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Metabolic Processes during Seed Germination

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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 December 2021) | Viewed by 44563

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Prof. Dr. Alma Balestrazzi

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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
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Dr. Andrea Pagano

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Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, 27100 Pavia, Italy
Interests: seed quality; seed vigor; seed germination; seed priming; pre-germinative metabolism; DNA damage response
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Dr. Łukasz Wojtyla

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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. Andrea Pagano
Dr. Łukasz Wojtyla
Guest Editors

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Keywords

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

Published Papers (11 papers)

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18 pages, 1728 KiB

Open AccessArticle

Endogenous Polyamines and Ethylene Biosynthesis in Relation to Germination of Osmoprimed Brassica napus Seeds under Salt Stress

by Katarzyna Lechowska, Łukasz Wojtyla, Muriel Quinet, Szymon Kubala, Stanley Lutts and Małgorzata Garnczarska

Int. J. Mol. Sci. 2022, 23(1), 349; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23010349 - 29 Dec 2021

Cited by 9 | Viewed by 2047

Abstract

Currently, seed priming is reported as an efficient and low-cost approach to increase crop yield, which could not only promote seed germination and improve plant growth state but also increase abiotic stress tolerance. Salinity represents one of the most significant abiotic stresses that alters multiple processes in plants. The accumulation of polyamines (PAs) in response to salt stress is one of the most remarkable plant metabolic responses. This paper examined the effect of osmopriming on endogenous polyamine metabolism at the germination and early seedling development of Brassica napus in relation to salinity tolerance. Free, conjugated and bound polyamines were analyzed, and changes in their accumulation were discussed with literature data. The most remarkable differences between the corresponding osmoprimed and unprimed seeds were visible in the free (spermine) and conjugated (putrescine, spermidine) fractions. The arginine decarboxylase pathway seems to be responsible for the accumulation of PAs in primed seeds. The obvious impact of seed priming on tyramine accumulation was also demonstrated. Moreover, the level of ethylene increased considerably in seedlings issued from primed seeds exposed to salt stress. It can be concluded that the polyamines are involved in creating the beneficial effect of osmopriming on germination and early growth of Brassica napus seedlings under saline conditions through moderate changes in their biosynthesis and accumulation. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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18 pages, 14006 KiB

Open AccessArticle

Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening

by Xiang Li, Kewei Cai, Xiaona Pei, Yan Li, Yanbo Hu, Fanjuan Meng, Xingshun Song, Mulualem Tigabu, Changjun Ding and Xiyang Zhao

Int. J. Mol. Sci. 2021, 22(22), 12414; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212414 - 17 Nov 2021

Cited by 18 | Viewed by 2333

Abstract

The NAC (NAM, ATAF and CUC) gene family plays a crucial role in the transcriptional regulation of various biological processes and has been identified and characterized in multiple plant species. However, genome-wide identification of this gene family has not been implemented in Juglans mandshurica, and specific functions of these genes in the development of fruits remain unknown. In this study, we performed genome-wide identification and functional analysis of the NAC gene family during fruit development and identified a total of 114 JmNAC genes in the J. mandshurica genome. Chromosomal location analysis revealed that JmNAC genes were unevenly distributed in 16 chromosomes; the highest numbers were found in chromosomes 2 and 4. Furthermore, according to the homologues of JmNAC genes in Arabidopsis thaliana, a phylogenetic tree was constructed, and the results demonstrated 114 JmNAC genes, which were divided into eight subgroups. Four JmNAC gene pairs were identified as the result of tandem duplicates. Tissue-specific analysis of JmNAC genes during different developmental stages revealed that 39 and 25 JmNAC genes exhibited upregulation during the mature stage in walnut exocarp and embryos, indicating that they may serve key functions in fruit development. Furthermore, 12 upregulated JmNAC genes were common in fruit ripening stage in walnut exocarp and embryos, which demonstrated that these genes were positively correlated with fruit development in J. mandshurica. This study provides new insights into the regulatory functions of JmNAC genes during fruit development in J. mandshurica, thereby improving the understanding of characteristics and evolution of the JmNAC gene family. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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20 pages, 16136 KiB

