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Liu J, Wei L, Wu Y, Wang Z, Wang H, Xiao J, Wang X, Sun L. Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat. BMC Genomics 2024; 25:209. [PMID: 38408894 PMCID: PMC10895793 DOI: 10.1186/s12864-024-10114-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild relative of wheat. RESULTS To understand the evolution of SnRK2-V family genes and their roles in various stress conditions, we performed genome-wide identification of the SnRK2-V gene family in H. villosa. Ten SnRK2-V genes were identified and characterized for their structures, functions and spatial expressions. Analysis of gene exon/intron structure further revealed the presence of evolutionary paths and replication events of SnRK2-V gene family in the H. villosa. In addition, the features of gene structure, the chromosomal location, subcellular localization of the gene family were investigated and the phylogenetic relationship were determined using computational approaches. Analysis of cis-regulatory elements of SnRK2-V gene members revealed their close correlation with different phytohormone signals. The expression profiling revealed that ten SnRK2-V genes expressed at least one tissue (leave, stem, root, or grain), or in response to at least one of the biotic (stripe rust or powdery mildew) or abiotic (drought or salt) stresses. Moreover, SnRK2.9-V was up-regulated in H. villosa under the drought and salt stress and overexpressing of SnRK2.9-V in wheat enhanced drought and salt tolerances via enhancing the genes expression of antioxidant enzymes, revealing a potential value of SnRK2.9-V in wheat improvement for salt tolerance. CONCLUSION Our present study provides a basic genome-wide overview of SnRK2-V genes in H. villosa and demonstrates the potential use of SnRK2.9-V in enhancing the drought and salt tolerances in common wheat.
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Affiliation(s)
- Jia Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
- Jinhua Academy, Zhejiang Chinese Medical University, Jinhua, 321000, China
| | - Luyang Wei
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Yirong Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Zongkuan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Haiyan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Jin Xiao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Xiue Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.
| | - Li Sun
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.
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Ding N, Cai J, Xiao S, Jiang L. Heterologous expression of rice OsEXO70FX1 confers tolerance to cadmium in Arabidopsis thaliana and fission yeast. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108268. [PMID: 38091933 DOI: 10.1016/j.plaphy.2023.108268] [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: 06/13/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024]
Abstract
Cadmium (Cd) is an environmental toxicant that accumulates in grains, which greatly increases the risk of human exposure to Cd via food chain. The exocytosis of Cd is one of the essential detoxification mechanisms in plants. OsEXO70s, which facilitate the fusion of secretory vesicles and target membranes, has undergone significant expansion in rice. Here, we uncovered 40 OsEXO70 genes characterized by genome-wide profiling and focused on the potential functions of OsEXO70s, especially OsEXO70FX1, in Cd stress. Overexpression of OsEXO70FX1 enhanced both diamide and Cd tolerances in Schizosaccharomyces pombe (S. pombe), and in Arabidopsis resulted in 11% more seedlings survival rate and about 70% longer primary roots under Cd treatment compared with WT (empty vector). Meanwhile, Cd treatment upregulated the expression levels of some exocyst subunits in overexpression lines. Trichomes isolated from overexpression lines were observed to accumulate more Cd. Also, reactive oxygen species (ROS) induced by Cd stress reflected less sensitivity of OsEXO70FX1 overexpression lines to Cd stress, which was evidenced in the Cd determination assay. These results provide the fundament to future research on rice EXO70 family and suggest that it may have evolved a specialized role in response to Cd stress.
