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Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life

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A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Plant, Algae and Fungi Cell Biology".

Deadline for manuscript submissions: closed (10 December 2021) | Viewed by 37669

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Special Issue Editors

Prof. Dr. Avtar K. Handa

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Guest Editor

Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA
Interests: molecular regulation of plant growth and development; postharvest biology and fruit ripening; molecular engineering of fruits to enhance quality attributes; modulating heat stress to enhance crop productivity; production of vaccines in plants
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Gopinadhan Paliyath

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Guest Editor

Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
Interests: functional foods; nutraceuticals; signal transduction pathways; inflammation; chronic disease prevention
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The last decade has seen remarkable progress in the understanding of the molecular regulation of fruit sets, development, maturation, ripening and shelf-life. Most of this knowledge has emerged from the use of a tomato as a model system for fleshy fruits. However, in recent years, a significant understanding about the molecular mechanisms regulating development of edible fruits is emerging from many other fruit systems. Furthermore, the interest of physiologists, biochemists and geneticists has greatly increased, as the emphasis of human health has begun to shift from the treatment to prevention of diseases. This Special Issue of Cells (IF 4.366) will publish manuscripts that emphasize the new emerging knowledge at biochemical, genetic and epigenetic levels, which regulate the quality attributes and shelf-lives of fruits.

As guidelines to the authors, this Special Issue will accept manuscripts containing fundamental information about the mechanisms regulating fruit biology, at all stages of flowering, anthesis, fruit-set, growth, maturation, ripening and senescence. Manuscripts providing advancements in the molecular mechanisms regulating biochemical homeostasis during fruit development and the accumulation of antioxidants/ phytonutrients will be of special interest. For more information, see Instructions for Authors (https://0-www-mdpi-com.brum.beds.ac.uk/journal/cells/instructions).

Prof. Avtar K. Handa
Prof. Dr. Gopinadhan Paliyath
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. Cells 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

Genetics
Epigenetics
Metabolism
Gene regulation
Proteomics
Transcriptional regulation
Translational regulation
DNA methylation
Signal transduction
Hormones
Ethylene
Calcium
Ion channels and transport
Protein Phosphorylation
Membrane biology
Enzymes
Cell walls
Shelf-life
Phytonutrients
Other factors that control fruit set to senescence

Published Papers (9 papers)

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Research

Jump to: Review

19 pages, 3557 KiB

Open AccessArticle

Ripening of Pomegranate Skin as Revealed by Developmental Transcriptomics

by Idit Ginzberg and Adi Faigenboim

Cells 2022, 11(14), 2215; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11142215 - 16 Jul 2022

Cited by 3 | Viewed by 1861

Abstract

The appearance of pomegranate (Punica granatum L.) fruit is highly important for its marketing. The primary concerns are obtaining sufficient red pigment accumulation and minimal cracking of the fruit skin (the outer red layer of the peel). We analyzed the skin transcriptome of pomegranate cv. Wonderful at distinct time points of fruit development to characterize the processes that occur in the skin during fruit ripening and which may reflect on processes in the whole fruit, such as the non-climacteric nature of pomegranate. The data suggested a ripening mechanism in pomegranate skin that differs from that in strawberry—the model plant for non-climacteric fruit where abscisic acid is the growth regulator that drives ripening—involving ethylene, polyamine, and jasmonic acid pathways. The biosynthetic pathways of important metabolites in pomegranate—hydrolyzable tannins and anthocyanins—were co-upregulated at the ripening stage, in line with the visual enhancement of red coloration. Interestingly, cuticle- and cell-wall-related genes that showed differential expression between the developmental stages were mainly upregulated in the skin of early fruit, with lower expression at mid-growth and ripening stages. Nevertheless, lignification may be involved in skin hardening in the mature fruit. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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13 pages, 2226 KiB

Open AccessFeature PaperArticle

Ethylene Induced by Sound Stimulation Enhances Anthocyanin Accumulation in Grape Berry Skin through Direct Upregulation of UDP-Glucose: Flavonoid 3-O-Glucosyltransferase

by Mone Yamazaki, Akari Ishida, Yutaka Suzuki, Yoshinao Aoki, Shunji Suzuki and Shinichi Enoki