Open AccessArticle

Hydro-Electro Hybrid Priming Promotes Carrot (Daucus carota L.) Seed Germination by Activating Lipid Utilization and Respiratory Metabolism

by Shuo Zhao, Daniel Garcia, Yinglei Zhao and Danfeng Huang

Int. J. Mol. Sci. 2021, 22(20), 11090; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222011090 - 14 Oct 2021

Cited by 8 | Viewed by 2319

Abstract

Carrot (Daucus carota L.) is widely cultivated as one of the most important root crops, and developing an effective presowing treatment method can promote the development of modern mechanized precision sowing. In the present study, a novel seed priming technology, named hydro-electro hybrid priming (HEHP), was used to promote the germination of carrot seeds. Seed germination experiments showed that HEHP was able to increase the germination index (GI) and vigor index (VI) by 3.1-fold and 6.8-fold, respectively, and the effect was significantly superior to that of hydro-priming (HYD) and electrostatic field treatment (EF). The consumption and utilization rate of seed storage reserves were also greatly improved. Meanwhile, both glyoxysomes and mitochondria were found to appear ahead of time in the endosperm cells of HEHP through observations of the subcellular structure of the endosperm. Activities of isocitrate lyase (ICL), NAD-dependent malate dehydrogenase (MDH), pyruvate kinase (PK), and alcohol dehydrogenase (ADH) were significantly increased by HEHP. From transcriptome results, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to the glyoxylate cycle, glycolysis, gluconeogenesis, and the citrate cycle were significantly enriched and real-time quantitative PCR (qRT-PCR) analysis confirmed the expression pattern of 15 critical differentially expressed genes (DEGs) in these pathways. All DEGs encoding MDH, phosphoenolpyruvate carboxykinase (PEPCK), and PK were upregulated in HEHP; thus, it is reasonable to infer that the transformation of malate, oxalacetate, phosphoenolpyruvate, and pyruvate in the cytoplasm may be pivotal for the energy supply during early germination. The results suggest that the optimal effect of HEHP is achieved by initiating stored lipid utilization and respiratory metabolism pathways related to germination. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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17 pages, 4863 KiB

Open AccessArticle

Probing the Energetic Metabolism of Resting Cysts under Different Conditions from Molecular and Physiological Perspectives in the Harmful Algal Blooms-Forming Dinoflagellate Scrippsiella trochoidea

by Fengting Li, Aoao Yang, Zhangxi Hu, Siheng Lin, Yunyan Deng and Ying Zhong Tang

Int. J. Mol. Sci. 2021, 22(14), 7325; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147325 - 07 Jul 2021

Cited by 3 | Viewed by 2425

Abstract

Energetic metabolism is essential in maintaining the viability of all organisms. Resting cysts play important roles in the ecology of dinoflagellates, particularly for harmful algal blooms (HABs)-causative species. However, the energetic metabolism underlying the germination potency maintenance of resting cysts of dinoflagellate have been extremely scarce in studies from physiological and, particularly, molecular perspectives. Therefore, we used the cosmopolitan Scrippsiella trochoidea as a representative of HABs-forming and cyst-producing dinoflagellates in this work to obtain novel insights into the molecular mechanisms, regulating the energetic metabolism in dinoflagellate resting cysts, under different physical condition. As the starting step, we established a cDNA subtractive library via suppression subtractive hybridization (SSH) technology, from which we screened an incomplete sequence for the β subunit of ATP synthase gene (β-F₁-ATPase), a key indicator for the status of cell’s energetic metabolism. The full-length cDNA of β-F₁-ATPase gene from S.trochoidea (Stβ-F₁-ATPase) was then obtained via rapid amplification of cDNA ends (RACE) (Accession: MZ343333). Our real-time qPCR detections, in vegetative cells and resting cysts treated with different physical conditions, revealed that (1) the expression of Stβ-F₁-ATPase in resting cysts was generally much lower than that in vegetative cells, and (2) the Stβ-F₁-ATPase expressions in the resting cysts under darkness, lowered temperature, and anoxia, and during an extended duration of dormancy, were significantly lower than that in cysts under the condition normally used for culture-maintaining (a 12 h light:12 h dark cycle, 21 °C, aerobic, and newly harvested). Our detections of the viability (via Neutral Red staining) and cellular ATP content of resting cysts, at the conditions corresponding to the abovementioned treatments, showed that both the viability and ATP content decreased rapidly within 12 h and then maintained at low levels within the 4-day experimentation under all the three conditions applied (4 °C, darkness, and anoxia), which are well in accordance with the measurements of the transcription of Stβ-F₁-ATPase. These results demonstrated that the energy consumption of resting cysts reaches a low, but somehow stable, level within a short time period and is lower at low temperature, darkness, and anoxia than that at ambient temperature. Our work provides an important basis for explaining that resting cysts survive long-term darkness and low temperature in marine sediments from molecular and physiological levels. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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15 pages, 1610 KiB

