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Lei C, Dang Z, Zhu M, Zhang M, Wang H, Chen Y, Zhang H. Identification of the ERF gene family of Mangifera indica and the defense response of MiERF4 to Xanthomonas campestris pv. mangiferaeindicae. Gene 2024; 912:148382. [PMID: 38493974 DOI: 10.1016/j.gene.2024.148382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/03/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
An important regulatory role for ethylene-responsive transcription factors (ERFs) is in plant growth and development, stress response, and hormone signaling. However, AP2/ERF family genes in mango have not been systematically studied. In this study, a total of 113 AP2/ERF family genes were identified from the mango genome and phylogenetically classified into five subfamilies: AP2 (28 genes), DREB (42 genes), ERF (33 genes), RAV (6 genes), and Soloist (4 genes). Of these, the ERF family, in conjunction with Arabidopsis and rice, forms a phylogenetic tree divided into seven groups, five of which have MiERF members. Analysis of gene structure and cis-elements showed that each MiERF gene contains only one AP2 structural domain, and that MiERF genes contain a large number of cis-elements associated with hormone signaling and stress response. Collinearity tests revealed a high degree of homology between MiERFs and CsERFs. Tissue-specific and stress-responsive expression profiling revealed that MiERF genes are primarily involved in the regulation of reproductive growth and are differentially and positively expressed in response to external hormones and pathogenic bacteria. Physiological results from a gain-of-function analysis of MiERF4 transiently overexpressed in tobacco and mango showed that transient expression of MiERF4 resulted in decreased colony count and callose deposition, as well as varying degrees of response to hormonal signals such as ETH, JA, and SA. Thus, MiERF4 may be involved in the JA/ETH signaling pathway to enhance plant defense against pathogenic bacteria. This study provides a basis for further research on the function and regulation of MiERF genes and lays a foundation for the selection of disease-resistant genes in mango.
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Affiliation(s)
- Chen Lei
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhiguo Dang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Min Zhu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
| | - Mengting Zhang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Huiliang Wang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China.
| | - He Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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Gao W, Zhang L, Zhang Y, Zhang P, Shahinnia F, Chen T, Yang D. Genome‑wide identification and expression analysis of the UBC gene family in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:341. [PMID: 38671351 PMCID: PMC11047035 DOI: 10.1186/s12870-024-05042-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Ubiquitination is an important regulatory step of selective protein degradation in the plant UPS (ubiquitin-proteasome system), which is involved in various biological processes in eukaryotes. Ubiquitin-conjugating enzymes play an intermediate role in the process of protein ubiquitination reactions and thus play an essential role in regulating plant growth and response to adverse environmental conditions. However, a genome-wide analysis of the UBC gene family in wheat (Triticum aestivum L.) has not yet been performed. RESULTS In this study, the number, physiochemical properties, gene structure, collinearity, and phylogenetic relationships of TaUBC family members in wheat were analyzed using bioinformatics methods. The expression pattern of TaUBC genes in different tissues/organs and developmental periods, as well as the transcript levels under abiotic stress treatment, were analyzed using RNA-Seq data and qRT-PCR. Meanwhile, favorable haplotypes of TaUBC25 were investigated based on wheat resequencing data of 681 wheat cultivars from the Wheat Union Database. The analyses identified a total of 93 TaUBC family members containing a UBC domain in wheat genome. These genes were unevenly distributed across 21 chromosomes, and numerous duplication events were observed between gene members. Based on phylogenetic analysis, the TaUBC family was divided into 13 E2 groups and a separate UEV group. We investigated the expression of TaUBC family genes under different tissue/organ and stress conditions by quantitative real-time PCR (qRT-PCR) analysis. The results showed that some TaUBC genes were specifically expressed in certain tissues/organs and that most TaUBC genes responded to NaCl, PEG6000, and ABA treatment with different levels of expression. In addition, we performed association analysis for the two haplotypes based on key agronomic traits such as thousand-kernel weight (TKW), kernel length (KL), kernel weight (KW), and kernel thickness (KT), examining 122 wheat accessions at three environmental sites. The results showed that TaUBC25-Hap II had significantly higher TKW, KL, KW, and KT than TaUBC25-Hap I. The distribution analysis of haplotypes showed that TaUBC25-Hap II was preferred in the natural population of wheat. CONCLUSION Our results identified 93 members of the TaUBC family in wheat, and several genes involved in grain development and abiotic stress response. Based on the SNPs detected in the TaUBC sequence, two haplotypes, TaUBC25-Hap I and TaUBC25-Hap II, were identified among wheat cultivars, and their potential value for wheat breeding was validated by association analysis. The above results provide a theoretical basis for elucidating the evolutionary relationships of the TaUBC gene family and lay the foundation for studying the functions of family members in the future.
