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Gene Networks in Seeds
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Gene Networks in Seeds

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (27 April 2023) | Viewed by 21246

Special Issue Editors

Prof. Dr. Raquel Iglesias Fernandez

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Guest Editor
1. Centro de Biotecnología y Genómica de Plantas (CBGP-UPM), 28223 Madrid, Spain
2. Department of Biotechnology-Plant Biology, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (ETSIAAB-UPM), Universidad Politécnica de Madrid, 28040 Madrid, Spain
Interests: molecular physiology of seed germination of species with agricultural importance (Hordeum vulgare, Prunus domestica); model plants (Brachypodium distachyon and Arabidopsis thaliana L.)
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jesús Vicente-Carbajosa

E-Mail Website
Guest Editor
1. Centro de Biotecnología y Genómica de Plantas (CBGP-UPM), 28223 Madrid, Spain
2. Department of Biotechnology-Plant Biology, Universidad Politécnica de Madrid, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (ETSIAAB- UPM), 28040-Madrid, Spain
Interests: abiotic stress; seed development; transcriptional regulation; regulatoy networks

Special Issue Information

Dear Colleagues,

Seeds are the first world crop and constitute the staple food for human livings. From a biological point of view, the seed is the dispersion unit of spermatophyte plants and guarantees the survival of the species. Numerous studies have shed light on the molecular and physiological basis governing seed development (embryogenesis, maturation and germination). Classically, seed regulatory networks have involved transcription factors (TFs), such as those belonging to bZIP, DOF, MYB and B3 (VP1/ABI3, FUS3 and LEC2) classes. The maize Viviparous-1 (Vp-1) TF has been reported as the main player of Pre-Harvest Sprouting; its barley ortholog (HvVP1) also plays an essential role in the regulation of genes during seed maturation and germination, and its physical interaction with GAMYB, BPBF and BLZ2 TFs has been also described. However, gene expression not only depends on transcription factor regulation; other molecular mechanisms also participate, such as the epigenetic, post-transcriptional, and post-translational mechanisms. Recent works have demonstrated the relevance of DNA methylation controlling seed gene expression, and how the oxidation of specific nucleotides produced by reactive oxygen species (ROS) modify the stability of the seed stored mRNAs. The main purpose of this Special Issue entitled “Regulatory Networks in Seeds” is to compile the most recent discoveries on seed genetics, epigenetics, and biochemistry with the aim of drawing an updated and detailed landscape of the seed biology.

Dr. Raquel Iglesias Fernández
Prof. Dr. Jesús Vicente-Carbajosa
Guest Editors

Manuscript Submission Information

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

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. 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

  • epigenetics
  • genetics
  • germination
  • post-transcriptional regulation
  • post-translational regulation
  • seed
  • transcription factor

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Published Papers (6 papers)

