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Recent Advances in Plant Molecular Science in China 2023

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 (31 December 2023) | Viewed by 16769

Special Issue Editors

Dr. Ke Wang

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Guest Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: wheat; genetic transformation; gene editing; molecular genetics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Changning Liu

E-Mail Website
Guest Editor
CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
Interests: bioinformatics; disease; long non coding RNA; plant biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This special issue aims to provide a comprehensive overview of recent advances in plant molecular science in China by inviting contributions from Chinese research institutes/laboratories that consolidate our understanding of this area. Potential topics regarding plants include, but are not limited to, biophysics, biochemistry, and molecular biology; cell biology; physiology; genomics/epigenomics; proteomics and metabolomics; bioactive phytochemicals; plant–microbe interactions; developmental biology; pests and diseases; synthetic biology; computational biology; and the development of new technologies in plant sciences. In this Special Issue, we welcome submissions in the form of comprehensive reviews or new research advancements in all the abovementioned areas.

Dr. Ke Wang
Dr. Changning Liu
Guest Editors

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Published Papers (9 papers)

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Research

20 pages, 7501 KiB  
Article
New Insights into the TIFY Gene Family of Brassica napus and Its Involvement in the Regulation of Shoot Branching
by Yarong Li, Qian Zhang, Luman Wang, Xinfa Wang, Jiangwei Qiao and Hanzhong Wang
Int. J. Mol. Sci. 2023, 24(23), 17114; https://doi.org/10.3390/ijms242317114 - 4 Dec 2023
Cited by 3 | Viewed by 1327
Abstract
As plant-specific transcription factors, the TIFY family genes are involved in the responses to a series of biotic and abiotic stresses and the regulation of the development of multiple organs. To explore the potential roles of the TIFY gene family in shoot branching, [...] Read more.
As plant-specific transcription factors, the TIFY family genes are involved in the responses to a series of biotic and abiotic stresses and the regulation of the development of multiple organs. To explore the potential roles of the TIFY gene family in shoot branching, which can shape plant architecture and finally determine seed yield, we conducted comprehensive genome-wide analyses of the TIFY gene family in Brassica napus. Here, HMMER search and BLASTp were used to identify the TIFY members. A total of 70 TIFY members were identified and divided into four subfamilies based on the conserved domains and motifs. These TIFY genes were distributed across 19 chromosomes. The predicted subcellular localizations revealed that most TIFY proteins were located in the nucleus. The tissue expression profile analyses indicated that TIFY genes were highly expressed in the stem, flower bud, and silique at the transcriptional level. High-proportioned activation of the dormant axillary buds on stems determined the branch numbers of rapeseed plants. Here, transcriptome analyses were conducted on axillary buds in four sequential developing stages, that is, dormant, temporarily dormant, being activated, and elongating (already activated). Surprisingly, the transcription of the majority of TIFY genes (65 of the 70) significantly decreased on the activation of buds. GO enrichment analysis and hormone treatments indicated that the transcription of TIFY family genes can be strongly induced by jasmonic acid, implying that the TIFY family genes may be involved in the regulation of jasmonic acid-mediated branch development. These results shed light on the roles of TIFY family genes in plant architecture. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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18 pages, 4408 KiB  
Article
SET Domain Group 703 Regulates Planthopper Resistance by Suppressing the Expression of Defense-Related Genes
by Peizheng Wen, Jun He, Qiong Zhang, Hongzhi Qi, Aoran Zhang, Daoming Liu, Quanguang Sun, Yongsheng Wang, Qi Li, Wenhui Wang, Zhanghao Chen, Yunlong Wang, Yuqiang Liu and Jianmin Wan
Int. J. Mol. Sci. 2023, 24(16), 13003; https://doi.org/10.3390/ijms241613003 - 21 Aug 2023
Cited by 2 | Viewed by 1646
Abstract
Plant defense responses against insect pests are intricately regulated by highly complex regulatory networks. Post-translational modifications (PTMs) of histones modulate the expression of genes involved in various biological processes. However, the role of PTMs in conferring insect resistance remains unclear. Through the screening [...] Read more.