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Affiliation(s)
- Ning Ding
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Jiajia Cai
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shimin Xiao
- Shanwei Marine Industry Institute, Shanwei Institute of Technology, Shanwei, 516600, China
| | - Li Jiang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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Kotsaridis K, Michalopoulou VA, Tsakiri D, Kotsifaki D, Kefala A, Kountourakis N, Celie PHN, Kokkinidis M, Sarris PF. The functional and structural characterization of Xanthomonas campestris pv. campestris core effector XopP revealed a new kinase activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:100-111. [PMID: 37344990 DOI: 10.1111/tpj.16362] [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: 11/16/2022] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 06/23/2023]
Abstract
Exo70B1 is a protein subunit of the exocyst complex with a crucial role in a variety of cell mechanisms, including immune responses against pathogens. The calcium-dependent kinase 5 (CPK5) of Arabidopsis thaliana (hereafter Arabidopsis), phosphorylates AtExo70B1 upon functional disruption. We previously reported that, the Xanthomonas campestris pv. campestris effector XopP compromises AtExo70B1, while bypassing the host's hypersensitive response, in a way that is still unclear. Herein we designed an experimental approach, which includes biophysical, biochemical, and molecular assays and is based on structural and functional predictions, utilizing AplhaFold and DALI online servers, respectively, in order to characterize the in vivo XccXopP function. The interaction between AtExo70B1 and XccXopP was found very stable in high temperatures, while AtExo70B1 appeared to be phosphorylated at XccXopP-expressing transgenic Arabidopsis. XccXopP revealed similarities with known mammalian kinases and phosphorylated AtExo70B1 at Ser107, Ser111, Ser248, Thr309, and Thr364. Moreover, XccXopP protected AtExo70B1 from AtCPK5 phosphorylation. Together these findings show that XccXopP is an effector, which not only functions as a novel serine/threonine kinase upon its host target AtExo70B1 but also protects the latter from the innate AtCPK5 phosphorylation, in order to bypass the host's immune responses. Data are available via ProteomeXchange with the identifier PXD041405.
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Affiliation(s)
- Konstantinos Kotsaridis
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Vassiliki A Michalopoulou
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Dimitra Tsakiri
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
| | - Dina Kotsifaki
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
| | - Aikaterini Kefala
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Patrick H N Celie
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael Kokkinidis
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Panagiotis F Sarris
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
- Biosciences, University of Exeter, Exeter, UK
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Liu L, Gu C, Zhang J, Guo J, Zhang X, Zhou Z. Genome-Wide Analysis of Exocyst Complex Subunit Exo70 Gene Family in Cucumber. Int J Mol Sci 2023; 24:10929. [PMID: 37446106 DOI: 10.3390/ijms241310929] [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: 05/24/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Cucumber (Cucumis sativus L.) is an important vegetable worldwide, but its yield is affected by a wide range of pathogens and pests. As the major subunit of the exocyst complex, the roles of Exo70 members have been shown in Arabidopsis and rice, but their function are unknown in cucumber. Here, we identified 18 CsExo70 members in cucumber, which were divided into three groups (Exo70.1-Exo70.3) and nine subgroups (Exo70A-Exo70I) based on the phylogenetic tree. Subsequently, systematical analyses were performed, including collinearity, gene structure, cis-acting elements, conserved motifs, expression patterns, and subcellular localization. Our results showed that CsExo70 genes were generally expressed in all tissues, and CsExo70C1 and CsExo70C2 were highly expressed in the stamen. Moreover, the expression levels of most CsExo70 genes were induced by Pseudomonas syringae pv. lachrymans (Psl) and Fusarium oxysporum f. sp. cucumerinum Owen (Foc), especially CsExo70E2 and CsExo70H3. In addition, these CsExo70s displayed similar location patterns with discrete and punctate signals in the cytoplasm. Together, our results indicate that CsExo70 members may be involved in plant development and resistance, and provide a reference for future in-depth studies of Exo70 genes in cucumber.
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Affiliation(s)
- Liu Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Chaoheng Gu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Jiahao Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Jingyu Guo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaolan Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Zhaoyang Zhou
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
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Yannam VRR, Caicedo M, Malvar RA, Ordás B. Genome-Wide Association Analysis of Senescence-Related Traits in Maize. Int J Mol Sci 2022; 23:ijms232415897. [PMID: 36555534 PMCID: PMC9782587 DOI: 10.3390/ijms232415897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Senescence is a programmed process that involves the destruction of the photosynthesis apparatus and the relocation of nutrients to the grain. Identifying senescence-associated genes is essential to adapting varieties for the duration of the cultivation cycle. A genome-wide association study (GWAS) was performed using 400 inbred maize lines with 156,164 SNPs to study the genetic architecture of senescence-related traits and their relationship with agronomic traits. We estimated the timing of senescence to be 45 days after anthesis in the whole plant and specifically in the husks. A list of genes identified in a previous RNAseq experiment as involved in senescence (core senescence genes) was used to propose candidate genes in the vicinity of the significant SNPs. Forty-six QTLs of moderate to high effect were found for senescence traits, including specific QTLs for husk senescence. The allele that delayed senescence primarily increased grain yield and moisture. Seven and one significant SNPs were found in the coding and promoter regions of eight core senescence genes, respectively. These genes could be potential candidates for generating a new variation by genome editing for functional analysis and breeding purposes, particularly Zm00001d014796, which could be responsible for a QTL of senescence found in multiple studies.