Cells 2021, 10(10), 2799; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10102799 - 19 Oct 2021

Cited by 11 | Viewed by 3157

Abstract

Global warming has resulted in the loss of anthocyanin accumulation in berry skin. Sound stimulation can be used as a potential method for enhancing fruit color development since many plants recognize sound vibration as an external stimulus and alter their physiological status in response to it. Sound stimulation (sine wave sound at 1000 Hz) enhanced anthocyanin accumulation in grape cultured cells and berry skins in field-grown grapevines at the early stage of ripening. The transcription of UFGT and ACO2, which encode the key enzymes in anthocyanin and ethylene biosynthesis, respectively, was upregulated in grape cultured cells exposed to sound stimulation. In contrast, the transcription of MybA1 and NCED1, which encode a transcription factor for UFGT and a key enzyme in abscisic acid biosynthesis, respectively, was not affected by the sound stimulation. A treatment with an ethylene biosynthesis inhibitor, aminoethoxyvinyl glycine hydrochloride, revered the enhancement of anthocyanin accumulation by sound stimulation. As the promoter assay using a GUS reporter gene demonstrated that UFGT promoter was directly activated by the ethylene-releasing compound ethephon, which enhanced anthocyanin accumulation in grape cultured cells, we conclude that sound stimulation enhanced anthocyanin accumulation through the direct upregulation of UFGT by ethylene biosynthesis. Our findings suggest that sound stimulation contributes to alleviating poor coloration in berry skin as a novel and innovative practical technique in viticulture. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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20 pages, 4072 KiB

Open AccessFeature PaperArticle

Systems Biology Applied to the Study of Papaya Fruit Ripening: The Influence of Ethylene on Pulp Softening

by Caroline Giacomelli Soares, Samira Bernardino Ramos do Prado, Sónia C. S. Andrade and João Paulo Fabi

Cells 2021, 10(9), 2339; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10092339 - 07 Sep 2021

Cited by 7 | Viewed by 5675

Abstract

Papaya is a fleshy fruit that undergoes fast ethylene-induced modifications. The fruit becomes edible, but the fast pulp softening is the main factor that limits the post-harvest period. Papaya fast pulp softening occurs due to cell wall disassembling coordinated by ethylene triggering that massively expresses pectinases. In this work, RNA-seq analysis of ethylene-treated and non-treated papayas enabled a wide transcriptome overview that indicated the role of ethylene during ripening at the gene expression level. Several families of transcription factors (AP2/ERF, NAC, and MADS-box) were differentially expressed. ACO, ACS, and SAM-Mtase genes were upregulated, indicating a high rate of ethylene biosynthesis after ethylene treatment. The correlation among gene expression and physiological data demonstrated ethylene treatment can indeed simulate ripening, and regulation of changes in fruit color, aroma, and flavor could be attributed to the coordinated expression of several related genes. Especially about pulp firmness, the identification of 157 expressed genes related to cell wall metabolism demonstrated that pulp softening is accomplished by a coordinated action of several different cell wall-related enzymes. The mechanism is different from other commercially important fruits, such as strawberry, tomato, kiwifruit, and apple. The observed behavior of this new transcriptomic data confirms ethylene triggering is the main event that elicits fast pulp softening in papayas. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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20 pages, 15795 KiB

Open AccessArticle

Genome-Wide Characterization of R2R3-MYB Transcription Factors in Pitaya Reveals a R2R3-MYB Repressor HuMYB1 Involved in Fruit Ripening through Regulation of Betalain Biosynthesis by Repressing Betalain Biosynthesis-Related Genes

by Fangfang Xie, Qingzhu Hua, Canbin Chen, Zhike Zhang, Rong Zhang, Jietang Zhao, Guibing Hu, Jianye Chen and Yonghua Qin

Cells 2021, 10(8), 1949; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10081949 - 31 Jul 2021