Plant defense responses against insect pests are intricately regulated by highly complex regulatory networks. Post-translational modifications (PTMs) of histones modulate the expression of genes involved in various biological processes. However, the role of PTMs in conferring insect resistance remains unclear. Through the screening of a T-DNA insertion activation-tagged mutant collection in rice, we identified the mutant planthopper susceptible 1 (phs1), which exhibits heightened expression of SET domain group 703 (SDG703). This overexpression is associated with increased susceptibility to the small brown planthopper (SBPH), an economically significant insect pest affecting rice crops. SDG703 is constitutively expressed in multiple tissues and shows substantial upregulation in response to SBPH feeding. SDG703 demonstrates the activity of histone H3K9 methyltransferase. Transcriptomic analysis revealed the downregulation of genes involved in effector-triggered immunity (ETI) and pattern-triggered immunity (PTI) in plants overexpressing SDG703. Among the downregulated genes, the overexpression of SDG703 in plants resulted in a higher level of histone H3K9 methylation compared to control plants. Collectively, these findings indicate that SDG703 suppresses the expression of defense-related genes through the promotion of histone methylation, consequently leading to reduced resistance against SBPH. The defense-related genes regulated by histone methylation present valuable targets for developing effective pest management strategies in future studies. Furthermore, our study provides novel insight into the epigenetic regulation involved in plant-insect resistance. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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18 pages, 4228 KiB  
Article
Crosstalk between 5-Aminolevulinic Acid and Abscisic Acid Adjusted Leaf Iron Accumulation and Chlorophyll Synthesis to Enhance the Cold Tolerance in Solanum lycopersicum Seedlings
by Zhen Kang, Yong Zhang, Xiongchun Cai, Zhengda Zhang, Zijian Xu, Xiangguang Meng, Xiaojing Li and Xiaohui Hu
Int. J. Mol. Sci. 2023, 24(13), 10781; https://doi.org/10.3390/ijms241310781 - 28 Jun 2023
Cited by 6 | Viewed by 1364
Abstract
Previous studies found that 5-aminolevulinic acid (ALA) and abscisic acid (ABA) can mitigate damage from adversity by enhancing photosynthesis. However, it is not clear whether they have positive effects on iron utilization and chlorophyll synthesis of tomato seedlings under low-temperature stress. To investigate [...] Read more.
Previous studies found that 5-aminolevulinic acid (ALA) and abscisic acid (ABA) can mitigate damage from adversity by enhancing photosynthesis. However, it is not clear whether they have positive effects on iron utilization and chlorophyll synthesis of tomato seedlings under low-temperature stress. To investigate the possible functional relationship between ABA and ALA and elucidate the possible mechanisms of action of ALA to alleviate low-temperature stress in tomato seedlings, this experiment analyzed the effects of ALA and ABA on chlorophyll synthesis in tomato seedling leaves sprayed with exogenous of ALA (25 mg·L−1) or ABA (100 µM) under low-temperature stress (8–18 °C/8–12 °C, day/night). The results show that exogenous ALA increased the Fv/Fm of tomato leaves by 5.31% and increased the accumulation of iron and chlorophyll by 101.15% and 15.18%, respectively, compared to the low-temperature treatment alone, and tomato resistance of low-temperature stress was enhanced. Meanwhile, exogenous application of ALA increased the ABA content by 39.43%, and subsequent application of exogenous ABA revealed that tomato seedlings showed similar effects to exogenous ALA under low-temperature stress, with increased accumulation of iron and chlorophyll in tomato seedlings, which eventually increased the maximum photochemical efficiency of PS II. Under low-temperature stress, application of exogenous ABA significantly reduced ALA content, but the expression of key enzyme genes (PPGD, HEMB1, HEME1, and HEMF1), precursors of chlorophyll synthesis by ALA, was significantly elevated, presumably because the increased activity of these enzymes after external application of ABA accelerated ALA consumption. In conclusion, ABA may crosstalk with ALA to improve the photochemical efficiency and low temperature resistance of tomatoes by regulating chlorophyll synthesis and iron accumulation. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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20 pages, 11846 KiB  
Article
Physiological and Transcriptomic Analyses Reveal the Effects of Carbon-Ion Beam on Taraxacum kok-saghyz Rodin Adventitious Buds
by Xia Chen, Yan Du, Shanwei Luo, Ying Qu, Wenjie Jin, Shizhong Liu, Zhuanzi Wang, Xiao Liu, Zhuo Feng, Bi Qin and Libin Zhou
