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Physiological and Environmental Regulation of Seed Germination: From Signaling Events to Molecular Responses

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 (31 March 2021) | Viewed by 39053

Special Issue Editors


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Guest Editor
Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), UMR7622 “Biologie du Développement”, Paris, France
Interests: seeds; germination; dormancy; signal transduction; protein phosphorylation; MAP kinases; ROS and NO signaling; environmental responses; biochemistry; molecular biology; cell biology

E-Mail Website
Guest Editor
Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), UMR7622 “Biologie du Développement”, Paris, France
Interests: seeds; germination; dormancy; signal transduction; MAP kinases; TCP transcription factors; lipid metabolism and signaling; post-translational modifications; molecular biology; biochemistry; cell biology

E-Mail Website
Guest Editor
Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), UMR7622 “Biologie du Développement”, Paris, France
Interests: seed; dormancy; germination; longevity; reactive oxygen species; transcriptome; RNA metabolism; abiotic stress

Special Issue Information

Dear Colleagues,

Seed germination is a critical event in plant life cycle and a major determinant of wild species and crop global performances. During their development and following their dispersal from the mother plant, seeds integrate a tremendous variety of hormonal and environmental signals that are converted into molecular responses, triggering or restricting germination. Thus, ongoing global warming will deeply impact germination phenology, and gaining a better understanding of how environmental cues are perceived and integrated is therefore crucial to develop strategies to mitigate climate-change effects.

During the last decade, numerous actors controlling seed germination have been identified. The deciphering of their function and regulation recently ended in major breakthroughs, and the conservation of such mechanisms can now be addressed through the prisma of species evolution and crop genetic selection. In parallel, the application of omic technologies (transcriptomics, proteomics, and metabolomics) to seed biology has provided valuable information on the comprehensive molecular networks associated with the germination process and their modification by environmental and hormonal cues. Although challenging, obtaining dynamic spatio-temporal models integrating these data and more is now realistic and within easy reach.

In this context, this Special Issue aims to address ongoing questions and emerging topics related to the molecular regulation of seed germination by hormonal and environmental factors. As examples, contributions exploring the following aspects will be particularly welcomed:

  • Regulatory networks associated with light/temperature perception and transduction;
  • Integration of molecular and mechanical signals for radicle elongation and their regulation by hormones and environment;
  • Emerging roles of post-transcriptional, post-translational, and epigenetic mechanisms;
  • Functions and interplay of seed compartments (endosperm…) in dormancy and germination reexamined;
  • Molecular networks integrating maternal effects in seed physiology;
  • DOG1 and beyond: functions and regulation of dormancy factors and roles in integrating environmental signals;
  • Primary dormancy, secondary dormancy, and dormancy cycling: generic versus specific molecular regulations;
  • Are lessons from model plants translatable to crops? Advances in comparative and translational biology.

Dr. Emmanuel Baudouin
Dr. Juliette Puyaubert
Dr. Christophe Bailly
Guest Editor

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.

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Keywords

  • Seed germination and dormancy
  • Environmental signals
  • Signaling pathways
  • Hormones
  • Transcriptional, post-trancriptional, translational, and post-translational regulation
  • Epigenetic regulation
  • Omics
  • Model plants and crops

Published Papers (9 papers)

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Editorial

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4 pages, 196 KiB  
Editorial
Physiological and Environmental Regulation of Seed Germination: From Signaling Events to Molecular Responses
by Emmanuel Baudouin, Juliette Puyaubert and Christophe Bailly
Int. J. Mol. Sci. 2022, 23(9), 4839; https://doi.org/10.3390/ijms23094839 - 27 Apr 2022
Viewed by 1363
Abstract
A timely and efficient seed germination is critical for plantlets’ establishment and robustness as well as plant development and plant performance in both natural ecosystems and agrosystems [...] Full article

