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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 (30 September 2022) | Viewed by 25686

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Special Issue Editors

Prof. Dr. Fure Chyi Chen

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Guest Editor

Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
Interests: orchids; biotechnology; breeding; genetics; micropropagation; mutant characterization; genetic transformation; tropical ornamentals
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. So-Young Park

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Guest Editor

Department of Horticultural Science, Division of Animal, Horticulture and Food Sciences, Chungbuk National University, Cheongju 28644, Korea
Interests: ornamental plant; polyploid breeding; functional metabolites; cell regeneration capacity; bioreactor; somatic embryogenesis; protoplast culture; gene editing

Special Issue Information

Dear Colleagues,

Ornamentals are grown for their showy flowers, foliage or variegation of diverse patterns. They are produced worldwide and most are from tropical and subtropical regions, in addition to temperate areas. Some potted plants are produced by grafting clean scion to the phytoplasma-infected stock plants to show their ornamental values of multiple branching, such as the common poinsettia. Tulips with the striped flower patterns were highly priced in the 17th century in the Netherlands. Horticultural practices are usually adopted during the cultivation and production process of ornamentals, including the use of prunning, pinching and chemicals such as growth retardants, to achieve desirable appearances of the flowering potted plant, foliage plant, cut green, or any form of plant parts. Tissue culture technology, or micropropagation, has contributed mass production of young plants for commercial use to the flower industry. Mutations of ornamentals may have ornamental values but the rate is low.

Recent developments in modern molecular tools, such as genomics, proteomics, transcriptomes, genetic transformation and gene editing, has provided opportunities to improve or introduce desirable genes or traits into the genome of ornamental plants. The aim of this Special Issue is to focus on the use of molecular tools of all aspects to generate novelty ornamentals, such as color, fragrance, plant architecture, disease and pest resistance, and so on.

This Special Issue will welcome submissions of original research papers and reviews, including but not limited to studies in:

Ornamental genomics and transcriptomics (functional and comparative); molecular genetics and development; molecular breeding; marker-assisted selection breeding; non-coding RNA regulation; gene editing; ornamental transformation; micropropagation and somaclonal variation.

Prof. Dr. Fure Chyi Chen
Prof. Dr. So-Young Park
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

breeding
flower color
leaf variegation
abiotic stress
biotic stress
fragrance
molecular markers
somaclonal variegation
ornamental plant
functional metabolites
somatic embryogenesis
bioreactor culture
gene editing

Published Papers (9 papers)

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Research

Jump to: Review

22 pages, 3552 KiB

Open AccessArticle

Allopatric Lineage Divergence of the East Asian Endemic Herb Conandron ramondioides Inferred from Low-Copy Nuclear and Plastid Markers

by Kuan-Ting Hsin, Hao-Chih Kuo, Goro Kokubugata, Michael Möller, Chun-Neng Wang and Yi-Sheng Cheng

Int. J. Mol. Sci. 2022, 23(23), 14932; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232314932 - 29 Nov 2022

Viewed by 1312

Abstract

The evolutionary histories of ornamental plants have been receiving only limited attention. We examined the origin and divergence processes of an East Asian endemic ornamental plant, Conandron ramondioides. C. ramondioides is an understory herb occurring in primary forests, which has been grouped into two varieties. We reconstructed the evolutionary and population demography history of C. ramondioides to infer its divergence process. Nuclear and chloroplast DNA sequences were obtained from 21 Conandron populations on both sides of the East China Sea (ECS) to explore its genetic diversity, structure, and population differentiation. Interestingly, the reconstructed phylogeny indicated that the populations should be classified into three clades corresponding to geographical regions: the Japan (Honshu+Shikoku) clade, the Taiwan–Iriomote clade, and the Southeast China clade. Lineage divergence between the Japan clade and the Taiwan–Iriomote and Southeast China clades occured 1.14 MYA (95% HPD: 0.82–3.86), followed by divergence between the Taiwan–Iriomote and Southeast China clades approximately 0.75 MYA (95% HPD: 0.45–1.3). Furthermore, corolla traits (floral lobe length to tube length ratios) correlated with geographical distributions. Moreover, restricted gene flow was detected among clades. Lastly, the lack of potential dispersal routes across an exposed ECS seafloor during the last glacial maximum suggests that migration among the Conandron clades was unlikely. In summary, the extant Conandron exhibits a disjunct distribution pattern as a result of vicariance rather than long-distance dispersal. We propose that allopatric divergence has occurred in C. ramondioides since the Pleistocene. Our findings highlight the critical influence of species’ biological characteristics on shaping lineage diversification of East Asian relic herb species during climate oscillations since the Quaternary. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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18 pages, 14816 KiB

