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Metabolic Processes during Seed Germination 2.0
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Metabolic Processes during Seed Germination 2.0

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 June 2023) | Viewed by 12182

Special Issue Editors

Prof. Dr. Alma Balestrazzi

E-Mail Website
Guest Editor
Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
Interests: seed germination; DNA repair; genotoxic stress; antioxidant response
Special Issues, Collections and Topics in MDPI journals
Dr. Łukasz Wojtyla

E-Mail Website
Guest Editor
Department of Plant Physiology, Adam Mickiewicz University in Poznan, 61-712 Poznan, Poland
Interests: seed germination; seed priming; abiotic stress response; proteomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Seeds, the main propagating vectors in higher plants, represent a fascinating as well as challenging subject for research. The reactivation of seed metabolism following imbibition involves the ex novo synthesis of antioxidant molecules and triggers DNA repair pathways from the early stages of seed pre-germinative metabolism while creating a suitable rehydrated environment for enzymatic activities. This complex picture still contains many knowledge gaps related to the roles of hormones and many other actors involved in seed stress response, including ROS-mediated signaling, miRNA-mediated regulation, modulation by long noncoding RNA, epigenetic information and chromatin condensation state. Such a complex landscape requires the use of integrative and multilevel approaches, as well as dedicated experimental models, to be properly understood.

This Special Issue aims to reveal the current state and recent advancements in the understanding of seed metabolism from genetic, epigenetic, biochemical, physiological and ecological perspectives, taking into account its implications for seed preservation and quality enhancement. As examples, original contributions on the following aspects will be welcomed:

  • Control of germination mediated by dormancy: actors and genetic and epigenetic backgrounds;
  • Molecular networks integrating hormonal and environmental signals in seed germination;
  • Reactive oxygen species in germination and dormancy;
  • Pathways in pre-germinative metabolism;
  • Adaptability and stress responses in seeds;
  • Seed vigor and genome integrity;
  • Seed priming: molecular bases and technical advancements;
  • Seed longevity: metabolic aspects;
  • Understanding seed metabolism to assess seed quality using multilevel approaches.

Prof. Dr. Alma Balestrazzi
Dr. Łukasz Wojtyla
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • seed germination
  • dormancy
  • pre-germinative metabolism
  • seed priming
  • genome integrity
  • seed longevity

Published Papers (6 papers)