Open AccessArticle

The Effect of Exogenous Application of Quercetin Derivative Solutions on the Course of Physiological and Biochemical Processes in Wheat Seedlings

by Marta Jańczak-Pieniążek, Dagmara Migut, Tomasz Piechowiak, Jan Buczek and Maciej Balawejder

Int. J. Mol. Sci. 2021, 22(13), 6882; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22136882 - 26 Jun 2021

Cited by 13 | Viewed by 2076

Abstract

Quercetin, classified as a flavonoid, is a strong antioxidant that plays a significant role in the regulation of physiological processes in plants, which is particularly important in the case of biotic and abiotic stresses. The study investigated the effect of the use of potassium quercetin solutions in various concentrations (0.5%, 1.0%, 3.0% and 5.0%) on the physiological and biochemical properties of wheat seedlings. A pot experiment was carried out in order to determine the most beneficial dose of this flavonoid acting as a bio-stimulant for wheat plants. Spraying with quercetin derivative solutions was performed twice, and physiological measurements (chlorophyll content and fluorescence as well as gas exchange) were carried out on the first and seventh days after each application. The total phenolic compounds content and the total antioxidant capacity were also determined. It was shown that the concentrations of potassium quercetin applied have a stimulating effect on the course of physiological processes. In the case of most of the tested physiological parameters (chlorophyll content and fluorescence and gas exchange) and the total antioxidant capacity, no significant differences were observed in their increase as a result of application with concentrations of 3.0 and 5.0%. Therefore, the beneficial effect of quercetin on the analysed parameters is already observed when spraying with a concentration of 3.0%. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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19 pages, 2438 KiB

Open AccessArticle

Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice

by Hedia Tnani, Dmytro Chebotarov, Ranjita Thapa, John Carlos I. Ignacio, Walter K. Israel, Fergie A. Quilloy, Shalabh Dixit, Endang M. Septiningsih and Tobias Kretzschmar

Int. J. Mol. Sci. 2021, 22(9), 4445; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22094445 - 24 Apr 2021

Cited by 8 | Viewed by 4926

Abstract

Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of “enriched haplotype” genome-wide association study based on the Ma-Zhan Red haplotype in the AG2 region was successfully used to narrow down AG2 from more than 7 Mb to less than 0.7 Mb. The AG2 peak region contained 27 genes, including the Rc gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling AG2 were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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22 pages, 3569 KiB

Open AccessArticle

AtFAHD1a: A New Player Influencing Seed Longevity and Dormancy in Arabidopsis?

by Davide Gerna, Erwann Arc, Max Holzknecht, Thomas Roach, Pidder Jansen-Dürr, Alexander K.H. Weiss and Ilse Kranner

Int. J. Mol. Sci. 2021, 22(6), 2997; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22062997 - 15 Mar 2021