Cited by 26 | Viewed by 3108

Abstract

The MYB (myeloblastosis) superfamily constitutes one of the most abundant transcription factors (TFs) regulating various biological processes in plants. However, the molecular characteristics and functions of MYB TFs in pitaya remain unclear. To date, no genome-wide characterization analysis of this gene family has been conducted in the Cactaceae species. In this study, 105 R2R3-MYB members were identified from the genome data of Hylocereus undatus and their conserved motifs, physiological and biochemical characteristics, chromosome locations, synteny relationship, gene structure and phylogeny were further analyzed. Expression analyses suggested that three up-regulated HuMYBs and twenty-two down-regulated HuMYBs were probably involved in fruit ripening of pitaya. Phylogenetic analyses of R2R3-MYB repressors showed that seven HuMYBs (HuMYB1, HuMYB21, HuMYB48, HuMYB49, HuMYB72, HuMYB78 and HuMYB101) were in clades containing R2R3-MYB repressors. HuMYB1 and HuMYB21 were significantly down-regulated with the betalain accumulation during fruit ripening of ‘Guanhuahong’ pitaya (H. monacanthus). However, only HuMYB1 had R2 and R3 repeats with C1, C2, C3 and C4 motifs. HuMYB1 was localized exclusively to the nucleus and exhibited transcriptional inhibition capacities. Dual luciferase reporter assay demonstrated that HuMYB1 inhibited the expression of betalain-related genes: HuADH1, HuCYP76AD1-1 and HuDODA1. These results suggested that HuMYB1 is a potential repressor of betalain biosynthesis during pitaya fruit ripening. Our results provide the first genome-wide analyses of the R2R3-MYB subfamily involved in pitaya betalain biosynthesis and will facilitate functional analysis of this gene family in the future. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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18 pages, 5006 KiB

Open AccessArticle

Characterization of RIN Isoforms and Their Expression in Tomato Fruit Ripening

by Maria A. Slugina, Gleb I. Efremov, Anna V. Shchennikova and Elena Z. Kochieva

Cells 2021, 10(7), 1739; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10071739 - 09 Jul 2021

Cited by 2 | Viewed by 2366

Abstract

Ripening of tomato fleshy fruit is coordinated by transcription factor RIN, which triggers ethylene and carotenoid biosynthesis, sugar accumulation, and cell wall modifications. In this study, we identified and characterized complete sequences of the RIN chromosomal locus in two tomato Solanum lycopersicum cultivars, its rin/RIN genotype, and three wild green-fruited species differing in fruit color and composition. The results reveal that S. lycopersicum cultivars and some wild species (S. pennellii, S. habrochaites, and S. huaylasense) had a 3′-splicing site enabling the transcription of RIN1i and RIN2i isoforms. The other wild species (S. arcanum, S. chmielewskii, S. neorickii, and S. peruvianum) had a 3′-splicing site only for RIN2i, which was consistent with RIN1i and RIN2i expression patterns. The genotype rin/RIN, which had an extended 3′-terminal deletion in the rin allele, mainly expressed the chimeric RIN–MC transcript, which was also found in cultivars (RIN/RIN). The RIN1, but not RIN2, protein is able to induce the transcription of the reporter gene in the Y2H system, which positively correlated with the transcription profile of RIN1i and RIN target genes. We suggest that during fruit ripening, RIN1 activates ripening-related genes, whereas RIN2 and RIN–MC act as modulators by competing for RIN-binding sites in gene promoters, which should be confirmed by further studies on the association between RIN-splicing mechanisms and tomato fruit ripening. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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17 pages, 3782 KiB

Open AccessArticle

Crosstalk Pathway between Trehalose Metabolism and Cytokinin Degradation for the Determination of the Number of Berries per Bunch in Grapes

by Ayane Moriyama, Chiho Yamaguchi, Shinichi Enoki, Yoshinao Aoki and Shunji Suzuki

Cells 2020, 9(11), 2378; https://0-doi-org.brum.beds.ac.uk/10.3390/cells9112378 - 29 Oct 2020