Open AccessArticle

Insights into the Cytochrome P450 Monooxygenase Superfamily in Osmanthus fragrans and the Role of OfCYP142 in Linalool Synthesis

by Jiawei Liu, Hongmin Hu, Huimin Shen, Qingyin Tian, Wenjie Ding, Xiulian Yang, Lianggui Wang and Yuanzheng Yue

Int. J. Mol. Sci. 2022, 23(20), 12150; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232012150 - 12 Oct 2022

Cited by 5 | Viewed by 1687

Abstract

Osmanthus fragrans flowers have long been used as raw materials in food, tea, beverage, and perfume industries due to their attractive and strong fragrance. The P450 superfamily proteins have been reported to widely participate in the synthesis of plant floral volatile organic compounds (VOCs). To investigate the potential functions of P450 superfamily proteins in the fragrance synthesis of O. fragrans, we investigated the P450 superfamily genome wide. A total of 276 P450 genes were identified belonging to 40 families. The RNA-seq data suggested that many OfCYP genes were preferentially expressed in the flower or other organs, and some were also induced by multiple abiotic stresses. The expression patterns of seven flower-preferentially expressed OfCYPs during the five different flower aroma content stages were further explored using quantitative real-time PCR, showing that the CYP94C subfamily member OfCYP142 had the highest positive correlation with linalool synthesis gene OfTPS2. The transient expression of OfCYP142 in O. fragrans petals suggested that OfCYP142 can increase the content of linalool, an important VOC of the O. fragrans floral aroma, and a similar result was also obtained in flowers of OfCYP142 transgenic tobacco. Combined with RNA-seq data of the transiently transformed O. fragrans petals, we found that the biosynthesis pathway of secondary metabolites was significantly enriched, and many 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway genes were also upregulated. This evidence indicated that the OfCYP proteins may play critical roles in the flower development and abiotic response of O. fragrans, and that OfCYP142 can participate in linalool synthesis. This study provides valuable information about the functions of P450 genes and a valuable guide for studying further functions of OfCYPs in promoting fragrance biosynthesis of ornamental plants. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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16 pages, 3018 KiB

Open AccessArticle

Transcriptome Analysis Reveals Endogenous Hormone Changes during Spike Development in Phalaenopsis

by Zuo Li, Wenfang Xiao, Heming Chen, Genfa Zhu and Fubing Lv

Int. J. Mol. Sci. 2022, 23(18), 10461; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810461 - 09 Sep 2022

