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Plants
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Molecular Regulation of Seed Development and Germination
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Molecular Regulation of Seed Development and Germination

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Physiology and Metabolism".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 6209

Special Issue Editor

Dr. Justyna Fidler

E-Mail Website
Guest Editor
Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
Interests: plant molecular biology and biochemistry; phytohormones; abscisic acid metabolism and signaling; molecular regulation of seed development and germination
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, Molecular Regulation of Seed Development and Germination, will focus on the latest discoveries on molecular mechanisms that control seed development, dormancy, and germination. It aims to outline the role of molecular factors, proteins, and plant hormones, and the interactions of different signaling pathways involved in these processes. Additionally, attention will be paid to how changing environmental conditions and abiotic and biotic stresses influence these mechanisms. This is crucial for understanding the ability of seeds to adapt and survive in different environments and exploring ways to enhance this process through seed priming. The Special Issue will also aim to present new tools and technologies used to study molecular mechanisms of seed development and germination, including the application of genomics, genome editing, and proteomics. These studies have the potential to support the development of more resilient plants, which is particularly important in the context of climate change and the pressing demand for improved agricultural productivity.

Dr. Justyna Fidler
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 250 words) can be sent to the Editorial Office for assessment.

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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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 dormancy
  • seed development
  • germination
  • phytohormones
  • abscisic acid
  • gibberellins
  • signaling pathways
  • environmental stresses
  • priming

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Published Papers (6 papers)