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Affiliation(s)
- Venkata Rami Reddy Yannam
- Mision Biológica de Galicia, Spanish National Research Council (CSIC), 36001 Pontevedra, Spain
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
| | - Marlon Caicedo
- Estación Experimental Tropical Pichilingue, Programa de Maíz, Instituto Nacional de Investigaciones Agropecuarias (INIAP), Quito 170518, Ecuador
| | - Rosa Ana Malvar
- Mision Biológica de Galicia, Spanish National Research Council (CSIC), 36001 Pontevedra, Spain
| | - Bernardo Ordás
- Mision Biológica de Galicia, Spanish National Research Council (CSIC), 36001 Pontevedra, Spain
- Correspondence:
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A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize. Int J Mol Sci 2022; 23:ijms23179755. [PMID: 36077153 PMCID: PMC9456493 DOI: 10.3390/ijms23179755] [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: 08/04/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Salinization seriously threatens the normal growth of maize, especially at the seedling stage. Recent studies have demonstrated that circular RNAs (circRNAs) play vital roles in the regulation of plant stress resistance. Here, we performed a genome-wide association study (GWAS) on the survival rate of 300 maize accessions under a salt stress treatment. A total of 5 trait-associated SNPs and 86 candidate genes were obtained by the GWAS. We performed RNA sequencing for 28 transcriptome libraries derived from 2 maize lines with contrasting salt tolerance under normal and salt treatment conditions. A total of 1217 highly expressed circRNAs were identified, of which 371 were responsive to a salt treatment. Using PCR and Sanger sequencing, we verified the reliability of these differentially expressed circRNAs. An integration of the GWAS and RNA-Seq analyses uncovered two differentially expressed hub genes (Zm00001eb013650 and Zm00001eb198930), which were regulated by four circRNAs. Based on these results, we constructed a regulation model of circRNA/miRNA/mRNA that mediated salt stress tolerance in maize. By conducting hub gene-based association analyses, we detected a favorable haplotype in Zm00001eb198930, which was responsible for high salt tolerance. These results help to clarify the regulatory relationship between circRNAs and their target genes as well as to develop salt-tolerant lines for maize breeding.
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Khan H, Krishnappa G, Kumar S, Mishra CN, Krishna H, Devate NB, Rathan ND, Parkash O, Yadav SS, Srivastava P, Biradar S, Kumar M, Singh GP. Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.). Front Genet 2022; 13:982589. [PMID: 36092913 PMCID: PMC9458894 DOI: 10.3389/fgene.2022.982589] [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: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
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Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Hari Krishna
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonu Singh Yadav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Suma Biradar
- University of Agricultural Sciences, Dharwad, India
| | - Monu Kumar
- ICAR-Indian Agricultural Research Institute, Jharkhand, India
| | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
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Yu Z, Tian C, Guan Y, He J, Wang Z, Wang L, Lin S, Guan Z, Fang W, Chen S, Zhang F, Jiang J, Chen F, Wang H. Expression Analysis of TCP Transcription Factor Family in Autopolyploids of Chrysanthemum nankingense. FRONTIERS IN PLANT SCIENCE 2022; 13:860956. [PMID: 35720599 PMCID: PMC9201386 DOI: 10.3389/fpls.2022.860956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Autopolyploids often exhibit plant characteristics different from their diploid ancestors and are frequently associated with altered genes expression controlling growth and development. TCP is a unique transcription factor family in plants that is closely related to plant growth and development. Based on transcriptome sequencing of Chrysanthemum nankingense, 23 full-length TCP genes were cloned. The expression of CnTCP9 was most variable in tetraploids, at least threefold greater than diploids. Due to the lack of a C. nankingense transgenic system, we overexpressed CnTCP9 in Arabidopsis thaliana (Col-0) and Chrysanthemum morifolium. Overexpression of CnTCP9 caused enlargement of leaves in A. thaliana and petals in C. morifolium, and the expression of genes downstream of the GA pathway in C. morifolium were increased. Our results suggest that autopolyploidization of C. nankingense led to differential expression of TCP family genes, thereby affecting plant characteristics by the GA pathway. This study improves the understanding of enlarged plant size after autopolyploidization.
