Molecular Biology of Ornamental Plants

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 29292

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Guest Editor
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Interests: ornamental plants; bioinformatics; biotechnology; gene editing
Special Issues, Collections and Topics in MDPI journals
College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
Interests: plant molecular biology; protein modification mechanism of plant abiotic stress tolerance; forage and turfgrass breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As is well known, relative to model plants, ornamental plants have many special characteristics. However, current regulatory models are mainly based on model plants. With the development of sequencing technology and omics tools, we can apply high-throughput sequencing and other omics methods to discover core regulatory networks and genes related to specific ornamental traits. These advances can provide assistance and candidate excellent genes for directional breeding. On the other hand, classical molecular biology methods have also been used to discover the regulatory mechanism of ornamental traits. This will also enrich our understanding of the development mechanism of plant specific organs. Based on these, we have decided to launch this Special Issue on “Molecular Biology of Ornamental Plants”.

This Special Issue welcomes contributions from researchers working in the field of molecular biology of ornamental plants. Original research articles are encouraged for submission, focusing on but not limited to the following areas:

  • Biotechnology and genome editing;
  • Biotic or abiotic stress resistant gene function in ornamental plants;
  • Integrative analysis of multi-omics;
  • Molecular regulatory mechanism of ornamental traits.

Dr. Aiping Song
Dr. Yu Chen
Guest Editors

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Keywords

  • biotechnology
  • development
  • molecular regulatory mechanism
  • multi-omics
  • ornamental plants
  • stress response

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Published Papers (17 papers)

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Editorial

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3 pages, 188 KiB  
Editorial
Molecular Biology of Ornamental Plants
by Aiping Song and Yu Chen
Plants 2023, 12(19), 3493; https://doi.org/10.3390/plants12193493 - 07 Oct 2023
Viewed by 718
Abstract
Relative to model plants, ornamental plants have many special characteristics, such as their flower color and shape, and a floral fragrance [...] Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)

