used to evaluate the existence of a transgenerational memory. The results demonstrated that the ability to take up high amounts of nitrate is induced more quickly as a result of multigenerational stress exposure. This behavior was paralleled by changes in the expression of nitrate responsive genes. RNAseq analyses revealed the enduring modulation of genes in downstream generations, despite the lack of stress stimulus in these plants. The modulation of signaling and transcription factors, such as NIGTs, NFYA and CIPK23 might indicate that there is a complex network operating to maintain the expression of N-responsive genes, such as NRT2.1, NIA1 and NIR. This behavior indicates a rapid acclimation of plants to changes in N availability. Indeed, when fourth generation plants were exposed to N limitation, they showed a rapid induction of N-deficiency responses. This suggests the possible involvement of a transgenerational memory in Arabidopsis that allows plants to adapt efficiently to the environment and this gives an edge to the next generation that presumably will grow in similar stressful conditions. Full article
(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development)
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17 pages, 5775 KiB  
Article
Nitrogen Starvation Differentially Influences Transcriptional and Uptake Rate Profiles in Roots of Two Maize Inbred Lines with Different NUE
by Maria Mascia, Davide Sega, Anita Zamboni and Zeno Varanini
Int. J. Mol. Sci. 2019, 20(19), 4856; https://doi.org/10.3390/ijms20194856 - 30 Sep 2019
Cited by 12 | Viewed by 2846
Abstract
Nitrogen use efficiency (NUE) of crops is estimated to be less than 50%, with a strong impact on environment and economy. Genotype-dependent ability to cope with N shortage has been only partially explored in maize and, in this context, the comparison of molecular [...] Read more.
Nitrogen use efficiency (NUE) of crops is estimated to be less than 50%, with a strong impact on environment and economy. Genotype-dependent ability to cope with N shortage has been only partially explored in maize and, in this context, the comparison of molecular responses of lines with different NUE is of particular interest in order to dissect the key elements underlying NUE. Changes in root transcriptome and NH4+/NO3− uptake rates during growth (after 1 and 4 days) without N were studied in high (Lo5) and low (T250) NUE maize inbred lines. Results suggests that only a small set of transcripts were commonly modulated in both lines in response to N starvation. However, in both lines, transcripts linked to anthocyanin biosynthesis and lateral root formation were positively affected. On the contrary, those involved in root elongation were downregulated. The main differences between the two lines reside in the ability to modulate the transcripts involved in the transport, distribution and assimilation of mineral nutrients. With regard to N mineral forms, only the Lo5 line responded to N starvation by increasing the NH4+ fluxes as supported by the upregulation of a transcript putatively involved in its transport. Full article
(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development)
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22 pages, 4851 KiB  
Article
Dynamic Changes in Metabolite Accumulation and the Transcriptome during Leaf Growth and Development in Eucommia ulmoides
by Long Li, Minhao Liu, Kan Shi, Zhijing Yu, Ying Zhou, Ruishen Fan and Qianqian Shi
Int. J. Mol. Sci. 2019, 20(16), 4030; https://doi.org/10.3390/ijms20164030 - 18 Aug 2019
Cited by 33 | Viewed by 5210
Abstract
Eucommia ulmoides Oliver is widely distributed in China. This species has been used mainly in medicine due to the high concentration of chlorogenic acid (CGA), flavonoids, lignans, and other compounds in the leaves and barks. However, the categories of metabolites, dynamic changes in [...] Read more.
Eucommia ulmoides Oliver is widely distributed in China. This species has been used mainly in medicine due to the high concentration of chlorogenic acid (CGA), flavonoids, lignans, and other compounds in the leaves and barks. However, the categories of metabolites, dynamic changes in metabolite accumulation and overall molecular mechanisms involved in metabolite biosynthesis during E. ulmoides leaf growth and development remain unknown. Here, a total of 515 analytes, including 127 flavonoids, 46 organic acids, 44 amino acid derivatives, 9 phenolamides, and 16 vitamins, were identified from four E. ulmoides samples using ultraperformance liquid chromatography–mass spectrometry (UPLC-MS) (for widely targeted metabolites). The accumulation of most flavonoids peaked in growing leaves, followed by old leaves. UPLC-MS analysis indicated that CGA accumulation increased steadily to a high concentration during leaf growth and development, and rutin showed a high accumulation level in leaf buds and growing leaves. Based on single-molecule long-read sequencing technology, 69,020 transcripts and 2880 novel loci were identified in E. ulmoides. Expression analysis indicated that isoforms in the flavonoid biosynthetic pathway and flavonoid metabolic pathway were highly expressed in growing leaves and old leaves. Co-expression network analysis suggested a potential direct link between the flavonoid and phenylpropanoid biosynthetic pathways via the regulation of transcription factors, including MYB (v-myb avian myeloblastosis viral oncogene homolog) and bHLH (basic/helix-loop-helix). Our study predicts dynamic metabolic models during leaf growth and development and will support further molecular biological studies of metabolite biosynthesis in E. ulmoides. In addition, our results significantly improve the annotation of the E. ulmoides genome. Full article
(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development)
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Review

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16 pages, 2092 KiB  
Review
Impact of Nitrogen Nutrition on Cannabis sativa: An Update on the Current Knowledge and Future Prospects
by Simone Landi, Roberto Berni, Giorgia Capasso, Jean-Francois Hausman, Gea Guerriero and Sergio Esposito
Int. J. Mol. Sci. 2019, 20(22), 5803; https://doi.org/10.3390/ijms20225803 - 18 Nov 2019
Cited by 27 | Viewed by 8298
Abstract
Nitrogen (N) availability represents one of the most critical factors affecting cultivated crops. N is indeed a crucial macronutrient influencing major aspects, from plant development to productivity and final yield of lignocellulosic biomass, as well as content of bioactive molecules. N metabolism is [...] Read more.
Nitrogen (N) availability represents one of the most critical factors affecting cultivated crops. N is indeed a crucial macronutrient influencing major aspects, from plant development to productivity and final yield of lignocellulosic biomass, as well as content of bioactive molecules. N metabolism is fundamental as it is at the crossroad between primary and secondary metabolic pathways: Besides affecting the synthesis of fundamental macromolecules, such as nucleic acids and proteins, N is needed for other types of molecules intervening in the response to exogenous stresses, e.g. alkaloids and glucosinolates. By partaking in the synthesis of phenylalanine, N also directly impacts a central plant metabolic ‘hub’—the phenylpropanoid pathway—from which important classes of molecules are formed, notably monolignols, flavonoids and other types of polyphenols. In this review, an updated analysis is provided on the impact that N has on the multipurpose crop hemp (Cannabis sativa L.) due to its renewed interest as a multipurpose crop able to satisfy the needs of a bioeconomy. The hemp stalk provides both woody and cellulosic fibers used in construction and for biocomposites; different organs (leaves/flowers/roots) are sources of added-value secondary metabolites, namely cannabinoids, terpenes, flavonoids, and lignanamides. We survey the available literature data on the impact of N in hemp and highlight the importance of studying those genes responding to both N nutrition and abiotic stresses. Available hemp transcriptomic datasets obtained on plants subjected to salt and drought are here analyzed using Gene Ontology (GO) categories related to N metabolism. The ultimate goal is to shed light on interesting candidate genes that can be further studied in hemp varieties growing under different N feeding conditions and showing high biomass yield and secondary metabolite production, even under salinity and drought. Full article
(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development)
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