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Affiliation(s)
- Weidong Gao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Long Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yanyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Fahimeh Shahinnia
- Bioanalytics Gatersleben, Am Schwabenplan 1b, Seeland, 06466, Germany
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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Liu J, Wu Y, Zhou L, Zhang A, Wang S, Liu Y, Yang D, Wang S. Influence of flowering on the anatomical structure, chemical components and carbohydrate metabolism of Bambusa tuldoides culms at different ages. FRONTIERS IN PLANT SCIENCE 2023; 14:1260302. [PMID: 38023931 PMCID: PMC10656694 DOI: 10.3389/fpls.2023.1260302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
Bamboo forests, which have come to occupy large areas in recent years, naturally undergo the process of blooming. However, bamboo culms and rhizomes degenerate after the plants bloom, resulting in widespread loss of raw materials. Systematic research on the properties and physiology of bamboo culms after flowering is lacking, and whether flowering bamboo culms could be used as raw materials in industry is unclear. In this paper, we compared and measured the fiber morphology, chemical components, and sugar metabolism indexes of non-flowering and flowering Bambusa tuldoides culms at different ages. The results showed that the fibers in the middle internodes of both non-flowering and flowering B. tuldoides culms had the longest length. The fibers completed their elongation within 1 year, but the fiber walls were continually deposited with age. The levels of the chemical components in the nonflowering culms also continually increased with age. The nonstructural carbohydrate (NSC) content and sugar metabolism indexes showed the highest levels in the 2-year culms and then declined in the 3-year culms. Compared to young culms that had not yet flowered, the 3-month-old and 1-year-old flowering culms had a significant decrease in the fiber length and tangential diameter, and their holocellulose and lignin levels also decreased, while the levels of ash, SiO2, 1% NaOH extractives, and benzene-ethanol extractives increased. A correlation analysis showed that sugar catabolism was accelerated in the flowering cluster, which could lead to "starvation death" in bamboo and which had a significant negative impact on the anatomical and chemical properties of the bamboo culms. Generally, the flowering bamboo culms had shorter fibers, higher levels of extractives and ash, and lower holocellulose content, which indicated that bamboo flowering has an adverse effect on the application of such components in the production of pulp, in papermaking, and in other processing and utilization activities. This study revealed the physiological changes in flowering B. tuldoides culms and provided a theoretical basis to inform the utilization of culms in this species.
