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Seed Biology at the System Level
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Seed Biology at the System Level

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

Deadline for manuscript submissions: closed (20 August 2023) | Viewed by 28624

Special Issue Editors

Dr. Daoquan Xiang

E-Mail Website
Guest Editor
Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
Interests: seed development; embryogenesis; transcriptomics; proteomics; functional genomics; epigenetics; development biology
Dr. Teagen D. Quilichini

E-Mail Website
Guest Editor
Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
Interests: cell and developmental biology; plant reproduction; embryogenesis; plant metabolism; seed and pollen biology

Special Issue Information

Dear Colleagues,

Seed development in angiosperms represents a crucial sexual phase in the life cycle of flowering plants, including crop species. Seeds require the formation of three genetically distinct subcompartments, including the embryo and endosperm as products of fertilization, within a maternally derived seed coat capsule (or testa). The development of this complex, self-contained vessel requires genetic, proteomic, and metabolic inputs to ensure that each seed carries the germline information, storage reserves, and nutrients necessary for successful reproduction and survival. Despite progress in the fundamental understanding of seed development, our understanding of the regulating networks and metabolic programs involved in producing a seed and their implications for improving seed yield and nutritional quality remains incomplete, particularly for crop plants. A holistic understanding of the complexities and interactions that drive seed development is becoming increasingly possible with the application of “omics” tools to decipher gene, protein, and metabolite networks. Together with computational analysis and modeling, these interdisciplinary efforts offer opportunities to uncover the underpinning mechanisms that support seed formation.

This Special Issue will highlight current efforts to develop comprehensive systems-level understanding of seed biology, with insights into the transcriptional, proteomic, and metabolic networks that support seed development in model and crop plants. Studies included in this issue will apply integrated systems-level approaches, including genomics, transcriptomics, proteomics, metabolomics, and/or modeling to examine key processes in the formation of seeds, from fertilization to the onset of dormancy and/or germination, and provide foundational and comprehensive insights into seed biology. There is particular interest in research that examines the nutritional value, agronomic performance, gene regulatory networks, and/or molecular mechanisms that control the development of the three seed subcompartments and provide insights to improve yield, resilience, or meal quality.

Dr. Daoquan Xiang
Dr. Teagen D. Quilichini
Guest Editors

Manuscript Submission Information

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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 development
  • embryogenesis
  • storage reserves
  • transcriptomics
  • proteomics
  • functional genomics
  • genetics
  • epigenetics
  • genomics
  • fatty acid
  • antinutritional compound
  • development biology

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Published Papers (9 papers)