Cited by 2 | Viewed by 2088

Abstract

Phalaenopsis orchids are popular worldwide due to their high ornamental and economic value; the spike and inflorescence formation of their flowers could be efficiently controlled under proper conditions. In this study, transcriptomic profiles and endogenous hormone changes were investigated to better understand the spike formation of Phalaenopsis. Morphological observations revealed four spike initiation statuses (i.e., S0: the status refers to axillary buds remaining dormant in the leaf axils; S1: the status refers to the 0.5 cm-long initial spike; S2: the status refers to the 1 cm-long spike; S3: the status refers to the 3 cm-long spike) during the process of spike development, while anatomical observations revealed four related statuses of inflorescence primordium differentiation. A total of 4080 differentially expressed genes were identified based on pairwise comparisons of the transcriptomic data obtained from the S0 to S3 samples; high levels of differential gene expression were mostly observed in S1 vs. S2, followed by S0 vs. S1. Then, the contents of 12 endogenous hormones (e.g., irindole-3-acetic acid (IAA), salicylic acid (SA), abscisic acid (ABA), gibberellins, and cytokinins) were measured. The results showed that the ABA content was decreased from S0 to S1, while the gibberellic acid 1 (GA1) content exhibited an opposite trend, indicating the reduction in ABA levels combined with the increase in GA1 levels in S0 promoted the axillary bud dormancy breaking, preparing for the following spike initiation. The GA20 oxidase and ABA 8′-hydroxylase genes, which are involved in endogenous hormone metabolism and signaling pathways, displayed similar expression patterns, suggesting they were probably the key genes participating in the GA and ABA regulation. Taken together, the findings of this study indicate that GA and ABA may be the key endogenous hormones breaking the dormancy and promoting the germination of axillary buds in Phalaenopsis. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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14 pages, 2582 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Role of GA₃ in Regulating the Asynchronism of Floral Bud Differentiation and Development in Heterodichogamous Cyclocarya paliurus (Batal.) Iljinskaja

by Yinquan Qu, Xiaolin Chen, Xia Mao, Peng Huang and Xiangxiang Fu

Int. J. Mol. Sci. 2022, 23(12), 6763; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23126763 - 17 Jun 2022

Cited by 6 | Viewed by 1561

Abstract

Cyclocarya paliurus is an important medical plant owing to the diverse bioactive compounds in its leaves. However, the heterodichogamy with female and male functions segregation within protandry (PA) or protogyny (PG) may greatly affect seed quality and its plantations for medicinal use. To speculate on the factor playing the dominant role in regulating heterodichogamy in C. paliurus, based on phenotypic observations, our study performed a multi comparison transcriptome analysis on female and male buds (PG and PA types) using RNA-seq. For the female and male bud comparisons, a total of 6753 differentially expressed genes (DEGs) were detected. In addition, functional analysis revealed that these DEGs were significantly enriched in floral development, hormone, and GA-related pathways. As the dominant hormones responsible for floral differentiation and development, gibberellins (GAs) in floral buds from PG and PA types were quantified using HPLC-MS. Among the tested GAs, GA₃ positively regulated the physiological differentiation (S0) and germination (S2) of floral buds. The dynamic changes of GA₃ content and floral morphological features were consistent with the expression levels of GA-related genes. Divergences of GA₃ contents at S0 triggered the asynchronism of physiological differentiation between male and female buds of intramorphs (PA-M vs. PA-F and PG-F vs. PG-M). A significant difference in GA₃ content enlarged this asynchronism at S2. Thus, we speculate that GA₃ plays the dominant role in the formation of heterodichogamy in C. paliurus. Meanwhile, the expression patterns of GA-related DEGs, including CPS, KO, GA20ox, GA2_OX, GID1, and DELLA genes, which play central roles in regulating flower development, coincided with heterodichogamous characteristics. These results support our speculations well, which should be further confirmed. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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16 pages, 11833 KiB

Open AccessArticle

Profiles of Cytokinins Metabolic Genes and Endogenous Cytokinins Dynamics during Shoot Multiplication In Vitro of Phalaenopsis

by Yuan-Yuan Li, Zhi-Gang Hao, Shuo Miao, Xiong Zhang, Jian-Qiang Li, Shun-Xing Guo and Yung-I Lee

Int. J. Mol. Sci. 2022, 23(7), 3755; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23073755 - 29 Mar 2022

