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Transcriptome Analysis and Gene Regulation in Plant Growth Development II

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

Deadline for manuscript submissions: 31 October 2024 | Viewed by 4449

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Dr. Yi He

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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

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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

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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

Transcriptome Analysis and Gene Regulation in Plant Growth Development in Plants (10 articles)

Published Papers (5 papers)

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Research

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16 pages, 2936 KiB

Open AccessArticle

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

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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 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

Open AccessArticle

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

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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 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

Open AccessArticle

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 - 09 Jan 2024

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Abstract

The morphological characteristics of the rice panicle play a pivotal role in influencing yield. In our research, we employed F₂ and F_2:3 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 F_2:3 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

Open AccessArticle

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 1087

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 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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Review

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14 pages, 1765 KiB

Open AccessReview

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 - 09 Oct 2023

Viewed by 1150

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 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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