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Research

9 pages, 1228 KB  
Communication
H2O2-GA3-Na2WO4 Synergistically Promotes Germination of Immature Winter Wheat Grains for Speed Breeding
by Dong Yan, Pengcheng Lv, Lichao Zhang, Dengke Wang, Tianyi Chen, Zefu Lu, Jizeng Jia and Lifeng Gao
Plants 2026, 15(9), 1313; https://doi.org/10.3390/plants15091313 - 24 Apr 2026
Viewed by 305
Abstract
Seed germination is a critical initial stage of the plant life cycle, regulated by signaling pathways such as phytohormones and reactive oxygen species (ROS). However, the low germination rate of immature grains is a key bottleneck limiting wheat speed breeding. This study used [...] Read more.
Seed germination is a critical initial stage of the plant life cycle, regulated by signaling pathways such as phytohormones and reactive oxygen species (ROS). However, the low germination rate of immature grains is a key bottleneck limiting wheat speed breeding. This study used immature grains of the winter wheat cultivar Kenong 199 (KN199) collected 18 days post anthesis to establish an efficient germination protocol. By screening individual and combined treatments of hydrogen peroxide (H2O2, 1%), gibberellin (GA3, 20 μM), and varying concentrations of abscisic acid (ABA) synthesis inhibitor sodium tungstate (Na2WO4), alongside transcriptome analysis, we identified the optimal reagent combination and gained preliminary insight into its molecular basis. The triple reagent combination of 0.5 mM Na2WO4 + 20 μM GA3 + 1% H2O2 exhibited the highest germination rate of 80%, approximately sevenfold higher than single reagent treatments, with germination rate peaking after 4 days. Transcriptome profiling revealed that this combination modulated the expression of key genes related to dormancy release and germination, including upregulation of GA biosynthesis gene GA3ox2 and ABA catabolism gene TaCYP707A2, and downregulation of ABA biosynthesis and signaling genes (ABI5, TaNCED1, etc.). Additionally, genes associated with energy metabolism and transport pathways were enhanced. This optimized reagent combination significantly improves immature grain germination, shortens the breeding cycle, and provides a practical tool for achieving “five generations per year” speed breeding in winter wheat. Our findings contribute to seed biology by offering a chemical strategy to overcome dormancy in immature cereal grains. Full article
(This article belongs to the Special Issue Molecular Regulation of Seed Development and Germination)
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22 pages, 3009 KB  
Article
Seed Nanopriming with Spirulina-Derived Carbon Dots Enhances Rice (Oryza sativa L.) Germination, Crop Establishment, and Seedling Metabolic Performance
by Luana Vanessa Peretti Minello, Cesar Aguzzoli, Aline Nunes, Eva Regina Oliveira, Marcelo Maraschin, Roberta Pena da Paschoa, Vanildo Silveira and Raul Antonio Sperotto
Plants 2026, 15(5), 770; https://doi.org/10.3390/plants15050770 - 3 Mar 2026
Cited by 1 | Viewed by 915
Abstract
Biogenic carbon dots (CDs) are emerging as promising plant biostimulants, yet their effects during early crop establishment remain underexplored. Here, we synthesized and characterized Spirulina-derived CDs and evaluated their efficacy as seed nanopriming agents in rice (Oryza sativa L.). CDs exhibited nanoscale [...] Read more.
Biogenic carbon dots (CDs) are emerging as promising plant biostimulants, yet their effects during early crop establishment remain underexplored. Here, we synthesized and characterized Spirulina-derived CDs and evaluated their efficacy as seed nanopriming agents in rice (Oryza sativa L.). CDs exhibited nanoscale size, abundant surface functionalities, and a highly negative ζ-potential, indicative of stable aqueous dispersions. Spectroscopic characterization (Raman and FTIR) confirmed a graphitic–amorphous carbon structure. Near-infrared spectroscopy coupled to principal component analysis revealed time-dependent metabolic changes during imbibition, identifying 8–12 h as the optimal priming window. Nanopriming with Spirulina CDs (0.2 mg mL−1 for 12 h) increased the seed germination rate (25%), the germination speed index (17%), vigor index I (22%), and root length (37%) compared to hydropriming. Biochemically, the nanoprimed seedlings accumulated higher levels of starch (24%), total carbohydrates (8%), and total phenolics (20%), without evidence of oxidative imbalance, based on antioxidant capacity measurements and proteomic profiling. Proteomic analysis revealed coordinated metabolic reprogramming, characterized by increased abundance of proteins involved in translation, energy metabolism, and ion/nutrient homeostasis, alongside reduced abundance of proteins associated with defense and catabolic processes. This shift from stress-preparation to growth-oriented metabolism supports improved seedling establishment. Overall, Spirulina-derived CDs function as effective nanobiostimulants that promote early metabolic activation and resource mobilization, offering a sustainable strategy to enhance rice seedling establishment. Full article
(This article belongs to the Special Issue Molecular Regulation of Seed Development and Germination)
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16 pages, 3196 KB  
Article
