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Transcriptome Analysis and Gene Regulation in Plant Growth Development II
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Transcriptome Analysis and Gene Regulation in Plant Growth Development II

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

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 10439

Special Issue Editors

Dr. Yi He

E-Mail Website
Guest Editor
College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: photosynthesis; signal transduction; gene regulation; flower development
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Dali Zeng

E-Mail Website
Guest Editor
College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: molecular breeding; gene regulation; plant genetics and genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Transcriptome sequencing has become more and more important in order to understand biological phenomena, and provides a vital insight for understanding gene regulatory mechanisms in the process of plant growth development. Therefore, it is a hot topic for many plant biologists on how to efficiently explore the information underlying the transcriptome sequencing to understand the gene regulatory mechanism for the phenomenon. In addition, an integrated multi-omics framework based on transcriptome has provided insight into the gene regulatory mechanism of plant growth development, especially in some non-model plants. The importance of new mathematical and statistical methods for transcriptome analysis will also help us better understand the hidden secrets of plant growth and development. This Special Issue of Plants will highlight the new tools, methods, strategies, and perspectives of transcriptome analysis and their role in explaining gene regulatory networks.

Dr. Yi He
Prof. Dr. Dali Zeng
Guest Editors

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Related Special Issue

Published Papers (7 papers)