Research

Jump to: Editorial, Review

17 pages, 3174 KiB  
Article
Transcriptomic Analysis Reveals the Regulatory Mechanism of Color Diversity in Rhododendron pulchrum Sweet (Ericaceae)
by Nanyan Zhu and Chunhua Zhou
Plants 2023, 12(14), 2656; https://doi.org/10.3390/plants12142656 - 15 Jul 2023
Cited by 1 | Viewed by 916
Abstract
Rhododendron pulchrum Sweet is a traditional ornamental plant cultivated in China and presents a great variation in petal coloration. However, few studies have been performed to reveal the genes involved and the regulatory mechanism of flower color formation in this plant. In this [...] Read more.
Rhododendron pulchrum Sweet is a traditional ornamental plant cultivated in China and presents a great variation in petal coloration. However, few studies have been performed to reveal the genes involved and the regulatory mechanism of flower color formation in this plant. In this study, to explore the underlying genetic basis of flower color formation, transcriptome analysis was performed by high-throughput sequencing techniques on four petal samples of different colors: purple, pink, light pink, and white. Results show that a total of 35.55 to 40.56 million high-quality clean reads were obtained, of which 28.56 to 32.65 million reads were mapped to the reference genome. For their annotation, 28,273, 18,054, 24,301, 19,099, and 11,507 genes were allocated to Nr, Swiss-Prot, Pfam, GO, and KEGG databases, correspondingly. There were differentially expressed genes among the four different petal samples, including signal-transduction-related genes, anthocyanin biosynthesis genes, and transcription factors. We found that the higher expressed levels of genes associated with flavonol synthase (FLS) might be the key to white formation, and the formation of red color may be related to the higher expression of flavanone 4-reductase (DFR) families. Overall, our study provides some valuable information for exploring and understanding the flower color intensity variation in R. pulchrum. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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13 pages, 1885 KiB  
Article
Establishing a Virus-Induced Gene Silencing System in Lycoris chinensis
by Guanghao Cheng, Xiaochun Shu, Zhong Wang, Ning Wang and Fengjiao Zhang
Plants 2023, 12(13), 2458; https://doi.org/10.3390/plants12132458 - 27 Jun 2023
Cited by 3 | Viewed by 991
Abstract
Lycoris is an important plant with both medicinal and ornamental values. However, it does not have an efficient genetic transformation system, which makes it difficult to study gene function of the genus. Virus-induced gene silencing (VIGS) is an effective technique for studying gene [...] Read more.
Lycoris is an important plant with both medicinal and ornamental values. However, it does not have an efficient genetic transformation system, which makes it difficult to study gene function of the genus. Virus-induced gene silencing (VIGS) is an effective technique for studying gene functions in plants. In this study, we develop an efficient virus-induced gene-silencing (VIGS) system using the leaf tip needle injection method. The widely used TRV vector is constructed, and the Cloroplastos Alterados 1 (CLA1) and Phytoene Desaturase (PDS) genes are selected as visual indicators in the VIGS system. As a result, it is observed that leaves infected with TRV-LcCLA1 and TRV-LcPDS both show a yellowing phenotype (loss of green), and the chlorosis range of TRV-LcCLA1 was larger and deeper than that of TRV-LcPDS. qRT-PCR results show that the expression levels of LcCLA1 and LcPDS are significantly reduced, and the silencing efficiency of LcCLA1 is higher than that of LcPDS. These results indicate that the VIGS system of L. chinensis was preliminarily established, and LcCLA1 is more suitable as a gene-silencing indicator. For the monocotyledonous plant leaves with a waxy surface, the leaf tip injection method greatly improves the infiltration efficiency. The newly established VIGS system will contribute to gene functional research in Lycoris species. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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22 pages, 5658 KiB  
Article
Selection and Validation of Optimal RT-qPCR Reference Genes for the Normalization of Gene Expression under Different Experimental Conditions in Lindera megaphylla
by Hongli Liu, Jing Liu, Peng Chen, Xin Zhang, Ke Wang, Jiuxing Lu and Yonghua Li
Plants 2023, 12(11), 2185; https://doi.org/10.3390/plants12112185 - 31 May 2023
Cited by 1 | Viewed by 1083
Abstract
Lindera megaphylla, a broad-leaved evergreen that is used as a landscape ornamental plant and medicinal plant, is an ecologically important and dominant tree species. However, little is known about the molecular mechanisms of its growth, development, and metabolism. The selection of suitable [...] Read more.