Research

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15 pages, 2007 KiB  
Article
A New Role for Plastid Thioredoxins in Seed Physiology in Relation to Hormone Regulation
by Guillaume Née, Gilles Châtel-Innocenti, Patrice Meimoun, Juliette Leymarie, Françoise Montrichard, Pascale Satour, Christophe Bailly and Emmanuelle Issakidis-Bourguet
Int. J. Mol. Sci. 2021, 22(19), 10395; https://doi.org/10.3390/ijms221910395 - 27 Sep 2021
Cited by 6 | Viewed by 1816
Abstract
In Arabidopsis seeds, ROS have been shown to be enabling actors of cellular signaling pathways promoting germination, but their accumulation under stress conditions or during aging leads to a decrease in the ability to germinate. Previous biochemical work revealed that a specific class [...] Read more.
In Arabidopsis seeds, ROS have been shown to be enabling actors of cellular signaling pathways promoting germination, but their accumulation under stress conditions or during aging leads to a decrease in the ability to germinate. Previous biochemical work revealed that a specific class of plastid thioredoxins (Trxs), the y-type Trxs, can fulfill antioxidant functions. Among the ten plastidial Trx isoforms identified in Arabidopsis, Trx y1 mRNA is the most abundant in dry seeds. We hypothesized that Trx y1 and Trx y2 would play an important role in seed physiology as antioxidants. Using reverse genetics, we found important changes in the corresponding Arabidopsis mutant seeds. They display remarkable traits such as increased longevity and higher and faster germination in conditions of reduced water availability or oxidative stress. These phenotypes suggest that Trxs y do not play an antioxidant role in seeds, as further evidenced by no changes in global ROS contents and protein redox status found in the corresponding mutant seeds. Instead, we provide evidence that marker genes of ABA and GAs pathways are perturbed in mutant seeds, together with their sensitivity to specific hormone inhibitors. Altogether, our results suggest that Trxs y function in Arabidopsis seeds is not linked to their previously identified antioxidant roles and reveal a new role for plastid Trxs linked to hormone regulation. Full article
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17 pages, 2609 KiB  
Article
The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination
by Elodie Layat, Marie Bourcy, Sylviane Cotterell, Julia Zdzieszyńska, Sophie Desset, Céline Duc, Christophe Tatout, Christophe Bailly and Aline V. Probst
Int. J. Mol. Sci. 2021, 22(8), 4031; https://doi.org/10.3390/ijms22084031 - 14 Apr 2021
Cited by 9 | Viewed by 3129
Abstract
Histone chaperones regulate the flow and dynamics of histone variants and ensure their assembly into nucleosomal structures, thereby contributing to the repertoire of histone variants in specialized cells or tissues. To date, not much is known on the distribution of histone variants and [...] Read more.
Histone chaperones regulate the flow and dynamics of histone variants and ensure their assembly into nucleosomal structures, thereby contributing to the repertoire of histone variants in specialized cells or tissues. To date, not much is known on the distribution of histone variants and their modifications in the dry seed embryo. Here, we bring evidence that genes encoding the replacement histone variant H3.3 are expressed in Arabidopsis dry seeds and that embryo chromatin is characterized by a low H3.1/H3.3 ratio. Loss of HISTONE REGULATOR A (HIRA), a histone chaperone responsible for H3.3 deposition, reduces cellular H3 levels and