Cited by 1 | Viewed by 1647

Abstract

Shoot multiplication induced by exogenous cytokinins (CKs) has been commonly used in Phalaenopsis micropropagation for commercial production. Despite this, mechanisms of CKs action on shoot multiplication remain unclear in Phalaenopsis. In this study, we first identified key CKs metabolic genes, including six isopentenyltransferase (PaIPTs), six cytokinin riboside 5′ monophosphate phosphoribohydrolase (PaLOGs), and six cytokinin dehydrogenase (PaCKXs), from the Phalaenopsis genome. Then, we investigated expression profiles of these CKs metabolic genes and endogenous CKs dynamics in shoot proliferation by thidiazuron (TDZ) treatments (an artificial plant growth regulator with strong cytokinin-like activity). Our data showed that these CKs metabolic genes have organ-specific expression patterns. The shoot proliferation in vitro was effectively promoted with increased TDZ concentrations. Following TDZ treatments, the highly expressed CKs metabolic genes in micropropagated shoots were PaIPT1, PaLOG2, and PaCKX4. By 30 days of culture, TDZ treatments significantly induced CK-ribosides levels in micropropagated shoots, such as tZR and iPR (2000-fold and 200-fold, respectively) as compared to the controls, whereas cZR showed only a 10-fold increase. Overexpression of PaIPT1 and PaLOG2 by agroinfiltration assays resulted in increased CK-ribosides levels in tobacco leaves, while overexpression of PaCKX4 resulted in decreased CK-ribosides levels. These findings suggest de novo biosynthesis of CKs induced by TDZ, primarily in elevation of tZR and iPR levels. Our results provide a better understanding of CKs metabolism in Phalaenopsis micropropagation. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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20 pages, 2926 KiB

Open AccessArticle

Transcriptomic Analysis Suggests Auxin Regulation in Dorsal-Ventral Petal Asymmetry of Wild Progenitor Sinningia speciosa

by Zhao-Jun Pan, Ya-Chi Nien, Yu-An Shih, Tsun-Ying Chen, Wen-Dar Lin, Wen-Hsi Kuo, Hao-Chun Hsu, Shih-Long Tu, Jen-Chih Chen and Chun-Neng Wang

Int. J. Mol. Sci. 2022, 23(4), 2073; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23042073 - 13 Feb 2022

Cited by 2 | Viewed by 2389

Abstract

The establishment of dorsal–ventral (DV) petal asymmetry is accompanied by differential growth of DV petal size, shape, and color differences, which enhance ornamental values. Genes involved in flower symmetry in Sinningia speciosa have been identified as CYCLOIDEA (SsCYC), but which gene regulatory network (GRN) is associated with SsCYC to establish DV petal asymmetry is still unknown. To uncover the GRN of DV petal asymmetry, we identified 630 DV differentially expressed genes (DV-DEGs) from the RNA-Seq of dorsal and ventral petals in the wild progenitor, S. speciosa ‘ES’. Validated by qRT-PCR, genes in the auxin signaling transduction pathway, SsCYC, and a major regulator of anthocyanin biosynthesis were upregulated in dorsal petals. These genes correlated with a higher endogenous auxin level in dorsal petals, with longer tube length growth through cell expansion and a purple dorsal color. Over-expression of SsCYC in Nicotiana reduced petal size by regulating cell growth, suggesting that SsCYC also controls cell expansion. This suggests that auxin and SsCYC both regulate DV petal asymmetry. Transiently over-expressed SsCYC, however, could not activate most major auxin signaling genes, suggesting that SsCYC may not trigger auxin regulation. Whether auxin can activate SsCYC or whether they act independently to regulate DV petal asymmetry remains to be explored in the future. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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14 pages, 5209 KiB

Open AccessArticle

Comparative Transcriptome Analysis Revealed Two Alternative Splicing bHLHs Account for Flower Color Alteration in Chrysanthemum

by Lili Xiang, Xiaofen Liu, Yanna Shi, Yajing Li, Weidong Li, Fang Li and Kunsong Chen

Int. J. Mol. Sci. 2021, 22(23), 12769; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222312769 - 25 Nov 2021