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Affiliation(s)
- Jiaxin Liu
- Faculty of Life Sciences, Southwest Forestry University, Kunming, China
- Faculty of Bamboo and Rattan, Southwest Forestry University, Kunming, China
| | - Yufang Wu
- Faculty of Life Sciences, Southwest Forestry University, Kunming, China
- Faculty of Bamboo and Rattan, Southwest Forestry University, Kunming, China
| | - Li Zhou
- Faculty of Life Sciences, Southwest Forestry University, Kunming, China
- Faculty of Bamboo and Rattan, Southwest Forestry University, Kunming, China
| | - Anmian Zhang
- Faculty of Life Sciences, Southwest Forestry University, Kunming, China
| | - Sushuang Wang
- Faculty of Life Sciences, Southwest Forestry University, Kunming, China
- Faculty of Bamboo and Rattan, Southwest Forestry University, Kunming, China
| | - Yi Liu
- Faculty of Life Sciences, Southwest Forestry University, Kunming, China
- Faculty of Bamboo and Rattan, Southwest Forestry University, Kunming, China
| | - Dejia Yang
- Faculty of Life Sciences, Southwest Forestry University, Kunming, China
- Faculty of Bamboo and Rattan, Southwest Forestry University, Kunming, China
| | - Shuguang Wang
- Faculty of Life Sciences, Southwest Forestry University, Kunming, China
- Faculty of Bamboo and Rattan, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Zhan Y, Wu T, Zhao X, Wang J, Guo S, Chen S, Qu S, Zheng Z. Genome-wide identification and expression of monoacylglycerol lipase (MAGL) gene family in peanut (Arachis hypogaea L.) and functional analysis of AhMGATs in neutral lipid metabolism. Int J Biol Macromol 2023; 243:125300. [PMID: 37315669 DOI: 10.1016/j.ijbiomac.2023.125300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/25/2023] [Accepted: 06/04/2023] [Indexed: 06/16/2023]
Abstract
Monoacylglycerol lipase (MAGL) involved in regulating plant growth and development and stress responses, hydrolyzes monoacylglycerol (MAG) into free fatty acid and glycerol, which is the last step of triacylglycerol (TAG) breakdown. Here, a genome-wide characterization of MAGL gene family from cultivated peanut (Arachis hypogaea L.) was performed. In total, 24 MAGL genes were identified and unevenly distributed on 14 chromosomes, encoding 229-414 amino acids with molecular weights ranging from 25.91 to 47.01 kDa. Spatiotemporal and stress-induced expression was analyzed by qRT-PCR. Multiple sequence alignment revealed that AhMAGL1a/b and AhMAGL3a/b were the only four bifunctional enzymes with conserved regions of hydrolase and acyltransferase, which could also be named as AhMGATs. GUS histochemical assay showed that AhMAGL1a and -1b were strongly expressed in all tissues of the plants; whereas both AhMAGL3a and -3b were weakly expressed in plants. Subcellular localization analysis indicated that AhMGATs were localized in the endoplasmic reticulum and/or Golgi complex. Seed-specific overexpression of AhMGATs in Arabidopsis decreased the oil content of the seeds and altered the fatty acid compositions, indicating that AhMGATs were involved in TAG breakdown but not TAG biosynthesis in plant seeds. This study lays the foundation for better understanding AhMAGL genes biological function in planta.
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Affiliation(s)
- Yihua Zhan
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China.
| | - Tingting Wu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Xuan Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Jing Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Shixian Guo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Shutong Chen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Shengtao Qu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Zhifu Zheng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China
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Li K, Wei Y, Wang Y, Tan B, Chen S, Li H. Genome-Wide Identification of LBD Genes in Foxtail Millet ( Setaria italica) and Functional Characterization of SiLBD21. Int J Mol Sci 2023; 24:ijms24087110. [PMID: 37108274 PMCID: PMC10138450 DOI: 10.3390/ijms24087110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
Plant-specific lateral organ boundaries domain (LBD) proteins play important roles in plant growth and development. Foxtail millet (Setaria italica) is one new C4 model crop. However, the functions of foxtail millet LBD genes are unknown. In this study, a genome-wide identification of foxtail millet LBD genes and a systematical analysis were conducted. A total of 33 SiLBD genes were identified. They are unevenly distributed on nine chromosomes. Among these SiLBD genes, six segmental duplication pairs were detected. The thirty-three encoded SiLBD proteins could be classified into two classes and seven clades. Members in the same clade have similar gene structure and motif composition. Forty-seven kinds of cis-elements were found in the putative promoters, and they are related to development/growth, hormone, and abiotic stress response, respectively. Meanwhile, the expression pattern was investigated. Most SiLBD genes are expressed in different tissues, while several genes are mainly expressed in one or two kinds of tissues. In addition, most SiLBD genes respond to different abiotic stresses. Furthermore, the function of SiLBD21, which is mainly expressed in roots, was characterized by ectopic expression in Arabidopsis and rice. Compared to controls, transgenic plants generated shorter primary roots and more lateral roots, indicating the function of SiLBD21 in root development. Overall, our study laid the foundation for further functional elucidation of SiLBD genes.