Lindera megaphylla, a broad-leaved evergreen that is used as a landscape ornamental plant and medicinal plant, is an ecologically important and dominant tree species. However, little is known about the molecular mechanisms of its growth, development, and metabolism. The selection of suitable reference genes is critical for molecular biological analyses. To date, no research on reference genes as a foundation for gene expression analysis has been undertaken in L. megaphylla. In this study, 14 candidate genes were selected from the transcriptome database of L. megaphylla for RT-qPCR assay under different conditions. Results showed that helicase-15 and UBC28 were most stable in different tissues of seedlings and adult trees. For different leaf developmental stages, the best combination of reference genes was ACT7 and UBC36. UBC36 and TCTP were the best under cold treatment, while PAB2 and CYP20-2 were the best under heat treatment. Finally, a RT-qPCR assay of LmNAC83 and LmERF60 genes were used to further verify the reliability of selected reference genes above. This work is the first to select and evaluate the stability of reference genes for the normalization of gene expression analysis in L. megaphylla and will provide an important foundation for future genetic studies of this species. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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19 pages, 10470 KiB  
Article
Genome-Wide Identification of the Rose SWEET Gene Family and Their Different Expression Profiles in Cold Response between Two Rose Species
by Xiangshang Song, Yaping Kou, Mingao Duan, Bo Feng, Xiaoyun Yu, Ruidong Jia, Xin Zhao, Hong Ge and Shuhua Yang
Plants 2023, 12(7), 1474; https://doi.org/10.3390/plants12071474 - 28 Mar 2023
Cited by 3 | Viewed by 1322
Abstract
Sugars Will Eventually be Exported Transporter (SWEET) gene family plays indispensable roles in plant physiological activities, development processes, and responses to biotic and abiotic stresses, but no information is known for roses. In this study, a total of 25 RcSWEET genes were identified [...] Read more.
Sugars Will Eventually be Exported Transporter (SWEET) gene family plays indispensable roles in plant physiological activities, development processes, and responses to biotic and abiotic stresses, but no information is known for roses. In this study, a total of 25 RcSWEET genes were identified in Rosa chinensis ‘Old Blush’ by genome-wide analysis and clustered into four subgroups based on their phylogenetic relationships. The genomic features, including gene structures, conserved motifs, and gene duplication among the chromosomes of RcSWEET genes, were characterized. Seventeen types of cis-acting elements among the RcSWEET genes were predicted to exhibit their potential regulatory roles during biotic and abiotic stress and hormone responses. Tissue-specific and cold-response expression profiles based on transcriptome data showed that SWEETs play widely varying roles in development and stress tolerance in two rose species. Moreover, the different expression patterns of cold-response SWEET genes were verified by qRT-PCR between the moderately cold-resistant species R. chinensis ‘Old Blush’ and the extremely cold-resistant species R. beggeriana. Especially, SWEET2a and SWEET10c exhibited species differences after cold treatment and were sharply upregulated in the leaves of R. beggeriana but not R. chinensis ‘Old Blush’, indicating that these two genes may be the crucial candidates that participate in cold tolerance in R. beggeriana. Our results provide the foundation for function analysis of the SWEET gene family in roses, and will contribute to the breeding of cold-tolerant varieties of roses. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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9 pages, 3417 KiB  
Article
Genome-Wide Identification and Analysis of MYB Transcription Factor Family in Hibiscus hamabo
by Dina Liu, Chunsun Gu, Zekai Fu and Zhiquan Wang
Plants 2023, 12(7), 1429; https://doi.org/10.3390/plants12071429 - 23 Mar 2023
Cited by 2 | Viewed by 1210
Abstract
MYB transcription factors constitute one of the largest gene families in plants and play essential roles in the regulation of plant growth, responses to stress, and a wide variety of physiological and biochemical processes. In this study, 204 MYB proteins (HhMYBs) were identified [...] Read more.
MYB transcription factors constitute one of the largest gene families in plants and play essential roles in the regulation of plant growth, responses to stress, and a wide variety of physiological and biochemical processes. In this study, 204 MYB proteins (HhMYBs) were identified in the Hibiscus hamabo Sieb. et Zucc (H. hamabo) genome and systematically analyzed based on their genomic sequence and transcriptomic data. The candidate HhMYB proteins and MYBs of Arabidopsis thaliana were divided into 28 subfamilies based on the analysis of their phylogenetic relationships and their motif patterns. Expression analysis using RNA-seq and quantitative real-time PCR (qRT-PCR) indicated that most HhMYBs are differentially regulated under drought and salt stresses. qRT-PCR analysis of seven selected HhMYBs suggested that the HhMYB family may have regulatory roles in the responses to stress and hormones. This study provides a framework for a more comprehensive analysis of the role of MYBs in the response to abiotic stress in H. hamabo. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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18 pages, 4830 KiB  
Article
Genome-Wide Analysis of the Rhododendron AP2/ERF Gene Family: Identification and Expression Profiles in Response to Cold, Salt and Drought Stress
by Zhenhao Guo, Lisi He, Xiaobo Sun, Chang Li, Jiale Su, Huimin Zhou and Xiaoqing Liu
Plants 2023, 12(5), 994; https://doi.org/10.3390/plants12050994 - 22 Feb 2023
Cited by 6 | Viewed by 1797
Abstract
The AP2/ERF gene family is one of the most conserved and important transcription factor families mainly occurring in plants with various functions in regulating plant biological and physiological processes. However, little comprehensive research has been conducted on the AP2/ERF gene family in Rhododendron [...] Read more.