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Research

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19 pages, 2021 KiB  
Article
Identifying SSR Markers Related to Seed Fatty Acid Content in Perilla Crop (Perilla frutescens L.)
by Hyeon Park, Kyu Jin Sa, Do Yoon Hyun, Sookyeong Lee and Ju Kyong Lee
Plants 2021, 10(7), 1404; https://doi.org/10.3390/plants10071404 - 9 Jul 2021
Cited by 19 | Viewed by 3405
Abstract
Perilla seed oil has been attracting attention in South Korea as a health food. Five fatty acids of 100 Perilla accessions were identified as follows: palmitic acid (PA) (5.10–9.13%), stearic acid (SA) (1.70–3.99%), oleic acid (OA) (11.1–21.9%), linoleic acid (LA) (10.2–23.4%), and linolenic [...] Read more.
Perilla seed oil has been attracting attention in South Korea as a health food. Five fatty acids of 100 Perilla accessions were identified as follows: palmitic acid (PA) (5.10–9.13%), stearic acid (SA) (1.70–3.99%), oleic acid (OA) (11.1–21.9%), linoleic acid (LA) (10.2–23.4%), and linolenic acid (LNA) (54.3–75.4%). Additionally, the 100 Perilla accessions were divided into two groups (high or low) based on the total fatty acid content (TFAC). By using an association analysis of 40 simple sequence repeat (SSR) markers and the six Perilla seed oil traits in the 100 Perilla accessions, we detected four SSR markers associated with TFAC, five SSR markers associated with LNA, one SSR marker associated with LA, two SSR markers each associated with OA and PA, and four SSR markers associated with SA. Among these SSR markers, four SSR markers (KNUPF14, KNUPF62, KNUPF72, KNUPF85) were all associated with TFAC and LNA. Moreover, two SSR markers (KNUPF62, KNUPF85) were both associated with TFAC, LNA, and OA. Therefore, these SSR markers are considered to be useful molecular markers for selecting useful accessions related to fatty acid contents in Perilla germplasm and for improving the seed oil quality of Perilla crop through marker-assisted selection (MAS) breeding programs. Full article
(This article belongs to the Special Issue Gene Networks in Seeds)
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13 pages, 1317 KiB  
Article
The EAR Motif in the Arabidopsis MADS Transcription Factor AGAMOUS-Like 15 Is Not Necessary to Promote Somatic Embryogenesis
by Sanjay Joshi, Christian Keller and Sharyn E. Perry
Plants 2021, 10(4), 758; https://doi.org/10.3390/plants10040758 - 13 Apr 2021
Cited by 8 | Viewed by 3064
Abstract
AGAMOUS-like 15 (AGL15) is a member of the MADS domain family of transcription factors (TFs) that can directly induce and repress target gene expression, and for which promotion of somatic embryogenesis (SE) is positively correlated with accumulation. An ethylene-responsive element binding factor-associated amphiphilic [...] Read more.
AGAMOUS-like 15 (AGL15) is a member of the MADS domain family of transcription factors (TFs) that can directly induce and repress target gene expression, and for which promotion of somatic embryogenesis (SE) is positively correlated with accumulation. An ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif of form LxLxL within the carboxyl-terminal domain of AGL15 was shown to be involved in repression of gene expression. Here, we examine whether AGL15′s ability to repress gene expression is needed to promote SE. While a form of AGL15 where the LxLxL is changed to AxAxA can still promote SE, another form with a strong transcriptional activator at the carboxy-terminal end, does not promote SE and, in fact, is detrimental to SE development. Select target genes were examined for response to the different forms of AGL15. Full article
(This article belongs to the Special Issue Gene Networks in Seeds)
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8 pages, 1603 KiB  
Communication
The Arabidopsis MADS-Domain Transcription Factor SEEDSTICK Controls Seed Size via Direct Activation of E2Fa
by Dario Paolo, Lisa Rotasperti, Arp Schnittger, Simona Masiero, Lucia Colombo and Chiara Mizzotti
Plants 2021, 10(2), 192; https://doi.org/10.3390/plants10020192 - 20 Jan 2021
Cited by 15 | Viewed by 3684
Abstract
Seed size is the result of complex molecular networks controlling the development of the seed coat (of maternal origin) and the two fertilization products, the embryo and the endosperm. In this study we characterized the role of Arabidopsis thaliana MADS-domain transcription factor SEEDSTICK [...] Read more.
Seed size is the result of complex molecular networks controlling the development of the seed coat (of maternal origin) and the two fertilization products, the embryo and the endosperm. In this study we characterized the role of Arabidopsis thaliana MADS-domain transcription factor SEEDSTICK (STK) in seed size control. STK is known to regulate the differentiation of the seed coat as well as the structural and mechanical properties of cell walls in developing seeds. In particular, we further characterized stk mutant seeds. Genetic evidence (reciprocal crosses) of the inheritance of the small-seed phenotype, together with the provided analysis of cell division activity (flow cytometry), demonstrate that STK acts in the earlier phases of seed development as a maternal activator of growth. Moreover, we describe a molecular mechanism underlying this activity by reporting how STK positively regulates cell cycle progression via directly activating the expression of E2Fa, a key regulator of the cell cycle. Altogether, our results unveil a new genetic network active in the maternal control of seed size in Arabidopsis. Full article
(This article belongs to the Special Issue Gene Networks in Seeds)
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Review