increases chromatin accessibility in dry seeds. These molecular differences are accompanied by increased seed dormancy in hira-1 mutant seeds. The loss of HIRA negatively affects seed germination even in the absence of HISTONE MONOUBIQUITINATION 1 or TRANSCRIPTION ELONGATION FACTOR II S, known to be required for seed dormancy. Finally, hira-1 mutant seeds show lower germination efficiency when aged under controlled deterioration conditions or when facing unfavorable environmental conditions such as high salinity. Altogether, our results reveal a dependency of dry seed chromatin organization on the replication-independent histone deposition pathway and show that HIRA contributes to modulating seed dormancy and vigor. Full article
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21 pages, 6406 KiB  
Article
Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (Glycine max) Tissues during Early Seed Development
by Shuo Sun, Changyu Yi, Jing Ma, Shoudong Wang, Marta Peirats-Llobet, Mathew G. Lewsey, James Whelan and Huixia Shou
Int. J. Mol. Sci. 2020, 21(20), 7603; https://doi.org/10.3390/ijms21207603 - 14 Oct 2020
Cited by 9 | Viewed by 3558
Abstract
Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity [...] Read more.
Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development. Full article
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12 pages, 723 KiB  
Communication
Temperature Regulation of Primary and Secondary Seed Dormancy in Rosa canina L.: Findings from Proteomic Analysis
by Tomasz A. Pawłowski, Barbara Bujarska-Borkowska, Jan Suszka, Tadeusz Tylkowski, Paweł Chmielarz, Ewelina A. Klupczyńska and Aleksandra M. Staszak
Int. J. Mol. Sci. 2020, 21(19), 7008; https://doi.org/10.3390/ijms21197008 - 23 Sep 2020
Cited by 8 | Viewed by 2356
Abstract
Temperature is a key environmental factor restricting seed germination. Rose (Rosa canina L.) seeds are characterized by physical/physiological dormancy, which is broken during warm, followed by cold stratification. Exposing pretreated seeds to 20 °C resulted in the induction of secondary dormancy. The [...] Read more.
Temperature is a key environmental factor restricting seed germination. Rose (Rosa canina L.) seeds are characterized by physical/physiological dormancy, which is broken during warm, followed by cold stratification. Exposing pretreated seeds to 20 °C resulted in the induction of secondary dormancy. The aim of this study was to identify and functionally characterize the proteins associated with dormancy control of rose seeds. Proteins from primary dormant, after warm and cold stratification (nondormant), and secondary dormant seeds were analyzed using 2-D electrophoresis. Proteins that varied in abundance were identified by mass spectrometry. Results showed that cold stratifications affected the variability of the highest number of spots, and there were more common spots with secondary dormancy than with warm stratification. The increase of mitochondrial proteins and actin during dormancy breaking suggests changes in cell functioning and seed preparation to germination. Secondary dormant seeds were characterized by low levels of legumin, metabolic enzymes, and actin, suggesting the consumption of storage materials, a decrease in metabolic activity, and cell elongation. Breaking the dormancy of rose seeds increased the abundance of cellular and metabolic proteins that promote germination. Induction of secondary dormancy caused a decrease in these proteins and germination arrest. Full article
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Review