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Research

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15 pages, 2666 KiB  
Article
Effects of Chloride and Sulfate Salts on Seed Germination and Seedling Growth of Ballota hirsuta Benth. and Myrtus communis L.
by Mohammed Dadach, Muhammad Zaheer Ahmed, Arvind Bhatt, Emanuele Radicetti and Roberto Mancinelli
Plants 2023, 12(22), 3906; https://doi.org/10.3390/plants12223906 - 20 Nov 2023
Viewed by 1979
Abstract
Soil salinity is a well-known abiotic factor affecting the germination and seedling growth of various plant species. Therefore, we evaluated the effects of different chloride salts (NaCl, KCl and MgCl2) and sulfate salts (Na2SO4, K2SO [...] Read more.
Soil salinity is a well-known abiotic factor affecting the germination and seedling growth of various plant species. Therefore, we evaluated the effects of different chloride salts (NaCl, KCl and MgCl2) and sulfate salts (Na2SO4, K2SO4 and MgSO4) on the seed germination and early seedling growth of two important ethnomedicinal shrubs of North Africa and the Mediterranean basin (Ballota hirsuta and Myrtus communis). Seeds of these species were subjected to five salinity levels (0–100 mM) and incubated at 20 °C under a light regime (12 h photoperiod). Both species demonstrated their highest germination percentage under control conditions (i.e., without salinity). However, as salinity levels increased, the germination percentages for both species decreased, regardless of the type of salt used. Cations appeared to be more determinative than the anions in regulating the seed germination of both species. M. communis seeds displayed greater sensitivity to sodium (Na+) salts, especially when accompanied with chloride (Cl−) anions. At the higher salt concentrations (75 and 100 mM), Na+ salts had a more pronounced inhibitory effect on M. communis seedling growth compared to potassium (K+) and magnesium (Mg2+) salts. Conversely, Mg2+ salts were more detrimental to seedling growth in B. hirsuta. Based on our results, it can be concluded that both of these species are able to tolerate a moderate level of salinity. Overall, B. hirsuta may be a promising choice for rehabilitating the soils dominated by chloride salts, while M. communis could be utilized for restoring sulfate-dominated soils. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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24 pages, 5900 KiB  
Article
Quantitative Analysis of Seed Surface Tubercles in Silene Species
by José Luis Rodríguez-Lorenzo, José Javier Martín-Gómez, Ana Juan, Ángel Tocino and Emilio Cervantes
Plants 2023, 12(19), 3444; https://doi.org/10.3390/plants12193444 - 29 Sep 2023
Cited by 3 | Viewed by 1524
Abstract
In the Caryophyllaceae, seed surfaces contain cell protrusions, of varying sizes and shapes, called tubercles. Tubercles have long been described in many species, but quantitative analyses with measurements of size and shape are lacking in the literature. Based on optical photography, the seeds [...] Read more.
In the Caryophyllaceae, seed surfaces contain cell protrusions, of varying sizes and shapes, called tubercles. Tubercles have long been described in many species, but quantitative analyses with measurements of size and shape are lacking in the literature. Based on optical photography, the seeds of Silene were classified into four types: smooth, rugose, echinate and papillose. Seeds in each of these groups have characteristic geometrical properties: smooth seeds lack tubercles and have the highest values of circularity and solidity in their lateral views, while papillose seeds have the largest tubercles and lowest values of circularity and solidity both in lateral and dorsal views. Here, tubercle width, height and slope, maximum and mean curvature values and maximum to mean curvature ratio were obtained for representative seeds of a total of 31 species, 12 belonging to Silene subg. Behenantha and 19 to S. subg. Silene. The seeds of the rugose type had lower values of curvature. Additionally, lower values of curvature were found in species of S. subg. Silene in comparison with S. subg. Behenantha. The seeds of S. subg. Behenantha had higher values of tubercle height and slope and higher values of maximum and average curvature and maximum to mean curvature ratio. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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15 pages, 2985 KiB  
Article
Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax
by Peng Gao, Shuqing Qiu, Xingliang Ma, Isobel A. P. Parkin, Daoquan Xiang and Raju Datla
Plants 2022, 11(15), 2031; https://doi.org/10.3390/plants11152031 - 4 Aug 2022
Cited by 2 | Viewed by 2194
Abstract
Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing [...] Read more.
Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing methods to generate in-depth transcriptome profiles of flax tissues with emphasis on the reproductive phases of five key stages of embryogenesis (globular embryo, heart embryo, torpedo embryo, cotyledon embryo, and mature embryo), mature seed, and vegetative tissues viz. ovary, anther, and root. These datasets were used to establish the co-expression networks covering 36 gene modules based on the expression patterns for each gene through weighted gene co-expression network analysis (WGCNA). Functional interrogation with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) of dominantly expressed genetic modules in tissues revealed pathways involved in the development of different tissues. Moreover, the essential genes in embryo development and synthesis of storage reserves were identified based on their dynamic expression patterns. Together, this comprehensive dataset for developing embryos, mature seeds and vegetative tissues provides new insights into molecular mechanisms of seed development with potential for flax crop improvement. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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18 pages, 999 KiB  
Article
Quantifying Cardinal Temperatures of Chia (Salvia hispanica L.) Using Non-Linear Regression Models
by Daniel Cabrera-Santos, Cesar A. Ordoñez-Salanueva, Salvador Sampayo-Maldonado, Jorge E. Campos, Alma Orozco-Segovia and Cesar M. Flores-Ortiz
Plants 2022, 11(9), 1142; https://doi.org/10.3390/plants11091142 - 22 Apr 2022
Cited by 7 | Viewed by 2577
Abstract