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20 pages, 413 KiB  
Review
The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance
by Angel J. Matilla
Plants 2022, 11(1), 20; https://doi.org/10.3390/plants11010020 - 22 Dec 2021
Cited by 28 | Viewed by 5184
Abstract
To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability [...] Read more.
To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular “glass state”. This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity. Full article
(This article belongs to the Special Issue Gene Networks in Seeds)
21 pages, 798 KiB  
Review
The Relevance of a Physiological-Stage Approach Study of the Molecular and Environmental Factors Regulating Seed Germination in Wild Plants
by Ximena Gómez-Maqueo, Laura Figueroa-Corona, Jorge Arturo Martínez-Villegas, Diana Soriano and Alicia Gamboa-deBuen
Plants 2021, 10(6), 1084; https://doi.org/10.3390/plants10061084 - 28 May 2021
Cited by 3 | Viewed by 3146
Abstract
Germination represents the culmination of the seed developmental program and is affected by the conditions prevailing during seed maturation in the mother plant. During maturation, the dormancy condition and tolerance to dehydration are established. These characteristics are modulated by the environment to which [...] Read more.
Germination represents the culmination of the seed developmental program and is affected by the conditions prevailing during seed maturation in the mother plant. During maturation, the dormancy condition and tolerance to dehydration are established. These characteristics are modulated by the environment to which they are subjected, having an important impact on wild species. In this work, a review was made of the molecular bases of the maturation, the processes of dormancy imposition and loss, as well as the germination process in different wild species with different life histories, and from diverse habitats. It is also specified which of these species present a certain type of management. The impact that the domestication process has had on certain characteristics of the seed is discussed, as well as the importance of determining physiological stages based on morphological characteristics, to face the complexities of the study of these species and preserve their genetic diversity and physiological responses. Full article
(This article belongs to the Special Issue Gene Networks in Seeds)
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Other

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9 pages, 848 KiB  
Perspective
A View into Seed Autophagy: From Development to Environmental Responses
by Raquel Iglesias-Fernández and Jesús Vicente-Carbajosa
Plants 2022, 11(23), 3247; https://doi.org/10.3390/plants11233247 - 26 Nov 2022
Cited by 2 | Viewed by 1663
Abstract
Autophagy is a conserved cellular mechanism involved in the degradation and subsequent recycling of cytoplasmic components. It is also described as a catabolic process implicated in the specific degradation of proteins in response to several stimuli. In eukaryotes, the endoplasmic reticulum accumulates an [...] Read more.
Autophagy is a conserved cellular mechanism involved in the degradation and subsequent recycling of cytoplasmic components. It is also described as a catabolic process implicated in the specific degradation of proteins in response to several stimuli. In eukaryotes, the endoplasmic reticulum accumulates an excess of proteins in response to environmental changes, and is the major cellular organelle at the crossroads of stress responses. Return to proteostasis involves the activation of the Unfolded Protein Response (UPR) and eventually autophagy as a feedback mechanism to relieve protein overaccumulation. Recent publications have focused on the relevance of autophagy in two central processes of seed biology: (i) seed storage protein accumulation upon seed maturation and (ii) reserve mobilization during seed imbibition. Although ER-protein accumulation and the subsequent activation of autophagy resemble the Seed Storage Protein (SSP) deposition during seed maturation, the molecular connection between seed development, autophagy, and seed response to abiotic stresses is still an underexplored field. This mini-review presents current advances in autophagy in seeds, highlighting its participation in the normal course of seed development from embryogenesis to germination. Finally, the function of autophagy in response to the seed environment is also considered, as is its involvement in controlling seed dormancy and germination. Full article
(This article belongs to the Special Issue Gene Networks in Seeds)
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