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Research

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20 pages, 3687 KiB  
Article
Identification of Reference Genes for Precise Expression Analysis during Germination in Chenopodium quinoa Seeds under Salt Stress
by Estefanía Contreras, Lucía Martín-Fernández, Arafet Manaa, Jesús Vicente-Carbajosa and Raquel Iglesias-Fernández
Int. J. Mol. Sci. 2023, 24(21), 15878; https://doi.org/10.3390/ijms242115878 - 01 Nov 2023
Viewed by 982
Abstract
Chenopodium quinoa Willd. (quinoa), a member of the Amaranthaceae family, is an allotetraploid annual plant, endemic to South America. The plant of C. quinoa presents significant ecological plasticity with exceptional adaptability to several environmental stresses, including salinity. The resilience of quinoa to several [...] Read more.
Chenopodium quinoa Willd. (quinoa), a member of the Amaranthaceae family, is an allotetraploid annual plant, endemic to South America. The plant of C. quinoa presents significant ecological plasticity with exceptional adaptability to several environmental stresses, including salinity. The resilience of quinoa to several abiotic stresses, as well as its nutritional attributes, have led to significant shifts in quinoa cultivation worldwide over the past century. This work first defines germination sensu stricto in quinoa where the breakage of the pericarp and the testa is followed by endosperm rupture (ER). Transcriptomic changes in early seed germination stages lead to unstable expression levels in commonly used reference genes that are typically stable in vegetative tissues. Noteworthy, no suitable reference genes have been previously identified specifically for quinoa seed germination under salt stress conditions. This work aims to identify these genes as a prerequisite step for normalizing qPCR data. To this end, germinating seeds from UDEC2 and UDEC4 accessions, with different tolerance to salt, have been analyzed under conditions of absence (0 mM NaCl) and in the presence (250 mM NaCl) of sodium chloride. Based on the relevant literature, six candidate reference genes, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Monensin sensitivity1 (MON1), Polypyrimidine tract-binding protein (PTB), Actin-7 (ACT7), Ubiquitin-conjugating enzyme (UBC), and 18S ribosomal RNA (18S), were selected and assessed for stability using the RefFinder Tool encompassing the statistical algorithms geNorm, NormFinder, BestKeeper, and ΔCt in the evaluation. The data presented support the suitability of CqACT7 and CqUBC as reference genes for normalizing gene expression during seed germination under salinity stress. These recommended reference genes can be valuable tools for consistent qPCR studies on quinoa seeds. Full article
(This article belongs to the Special Issue Metabolic Processes during Seed Germination 2.0)
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15 pages, 2660 KiB  
Article
Identification of DNA Methylation Changes in European Beech Seeds during Desiccation and Storage
by Marcin Michalak, Beata Patrycja Plitta-Michalak, Jan Suszka, Mirosława Zofia Naskręt-Barciszewska, Szymon Kotlarski, Jan Barciszewski and Paweł Chmielarz
Int. J. Mol. Sci. 2023, 24(4), 3557; https://doi.org/10.3390/ijms24043557 - 10 Feb 2023
Cited by 3 | Viewed by 1340
Abstract
Ageing and deterioration of seeds is a major problem for the maintenance of seed quality and viability during long-term storage. Prediction of early stages of seed deterioration in order to point out the plantlets’ regeneration time is a major challenge of successful storage. [...] Read more.
Ageing and deterioration of seeds is a major problem for the maintenance of seed quality and viability during long-term storage. Prediction of early stages of seed deterioration in order to point out the plantlets’ regeneration time is a major challenge of successful storage. In preserved seeds, damages accumulate within cells at the rate mainly related to their moisture content and temperature of storage. Current research reveals global alterations in DNA methylation in lipid-rich intermediate seeds during desiccation and storage at various regimes covering nonoptimal and optimal conditions. We show for the first time that monitoring of 5-methylcytosine (m5C) level in seeds can be used as a truly universal viability marker regardless of postharvest category of seeds and their composition. For seeds stored up to three years, in varied conditions, moisture content, temperature, and time of storage had significant influence on seedling emergence and DNA methylation (p < 0.05). Similarities among lipid-rich intermediate and orthodox seeds regarding different reactions of embryonic axes and cotyledons to desiccation are newly revealed. Along with previous studies on seeds dramatically different in desiccation tolerance (recalcitrant vs. orthodox), results regarding lipid-rich seeds positioned in-between (intermediate) prove that maintaining global DNA methylation status is crucial for maintaining seed viability. Full article
(This article belongs to the Special Issue Metabolic Processes during Seed Germination 2.0)
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18 pages, 3506 KiB  
Article
Influence of Light of Different Spectral Compositions on Growth Parameters, Photosynthetic Pigment Contents and Gene Expression in Scots Pine Plantlets
by Pavel Pashkovskiy, Yury Ivanov, Alexandra Ivanova, Vladimir D. Kreslavski, Mikhail Vereshchagin, Polina Tatarkina, Vladimir V. Kuznetsov and Suleyman I. Allakhverdiev
Int. J. Mol. Sci. 2023, 24(3), 2063; https://doi.org/10.3390/ijms24032063 - 20 Jan 2023
Cited by 3 | Viewed by 1410
Abstract
The photoreceptors of red light (phytochromes) and blue light (cryptochromes) impact plant growth and metabolism. However, their action has been barely studied, especially in coniferous plants. Therefore, the influence of blue (maximum 450 nm), red (maximum 660 nm), white light (maxima 450 nm [...] Read more.