Int. J. Mol. Sci. 2023, 24(11), 9287; https://doi.org/10.3390/ijms24119287 - 26 May 2023
Viewed by 1940
Abstract
Taraxacum kok-saghyz Rodin (TKS) has great potential as an alternative natural-rubber (NR)-producing crop. The germplasm innovation of TKS still faces great challenges due to its self-incompatibility. Carbon-ion beam (CIB) irradiation is a powerful and non-species-specific physical method for mutation creation. Thus far, the [...] Read more.
Taraxacum kok-saghyz Rodin (TKS) has great potential as an alternative natural-rubber (NR)-producing crop. The germplasm innovation of TKS still faces great challenges due to its self-incompatibility. Carbon-ion beam (CIB) irradiation is a powerful and non-species-specific physical method for mutation creation. Thus far, the CIB has not been utilized in TKS. To better inform future mutation breeding for TKS by the CIB and provide a basis for dose-selection, adventitious buds, which not only can avoid high levels of heterozygosity, but also further improve breeding efficiency, were irradiated here, and the dynamic changes of the growth and physiologic parameters, as well as gene expression pattern were profiled, comprehensively. The results showed that the CIB (5–40 Gy) caused significant biological effects on TKS, exhibiting inhibitory effects on the fresh weight and the number of regenerated buds and roots. Then,15 Gy was chosen for further study after comprehensive consideration. CIB-15 Gy resulted in significant oxidative damages (hydroxyl radical (OH•) generation activity, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity and malondialdehyde (MDA) content) and activated the antioxidant system (superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX)) of TKS. Based on RNA-seq analysis, the number of differentially expressed genes (DEGs) peaked at 2 h after CIB irradiation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DNA-replication-/repair- (mainly up-regulated), cell-death- (mainly up-regulated), plant-hormone- (auxin and cytokinin, which are related to plant morphogenesis, were mainly down-regulated), and photosynthesis- (mainly down-regulated) related pathways were involved in the response to the CIB. Furthermore, CIB irradiation can also up-regulate the genes involved in NR metabolism, which provides an alternative strategy to elevate the NR production in TKS in the future. These findings are helpful to understand the radiation response mechanism and further guide the future mutation breeding for TKS by the CIB. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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19 pages, 27562 KiB  
Article
Identification of the GDP-L-Galactose Phosphorylase Gene as a Candidate for the Regulation of Ascorbic Acid Content in Fruits of Capsicum annuum L.
by Yixin Wang, Zheng Wang, Sansheng Geng, Heshan Du, Bin Chen, Liang Sun, Guoyun Wang, Meihong Sha, Tingting Dong, Xiaofen Zhang and Qian Wang
Int. J. Mol. Sci. 2023, 24(8), 7529; https://doi.org/10.3390/ijms24087529 - 19 Apr 2023
Cited by 4 | Viewed by 1877
Abstract
Ascorbic acid (AsA) is an antioxidant with significant functions in both plants and animals. Despite its importance, there has been limited research on the molecular basis of AsA production in the fruits of Capsicum annuum L. In this study, we used Illumina transcriptome [...] Read more.
Ascorbic acid (AsA) is an antioxidant with significant functions in both plants and animals. Despite its importance, there has been limited research on the molecular basis of AsA production in the fruits of Capsicum annuum L. In this study, we used Illumina transcriptome sequencing (RNA-seq) technology to explore the candidate genes involved in AsA biosynthesis in Capsicum annuum L. A total of 8272 differentially expressed genes (DEGs) were identified by the comparative transcriptome analysis. Weighted gene co-expression network analysis identified two co-expressed modules related to the AsA content (purple and light-cyan modules), and eight interested DEGs related to AsA biosynthesis were selected according to gene annotations in the purple and light-cyan modules. Moreover, we found that the gene GDP-L-galactose phosphorylase (GGP) was related to AsA content, and silencing GGP led to a reduction in the AsA content in fruit. These results demonstrated that GGP is an important gene controlling AsA biosynthesis in the fruit of Capsicum annuum L. In addition, we developed capsanthin/capsorubin synthase as the reporter gene for visual analysis of gene function in mature fruit, enabling us to accurately select silenced tissues and analyze the results of silencing. The findings of this study provide the theoretical basis for future research to elucidate AsA biosynthesis in Capsicum annuum L. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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15 pages, 5510 KiB  