The AP2/ERF gene family is one of the most conserved and important transcription factor families mainly occurring in plants with various functions in regulating plant biological and physiological processes. However, little comprehensive research has been conducted on the AP2/ERF gene family in Rhododendron (specifically, Rhododendron simsii), an important ornamental plant. The existing whole-genome sequence of Rhododendron provided data to investigate the AP2/ERF genes in Rhododendron on a genome-wide scale. A total of 120 Rhododendron AP2/ERF genes were identified. The phylogenetic analysis showed that RsAP2 genes were classified into five main subfamilies, AP2, ERF, DREB, RAV and soloist. Cis-acting elements involving plant growth regulators, response to abiotic stress and MYB binding sites were detected in the upstream sequences of RsAP2 genes. A heatmap of RsAP2 gene expression levels showed that these genes had different expression patterns in the five developmental stages of Rhododendron flowers. Twenty RsAP2 genes were selected for quantitative RT-PCR experiments to clarify the expression level changes under cold, salt and drought stress treatments, and the results showed that most of the RsAP2 genes responded to these abiotic stresses. This study generated comprehensive information on the RsAP2 gene family and provides a theoretical basis for future genetic improvement. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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12 pages, 2711 KiB  
Article
IlAP2, an AP2/ERF Superfamily Gene, Mediates Cadmium Tolerance by Interacting with IlMT2a in Iris lactea var. chinensis
by Zhiquan Wang, Longjie Ni, Liangqin Liu, Haiyan Yuan and Chunsun Gu
Plants 2023, 12(4), 823; https://doi.org/10.3390/plants12040823 - 12 Feb 2023
Cited by 2 | Viewed by 1231
Abstract
Cadmium (Cd) stress has a major impact on ecosystems, so it is important to find suitable Cd-tolerant plants while elucidating the responsible molecular mechanism for phytoremediation to manage Cd soil contamination. Iris lactea var. chinensis is an ornamental perennial groundcover plant with strong [...] Read more.
Cadmium (Cd) stress has a major impact on ecosystems, so it is important to find suitable Cd-tolerant plants while elucidating the responsible molecular mechanism for phytoremediation to manage Cd soil contamination. Iris lactea var. chinensis is an ornamental perennial groundcover plant with strong tolerance to Cd. Previous studies found that IlAP2, an AP2/ERF superfamily gene, may be an interacting partner of the metallothionein gene IlMT2a, which plays a key role in Cd tolerance. To study the role of IlAP2 in regulating Cd tolerance in I. lactea, we analyzed its regulation function and mechanism based on a yeast two-hybrid assay, a bimolecular fluorescence complementation test, quantitative real-time PCR, transgenics and transcriptome sequencing. The results showed that IlAP2 interacts with IlMT2a and may cooperate with other transcription factors to regulate genes involved in signal transduction and plant hormones, leading to reduced Cd toxicity by hindering Cd transport. These findings provide insights into the mechanism of IlAP2-mediated stress responses to Cd and important gene resources for improving plant stress tolerance in phytoremediation. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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13 pages, 2862 KiB  
Article
Elucidating Biological Functions of 9-cis-Epoxycarotenoid Dioxygenase Genes Involved in Seed Dormancy in Paeonia lactiflora
by Riwen Fei, Shixin Guan, Siyang Duan, Jiayuan Ge, Tianyi Sun and Xiaomei Sun
Plants 2023, 12(4), 710; https://doi.org/10.3390/plants12040710 - 06 Feb 2023
Cited by 4 | Viewed by 1300
Abstract
Abscisic acid (ABA) is a major phytohormone affecting seed dormancy and germination in plants. ABA is synthesized mainly through the C40 carotenoid pathway. In the ABA biosynthesis pathway, 9-cis-epoxycarotenoid dioxygenase (NCED) is a key rate-limiting enzyme that regulates the accumulation and [...] Read more.
Abscisic acid (ABA) is a major phytohormone affecting seed dormancy and germination in plants. ABA is synthesized mainly through the C40 carotenoid pathway. In the ABA biosynthesis pathway, 9-cis-epoxycarotenoid dioxygenase (NCED) is a key rate-limiting enzyme that regulates the accumulation and content of ABA. However, the role of the NCED gene in perennial plants with complex seed dormancy remains largely unknown. Here, we cloned two differentially expressed paralogs of herbaceous peony NCED genes, named PlNCED1 and PlNCED2, and further identified their involvement in seed dormancy from perennial herbaceous peony experiencing complex double seed dormancy. The deduced PlNCED amino acid sequences had high sequence homology with NCED sequences from other plants and contained the typical conserved RPE65 domain of the NCED family. Phylogenetic analysis showed that PlNCED1 and PlNCED2 have a close relationship with PoNCED in Paeonia ostii and VvNCED6 in Vitis vinifera, respectively. A subcellular localization assay demonstrated that the PlNCED1 protein resided within the nucleus, while the PlNCED2 protein was located in the cytoplasm, indicating their different roles in the biosynthesis of ABA. Furthermore, the content of endogenous ABA in transgenic calluses showed that PlNCEDs were positively correlated with ABA content. Both PlNCED transgenic Arabidopsis lines and the functional complementation of Arabidopsis NCED mutants found that PlNCEDs promoted seed dormancy and delayed seed germination. These results reveal that PlNCEDs participate in the seed dormancy of herbaceous peony by regulating the accumulation of endogenous ABA. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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19 pages, 7268 KiB  