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Affiliation(s)
- Kunjie Li
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yaning Wei
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yimin Wang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Bin Tan
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Shoukun Chen
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Haifeng Li
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
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Overexpression of <italic>PvSVP1</italic>, an <italic>SVP</italic>-like gene of bamboo, causes early flowering and abnormal floral organs in <italic>Arabidopsis</italic> and rice. Acta Biochim Biophys Sin (Shanghai) 2023; 55:237-249. [PMID: 36647724 PMCID: PMC10160235 DOI: 10.3724/abbs.2022199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
<p indent="0mm">Bamboo is a nontimber woody plant featuring a long vegetative stage and uncertain flowering time. Therefore, the genes belonging to flowering repressors might be essential in regulating the transition from the vegetative to reproductive stage in bamboo. The <italic>Short Vegetative Phase</italic> ( <italic>SVP</italic>) gene plays a pivotal role in floral transition and development. However, little is known about the bamboo <italic>SVP</italic> homologues. In this study, <italic>Phyllostachys violascens</italic> <italic>PvSVP1</italic> is isolated by analysis of the <italic>P</italic>. <italic>edulis</italic> transcriptome database. Phylogenetic analysis shows that <italic>PvSVP1</italic> is closely related to <italic>OsMADS55</italic> (rice <italic>SVP</italic> homolog). <italic>PvSVP1</italic> is ubiquitously expressed in various tissues, predominantly in vegetative tissues. To investigate the function of <italic>PvSVP1</italic>, <italic>PvSVP1</italic> is overexpressed in <italic>Arabidopsis</italic> and rice under the influence of the 35S promoter. Overexpression of <italic>PvSVP1</italic> in <italic>Arabidopsis</italic> causes early flowering and produces abnormal petals and sepals. Quantitative real-time PCR reveals that overexpression in <italic>Arabidopsis</italic> produces an early flowering phenotype by downregulating <italic>FLC</italic> and upregulating <italic>FT</italic> and produces abnormal floral organs by upregulating <italic>AP1</italic>, <italic>AP3</italic> and <italic>PI</italic> expressions. Simultaneously, overexpression of <italic>PvSVP1</italic> in rice alters the expressions of flowering-related genes such as <italic>Hd3a</italic>, <italic>RFT1</italic>, <italic>OsMADS56</italic> and <italic>Ghd7</italic> and promotes flowering under field conditions. In addition, PvSVP1 may be a nuclear protein which interacts with PvVRN1 and PvMADS56 on the yeast two-hybrid and BiFC systems. Our study suggests that <italic>PvSVP1</italic> may play a vital role in flowering time and development by interacting with PvVRN1 and PvMADS56 in the nucleus. Furthermore, this study paves the way toward understanding the complex flowering process of bamboo. </p>.
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Lee YM, Teoh DEJ, Yeung K, Liou YC. The kingdom of the prolyl-isomerase Pin1: The structural and functional convergence and divergence of Pin1. Front Cell Dev Biol 2022; 10:956071. [PMID: 36111342 PMCID: PMC9468764 DOI: 10.3389/fcell.2022.956071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
More than 20 years since its discovery, our understanding of Pin1 function in various diseases continues to improve. Pin1 plays a crucial role in pathogenesis and has been implicated in metabolic disorders, cardiovascular diseases, inflammatory diseases, viral infection, cancer and neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s disease. In particular, the role of Pin1 in neurodegenerative diseases and cancer has been extensively studied. Our understanding of Pin1 in cancer also led to the development of cancer therapeutic drugs targeting Pin1, with some currently in clinical trial phases. However, identifying a Pin1-specific drug with good cancer therapeutic effect remains elusive, thus leading to the continued efforts in Pin1 research. The importance of Pin1 is highlighted by the presence of Pin1 orthologs across various species: from vertebrates to invertebrates and Kingdom Animalia to Plantae. Among these Pin1 orthologs, their sequence and structural similarity demonstrate the presence of conservation. Moreover, their similar functionality between species further highlights the conservancy of Pin1. As researchers continue to unlock the mysteries of Pin1 in various diseases, using different Pin1 models might shed light on how to better target Pin1 for disease therapeutics. This review aims to highlight the various Pin1 orthologs in numerous species and their divergent functional roles. We will examine their sequence and structural similarities and discuss their functional similarities and uniqueness to demonstrate the interconnectivity of Pin1 orthologs in multiple diseases.