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Research

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18 pages, 4561 KiB  
Article
Comparative Transcriptome and sRNAome Analysis Suggest Coordinated Citrus Immune Responses against Huanglongbing Disease
by Muhammad Saqib Bilal, Gomes Paul, Ze Yu, Le Xu, Tang Cheng, Baoping Cheng, Muhammad Naveed Aslam, Ayesha Baig and Hongwei Zhao
Plants 2024, 13(11), 1496; https://doi.org/10.3390/plants13111496 - 29 May 2024
Viewed by 1234
Abstract
Citrus Huanglongbing (HLB), caused by the phloem-inhibiting bacterium Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease, intimidating citrus production worldwide. Although commercially cultivated citrus cultivars are vulnerable to CLas infection, HLB-tolerant attributes have, however, been observed in certain [...] Read more.
Citrus Huanglongbing (HLB), caused by the phloem-inhibiting bacterium Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease, intimidating citrus production worldwide. Although commercially cultivated citrus cultivars are vulnerable to CLas infection, HLB-tolerant attributes have, however, been observed in certain citrus varieties, suggesting a possible pathway for identifying innate defense regulators that mitigate HLB. By adopting transcriptome and small RNAome analysis, the current study compares the responses of HLB-tolerant lemon (Citrus limon L.) with HLB-susceptible Shatangju mandarin (Citrus reticulata Blanco cv. Shatangju) against CLas infection. Transcriptome analysis revealed significant differences in gene expression between lemon and Shatangju. A total of 1751 and 3076 significantly differentially expressed genes were identified in Shatangju and lemon, respectively. Specifically, CLas infected lemon tissues demonstrated higher expressions of genes involved in antioxidant enzyme activity, protein phosphorylation, carbohydrate, cell wall, and lipid metabolism than Shatangju. Wet-lab experiments further validated these findings, demonstrating increased antioxidant enzyme activity in lemon: APX (35%), SOD (30%), and CAT (64%) than Shatangju. Conversely, Shatangju plants exhibited higher levels of oxidative stress markers like H2O2 (44.5%) and MDA content (65.2%), alongside pronounced ion leakage (11.85%), than lemon. Moreover, microscopic investigations revealed that CLas infected Shatangju phloem exhibits significantly more starch and callose accumulation than lemon. Furthermore, comparative sRNA profiles revealed the potential defensive regulators for HLB tolerance. In Shatangju, increased expression of csi-miR166 suppresses the expression of disease-resistant proteins, leading to inadequate defense against CLas. Conversely, reduced expression of csi-miR166 in lemon plants enables them to combat HLB by activating disease-resistance proteins. The above findings indicate that when infected with CLas, lemon exhibits stronger antioxidative activity and higher expression of disease-resistant genes, contributing to its enhanced tolerance to HLB. In contrast, Shatangju shows lower antioxidative activity, reduced expression of disease-resistant genes, significant ion leakage, and extensive callose deposition, possibly related to damage to plant cell structure and blockage of phloem sieve tubes, thereby promoting the development of HLB symptoms. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development II)
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17 pages, 3215 KiB  
Article
Jasmonate ZIM Domain Protein (JAZ) Gene SLJAZ15 Increases Resistance to Orobanche aegyptiaca in Tomato
by Siyu Chen, Lu Zhang, Qianqian Ma, Meixiu Chen, Xiaolei Cao, Sifeng Zhao and Xuekun Zhang
Plants 2024, 13(11), 1493; https://doi.org/10.3390/plants13111493 - 29 May 2024
Viewed by 1313
Abstract
Orobanche aegyptiaca Pers. is a holoparasitic plant that severely reduces tomato (Solanum lycopersicum L.) production in China. However, there is a lack of effective control methods and few known sources of genetic resistance. In this study, we focused on key genes in [...] Read more.
Orobanche aegyptiaca Pers. is a holoparasitic plant that severely reduces tomato (Solanum lycopersicum L.) production in China. However, there is a lack of effective control methods and few known sources of genetic resistance. In this study, we focused on key genes in the JAZ family, comparing the JAZ family in Arabidopsis thaliana (L. Heynh.) to the tomato genome. After identifying the JAZ family members in S. lycopersicum, we performed chromosomal localization and linear analysis with phylogenetic relationship analysis of the JAZ family. We also analyzed the gene structure of the JAZ gene family members in tomato and the homology of the JAZ genes among the different species to study their relatedness. The key genes for O. aegyptiaca resistance were identified using VIGS (virus-induced gene silencing), and the parasitization rate of silenced tomato plants against O. aegyptiaca increased by 47.23–91.13%. The genes were localized in the nucleus by subcellular localization. Heterologous overexpression in A. thaliana showed that the key gene had a strong effect on the parasitization process of O. aegyptiaca, and the overexpression of the key gene reduced the parasitization rate of O. aegyptiaca 1.69-fold. Finally, it was found that the SLJAZ15 gene can positively regulate the hormone content in tomato plants and affect plant growth and development, further elucidating the function of this gene. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development II)
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16 pages, 2936 KiB  
Article