Article
Genome-Wide Identification and Expression Analysis of HSF Transcription Factors in Alfalfa (Medicago sativa) under Abiotic Stress
by Jin Ma, Guozhe Zhang, Yacheng Ye, Linxue Shang, Sidan Hong, Qingqing Ma, Yu Zhao and Cuihua Gu
Plants 2022, 11(20), 2763; https://doi.org/10.3390/plants11202763 - 19 Oct 2022
Cited by 7 | Viewed by 1717
Abstract
Alfalfa (Medicago sativa) is one of the most important legume forage species in the world. It is often affected by several abiotic stressors that result in reduced yields and poor growth. Therefore, it is crucial to study the resistance of M. [...] Read more.
Alfalfa (Medicago sativa) is one of the most important legume forage species in the world. It is often affected by several abiotic stressors that result in reduced yields and poor growth. Therefore, it is crucial to study the resistance of M. sativa to abiotic stresses. Heat shock transcription factors (HSF) are key players in a number of transcriptional regulatory pathways. These pathways play an essential role in controlling how plants react to different abiotic stressors. Studies on the HSF gene family have been reported in many species but have not yet undergone a thorough analysis in M. sativa. Therefore, in order to identify a more comprehensive set of HSF genes, from the genomic data, we identified 16 members of the MsHSF gene, which were unevenly distributed over six chromosomes. We also looked at their gene architectures and protein motifs, and phylogenetic analysis allowed us to divide them into 3 groups with a total of 15 subgroups. Along with these aspects, we then examined the physicochemical properties, subcellular localization, synteny analysis, GO annotation and enrichment, and protein interaction networks of amino acids. Finally, the analysis of 16 MsHSF genes’ expression levels across all tissues and under four abiotic stresses using publicly available RNA-Seq data revealed that these genes had significant tissue-specific expression. Moreover, the expression of most MsHSF genes increased dramatically under abiotic stress, further validating the critical function played by the MsHSF gene family in abiotic stress. These results provided basic information about MsHSF gene family and laid a foundation for further study on the biological role of MsHSF gene in response to stress in M. sativa. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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15 pages, 4633 KiB  
Article
Identification and Expression Analysis of NAC Gene Family in Weeping Trait of Lagerstroemia indica
by Cuihua Gu, Linxue Shang, Guozhe Zhang, Qun Wang, Qingqing Ma, Sidan Hong, Yu Zhao and Liyuan Yang
Plants 2022, 11(16), 2168; https://doi.org/10.3390/plants11162168 - 21 Aug 2022
Cited by 4 | Viewed by 1573
Abstract
Lagerstroemia indica is a widely used ornamental plant in summer gardens because of its desirable plant shape. The weeping traits of plants are related to secondary cell wall thickness and hormone signaling. NAC (NAM-ATAF1/2-CUC2), as one of the plant-specific transcription factors, is a [...] Read more.
Lagerstroemia indica is a widely used ornamental plant in summer gardens because of its desirable plant shape. The weeping traits of plants are related to secondary cell wall thickness and hormone signaling. NAC (NAM-ATAF1/2-CUC2), as one of the plant-specific transcription factors, is a switch for the secondary cell wall and also involved in leaf senescence, phytohormone signaling, and other growth processes. We identified a total of 21 LiNAC genes from the transcriptome data, which we divided into 14 subgroups and 2 groups. The physicochemical characteristics of amino acids, subcellular localization, transmembrane structure, GO and KEGG enrichment, and expression patterns were also examined. The qRT-PCR analysis showed that the expressions of LiNAC8 and LiNAC13 in upright L. indica ‘Shaoguifei’ and weeping L. indica ‘Xiariwuniang’ were significantly higher from the beginning to the end of growth stage (S1–S3), and the expressions of ‘Shaoguifei’ were always higher than those of ‘Xiariwuniang’. However, LiNAC2 showed a downward trend in S1–S3 and the relative expression level of ‘Shaoguifei’ was lower than that of ‘Xiariwuniang’. It is hypothesized that these LiNAC genes may be involved in the regulation of weeping traits in L. indica. The results of this study provide a basis for analyzing the functions of LiNAC genes and help to explore the molecular regulatory mechanisms related to the weeping traits in L. indica. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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16 pages, 13932 KiB  
Article
Genome-Wide Identification and Expression Analysis of Dof Transcription Factors in Lotus (Nelumbo nucifera Gaertn.)
by Xiaohan Cao, Wenyang Wan, Huimin Mao, Dandan Yin, Xianhui Deng, Huan Yan and Liping Ren
Plants 2022, 11(15), 2057; https://doi.org/10.3390/plants11152057 - 06 Aug 2022
Cited by 4 | Viewed by 1892
Abstract
Lotus (Nelumbo nucifera Gaertn.) is a traditional Chinese aquatic flower with high ornamental and economic value, but water salinity seriously affects lotus cultivation and distribution. The Dof transcription factors (TFs) play a crucial function in the regulatory network of growth and defense [...] Read more.