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26 pages, 1392 KiB  
Review
ABA Metabolism and Homeostasis in Seed Dormancy and Germination
by Naoto Sano and Annie Marion-Poll
Int. J. Mol. Sci. 2021, 22(10), 5069; https://doi.org/10.3390/ijms22105069 - 11 May 2021
Cited by 91 | Viewed by 7959
Abstract
Abscisic acid (ABA) is a key hormone that promotes dormancy during seed development on the mother plant and after seed dispersal participates in the control of dormancy release and germination in response to environmental signals. The modulation of ABA endogenous levels is largely [...] Read more.
Abscisic acid (ABA) is a key hormone that promotes dormancy during seed development on the mother plant and after seed dispersal participates in the control of dormancy release and germination in response to environmental signals. The modulation of ABA endogenous levels is largely achieved by fine-tuning, in the different seed tissues, hormone synthesis by cleavage of carotenoid precursors and inactivation by 8′-hydroxylation. In this review, we provide an overview of the current knowledge on ABA metabolism in developing and germinating seeds; notably, how environmental signals such as light, temperature and nitrate control seed dormancy through the adjustment of hormone levels. A number of regulatory factors have been recently identified which functional relationships with major transcription factors, such as ABA INSENSITIVE3 (ABI3), ABI4 and ABI5, have an essential role in the control of seed ABA levels. The increasing importance of epigenetic mechanisms in the regulation of ABA metabolism gene expression is also described. In the last section, we give an overview of natural variations of ABA metabolism genes and their effects on seed germination, which could be useful both in future studies to better understand the regulation of ABA metabolism and to identify candidates as breeding materials for improving germination properties. Full article
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23 pages, 6415 KiB  
Review
Molecular Control of Oil Metabolism in the Endosperm of Seeds
by Romane Miray, Sami Kazaz, Alexandra To and Sébastien Baud
Int. J. Mol. Sci. 2021, 22(4), 1621; https://doi.org/10.3390/ijms22041621 - 05 Feb 2021
Cited by 25 | Viewed by 4038
Abstract
In angiosperm seeds, the endosperm develops to varying degrees and accumulates different types of storage compounds remobilized by the seedling during early post-germinative growth. Whereas the molecular mechanisms controlling the metabolism of starch and seed-storage proteins in the endosperm of cereal grains are [...] Read more.
In angiosperm seeds, the endosperm develops to varying degrees and accumulates different types of storage compounds remobilized by the seedling during early post-germinative growth. Whereas the molecular mechanisms controlling the metabolism of starch and seed-storage proteins in the endosperm of cereal grains are relatively well characterized, the regulation of oil metabolism in the endosperm of developing and germinating oilseeds has received particular attention only more recently, thanks to the emergence and continuous improvement of analytical techniques allowing the evaluation, within a spatial context, of gene activity on one side, and lipid metabolism on the other side. These studies represent a fundamental step toward the elucidation of the molecular mechanisms governing oil metabolism in this particular tissue. In particular, they highlight the importance of endosperm-specific transcriptional controls for determining original oil compositions usually observed in this tissue. In the light of this research, the biological functions of oils stored in the endosperm of seeds then appear to be more diverse than simply constituting a source of carbon made available for the germinating seedling. Full article
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18 pages, 1037 KiB  
Review
Emerging Roles of RNA-Binding Proteins in Seed Development and Performance
by Lijuan Lou, Ling Ding, Tao Wang and Yong Xiang
Int. J. Mol. Sci. 2020, 21(18), 6822; https://doi.org/10.3390/ijms21186822 - 17 Sep 2020
Cited by 9 | Viewed by 3489
Abstract
Seed development, dormancy, and germination are key physiological events that are not only important for seed generation, survival, and dispersal, but also contribute to agricultural production. RNA-binding proteins (RBPs) directly interact with target mRNAs and fine-tune mRNA metabolism by governing post-transcriptional regulation, including [...] Read more.
Seed development, dormancy, and germination are key physiological events that are not only important for seed generation, survival, and dispersal, but also contribute to agricultural production. RNA-binding proteins (RBPs) directly interact with target mRNAs and fine-tune mRNA metabolism by governing post-transcriptional regulation, including RNA processing, intron splicing, nuclear export, trafficking, stability/decay, and translational control. Recent studies have functionally characterized increasing numbers of diverse RBPs and shown that they participate in seed development and performance, providing significant insight into the role of RBP–mRNA interactions in seed processes. In this review, we discuss recent research progress on newly defined RBPs that have crucial roles in RNA metabolism and affect seed development, dormancy, and germination. Full article
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13 pages, 1487 KiB  
Review
Seed Germination in Oil Palm (Elaeis guineensis Jacq.): A Review of Metabolic Pathways and Control Mechanisms
by Jing Cui, Emmanuelle Lamade and Guillaume Tcherkez
Int. J. Mol. Sci. 2020, 21(12), 4227; https://doi.org/10.3390/ijms21124227 - 13 Jun 2020
Cited by 13 | Viewed by 10404
Abstract
Oil palm is an oil-producing crop of major importance at the global scale. Oil palm mesocarp lipids are used for myriads industrial applications, and market demand has been growing for decades. In addition, oil palm seeds are oleaginous, and the oil extracted therefrom [...] Read more.
Oil palm is an oil-producing crop of major importance at the global scale. Oil palm mesocarp lipids are used for myriads industrial applications, and market demand has been growing for decades. In addition, oil palm seeds are oleaginous, and the oil extracted therefrom can be used for several purposes, from food to cosmetics. As such, there is a huge need in oil palm seeds to maintain the global cohort of more than 2 billion trees. However, oil palm seed germination is a rather difficult process, not only to break dormancy, but also because it is long and often reaches lower-than-expected germination rates. Surprisingly, despite the crucial importance of germination for oil palm plantation management, our knowledge is still rather limited, in particular about germinating oil palm seed metabolism. The present review incorporates different pieces of information that have been obtained in the past few years, in oil palm and in other palm species, in order to provide an overview of germination metabolism and its control. Further insights can also be gained from other oleaginous model plants, such as Arabidopsis or canola, however, palm seeds have peculiarities that must be accounted for, to gain a better understanding of germinating seed metabolism. Full article
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