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Sainz MM, Filippi CV, Eastman G, Sotelo-Silveira J, Borsani O, Sotelo-Silveira M. Analysis of Thioredoxins and Glutaredoxins in Soybean: Evidence of Translational Regulation under Water Restriction. Antioxidants (Basel) 2022; 11:antiox11081622. [PMID: 36009341 PMCID: PMC9405309 DOI: 10.3390/antiox11081622] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/10/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Soybean (Glycine max (L.) Merr.) establishes symbiosis with rhizobacteria, developing the symbiotic nodule, where the biological nitrogen fixation (BNF) occurs. The redox control is key for guaranteeing the establishment and correct function of the BNF process. Plants have many antioxidative systems involved in ROS homeostasis and signaling, among them a network of thio- and glutaredoxins. Our group is particularly interested in studying the differential response of nodulated soybean plants to water-deficit stress. To shed light on this phenomenon, we set up an RNA-seq experiment (for total and polysome-associated mRNAs) with soybean roots comprising combined treatments including the hydric and the nodulation condition. Moreover, we performed the initial identification and description of the complete repertoire of thioredoxins (Trx) and glutaredoxins (Grx) in soybean. We found that water deficit altered the expression of a greater number of differentially expressed genes (DEGs) than the condition of plant nodulation. Among them, we identified 12 thioredoxin (Trx) and 12 glutaredoxin (Grx) DEGs, which represented a significant fraction of the detected GmTrx and GmGrx in our RNA-seq data. Moreover, we identified an enriched network in which a GmTrx and a GmGrx interacted with each other and associated through several types of interactions with nitrogen metabolism enzymes.
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Affiliation(s)
- María Martha Sainz
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Avenida Garzón 780, Montevideo 12900, Uruguay
| | - Carla Valeria Filippi
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Avenida Garzón 780, Montevideo 12900, Uruguay
| | - Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo 11600, Uruguay
- Department of Biology, University of Virginia, 485 McCormick Rd., Charlottesville, VA 22904, USA
| | - José Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo 11600, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Omar Borsani
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Avenida Garzón 780, Montevideo 12900, Uruguay
| | - Mariana Sotelo-Silveira
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Avenida Garzón 780, Montevideo 12900, Uruguay
- Correspondence:
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Hou D, Li L, Ma T, Pei J, Zhao Z, Lu M, Wu A, Lin X. The SOC1-like gene BoMADS50 is associated with the flowering of Bambusa oldhamii. HORTICULTURE RESEARCH 2021; 8:133. [PMID: 34059654 PMCID: PMC8166863 DOI: 10.1038/s41438-021-00557-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 03/16/2021] [Accepted: 03/26/2021] [Indexed: 05/27/2023]
Abstract
Bamboo is known for its edible shoots and beautiful texture and has considerable economic and ornamental value. Unique among traditional flowering plants, many bamboo plants undergo extensive synchronized flowering followed by large-scale death, seriously affecting the productivity and application of bamboo forests. To date, the molecular mechanism of bamboo flowering characteristics has remained unknown. In this study, a SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)-like gene, BoMADS50, was identified from Bambusa oldhamii. BoMADS50 was highly expressed in mature leaves and the floral primordium formation period during B. oldhamii flowering and overexpression of BoMADS50 caused early flowering in transgenic rice. Moreover, BoMADS50 could interact with APETALA1/FRUITFULL (AP1/FUL)-like proteins (BoMADS14-1/2, BoMADS15-1/2) in vivo, and the