Lotus (Nelumbo nucifera Gaertn.) is a traditional Chinese aquatic flower with high ornamental and economic value, but water salinity seriously affects lotus cultivation and distribution. The Dof transcription factors (TFs) play a crucial function in the regulatory network of growth and defense in plants. However, no systematic investigations of the Dof TFs in lotus have been performed. In this study, comprehensive searches of the lotus genome yielded 29 potential NnDofs. We carried out a series of standardized analyses, which include physical properties, multiple sequence alignment, phylogenetic analysis, gene structure, motif composition, cis-acting element prediction, chromosome distribution, and synteny analysis. The results showed that segment duplication probably caused the NnDofs gene family expansion. The potential functions of NnDofs in lotus development and stress conditions are speculated by promoter analysis. Furthermore, a complete expression investigation of NnDofs utilizing an RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) was performed. The majority of the NnDofs exhibit tissue-specific expression patterns, and many genes have been identified as being extremely sensitive to salt stressors. Overall, this study is the first to report a genome-wide assessment of the Dof family in lotus, and the findings offer vital insights for prospective functional studies on lotus salinity stress. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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15 pages, 1762 KiB  
Article
A Comparative Study of Genetic Responses to Short- and Long-Term Habitat Fragmentation in a Distylous Herb Hedyotis chyrsotricha (Rubiaceae)
by Na Yuan, Shujing Wei, Hans Peter Comes, Sisheng Luo, Ruisen Lu and Yingxiong Qiu
Plants 2022, 11(14), 1800; https://doi.org/10.3390/plants11141800 - 07 Jul 2022
Cited by 1 | Viewed by 1198
Abstract
The genetic effects of habitat fragmentation are complex and are influenced by both species traits and landscape features. For plants with strong seed or pollen dispersal capabilities, the question of whether the genetic erosion of an isolated population becomes stronger or is counterbalanced [...] Read more.
The genetic effects of habitat fragmentation are complex and are influenced by both species traits and landscape features. For plants with strong seed or pollen dispersal capabilities, the question of whether the genetic erosion of an isolated population becomes stronger or is counterbalanced by sufficient gene flow across landscapes as the timescales of fragmentation increase has been less studied. In this study, we compared the population structure and genetic diversity of a distylous herb, Hedyotis chyrsotricha (Rubiaceae), in two contrasting island systems of southeast China. Based on RAD-Seq data, our results showed that populations from the artificially created Thousand-Island Lake (TIL) harbored significantly higher levels of genetic diversity than those from the Holocene-dated Zhoushan Archipelago (ZA) (π = 0.247 vs. 0.208, HO = 0.307 vs. 0.256, HE = 0.228 vs. 0.190), while genetic differences between island and mainland populations were significant in neither the TIL region nor the ZA region. A certain level of population substructure was found in TIL populations, and the level of gene flow among TIL populations was also lower than in ZA populations (m = 0.019 vs. 0.027). Overall, our comparative study revealed that genetic erosion has not become much stronger for the island populations of either the TIL or ZA regions. Our results emphasized that the matrix of water in the island system may facilitate the seed (fruit) dispersal of H. chrysotricha, thus maintaining population connectivity and providing ongoing resilience to the effects of habitat fragmentation over thousands of years. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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13 pages, 2605 KiB  
Article
Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of Luculia yunnanensis, an Endangered Species Endemic to Yunnan, Southwestern China
by Yao Zhang, Xi Liu, Yuying Li, Xiongfang Liu, Hong Ma, Suping Qu and Zhenghong Li
Plants 2022, 11(9), 1204; https://doi.org/10.3390/plants11091204 - 29 Apr 2022
Cited by 5 | Viewed by 1373
Abstract
Luculia yunnanensis (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence [...] Read more.
Luculia yunnanensis (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence of climate change and human factors, the distribution range of L. yunnanensis has exhibited a significant shrinking trend, and it has become a vulnerable species that is in urgent need of conservation and rational utilization research. In this study, the flower transcriptome sequencing of L. yunnanensis was conducted using an Illumina HiSeq platform. We designed and developed a series of EST-SSR primers based on the flower transcriptome data of L. yunnanensis. The results showed that 98,389 unigenes were obtained from the L. yunnanensis flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. The MISA (Microsatellite) tool was used to identify SSR loci from all unigenes, and a total of 15,384 SSRs were identified. Repeat motifs were given priority with mononucleotides, dinucleotides, and trinucleotides. The 81 primer pairs were synthesized randomly, of which 44 pairs showed effective amplification. A total of 17 primers showed stable amplification, and rich polymorphism was observed in 6 populations. We concluded via genetic diversity analysis that the average effective number of alleles (Ne), Shannon’s information index (I), and polymorphism information content (PIC) were 1.925, 0.837, and 0.403, respectively. In conclusion, 17 EST-SSR primers can be used for subsequent population genetic diversity analysis and molecular-marker-assisted breeding, which is of great significance for formulating resource conservation and utilization strategies for L. yunnanensis. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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17 pages, 5769 KiB  