Article
Molecular Cytological Analysis and Specific Marker Development in Wheat-Psathyrostachys huashanica Keng 3Ns Additional Line with Elongated Glume
by Jingyu Pang, Chenxi Huang, Yuesheng Wang, Xinyu Wen, Pingchuan Deng, Tingdong Li, Changyou Wang, Xinlun Liu, Chunhuan Chen, Jixin Zhao and Wanquan Ji
Int. J. Mol. Sci. 2023, 24(7), 6726; https://doi.org/10.3390/ijms24076726 - 4 Apr 2023
Viewed by 1949
Abstract
Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) is an excellent gene resource for wheat breeding, which is characterized by early maturity, low plant height, and disease resistance. The wheat-P. huashanica derivatives were created by the elite genes of P. [...] Read more.
Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) is an excellent gene resource for wheat breeding, which is characterized by early maturity, low plant height, and disease resistance. The wheat-P. huashanica derivatives were created by the elite genes of P. huashanica and permeate into common wheat through hybridization. Among them, a long-glume material 20JH1155 was identified, with larger grains and longer spike than its parents. In the present study, the methods of cytological observation, GISH, and sequential FISH analysis showed that 20JH1155 contained 21 pairs of wheat chromosomes and a pair of P. huashanica. There were some differences in 5A and 7B chromosomes between 20JH1155 and parental wheat 7182. Molecular marker, FISH, and sequence cloning indicated 20JH1155 alien chromosomes were 3Ns of P. huashanica. In addition, differentially expressed genes during immature spikelet development of 20JH1155 and 7182 and predicted transcription factors were obtained by transcriptome sequencing. Moreover, a total of 7 makers derived from Ph#3Ns were developed from transcriptome data. Taken together, the wheat-P. huashanica derived line 20JH1155 provides a new horizon on distant hybridization of wheat and accelerates the utilization of genes of P. huashanica. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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16 pages, 5324 KiB  
Article
Comparative Transcriptome Analysis Reveals a Potential Regulatory Network for Ogura Cytoplasmic Male Sterility in Cabbage (Brassica oleracea L.)
by Li Chen, Wenjing Ren, Bin Zhang, Huiling Guo, Zhiyuan Fang, Limei Yang, Mu Zhuang, Honghao Lv, Yong Wang, Jialei Ji, Xilin Hou and Yangyong Zhang
Int. J. Mol. Sci. 2023, 24(7), 6703; https://doi.org/10.3390/ijms24076703 - 4 Apr 2023
Cited by 2 | Viewed by 2059
Abstract
Ogura cytoplasmic male sterility (CMS) lines are widely used breeding materials in cruciferous crops and play important roles in heterosis utilization; however, the sterility mechanism remains unclear. To investigate the microspore development process and gene expression changes after the introduction of orf138 and [...] Read more.
Ogura cytoplasmic male sterility (CMS) lines are widely used breeding materials in cruciferous crops and play important roles in heterosis utilization; however, the sterility mechanism remains unclear. To investigate the microspore development process and gene expression changes after the introduction of orf138 and Rfo, cytological observation and transcriptome analysis were performed using a maintainer line, an Ogura CMS line, and a restorer line. Semithin sections of microspores at different developmental stages showed that the degradation of tapetal cells began at the tetrad stage in the Ogura CMS line, while it occurred at the bicellular microspore stage to the tricellular microspore stage in the maintainer and restorer lines. Therefore, early degradation of tapetal cells may be the cause of pollen abortion. Transcriptome analysis results showed that a total of 1287 DEGs had consistent expression trends in the maintainer line and restorer line, but were significantly up- or down-regulated in the Ogura CMS line, indicating that they may be closely related to pollen abortion. Functional annotation showed that the 1287 core DEGs included a large number of genes related to pollen development, oxidative phosphorylation, carbohydrate, lipid, and protein metabolism. In addition, further verification elucidated that down-regulated expression of genes related to energy metabolism led to decreased ATP content and excessive ROS accumulation in the anthers of Ogura CMS. Based on these results, we propose a transcriptome-mediated induction and regulatory network for cabbage Ogura CMS. Our research provides new insights into the mechanism of pollen abortion and fertility restoration in Ogura CMS. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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16 pages, 11720 KiB  
Article
Heterologous VvDREB2c Expression Improves Heat Tolerance in Arabidopsis by Inducing Photoprotective Responses