Temperature is the main factor that impacts germination and therefore the success of annual crops, such as chia (Salvia hispanica L.), whose seeds are known for their high nutritional value related to its oil. The effect of temperature on germination is related [...] Read more.
Temperature is the main factor that impacts germination and therefore the success of annual crops, such as chia (Salvia hispanica L.), whose seeds are known for their high nutritional value related to its oil. The effect of temperature on germination is related to cardinal-temperature concepts that describe the range of temperature over which seeds of a particular species can germinate. Therefore, in this study, in addition to calculated germinative parameters such as total germination and germination rate of S. hispanica seeds, the effectiveness of non-linear models for estimating the cardinal temperatures of chia seeds was also determined. We observed that germination of S. hispanica occurred in cold to moderate-high temperatures (10–35 °C), having an optimal range between 25 and 35 °C, with the highest GR and t50 at 30 °C. Temperatures higher than 35 °C significantly reduced germination. Output parameters of the different non-linear models showed that the response of chia germination to temperature was best explained by beta models (B). Cardinal temperatures calculated by the B1 model for chia germination were: 2.52 ± 6.82 °C for the base, 30.45 ± 0.32 °C for the optimum, and 48.58 ± 2.93 °C for the ceiling temperature. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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20 pages, 2692 KiB  
Article
Morphological and Structural Details of Tomato Seed Coat Formation: A Different Functional Role of the Inner and Outer Epidermises in Unitegmic Ovule
by Inna A. Chaban, Alexander A. Gulevich, Neonila V. Kononenko, Marat R. Khaliluev and Ekaterina N. Baranova
Plants 2022, 11(9), 1101; https://doi.org/10.3390/plants11091101 - 19 Apr 2022
Cited by 3 | Viewed by 3871
Abstract
In order to understand how and what structures of the tomato ovule with a single integument form the seed coat of a mature seed, a detailed study of the main development stages of the tomato ovule integument was carried out using the methods [...] Read more.
In order to understand how and what structures of the tomato ovule with a single integument form the seed coat of a mature seed, a detailed study of the main development stages of the tomato ovule integument was carried out using the methods of light and electron microscopy. The integument itself it was shown to transform in the course of development into the coat (skin) of a mature seed, but the outer and inner epidermises of the integument and some layers of the integument parenchyma are mainly involved in this process. The outer epidermis cells are highly modified in later stages; their walls are thickened and lignified, creating a unique relatively hard outer coat. The fate of the inner epidermis of integument is completely different. It is separated from the other parenchyma cells of integument and is transformed into an independent new secretory tissue, an endothelium, which fences off the forming embryo and endosperm from the death zone. Due to the secretory activity of the endothelium, the dying inner parenchyma cells of the integument are lysed. Soon after the cuticle covers the endosperm, the lysis of dead integument cells stops and their flattened remnants form dense layers, which then enter the final composition of the coat of mature tomato seed. The endothelium itself returns to the location of the integument inner epidermis. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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20 pages, 8459 KiB  
Article
Morphological and Ultrastructural Features of Formation of the Skin of Wheat (Triticum aestivum L.) Kernel
by Inna A. Chaban, Alexander A. Gulevich, Elena A. Smirnova and Ekaterina N. Baranova
Plants 2021, 10(11), 2538; https://doi.org/10.3390/plants10112538 - 21 Nov 2021
Cited by 5 | Viewed by 2585
Abstract
The integumentary tissues of plant seeds protect the embryo (new sporophyte) forming in them from unfavorable external conditions; therefore, comprehensive knowledge about the structural and functional specificity of seed covers in various plants may be of both theoretical and practical interest. As a [...] Read more.
The integumentary tissues of plant seeds protect the embryo (new sporophyte) forming in them from unfavorable external conditions; therefore, comprehensive knowledge about the structural and functional specificity of seed covers in various plants may be of both theoretical and practical interest. As a result of our study, additional data were obtained on the morphological and ultrastructural features of the formation of a multilayer skin of wheat (Triticum aestivum L.) kernel (caryopsis). The ultrastructure research analysis showed that differentiation of the pericarp and inner integument of the ovule leads to the formation of functionally different layers of the skin of mature wheat grain. Thus, the differentiation of exocarp and endocarp cells is accompanied by a significant thickening of the cell walls, which reliably protect the ovule from adverse external conditions. The cells of the two-layer inner integument of the ovule differentiate into cuticular and phenolic layers, which are critical for protecting daughter tissues from various pathogens. The epidermis of the nucellus turns into a layer of mucilage, which apparently helps to maintain the water balance of the seed. Morphological and ultrastructural data showed that the formation of the kernel’s skin occurs in coordination with the development of the embryo and endosperm up to the full maturity of the kernel. This is evidenced by the structure of the cytoplasm and nucleus, characteristic of metabolically active protoplasts of cells, which is observed in most integumentary layers at the late stages of maturation. This activity can also be confirmed by a significant increase in the thickness of the cell walls in the cells of two layers of the exocarp and in cross cells in comparison with the earlier stages. Based on these results, we came to the conclusion that the cells of a majority in the covering tissues of the wheat kernel during its ontogenesis are transformed into specialized layers of the skin by terminal differentiation. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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Review