Transcriptomic Insights: Phytogenic Modulation of Buffel Grass (Cenchrus ciliaris) Seedling Emergence
by Xipeng Ren, Tieneke Trotter, Nanjappa Ashwath, Dragana Stanley, Yadav S. Bajagai and Philip B. Brewer
Plants 2024, 13(9), 1174; https://doi.org/10.3390/plants13091174 - 23 Apr 2024
Viewed by 1096
Abstract
This study explores the impact of a novel phytogenic product containing citric acid, carvacrol, and cinnamaldehyde on buffel grass (Cenchrus ciliaris) seedling emergence. A dilution series of the phytogenic solution revealed a concentration range that promoted seedling emergence, with an optimal [...] Read more.
This study explores the impact of a novel phytogenic product containing citric acid, carvacrol, and cinnamaldehyde on buffel grass (Cenchrus ciliaris) seedling emergence. A dilution series of the phytogenic solution revealed a concentration range that promoted seedling emergence, with an optimal concentration of 0.5%. Transcriptomic analysis using RNA-seq was performed to investigate gene expression changes in seedlings under the influence of the phytogenic product. The results revealed that the phytogenic treatment significantly altered the gene expression, with a prevalent boost in transcriptional activity compared to the control. Functional analysis indicated the positive alteration of key metabolic pathways, including the tricarboxylic acid (TCA) cycle, glycolysis, and pentose phosphate pathways. Moreover, pathways related to amino acids, nucleotide biosynthesis, heme biosynthesis, and formyltetrahydrofolate biosynthesis showed substantial modulation. The study provides valuable insights into the molecular mechanisms underlying the phytogenic product’s effects on grass seedling establishment and highlights its ability to promote energy metabolism and essential biosynthetic pathways for plant growth. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development II)
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14 pages, 5826 KiB  
Article
Cytological, Physiological, and Transcriptomic Analyses of the Leaf Color Mutant Yellow Leaf 20 (yl20) in Eggplant (Solanum melongena L.)
by Bing Li, Jingjing Zhang, Peng Tian, Xiurui Gao, Xue Song, Xiuqing Pan and Yanrong Wu
Plants 2024, 13(6), 855; https://doi.org/10.3390/plants13060855 - 15 Mar 2024
Viewed by 1292
Abstract
Leaf color mutants are ideal materials for studying chlorophyll metabolism, chloroplast development, and photosynthesis in plants. We discovered a novel eggplant (Solanum melongena L.) mutant yl20 (yellow leaf 20) that exhibits yellow leaves. In this study, we compared the leaves of the [...] Read more.
Leaf color mutants are ideal materials for studying chlorophyll metabolism, chloroplast development, and photosynthesis in plants. We discovered a novel eggplant (Solanum melongena L.) mutant yl20 (yellow leaf 20) that exhibits yellow leaves. In this study, we compared the leaves of the mutant yl20 and wild type (WT) plants for cytological, physiological, and transcriptomic analyses. The results showed that the mutant yl20 exhibits abnormal chloroplast ultrastructure, reduced chlorophyll and carotenoid contents, and lower photosynthetic efficiency compared to the WT. Transcriptome data indicated 3267 and 478 differentially expressed genes (DEGs) between WT and yl20 lines in the cotyledon and euphylla stages, respectively, where most DEGs were downregulated in the yl20. Gene Ontology (GO) analysis revealed the “plastid-encoded plastid RNA polymerase complex” and the “chloroplast-related” terms were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the significantly enriched DEGs were involved in flavone and flavonol biosynthesis, porphyrin and chlorophyll metabolism, etc. We speculated that these DEGs involved in significant terms were closely related to the leaf color development of the mutant yl20. Our results provide a possible explanation for the altered phenotype of leaf color mutants in eggplant and lay a theoretical foundation for plant breeding. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development II)
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15 pages, 3013 KiB  
Article
Genetic Dissection of Panicle Morphology Traits in Super High-Yield Hybrid Rice Chaoyou 1000
by Jing Jiang, Li Wang, Gucheng Fan, Yu Long, Xueli Lu, Run Wang, Haiyang Liu, Xianjin Qiu, Dali Zeng and Zhixin Li
Plants 2024, 13(2), 179; https://doi.org/10.3390/plants13020179 - 9 Jan 2024
Cited by 1 | Viewed by 1019
Abstract
The morphological characteristics of the rice panicle play a pivotal role in influencing yield. In our research, we employed F2 and F2:3 populations derived from the high-yielding hybrid rice variety Chaoyou 1000. We screened 123 pairs of molecular markers, which were [...] Read more.
The morphological characteristics of the rice panicle play a pivotal role in influencing yield. In our research, we employed F2 and F2:3 populations derived from the high-yielding hybrid rice variety Chaoyou 1000. We screened 123 pairs of molecular markers, which were available, to construct the genetic linkage map. Subsequently, we assessed the panicle morphology traits of F2 populations in Lingshui County, Hainan Province, in 2017, and F2:3 populations in Hangzhou City, Zhejiang Province, in 2018. These two locations represent two types of ecology. Hangzhou’s climate is characterized by high temperatures and humidity, while Lingshui’s climate is characterized by a tropical monsoon climate. In total, 33 QTLs were identified, with eight of these being newly discovered, and two of them were consistently detected in two distinct environments. We identified fourteen QTL-by-environment interactions (QEs), which collectively explained 4.93% to 59.95% of the phenotypic variation. While most of the detected QTLs are consistent with the results of previous tests, the novel-detected QTLs will lay the foundation for rice yield increase and molecular breeding. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development II)