Article
Genome-Wide Identification and Expression Analysis of XTH Gene Family during Flower-Opening Stages in Osmanthus fragrans
by Yang Yang, Yunfeng Miao, Shiwei Zhong, Qiu Fang, Yiguang Wang, Bin Dong and Hongbo Zhao
Plants 2022, 11(8), 1015; https://doi.org/10.3390/plants11081015 - 08 Apr 2022
Cited by 3 | Viewed by 2210
Abstract
Osmanthus fragrans is an aromatic plant which is widely used in landscaping and garden greening in China. However, the process of flower opening is significantly affected by ambient temperature changes. Cell expansion in petals is the primary factor responsible for flower opening. Xyloglucan [...] Read more.
Osmanthus fragrans is an aromatic plant which is widely used in landscaping and garden greening in China. However, the process of flower opening is significantly affected by ambient temperature changes. Cell expansion in petals is the primary factor responsible for flower opening. Xyloglucan endoglycolase/hydrolase (XTH) is a cell-wall-loosening protein involved in cell expansion or cell-wall weakening. Through whole-genome analysis, 38 OfXTH genes were identified in O. fragrans which belong to the four main phylogenetic groups. The gene structure, chromosomal location, synteny relationship, and cis-acting elements prediction and expression patterns were analyzed on a genome-wide scale. The expression patterns showed that most OfXTHs were closely associated with the flower-opening period of O. fragrans. At the early flower-opening stage (S1 and S2), transcriptome and qRT-PCR analysis revealed the expression of OfXTH24, 27, 32, 35, and 36 significantly increased under low ambient temperature (19 °C). It is speculated that the five genes might be involved in the regulation of flower opening by responding to ambient temperature changes. Our results provide solid foundation for the functional analysis of OfXTH genes and help to explore the mechanism of flower opening responding to ambient temperature in O. fragrans. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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19 pages, 15293 KiB  
Article
Diversity and Functional Evolution of Terpene Synthases in Rosaceae
by Aidi Zhang, Yuhong Xiong, Jing Fang, Xiaohan Jiang, Tengfei Wang, Kangchen Liu, Huixiang Peng and Xiujun Zhang
Plants 2022, 11(6), 736; https://doi.org/10.3390/plants11060736 - 10 Mar 2022
Cited by 7 | Viewed by 2664
Abstract
Terpenes are organic compounds and play important roles in plant development and stress response. Terpene synthases (TPSs) are the key enzymes for the biosynthesis of terpenes. For Rosaceae species, terpene composition represents a critical quality attribute, but limited information is available regarding the [...] Read more.
Terpenes are organic compounds and play important roles in plant development and stress response. Terpene synthases (TPSs) are the key enzymes for the biosynthesis of terpenes. For Rosaceae species, terpene composition represents a critical quality attribute, but limited information is available regarding the evolution and expansion occurring in the terpene synthases gene family. Here, we selected eight Rosaceae species with sequenced and annotated genomes for the identification of TPSs, including three Prunoideae, three Maloideae, and two Rosoideae species. Our data showed that the TPS gene family in the Rosaceae species displayed a diversity of family numbers and functions among different subfamilies. Lineage and species-specific expansion of the TPSs accompanied by frequent domain loss was widely observed within different TPS clades, which might have contributed to speciation or environmental adaptation in Rosaceae. In contrast to Maloideae and Rosoideae species, Prunoideae species owned less TPSs, with the evolution of Prunoideae species, TPSs were expanded in modern peach. Both tandem and segmental duplication significantly contributed to TPSs expansion. Ka/Ks calculations revealed that TPSs genes mainly evolved under purifying selection except for several pairs, where the divergent time indicated TPS-e clade was diverged relatively anciently. Gene function classification of TPSs further demonstrated the function diversity among clades and species. Moreover, based on already published RNA-Seq data from NCBI, the expression of most TPSs in Malus domestica, Prunus persica, and Fragaria vesca displayed tissue specificity and distinct expression patterns either in tissues or expression abundance between species and TPS clades. Certain putative TPS-like proteins lacking both domains were detected to be highly expressed, indicating the underlying functional or regulatory potentials. The result provided insight into the TPS family evolution and genetic information that would help to improve Rosaceae species quality. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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Review