expression of BoMADS50 was significantly promoted by BoMADS14-1, further indicating a synergistic effect between BoMADS50 and BoAP1/FUL-like proteins in regulating B. oldhamii flowering. We also identified four additional transcripts of BoMADS50 (BoMADS50-1/2/3/4) with different nucleotide variations. Although the protein-CDS were polymorphic, they had flowering activation functions similar to those of BoMADS50. Yeast one-hybrid and transient expression assays subsequently showed that both BoMADS50 and BoMADS50-1 bind to the promoter fragment of itself and the SHORT VEGETATIVE PHASE (SVP)-like gene BoSVP, but only BoMADS50-1 can positively induce their transcription. Therefore, nucleotide variations likely endow BoMADS50-1 with strong regulatory activity. Thus, BoMADS50 and BoMADS50-1/2/3/4 are probably important positive flowering regulators in B. oldhamii. Moreover, the functional conservatism and specificity of BoMADS50 and BoMADS50-1 might be related to the synchronized and sporadic flowering characteristics of B. oldhamii.
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Affiliation(s)
- Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Ling Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Tengfei Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Zhongyu Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Aimin Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642, Guangzhou, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, Guangzhou, China.
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China.
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10
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Jiao Y, Hu Q, Zhu Y, Zhu L, Ma T, Zeng H, Zang Q, Li X, Lin X. Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens). BMC Bioinformatics 2019; 20:687. [PMID: 31874613 PMCID: PMC6929269 DOI: 10.1186/s12859-019-3261-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is still unclear. Results In this study, three successive stages of flowering buds and the corresponding vegetative buds (non-flowering stage) from Lei bamboo (Phyllostachys violascens) were collected for transcriptome analysis using Illumina RNA-Seq method. We generated about 442 million clean reads from the above samples, and 132,678 unigenes were acquired with N50 of 1080 bp. A total of 7266 differentially expressed genes (DEGs) were determined. According to expression profile and gene function analysis, some environmental stress responsive and plant hormone-related DEGs were highly expressed in the inflorescence meristem formation stage (TF_1) while some floral organ development related genes were up-regulated significantly in floral organs determination stage (TF_2) and floral organs maturation (TF_3) stage, implying the essential roles of these DEGs in flower induction and maturation of Lei bamboo. Additionally, a total of 25 MADS-box unigenes were identified. Based on the expression profile, B, C/D and E clade genes were more related to floral organs development compared with A clade genes in Lei bamboo. Conclusions This transcriptome data presents fundamental information about the genes and pathways involved in flower induction and development of Lei bamboo. Moreover, a critical sampling method is provided which could be benefit for bamboo flowering mechanism study.
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Affiliation(s)
- Yulian Jiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China.,Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Lin'an, 311300, Zhejiang, China
| | - Qiutao Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Yan Zhu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Longfei Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Tengfei Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Haiyong Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Qiaolu Zang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China. .,Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Lin'an, 311300, Zhejiang, China.