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14 pages, 1906 KiB  
Review
Saponin Biosynthesis in Pulses
by Bianyun Yu, Nii Patterson and L. Irina Zaharia
Plants 2022, 11(24), 3505; https://doi.org/10.3390/plants11243505 - 14 Dec 2022
Cited by 12 | Viewed by 3881
Abstract
Pulses are a group of leguminous crops that are harvested solely for their dry seeds. As the demand for plant-based proteins grows, pulses are becoming important food crops worldwide. In addition to being a rich source of nutrients, pulses also contain saponins that [...] Read more.
Pulses are a group of leguminous crops that are harvested solely for their dry seeds. As the demand for plant-based proteins grows, pulses are becoming important food crops worldwide. In addition to being a rich source of nutrients, pulses also contain saponins that are traditionally considered anti-nutrients, and impart bitterness and astringency. Saponins are plant secondary metabolites with great structural and functional diversity. Given their diverse functional properties and biological activities, both undesirable and beneficial, saponins have received growing attention. It can be expected that redirecting metabolic fluxes to control the saponin levels and produce desired saponins would be an effective approach to improve the nutritional and sensory quality of the pulses. However, little effort has been made toward understanding saponin biosynthesis in pulses, and, thus there exist sizable knowledge gaps regarding its pathway and regulatory network. In this paper, we summarize the research progress made on saponin biosynthesis in pulses. Additionally, phylogenetic relationships of putative biosynthetic enzymes among multiple pulse species provide a glimpse of the evolutionary routes and functional diversification of saponin biosynthetic enzymes. The review will help us to advance our understanding of saponin biosynthesis and aid in the development of molecular and biotechnological tools for the systematic optimization of metabolic fluxes, in order to produce the desired saponins in pulses. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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15 pages, 895 KiB  
Review
The Seed Coat’s Impact on Crop Performance in Pea (Pisum sativum L.)
by Teagen D. Quilichini, Peng Gao, Bianyun Yu, Dengjin Bing, Raju Datla, Pierre Fobert and Daoquan Xiang
Plants 2022, 11(15), 2056; https://doi.org/10.3390/plants11152056 - 6 Aug 2022
Cited by 11 | Viewed by 3287
Abstract
Seed development in angiosperms produces three genetically and developmentally distinct sub-compartments: the embryo, endosperm, and seed coat. The maternally derived seed coat protects the embryo and interacts closely with the external environment especially during germination and seedling establishment. Seed coat is a key [...] Read more.
Seed development in angiosperms produces three genetically and developmentally distinct sub-compartments: the embryo, endosperm, and seed coat. The maternally derived seed coat protects the embryo and interacts closely with the external environment especially during germination and seedling establishment. Seed coat is a key contributor to seed composition and an important determinant of nutritional value for humans and livestock. In this review, we examined pea crop productivity through the lens of the seed coat, its contribution to several valued nutritional traits of the pea crop, and its potential as a breeding target. Key discoveries made in advancing the knowledge base for sensing and transmission of external signals, the architecture and chemistry of the pea seed coat, and relevant insights from other important legumes were discussed. Furthermore, for selected seed coat traits, known mechanisms of genetic regulation and efforts to modulate these mechanisms to facilitate composition and productivity improvements in pea were discussed, alongside opportunities to support the continued development and improvement of this underutilized crop. This review describes the most important features of seed coat development in legumes and highlights the key roles played by the seed coat in pea seed development, with a focus on advances made in the genetic and molecular characterization of pea and other legumes and the potential of this key seed tissue for targeted improvement and crop optimization. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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9 pages, 628 KiB  
Review
Endosperm–Embryo Communications: Recent Advances and Perspectives
by Jingpu Song, Xin Xie, Yuhai Cui and Jitao Zou
Plants 2021, 10(11), 2511; https://doi.org/10.3390/plants10112511 - 19 Nov 2021
Cited by 9 | Viewed by 5161
Abstract
Seed maturation depends on well-coordinated communications between the processes of endosperm and embryo development. The endosperm is considered to be destined to support embryo development and the timing of endosperm cellularization is critical for embryo growth. Recent findings suggest that the endosperm development [...] Read more.
Seed maturation depends on well-coordinated communications between the processes of endosperm and embryo development. The endosperm is considered to be destined to support embryo development and the timing of endosperm cellularization is critical for embryo growth. Recent findings suggest that the endosperm development and the onset of embryo maturation are two independent processes during seed development. Meanwhile, it is lately reported that several mobile regulators originating from the endosperm are needed to ensure proper embryo growth and seed maturation. In this opinion article, we highlight processes on how endosperm communicates with embryo during seed development and discuss some intriguing questions in light of the latest advancements. Full article
(This article belongs to the Special Issue Seed Biology at the System Level)
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