Cited by 8 | Viewed by 2987

Abstract

Fumarylacetoacetate hydrolase (FAH) proteins form a superfamily found in Archaea, Bacteria, and Eukaryota. However, few fumarylacetoacetate hydrolase domain (FAHD)-containing proteins have been studied in Metazoa and their role in plants remains elusive. Sequence alignments revealed high homology between two Arabidopsis thaliana FAHD-containing proteins and human FAHD1 (hFAHD1) implicated in mitochondrial dysfunction-associated senescence. Transcripts of the closest hFAHD1 orthologue in Arabidopsis (AtFAHD1a) peak during seed maturation drying, which influences seed longevity and dormancy. Here, a homology study was conducted to assess if AtFAHD1a contributes to seed longevity and vigour. We found that an A. thaliana T-DNA insertional line (Atfahd1a-1) had extended seed longevity and shallower thermo-dormancy. Compared to the wild type, metabolite profiling of dry Atfahd1a-1 seeds showed that the concentrations of several amino acids, some reducing monosaccharides, and δ-tocopherol dropped, whereas the concentrations of dehydroascorbate, its catabolic intermediate threonic acid, and ascorbate accumulated. Furthermore, the redox state of the glutathione disulphide/glutathione couple shifted towards a more reducing state in dry mature Atfahd1a-1 seeds, suggesting that AtFAHD1a affects antioxidant redox poise during seed development. In summary, AtFAHD1a appears to be involved in seed redox regulation and to affect seed quality traits such as seed thermo-dormancy and longevity. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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17 pages, 4781 KiB

Open AccessArticle

The Rice Small Auxin-Up RNA Gene OsSAUR33 Regulates Seed Vigor via Sugar Pathway during Early Seed Germination

by Jia Zhao, Wenjun Li, Shan Sun, Liling Peng, Zhibo Huang, Yongqi He and Zhoufei Wang

Int. J. Mol. Sci. 2021, 22(4), 1562; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041562 - 04 Feb 2021

Cited by 24 | Viewed by 3617

Abstract

Seed vigor affects seed germination and seedling emergence, and therefore is an important agronomic trait in rice. Small auxin-up RNAs (SAURs) function in a range of developmental processes, but their role in seed vigor remains unclear. Here, we observed that disruption of OsSAUR33 resulted in reduced germination rates and low seed uniformity in early germination. Expression of OsSAUR33 was higher in mature grains and early germinating seeds. RNA-seq analysis revealed that OsSAUR33 modulated seed vigor by affecting the mobilization of stored reserves during germination. Disruption of OsSAUR33 increased the soluble sugar content in dry mature grains and seeds during early germination. OsSAUR33 interacted with the sucrose non-fermenting-1-related protein kinase OsSnRK1A, a regulator of the sugar signaling pathway, which influences the expression of sugar signaling-related genes during germination. Disruption of OsSAUR33 increased sugar-sensitive phenotypes in early germination, suggesting OsSAUR33 likely affects seed vigor through the sugar pathway. One elite haplotype of OsSAUR33 associated with higher seed vigor was identified mainly in indica accessions. This study provides insight into the effects of OsSAUR33 on seed vigor in rice. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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Review

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22 pages, 1787 KiB

Open AccessReview

Seed Dormancy and Pre-Harvest Sprouting in Rice—An Updated Overview

by Soo-In Sohn, Subramani Pandian, Thamilarasan Senthil Kumar, Yedomon Ange Bovys Zoclanclounon, Pandiyan Muthuramalingam, Jayabalan Shilpha, Lakkakula Satish and Manikandan Ramesh

Int. J. Mol. Sci. 2021, 22(21), 11804; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222111804 - 30 Oct 2021

Cited by 25 | Viewed by 5719

Abstract

Pre-harvest sprouting is a critical phenomenon involving the germination of seeds in the mother plant before harvest under relative humid conditions and reduced dormancy. As it results in reduced grain yield and quality, it is a common problem for the farmers who have cultivated the rice and wheat across the globe. Crop yields need to be steadily increased to improve the people’s ability to adapt to risks as the world’s population grows and natural disasters become more frequent. To improve the quality of grain and to avoid pre-harvest sprouting, a clear understanding of the crops should be known with the use of molecular omics approaches. Meanwhile, pre-harvest sprouting is a complicated phenomenon, especially in rice, and physiological, hormonal, and genetic changes should be monitored, which can be modified by high-throughput metabolic engineering techniques. The integration of these data allows the creation of tailored breeding lines suitable for various demands and regions, and it is crucial for increasing the crop yields and economic benefits. In this review, we have provided an overview of seed dormancy and its regulation, the major causes of pre-harvest sprouting, and also unraveled the novel avenues to battle pre-harvest sprouting in cereals with special reference to rice using genomics and transcriptomic approaches. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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17 pages, 887 KiB