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11
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Characteristics and Expression Pattern of MYC Genes in Triticum aestivum, Oryza sativa, and Brachypodium distachyon. PLANTS 2019; 8:plants8080274. [PMID: 31398900 PMCID: PMC6724133 DOI: 10.3390/plants8080274] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 11/16/2022]
Abstract
Myelocytomatosis oncogenes (MYC) transcription factors (TFs) belong to basic helix-loop-helix (bHLH) TF family and have a special bHLH_MYC_N domain in the N-terminal region. Presently, there is no detailed and systematic analysis of MYC TFs in wheat, rice, and Brachypodium distachyon. In this study, 26 TaMYC, 7 OsMYC, and 7 BdMYC TFs were identified and their features were characterized. Firstly, they contain a JAZ interaction domain (JID) and a putative transcriptional activation domain (TAD) in the bHLH_MYC_N region and a BhlH region in the C-terminal region. In some cases, the bHLH region is followed by a leucine zipper region; secondly, they display tissue-specific expression patterns: wheat MYC genes are mainly expressed in leaves, rice MYC genes are highly expressed in stems, and B. distachyon MYC genes are mainly expressed in inflorescences. In addition, three types of cis-elements, including plant development/growth-related, hormone-related, and abiotic stresses-related were identified in different MYC gene promoters. In combination with the previous studies, these results indicate that MYC TFs mainly function in growth and development, as well as in response to stresses. This study laid a foundation for the further functional elucidation of MYC genes.
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12
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Zhu Y, Li Y, Zhang S, Zhang X, Yao J, Luo Q, Sun F, Wang X. Genome-wide identification and expression analysis reveal the potential function of ethylene responsive factor gene family in response to Botrytis cinerea infection and ovule development in grapes (Vitis vinifera L.). PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:571-584. [PMID: 30468551 DOI: 10.1111/plb.12943] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/16/2018] [Indexed: 05/02/2023]
Abstract
The prevention of Botrytis cinerea infection and the study of grape seedlessness are very important for grape industries. Finding correlated regulatory genes is an important approach towards understanding their molecular mechanisms. Ethylene responsive factor (ERF) gene family play critical roles in defence networks and the growth of plants. To date, no large-scale study of the ERF proteins associated with pathogen defence and ovule development has been performed in grape (Vitis vinifera L.). In the present study, we identified 113 ERF genes (VvERF) and named them based on their chromosome locations. The ERF genes could be divided into 11 groups based on a multiple sequence alignment and a phylogenetic comparison with homologues from Arabidopsis thaliana. Synteny analysis and Ka/Ks ratio calculation suggested that segmental and tandem duplications contributed to the expansion of the ERF gene family. The evolutionary relationships between the VvERF genes were investigated by exon-intron structure characterisation, and an analysis of the cis-acting regulatory elements in their promoters suggested potential regulation after stress or hormone treatments. Expression profiling after infection with the fungus, B. cinerea, indicated that ERF genes function in responses to pathogen attack. In addition, the expression levels of most ERF genes were much higher during ovule development in seedless grapes, suggesting a role in ovule abortion related to seedlessness. Taken together, these results indicate that VvERF proteins are involved in responses to Botrytis cinerea infection and in grape ovule development. This information may help guide strategies to improve grape production.
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Affiliation(s)
- Y Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - Y Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - S Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - X Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - J Yao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - Q Luo
- Research Institute of Grapes and Melon in Xinjiang Uygur Autonomous Region, Shanshan, Xinjiang, China
| | - F Sun
- Research Institute of Grapes and Melon in Xinjiang Uygur Autonomous Region, Shanshan, Xinjiang, China
| | - X Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
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13