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Xu Z, Li F, Li M, He Y, Chen Y, Hu F. Functional analysis of ARF1 from Cymbidium goeringii in IAA response during leaf development. PeerJ 2022; 10:e13077. [PMID: 35291484 PMCID: PMC8918147 DOI: 10.7717/peerj.13077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Background Cymbidium is an economically important genus of flowering orchids cultivated in China because of showing graceful leaf shapes and elegant flower coloration. However, the deterioration of the ecological environment and the difficulty of conservation management have become increasing challenges for maintaining its germplasm resources. ARFs are critical transcription factors in the auxin signaling pathway and have been found to play pivotal roles in leaf growth and development in previous studies. However, their functions and mechanisms in Cymbidium goeringii remain to be clarified. Methods The sequence of the CgARF1 gene was analyzed by bioinformatics. The expression of this gene in different tissues and under IAA treatment was detected by quantitative real-time PCR analysis. The CgARF1 gene was overexpressed in wild-type Arabidopsis and Nicotiana benthamiana via the Agrobacterium infection method. Acetone-ethanol solvent extraction was applied for the determination of chlorophyll contents, and the contents of endogenous hormones were determined using the enzyme-linked immunosorbent assay technique. Results CgARF1 cloned from C. goeringii 'Songmei' was 2,049 bp in length and encoded 682 amino acids containing three typical domains: a B3 DNA binding domain, an Aux_resp domain and an AUX/IXX family domain. The expression pattern of CgARF1 in different tissues of C. goeringii showed that its expression was highest in the leaves and changed greatly under IAA treatment. Subcellular localization studies showed that the protein was mainly localized in the cell nucleus. CgARF1-overexpressing lines exhibited leaf senescence and a decreased chlorophyll content. Under IAA treatment, CgARF1 regulates the rooting length, rooting number and rooting rate from detached leaves. The levels of endogenous hormones in transgenic leaves were also significantly changed. Conclusion These results indicated that CgARF1 overexpression is responsive to IAA treatment during leaf development. This study provides a foundation for future research on the function of the ARF gene family in C. goeringii.
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Affiliation(s)
- Zihan Xu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Fangle Li
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Meng Li
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yuanhao He
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Fengrong Hu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
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Zhang H, Zhang X, Zhao J, Sun L, Wang H, Zhu Y, Xiao J, Wang X. Genome-Wide Identification of GDSL-Type Esterase/Lipase Gene Family in Dasypyrum villosum L. Reveals That DvGELP53 Is Related to BSMV Infection. Int J Mol Sci 2021; 22:ijms222212317. [PMID: 34830200 PMCID: PMC8624868 DOI: 10.3390/ijms222212317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/21/2022] Open
Abstract
GDSL-type esterase/lipase proteins (GELPs) characterized by a conserved GDSL motif at their N-terminus belong to the lipid hydrolysis enzyme superfamily. In plants, GELPs play an important role in plant growth, development and stress response. The studies of the identification and characterization of the GELP gene family in Triticeae have not been reported. In this study, 193 DvGELPs were identified in Dasypyrum villosum and classified into 11 groups (clade A–K) by means of phylogenetic analysis. Most DvGELPs contain only one GDSL domain, only four DvGELPs contain other domains besides the GDSL domain. Gene structure analysis indicated 35.2% DvGELP genes have four introns and five exons. In the promoter regions of the identified DvGELPs, we detected 4502 putative cis-elements, which were associated with plant hormones, plant growth, environmental stress and light responsiveness. Expression profiling revealed 36, 44 and 17 DvGELPs were highly expressed in the spike, the root and the grain, respectively. Further investigation of a root-specific expressing GELP, DvGELP53, indicated it was induced by a variety of biotic and abiotic stresses. The knockdown of DvGELP53 inhibited long-distance movement of BSMV in the tissue of D. villosum. This research provides a genome-wide glimpse of the D. villosum GELP genes and hints at the participation of DvGELP53 in the interaction between virus and plants.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (H.Z.); (Y.Z.)