Jump to: Editorial, Research

14 pages, 1313 KiB  
Review
The Role of Transcription Factors in the Regulation of Plant Shoot Branching
by Lingling Zhang, Weimin Fang, Fadi Chen and Aiping Song
Plants 2022, 11(15), 1997; https://doi.org/10.3390/plants11151997 - 31 Jul 2022
Cited by 9 | Viewed by 3899
Abstract
Transcription factors, also known as trans-acting factors, balance development and stress responses in plants. Branching plays an important role in plant morphogenesis and is closely related to plant biomass and crop yield. The apical meristem produced during plant embryonic development repeatedly produces the [...] Read more.
Transcription factors, also known as trans-acting factors, balance development and stress responses in plants. Branching plays an important role in plant morphogenesis and is closely related to plant biomass and crop yield. The apical meristem produced during plant embryonic development repeatedly produces the body of the plant, and the final aerial structure is regulated by the branching mode generated by axillary meristem (AM) activities. These branching patterns are regulated by two processes: AM formation and axillary bud growth. In recent years, transcription factors involved in regulating these processes have been identified. In addition, these transcription factors play an important role in various plant hormone pathways and photoresponses regulating plant branching. In this review, we start from the formation and growth of axillary meristems, including the regulation of hormones, light and other internal and external factors, and focus on the transcription factors involved in regulating plant branching and development to provide candidate genes for improving crop architecture through gene editing or directed breeding. Full article
(This article belongs to the Special Issue Molecular Biology of Ornamental Plants)
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