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Xiao G, Li B, Chen H, Chen W, Wang Z, Mao B, Gui R, Guo X. Overexpression of PvCO1, a bamboo CONSTANS-LIKE gene, delays flowering by reducing expression of the FT gene in transgenic Arabidopsis. BMC PLANT BIOLOGY 2018; 18:232. [PMID: 30314465 PMCID: PMC6186071 DOI: 10.1186/s12870-018-1469-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/04/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND In Arabidopsis, a long day flowering plant, CONSTANS (CO) acts as a transcriptional activator of flowering under long day (LD) condition. In rice, a short day flowering plant, Hd1, the ortholog of CO, plays dual functions in respond to day-length, activates flowering in short days and represses flowering in long days. In addition, alleles of Hd1 account for ~ 44% of the variation in flowering time observed in cultivated rice and sorghum. How does it work in bamboo? The function of CO in bamboo is similar to that in Arabidopsis? RESULTS Two CO homologous genes, PvCO1 and PvCO2, in Phyllostachys violascens were identified. Alignment analysis showed that the two PvCOLs had the highest sequence similarity to rice Hd1. Both PvCO1 and PvCO2 expressed in specific tissues, mainly in leaf. The PvCO1 gene had low expression before flowering, high expression during the flowering stage, and then declined to low expression again after flowering. In contrast, expression of PvCO2 was low during the flowering stage, but rapidly increased to a high level after flowering. The mRNA levels of both PvCOs exhibited a diurnal rhythm. Both PvCO1 and PvCO2 proteins were localized in nucleus of cells. PvCO1 could interact with PvGF14c protein which belonged to 14-3-3 gene family through B-box domain. Overexpression of PvCO1 in Arabidopsis significantly caused late flowering by reducing the expression of AtFT, whereas, transgenic plants overexpressing PvCO2 showed a similar flowering time with WT under LD conditions. Taken together, these results suggested that PvCO1 was involved in the flowering regulation, and PvCO2 may either not have a role in regulating flowering or act redundantly with other flowering regulators in Arabidopsis. Our data also indicated regulatory divergence between PvCOLs in Ph. violascens and CO in Arabidopsis as well as Hd1 in Oryza sativa. Our results will provide useful information for elucidating the regulatory mechanism of COLs involved in the flowering. CONCLUSIONS Unlike to the CO gene in Arabidopsis, PvCO1 was a negative regulator of flowering in transgenic Arabidopsis under LD condition. It was likely that long period of vegetative growth of this bamboo species was related with the regulation of PvCO1.
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Affiliation(s)
- Guohui Xiao
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 China
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029 China
| | - Bingjuan Li
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 China
| | - Hongjun Chen
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 China
| | - Wei Chen
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 China
| | - Zhengyi Wang
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029 China
| | - Bizeng Mao
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029 China
| | - Renyi Gui
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 China
| | - Xiaoqin Guo
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Hangzhou, 311300 China
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14
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Li B, Xiao G, Luo K, Wang Z, Mao B, Lin X, Guo X. Overexpression of PvGF14c from Phyllostachys violascens Delays Flowering Time in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:105. [PMID: 29491870 PMCID: PMC5817094 DOI: 10.3389/fpls.2018.00105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
14-3-3 Proteins are a family of highly conserved regulatory molecules expressed in all eukaryotic cells and regulate a diverse set of biological responses in plants. However, their functions in flowering of Phyllostachys violascens are poorly understood. In this study, four non-𝜀 Pv14-3-3 genes from P. violascens were identified and named PvGF14b, PvGF14c, PvGF14e, and PvGF14f. qRT-PCR analyses revealed that PvGF14b and PvGF14e exhibited widely expressed in all tested bamboo tissues. PvGF14b was highest expression in root and lowest in immature leaf. Whereas PvGF14c and PvGF14f showed tissue-specific expression. PvGF14c was mainly expressed in immature and mature leaves. PvGF14f was highest expression in mature leaves. These four genes were not significantly differentially expressed in mature leaf before bamboo flowering and during flower development. PvGF14b and PvGF14c were not induced by circadian rhythm. PvGF14c displayed subcellular localization in the cytoplasm and PvFT in nucleus and cytoplasm. Yeast two-hybrid screening and bimolecular fluorescence complementation confirmed the interaction between PvGF14c and PvFT. The overexpression of PvGF14b, PvGF14c, and PvGF14e significantly delayed flowering time in transgenic Arabidopsis under long-day condition. These findings suggested that at least three PvGF14 genes are involved in flowering and may act as a negative regulator of flowering by interacting with PvFT in bamboo.
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Affiliation(s)
- Bingjuan Li
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Guohui Xiao
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Kaisheng Luo
- School of Geography and Remote Sensing, Nanjing University of Information Science and Technology, Nanjing, China
| | - Zhengyi Wang
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bizeng Mao
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xinchun Lin
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Xiaoqin Guo
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Zhejiang A & F University, Hangzhou, China
- *Correspondence: Xiaoqin Guo,
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