The photoreceptors of red light (phytochromes) and blue light (cryptochromes) impact plant growth and metabolism. However, their action has been barely studied, especially in coniferous plants. Therefore, the influence of blue (maximum 450 nm), red (maximum 660 nm), white light (maxima 450 nm + 575 nm), far-red light (maximum 730 nm), white fluorescent light and dark on seed germination, growth, chlorophyll and carotenoid contents, as well as the transcript levels of genes involved in reception, photosynthesis, light and hormonal signaling of Scots pine plantlets, was investigated. The highest values of dry weight, root length and photosynthetic pigment contents were characteristic of 9-day-old plantlets grown under red light, whereas in the dark plantlet length, seed vigor, seed germination, dry weight and pigment contents were decreased. Under blue and white lights, the main studied morphological parameters were decreased or close to red light. The cotyledons were undeveloped under dark conditions, likely due to the reduced content of photosynthetic pigments, which agrees with the low transcript levels of genes encoding protochlorophyllide oxidoreductase (PORA) and phytoene synthase (PSY). The transcript levels of a number of genes involved in phytohormone biosynthesis and signaling, such as GA3ox, RRa, KAO and JazA, were enhanced under red light, unlike under dark conditions. We suggest that the observed phenomena of red light are the most important for the germination of the plantlets and may be based on earlier and enhanced expression of auxin, cytokinin, gibberellin and jasmonate signaling genes activated by corresponding photoreceptors. The obtained results may help to improve reforestation technology; however, this problem needs further study. Full article
(This article belongs to the Special Issue Metabolic Processes during Seed Germination 2.0)
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14 pages, 3397 KiB  
Article
Transcriptome Analyses Reveal the Role of Light in Releasing the Morphological Dormancy of Celery Seed by Integrating Plant Hormones, Sugar Metabolism and Endosperm Weakening
by Han Li, Jingbo Chen, Lizhong He, Hongfang Zhu, Zhiwu Huang, Minfen Zhu, Linhua Fan, Lingyun Wu, Li Yu, Weimin Zhu and Jun Yan
Int. J. Mol. Sci. 2022, 23(17), 10140; https://doi.org/10.3390/ijms231710140 - 04 Sep 2022
Cited by 3 | Viewed by 2147
Abstract
Celery seed is known to be difficult to germinate due to its morphological dormancy. Light is the key signal to release morphological dormancy and promote seed germination. However, this mechanism has rarely been studied. We performed physiological, transcriptome analyses on celery seed exposed [...] Read more.
Celery seed is known to be difficult to germinate due to its morphological dormancy. Light is the key signal to release morphological dormancy and promote seed germination. However, this mechanism has rarely been studied. We performed physiological, transcriptome analyses on celery seed exposed to light and dark to decipher the mechanism by which light promotes germination of celery seed. The results showed that light significantly enhanced the expression of gibberellin synthesis genes and abscisic acid degradation genes and inhibited the expression of abscisic acid synthesis genes and gibberellin degradation genes. Moreover, gibberellin synthesis inhibitor could completely inhibit the germination capacity of celery seed, indicating that gibberellin is indispensable in the process of celery seed germination. Compared with dark, light also increased the activity of α-amylase and β-amylase and the expression of related coding genes and promoted the degradation of starch and the increase of soluble sugar content, suggesting that light enhanced the sugar metabolism of celery seed. In addition, transcriptome analysis revealed that many genes related to endosperm weakening (cell wall remodeling enzymes, extension proteins) were up-regulated under light. It was also found that light promoted the accumulation of hydrogen peroxide in the radicle, which promoted the endosperm weakening process of celery seed. Our results thus indicated that light signal may promote the release of morphological dormancy through the simultaneous action of multiple factors. Full article
(This article belongs to the Special Issue Metabolic Processes during Seed Germination 2.0)
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20 pages, 3710 KiB  
Article
Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene
by Xu Wang, Marlène Davanture, Michel Zivy, Christophe Bailly, Eiji Nambara and Françoise Corbineau
Int. J. Mol. Sci. 2022, 23(16), 9352; https://doi.org/10.3390/ijms23169352 - 19 Aug 2022
Viewed by 1542
Abstract
In Arabidopsis thaliana, the breaking of seed dormancy in wild type (Col-0) by ethylene at 100 μL L−1 required at least 30 h application. A mutant of the proteolytic N-degron pathway, lacking the E3 ligase PROTEOLYSIS 6 (PRT6), was [...] Read more.
In Arabidopsis thaliana, the breaking of seed dormancy in wild type (Col-0) by ethylene at 100 μL L−1 required at least 30 h application. A mutant of the proteolytic N-degron pathway, lacking the E3 ligase PROTEOLYSIS 6 (PRT6), was investigated for its role in ethylene-triggered changes in proteomes during seed germination. Label-free quantitative proteomics was carried out on dormant wild type Col-0 and prt6 seeds treated with (+) or without (−) ethylene. After 16 h, 1737 proteins were identified, but none was significantly different in protein levels in response to ethylene. After longer ethylene treatment (30 h), 2552 proteins were identified, and 619 Differentially Expressed Proteins (DEPs) had significant differences in protein abundances between ethylene treatments and genotypes. In Col, 587 DEPs were enriched for those involved in signal perception and transduction, reserve mobilization and new material generation, which potentially contributed to seed germination. DEPs up-regulated by ethylene in Col included S-adenosylmethionine synthase 1, methionine adenosyltransferase 3 and ACC oxidase involved in ethylene synthesis and of Pyrabactin Resistance1 acting as an ABA receptor, while DEPs down-regulated by ethylene in Col included aldehyde oxidase 4 involved in ABA synthesis. In contrast, in prt6 seeds, ethylene did not result in strong proteomic changes with only 30 DEPs. Taken together, the present work demonstrates that the proteolytic N-degron pathway is essential for ethylene-mediated reprogramming of seed proteomes during germination. Full article
(This article belongs to the Special Issue Metabolic Processes during Seed Germination 2.0)
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Review