Cited by 2 | Viewed by 2109

Abstract

In grapes, the number of flowers per inflorescence determines the compactness of grape bunches. Grape cultivars with tight bunches and thin-skinned berries easily undergo berry splitting, especially in growing areas with heavy rainfall during the grapevine growing season, such as Japan. We report herein that grape cytokinin oxidase/dehydrogenase 5 (VvCKX5) determines the number of berries per inflorescence in grapes. The number of berries per bunch was inversely proportional to the VvCKX5 expression level in juvenile inflorescences among the cultivars tested. VvCKX5 overexpression drastically decreased the number of flower buds per inflorescence in Arabidopsis plants, suggesting that VvCKX5 might be one of the negative regulators of the number of flowers per inflorescence in grapes. Similarly, the overexpression of grape sister of ramose 3 (VvSRA), which encodes trehalose 6-phosphate phosphatase that catalyzes the conversion of trehalose-6-phosphate into trehalose, upregulated AtCKX7 expression in Arabidopsis plants, leading to a decrease in the number of flower buds per Arabidopsis inflorescence. VvCKX5 gene expression was upregulated in grapevine cultured cells and juvenile grape inflorescences treated with trehalose. Finally, injecting trehalose into swelling buds nearing bud break using a microsyringe decreased the number of berries per bunch by half. VvCKX5 overexpression in Arabidopsis plants had no effect on the number of secondary inflorescences from the main inflorescence, and similarly trehalose did not affect pedicel branching on grapevine inflorescences, suggesting that VvCKX5, as well as VvSRA-mediated trehalose metabolism, regulates flower formation but not inflorescence branching. These findings may provide new information on the crosstalk between VvSRA-mediated trehalose metabolism and VvCKX-mediated cytokinin degradation for determining the number of berries per bunch. Furthermore, this study is expected to contribute to the development of innovative cultivation techniques for loosening tight bunches. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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Review

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29 pages, 3120 KiB

Open AccessReview

NAC Transcription Factor Family Regulation of Fruit Ripening and Quality: A Review

by Gang-Shuai Liu, Hong-Li Li, Donald Grierson and Da-Qi Fu

Cells 2022, 11(3), 525; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11030525 - 02 Feb 2022

Cited by 51 | Viewed by 5472

Abstract

The NAC transcription factor (TF) family is one of the largest plant-specific TF families and its members are involved in the regulation of many vital biological processes during plant growth and development. Recent studies have found that NAC TFs play important roles during the ripening of fleshy fruits and the development of quality attributes. This review focuses on the advances in our understanding of the function of NAC TFs in different fruits and their involvement in the biosynthesis and signal transduction of plant hormones, fruit textural changes, color transformation, accumulation of flavor compounds, seed development and fruit senescence. We discuss the theoretical basis and potential regulatory models for NAC TFs action and provide a comprehensive view of their multiple roles in modulating different aspects of fruit ripening and quality. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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12 pages, 1303 KiB

Open AccessReview

Role of Glycoproteins during Fruit Ripening and Seed Development

by Angela Mendez-Yañez, Patricio Ramos and Luis Morales-Quintana

Cells 2021, 10(8), 2095; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10082095 - 15 Aug 2021

Cited by 5 | Viewed by 2552

Abstract

Approximately thirty percent of the proteins synthesized in animal or plant cells travel through the secretory pathway. Seventy to eighty percent of those proteins are glycosylated. Thus, glycosylation is an important protein modification that is related to many cellular processes, such as differentiation, recognition, development, signal transduction, and immune response. Additionally, glycosylation affects protein folding, solubility, stability, biogenesis, and activity. Specifically, in plants, glycosylation has recently been related to the fruit ripening process. This review aims to provide valuable information and discuss the available literature focused on three principal topics: (I) glycosylations as a key posttranslational modification in development in plants, (II) experimental and bioinformatics tools to analyze glycosylations, and (III) a literature review related to glycosylations in fruit ripening. Based on these three topics, we propose that it is necessary to increase the number of studies related to posttranslational modifications, specifically protein glycosylation because the specific role of glycosylation in the posttranslational process and how this process affects normal fruit development and ripening remain unclear to date. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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34 pages, 4131 KiB

Open AccessFeature PaperEditor’s ChoiceReview

Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening

by Shan Li, Kunsong Chen and Donald Grierson

Cells 2021, 10(5), 1136; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10051136 - 08 May 2021

Cited by 92 | Viewed by 10152

Abstract

This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of ‘master regulators’ indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits. Full article

(This article belongs to the Special Issue Molecular Regulation of Fruit-Set, Development, Maturation, Ripening and Shelf-Life)

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