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20 pages, 6062 KiB  
Article
Transcriptome Analysis Reveals the Response Mechanism of Digitaria sanguinalis, Arabidopsis thaliana and Poa annua under 4,8-Dihydroxy-1-tetralone Treatment
by Qiumin Sun, Tao Wang, Jiu Huang, Xinyi Gu, Yanling Dong, Ying Yang, Xiaowen Da, Xiaorong Mo, Xiaoting Xie, Hangjin Jiang, Daoliang Yan, Bingsong Zheng and Yi He
Plants 2023, 12(14), 2728; https://doi.org/10.3390/plants12142728 - 22 Jul 2023
Viewed by 1623
Abstract
4,8-dihydroxy-l-tetralone (4,8-DHT) is an allelochemical isolated from the outer bark of Carya cathayensis that acts as a plant growth inhibitor. In order to explore the mechanism of 4,8-DHT inhibiting weed activity, we treated three species of Digitaria sanguinalis, Arabidopsis thaliana, and Poa [...] Read more.
4,8-dihydroxy-l-tetralone (4,8-DHT) is an allelochemical isolated from the outer bark of Carya cathayensis that acts as a plant growth inhibitor. In order to explore the mechanism of 4,8-DHT inhibiting weed activity, we treated three species of Digitaria sanguinalis, Arabidopsis thaliana, and Poa annua with different concentrations of 4,8-DHT and performed phenotype observation and transcriptome sequencing. The results showed that with an increase in 4,8-DHT concentration, the degree of plant damage gradually deepened. Under the same concentration of 4,8-DHT, the damage degree of leaves and roots of Digitaria sanguinalis was the greatest, followed by Arabidopsis thaliana, while Poa annua had the least damage, and the leaves turned slightly yellow. Transcriptome data showed that 24536, 9913, and 1662 differentially expressed genes (DEGs) were identified in Digitaria sanguinalis, Arabidopsis thaliana, and Poa annua, respectively. These DEGs were significantly enriched in photosynthesis, carbon fixation, glutathione metabolism, phenylpropanoid biosynthesis, and oxidative phosphorylation pathways. In addition, DEGs were also enriched in plant hormone signal transduction and the MAPK signal pathway in Arabidopsis thaliana. Further analysis showed that after 4,8-DHT treatment, the transcript levels of photosynthesis PSI- and PSII-related genes, LHCA/B-related genes, Rubisco, and PEPC were significantly decreased in Digitaria sanguinalis and Arabidopsis thaliana. At the same time, the transcription levels of genes related to glutathione metabolism and the phenylpropanoid biosynthesis pathway in Digitaria sanguinalis were also significantly decreased. However, the expression of these genes was upregulated in Arabidopsis thaliana and Poa annua. These indicated that 4,8-DHT affected the growth of the three plants through different physiological pathways, and then played a role in inhibiting plant growth. Simultaneously, the extent to which plants were affected depended on the tested plants and the content of 4,8-DHT. The identification of weed genes that respond to 4,8-DHT has helped us to further understand the inhibition of plant growth by allelochemicals and has provided a scientific basis for the development of allelochemicals as herbicides. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development II)
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14 pages, 1765 KiB  
Review
Regulation of Flowering Time and Other Developmental Plasticities by 3’ Splicing Factor-Mediated Alternative Splicing in Arabidopsis thaliana
by Keh Chien Lee, Young-Cheon Kim, Jeong-Kook Kim, Horim Lee and Jeong Hwan Lee
Plants 2023, 12(19), 3508; https://doi.org/10.3390/plants12193508 - 9 Oct 2023
Viewed by 1827
Abstract
Plants, as sessile organisms, show a high degree of plasticity in their growth and development and have various strategies to cope with these alterations under continuously changing environments and unfavorable stress conditions. In particular, the floral transition from the vegetative and reproductive phases [...] Read more.
Plants, as sessile organisms, show a high degree of plasticity in their growth and development and have various strategies to cope with these alterations under continuously changing environments and unfavorable stress conditions. In particular, the floral transition from the vegetative and reproductive phases in the shoot apical meristem (SAM) is one of the most important developmental changes in plants. In addition, meristem regions, such as the SAM and root apical meristem (RAM), which continually generate new lateral organs throughout the plant life cycle, are important sites for developmental plasticity. Recent findings have shown that the prevailing type of alternative splicing (AS) in plants is intron retention (IR) unlike in animals; thus, AS is an important regulatory mechanism conferring plasticity for plant growth and development under various environmental conditions. Although eukaryotes exhibit some similarities in the composition and dynamics of their splicing machinery, plants have differences in the 3’ splicing characteristics governing AS. Here, we summarize recent findings on the roles of 3’ splicing factors and their interacting partners in regulating the flowering time and other developmental plasticities in Arabidopsis thaliana. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development II)
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