Integrating Metabolomics and Proteomics to Reveal the Regulatory Network Governing the Natural Variation in Rice Seed Germination Rate
by Xiaoxuan Zhang, Chenkun Yang, Yunyun Li, Ran Zhang, Jinjin Zhu, Wanghua Wu, Yuheng Shi, Xianqing Liu, Xiaoyan Han and Jie Luo
Plants 2026, 15(4), 559; https://doi.org/10.3390/plants15040559 - 10 Feb 2026
Viewed by 597
Abstract
Seed germination rate is a key early trait that strongly influences rice yield. Although germination is known to be regulated by classical phytohormones and certain metabolites, the systematic metabolic regulatory network underlying natural variation, especially the key hub metabolites with causal function, still [...] Read more.
Seed germination rate is a key early trait that strongly influences rice yield. Although germination is known to be regulated by classical phytohormones and certain metabolites, the systematic metabolic regulatory network underlying natural variation, especially the key hub metabolites with causal function, still lacks in-depth analysis. In this study, we investigated 56 rice accessions showing pronounced differences in germination performance and systematically identified metabolic pathways associated with germination rate by integrating metabolomic and proteomic analyses. Pathways involved in amino acid metabolism, energy metabolism, and glutathione metabolism were coordinately activated in Rapid Germination (RG) seeds compared with Delayed Germination (DG) seeds. Among them, glutamine was significantly enriched in the RG group. Exogenous application of glutamine selectively and significantly promoted radicle and shoot elongation in a subset of DG varieties, providing direct evidence for a positive causal role of glutamine in seed germination. The variety-specific response further suggests that germination is controlled by a complex, genotype-dependent regulatory network. Together, our results highlight a glutamine-centered metabolic program as an important basis for rapid rice seed germination and provide potential targets for improving early vigor through metabolic engineering and molecular breeding. Full article
(This article belongs to the Special Issue Molecular Regulation of Seed Development and Germination)
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22 pages, 1773 KB  
Article
Differential Regulation of Gene Expression, Ion Homeostasis, and Antioxidant Defense Confers Salinity Tolerance During Seed Germination in Wheat
by Ahmed Sallam, Nouran M. Hasseb, Mohamed A. Karam, Andreas Börner, Xu Zheng and Yasser S. Moursi
Plants 2026, 15(2), 230; https://doi.org/10.3390/plants15020230 - 12 Jan 2026
Cited by 2 | Viewed by 1087
Abstract
Salinity represents a major constraint on plant development and crop productivity in wheat, which represents one of the most critical sources of dietary calories worldwide. Its detrimental effects are particularly pronounced during the early stages of growth, including seed germination and seedling establishment. [...] Read more.
Salinity represents a major constraint on plant development and crop productivity in wheat, which represents one of the most critical sources of dietary calories worldwide. Its detrimental effects are particularly pronounced during the early stages of growth, including seed germination and seedling establishment. Salinity tolerance is a multifaceted trait governed by several interrelated mechanisms, notably ion homeostasis, osmotic adjustment, activation of enzymatic antioxidant systems, and transcriptional regulation of ion transporter genes. In the present study, contrasting wheat genotypes exhibiting differential salinity tolerance were selected from a panel of 172 accessions evaluated under salinity stress (175 mM NaCl) and control conditions (0 mM NaCl). The objectives of the current study are to confirm the underlying physiological and molecular mechanisms conferring salinity tolerance. Key physiological and molecular parameters including Na+, K+, and P homeostasis; activities of major antioxidant enzymes; and expression profiles of the salinity-responsive ion transporter genes TaAVP1 and NHX1 were quantified in six tolerant genotypes and one susceptible genotype. The tolerant genotypes exhibited higher concentrations of Na+ and K+ and elevated activities of all antioxidant enzymes, compared with the susceptible genotype. Furthermore, the tolerant genotypes showed differential expression of TaAVP1 and NHX1: both genes were upregulated in Javelin 48 and Kandahar, whereas they were downregulated in genotype 1018d. Notably, genotype Kule demonstrated the highest Na+ accumulation, accompanied by markedly elevated activities of all major antioxidant enzymes, with ascorbate peroxidase and glutathione reductase increasing by 9.20-fold and 2.32-fold, respectively, under salinity stress. Based on these findings, the tolerant genotypes can be categorized into two functional groups: Javelin 48, Ghati, and 1018d (characterized by high K+ and salinity tolerance) are better suited to soils affected by low Na+ salinity, whereas Kandahar, Kule, and 1049 (characterized by high Na+ and sodicity tolerance) are more adapted to soils with elevated Na+ levels. In conclusion, the tolerant genotypes exhibited distinct, coordinated mechanisms to mitigate salinity stress, underscoring the complexity and plasticity of adaptive responses in wheat. Full article