by Qian Zha, Xiangjing Yin, Xiaojun Xi and Aili Jiang
Int. J. Mol. Sci. 2023, 24(6), 5989; https://doi.org/10.3390/ijms24065989 - 22 Mar 2023
Cited by 4 | Viewed by 2023
Abstract
Extreme temperatures limit grape production and sustainability. Dehydration-responsive element-binding (DREB) transcription factors affect plant responses to temperature related stresses. Therefore, we investigated the role of VvDREB2c, a DREB-coding gene, found in grapes (Vitis vinifera L.). Protein characterization revealed that VvDREB2c is localized [...] Read more.
Extreme temperatures limit grape production and sustainability. Dehydration-responsive element-binding (DREB) transcription factors affect plant responses to temperature related stresses. Therefore, we investigated the role of VvDREB2c, a DREB-coding gene, found in grapes (Vitis vinifera L.). Protein characterization revealed that VvDREB2c is localized to the nucleus and that its AP2/ERF domain contains three β-sheets and one α-helix sheet. Analysis of the VvDREB2c promoter region revealed the presence of light-, hormone-, and stress-related cis-acting elements. Furthermore, we observed that the heterologous expression of VvDREB2c in Arabidopsis improved growth, drought tolerance, and heat tolerance. Furthermore, it improved the leaf quantum yield of regulated energy dissipation [Y(NPQ)], elevated the activities of RuBisCO, and phosphoenolpyruvate carboxylase and reduced the quantum yield of non-regulated energy dissipation [Y(NO)] in plants exposed to high temperatures. VvDREB2c-overexpressing lines also specifically upregulated several photosynthesis-related genes (CSD2, HSP21, and MYB102). In addition, VvDREB2c-overexpressing lines reduced light damage and enhanced photoprotective ability by dissipating excess light energy and converting it into heat, which eventually improves tolerance to high temperature. The contents of abscisic acid, jasmonic acid, and salicylic acid and differentially expressed genes (DEGs) in the mitogen-activated protein kinase (MAPK) signaling pathway were affected by heat stress in VvDREB2c-overexpressing lines, which indicated that VvDREB2c positively regulates heat tolerance via a hormonal pathway in Arabidopsis. VvDREB2c promotes heat tolerance in Arabidopsis by exerting effects on photosynthesis, hormones, and growth conditions. This study may provide useful insights into the enrichment of the heat-tolerance pathways in plants. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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25 pages, 6425 KiB  
Article
Data-Independent Acquisition Proteomics Reveals the Effects of Red and Blue Light on the Growth and Development of Moso Bamboo (Phyllostachys edulis) Seedlings
by Ke Li, Luyao Ji, Yaoyun Xing, Zecheng Zuo and Li Zhang
Int. J. Mol. Sci. 2023, 24(6), 5103; https://doi.org/10.3390/ijms24065103 - 7 Mar 2023
Cited by 5 | Viewed by 1854
Abstract
Moso bamboo is a rapidly growing species with significant economic, social, and cultural value. Transplanting moso bamboo container seedlings for afforestation has become a cost-effective method. The growth and development of the seedlings is greatly affected by the quality of light, including light [...] Read more.
Moso bamboo is a rapidly growing species with significant economic, social, and cultural value. Transplanting moso bamboo container seedlings for afforestation has become a cost-effective method. The growth and development of the seedlings is greatly affected by the quality of light, including light morphogenesis, photosynthesis, and secondary metabolite production. Therefore, studies on the effects of specific light wavelengths on the physiology and proteome of moso bamboo seedlings are crucial. In this study, moso bamboo seedlings were germinated in darkness and then exposed to blue and red light conditions for 14 days. The effects of these light treatments on seedling growth and development were observed and compared through proteomics analysis. Results showed that moso bamboo has higher chlorophyll content and photosynthetic efficiency under blue light, while it displays longer internode and root length, more dry weight, and higher cellulose content under red light. Proteomics analysis reveals that these changes under red light are likely caused by the increased content of cellulase CSEA, specifically expressed cell wall synthetic proteins, and up-regulated auxin transporter ABCB19 in red light. Additionally, blue light is found to promote the expression of proteins constituting photosystem II, such as PsbP and PsbQ, more than red light. These findings provide new insights into the growth and development of moso bamboo seedlings regulated by different light qualities. Full article
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2023)
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