Cited by 4 | Viewed by 1972

Abstract

‘Jimba’ is a white chrysanthemum cultivar, which occasionally and spontaneously produces red flower petals under natural cultivation due to cyanidin-based anthocyanin accumulation. To investigate the underlying mechanism of this process, a comparative transcriptome was analyzed between white and turning red ‘Jimba’. The structural and regulatory genes of anthocyanin pathway were significantly up-regulated in turning red ‘Jimba’. Among them, two alternative splicings, CmbHLH2 and CmbHLH2.1, showed the most significantly up-regulated in turning red tissue. Transiently over-expressed 35S::CmMYB6-CmbHLH2 strongly induced anthocyanin accumulation in ‘Jimba’ flower petals, while moderate amount of anthocyanin was detected when over-expressed 35S::CmMYB6-CmbHLH2.1. Both CmbHLH2 and CmbHLH2.1 could interact with CmMYB6 to activate CmDFR promoter according to Yeast two-hybrid and dual-luciferase assay. Moreover, CmMYB6-CmbHLH2 but not CmMYB6-CmbHLH2.1 could activate the CmbHLH2 promoter to provide positive feedback loop regulation. Taken together, it suggested that both CmbHLH2 and CmbHLH2.1 involved in regulation flower color alteration in turning red ‘Jimba’, and CmbHLH2 played a predominant role in this process. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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Review

Jump to: Research

24 pages, 1431 KiB

Open AccessReview

Towards the Improvement of Ornamental Attributes in Chrysanthemum: Recent Progress in Biotechnological Advances

by Manjulatha Mekapogu, Oh-Keun Kwon, Hyun-Young Song and Jae-A Jung

Int. J. Mol. Sci. 2022, 23(20), 12284; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232012284 - 14 Oct 2022

Cited by 15 | Viewed by 6249

Abstract

Incessant development and introduction of novel cultivars with improved floral attributes are vital in the dynamic ornamental industry. Chrysanthemum (Chrysanthemum morifolium) is a highly favored ornamental plant, ranking second globally in the cut flower trade, after rose. Development of new chrysanthemum cultivars with improved and innovative modifications in ornamental attributes, including floral color, shape, plant architecture, flowering time, enhanced shelf life, and biotic and abiotic stress tolerance, is a major goal in chrysanthemum breeding. Despite being an economically important ornamental plant, the application of conventional and molecular breeding approaches to various key traits of chrysanthemum is hindered owing to its genomic complexity, heterozygosity, and limited gene pool availability. Although classical breeding of chrysanthemum has resulted in the development of several hundreds of cultivars with various morphological variations, the genetic and transcriptional control of various important ornamental traits remains unclear. The coveted blue colored flowers of chrysanthemums cannot be achieved through conventional breeding and mutation breeding due to technical limitations. However, blue-hued flower has been developed by genetic engineering, and transgenic molecular breeding has been successfully employed, leading to substantial progress in improving various traits. The recent availability of whole-genome sequences of chrysanthemum offers a platform to extensively employ MAS to identify a large number of markers for QTL mapping, and GWAS to dissect the genetic control of complex traits. The combination of NGS, multi-omic platforms, and genome editing technologies has provided a tremendous scope to decipher the molecular and regulatory mechanisms. However, the application and integration of these technologies remain inadequate for chrysanthemum. This review, therefore, details the significance of floral attributes, describes the efforts of recent advancements, and highlights the possibilities for future application towards the improvement of crucial ornamental traits in the globally popular chrysanthemum plant. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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18 pages, 1223 KiB

Open AccessReview

Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution

by Francesca Lucibelli, Maria Carmen Valoroso and Serena Aceto

Int. J. Mol. Sci. 2022, 23(15), 8299; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158299 - 27 Jul 2022

Cited by 23 | Viewed by 5455

Abstract

DNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation. Full article

(This article belongs to the Special Issue From Functional Genomics to Biotechnology in Ornamental Plant)

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