(This article belongs to the Special Issue Molecular Regulation of Seed Development and Germination)
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19 pages, 3503 KB  
Article
Discovery of Hub Genes Involved in Seed Development and Lipid Biosynthesis in Sea Buckthorn (Hippophae rhamnoides L.) Using UID Transcriptome Sequencing
by Siyang Zhao, Chengjiang Ruan, Alexey A. Dmitriev and Hyun Uk Kim
Plants 2025, 14(15), 2436; https://doi.org/10.3390/plants14152436 - 6 Aug 2025
Viewed by 1331
Abstract
Sea buckthorn is a vital woody oil species valued for its role in soil conservation and its bioactive seed oil, which is rich in unsaturated fatty acids and other compounds. However, low seed oil content and small seed size are the main bottlenecks [...] Read more.
Sea buckthorn is a vital woody oil species valued for its role in soil conservation and its bioactive seed oil, which is rich in unsaturated fatty acids and other compounds. However, low seed oil content and small seed size are the main bottlenecks restricting the development and utilization of sea buckthorn. In this study, we tested the seed oil content and seed size of 12 sea buckthorn cultivars and identified the key genes and transcription factors involved in seed development and lipid biosynthesis via the integration of UID RNA-seq (Unique Identifiers, UID), WGCNA (weighted gene co-expression network analysis) and qRT-PCR (quantitative real-time PCR) analysis. The results revealed five cultivars (CY02, CY11, CY201309, CY18, CY21) with significantly higher oil contents and five cultivars (CY10, CY201309, CY18, CY21, CY27) with significantly heavier seeds. A total of 10,873 genes were significantly differentially expressed between the S1 and S2 seed developmental stages of the 12 cultivars. WGCNA was used to identify five modules related to seed oil content and seed weight/size, and 417 candidate genes were screened from these modules. Among them, multiple hub genes and transcription factors were identified; for instance, ATP synthase, ATP synthase subunit D and Acyl carrier protein 1 were related to seed development; plastid–lipid-associated protein, acyltransferase-like protein, and glycerol-3-phosphate 2-O-acyltransferase 6 were involved in lipid biosynthesis; and transcription factors DOF1.2, BHLH137 and ERF4 were associated with seed enlargement and development. These findings provide crucial insights into the genetic regulation of seed traits in sea buckthorn, offering targets for future breeding efforts aimed at improving oil yield and quality. Full article
(This article belongs to the Special Issue Molecular Regulation of Seed Development and Germination)
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22 pages, 5319 KB  
Article
Exogenous Sucrose Improves the Vigor of Aged Safflower Seeds by Mediating Fatty Acid Metabolism and Glycometabolism
by Tang Lv, Lin Zhong, Juan Li, Cuiping Chen, Bin Xian, Tao Zhou, Chaoxiang Ren, Jiang Chen, Jin Pei and Jie Yan
Plants 2025, 14(15), 2301; https://doi.org/10.3390/plants14152301 - 25 Jul 2025
Cited by 1 | Viewed by 1345
Abstract
Safflower (Carthamus tinctorius L.) seeds, rich in triacylglycerols, have poor fatty acid-to-sugar conversion during storage, affecting longevity and vigor. Previous experiments have shown that the aging of safflower seeds is mainly related to the impairment of energy metabolism pathways such as glycolysis, [...] Read more.
Safflower (Carthamus tinctorius L.) seeds, rich in triacylglycerols, have poor fatty acid-to-sugar conversion during storage, affecting longevity and vigor. Previous experiments have shown that the aging of safflower seeds is mainly related to the impairment of energy metabolism pathways such as glycolysis, fatty acid degradation, and the tricarboxylic acid cycle. The treatment with exogenous sucrose can partially promote the germination of aged seeds. However, the specific pathways through which exogenous sucrose promotes the germination of aged safflower seeds have not yet been elucidated. This study aimed to explore the molecular mechanism by which exogenous sucrose enhances the vitality of aged seeds. Phenotypically, it promoted germination and seedling establishment in CDT-aged seeds but not in unaged ones. Biochemical analyses revealed increased soluble sugars and fatty acids in aged seeds with sucrose treatment. Enzyme activity and transcriptome sequencing showed up-regulation of key enzymes and genes in related metabolic pathways in aged seeds, not in unaged ones. qPCR confirmed up-regulation of genes for triacylglycerol and fatty acid-to-sugar conversion. Transmission electron microscopy showed a stronger connection between the glyoxylate recycler and oil bodies, accelerating oil body degradation. In conclusion, our research shows that exogenous sucrose promotes aged safflower seed germination by facilitating triacylglycerol hydrolysis, fatty acid conversion, and glycometabolism, rather than simply serving as a source of energy to supplement the energy deficiency of aged seeds. These findings offer practical insights for aged seeds, especially offering an effective solution to the aging problem of seeds with high oil content. Full article
(This article belongs to the Special Issue Molecular Regulation of Seed Development and Germination)
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