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18 pages, 3208 KiB  
Review
Epigenetic Mechanisms of Tree Responses to Climatic Changes
by Barbara Kurpisz and Tomasz Andrzej Pawłowski
Int. J. Mol. Sci. 2022, 23(21), 13412; https://doi.org/10.3390/ijms232113412 - 02 Nov 2022
Cited by 3 | Viewed by 3811
Abstract
Forest trees are complex perennial organisms that are adapted to the local environment in the results of prevailing climate conditions in population history. Because they lead a sedentary lifestyle, plants are exposed to various environmental stimuli, such as changes which can lead to [...] Read more.
Forest trees are complex perennial organisms that are adapted to the local environment in the results of prevailing climate conditions in population history. Because they lead a sedentary lifestyle, plants are exposed to various environmental stimuli, such as changes which can lead to the rapid adjustment or failure of their defence mechanisms. As forests play a key role in environment homeostasis and are the source of many products, it is crucial to estimate the role of forest trees’ plasticity mechanisms in the face of the climate change. Fast epigenetic adjustment is the basis for surviving climate fluctuations, however the question is whether this mechanism will be also efficient if climate fluctuations increase. Epigenetic modifications enable rapid reactions to the inducing stimulus by establishing chromatin patterns and manipulating gene expression without affecting the DNA itself. This work aimed to gather information about the epigenetic mechanisms of tree responses to changing environmental conditions, in order to summarise what is known so far and emphasize the significance of the discussed issue. Applying this knowledge in the future to study the interactions between climate change and gene regulation at the levels of plant development could generate answers to questions about the limitations of plasticity of plant adaptation to changing environment. We still know very little about how organisms, especially trees, cope with climate change and we believe that this overview will encourage researchers to fill this gap in the knowledge, and that results will be applied in improving defensive capacity of this ecologically and economically important species. Full article
(This article belongs to the Special Issue Metabolic Processes during Seed Germination 2.0)
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