Open AccessReview

Regulation of Seed Dormancy and Germination Mechanisms in a Changing Environment

by Ewelina A. Klupczyńska and Tomasz A. Pawłowski

Int. J. Mol. Sci. 2021, 22(3), 1357; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22031357 - 29 Jan 2021

Cited by 40 | Viewed by 9398

Abstract

Environmental conditions are the basis of plant reproduction and are the critical factors controlling seed dormancy and germination. Global climate change is currently affecting environmental conditions and changing the reproduction of plants from seeds. Disturbances in germination will cause disturbances in the diversity of plant communities. Models developed for climate change scenarios show that some species will face a significant decrease in suitable habitat area. Dormancy is an adaptive mechanism that affects the probability of survival of a species. The ability of seeds of many plant species to survive until dormancy recedes and meet the requirements for germination is an adaptive strategy that can act as a buffer against the negative effects of environmental heterogeneity. The influence of temperature and humidity on seed dormancy status underlines the need to understand how changing environmental conditions will affect seed germination patterns. Knowledge of these processes is important for understanding plant evolution and adaptation to changes in the habitat. The network of genes controlling seed dormancy under the influence of environmental conditions is not fully characterized. Integrating research techniques from different disciplines of biology could aid understanding of the mechanisms of the processes controlling seed germination. Transcriptomics, proteomics, epigenetics, and other fields provide researchers with new opportunities to understand the many processes of plant life. This paper focuses on presenting the adaptation mechanism of seed dormancy and germination to the various environments, with emphasis on their prospective roles in adaptation to the changing climate. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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24 pages, 1365 KiB

Open AccessReview

Desiccation Tolerance as the Basis of Long-Term Seed Viability

by Galina Smolikova, Tatiana Leonova, Natalia Vashurina, Andrej Frolov and Sergei Medvedev

Int. J. Mol. Sci. 2021, 22(1), 101; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22010101 - 24 Dec 2020

Cited by 42 | Viewed by 4047

Abstract

Desiccation tolerance appeared as the key adaptation feature of photoautotrophic organisms for survival in terrestrial habitats. During the further evolution, vascular plants developed complex anatomy structures and molecular mechanisms to maintain the hydrated state of cell environment and sustain dehydration. However, the role of the genes encoding the mechanisms behind this adaptive feature of terrestrial plants changed with their evolution. Thus, in higher vascular plants it is restricted to protection of spores, seeds and pollen from dehydration, whereas the mature vegetative stages became sensitive to desiccation. During maturation, orthodox seeds lose up to 95% of water and successfully enter dormancy. This feature allows seeds maintaining their viability even under strongly fluctuating environmental conditions. The mechanisms behind the desiccation tolerance are activated at the late seed maturation stage and are associated with the accumulation of late embryogenesis abundant (LEA) proteins, small heat shock proteins (sHSP), non-reducing oligosaccharides, and antioxidants of different chemical nature. The main regulators of maturation and desiccation tolerance are abscisic acid and protein DOG1, which control the network of transcription factors, represented by LEC1, LEC2, FUS3, ABI3, ABI5, AGL67, PLATZ1, PLATZ2. This network is complemented by epigenetic regulation of gene expression via methylation of DNA, post-translational modifications of histones and chromatin remodeling. These fine regulatory mechanisms allow orthodox seeds maintaining desiccation tolerance during the whole period of germination up to the stage of radicle protrusion. This time point, in which seeds lose desiccation tolerance, is critical for the whole process of seed development. Full article

(This article belongs to the Special Issue Metabolic Processes during Seed Germination)

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