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Xu Zhang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Jia Zhao
- College of Agriculture, South China Agriculture University, Guangzhou 510642, China;
| | - Li Sun
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Haiyan Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (H.Z.); (Y.Z.)
| | - Jin Xiao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Xiue Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
- Correspondence: ; Tel.: +86-25-84395308
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Zhu YQ, Qiu L, Liu LL, Luo L, Han XP, Zhai YH, Wang WJ, Ren MZ, Xing YD. Identification and Comprehensive Structural and Functional Analyses of the EXO70 Gene Family in Cotton. Genes (Basel) 2021; 12:genes12101594. [PMID: 34680988 PMCID: PMC8536163 DOI: 10.3390/genes12101594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 11/24/2022] Open
Abstract
The EXO70 gene is a vital component of the exocytosis complex and participates in biological processes ranging from plant cell division to polar growth. There are many EXO70 genes in plants and their functions are extensive, but little is known about the EXO70 gene family in cotton. Here, we analyzed four cotton sequence databases, identified 165 EXO70 genes, and divided them into eight subgroups (EXO70A–EXO70H) based on their phylogenetic relationships. EXO70A had the most exons (≥11), whereas the other seven each had only one or two exons. Hence, EXO70A may have many important functions. The 84 EXO70 genes in Asian and upland cotton were expressed in the roots, stems, leaves, flowers, fibers, and/or ovules. Full-length GhEXO70A1-A cDNA was homologously cloned from upland cotton (Gossypium hirsutum, G. hirsutum). Subcellular analysis revealed that GhEXO70A1-A protein was localized to the plasma membrane. A yeast two-hybrid assay revealed that GhEXO70A1-A interacted with GhEXO84A, GhEXO84B, and GhEXO84C. GhEXO70A1-A silencing significantly altered over 4000 genes and changed several signaling pathways related to metabolism. Thus, the EXO70 gene plays critical roles in the physiological functions of cotton.
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Affiliation(s)
- Ya-Qian Zhu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.-Q.Z.); (L.Q.); (L.-L.L.); (L.L.); (X.-P.H.); (Y.-H.Z.); (W.-J.W.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Lu Qiu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.-Q.Z.); (L.Q.); (L.-L.L.); (L.L.); (X.-P.H.); (Y.-H.Z.); (W.-J.W.)
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lu-Lu Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.-Q.Z.); (L.Q.); (L.-L.L.); (L.L.); (X.-P.H.); (Y.-H.Z.); (W.-J.W.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Lei Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.-Q.Z.); (L.Q.); (L.-L.L.); (L.L.); (X.-P.H.); (Y.-H.Z.); (W.-J.W.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xin-Pei Han
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.-Q.Z.); (L.Q.); (L.-L.L.); (L.L.); (X.-P.H.); (Y.-H.Z.); (W.-J.W.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yao-Hua Zhai
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.-Q.Z.); (L.Q.); (L.-L.L.); (L.L.); (X.-P.H.); (Y.-H.Z.); (W.-J.W.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wen-Jing Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.-Q.Z.); (L.Q.); (L.-L.L.); (L.L.); (X.-P.H.); (Y.-H.Z.); (W.-J.W.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Mao-Zhi Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Correspondence: (M.-Z.R.); (Y.-D.X.)
| | - Ya-Di Xing
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.-Q.Z.); (L.Q.); (L.-L.L.); (L.L.); (X.-P.H.); (Y.-H.Z.); (W.-J.W.)
- Correspondence: (M.-Z.R.); (Y.-D.X.)
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12
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Xu J, Hu P, Tao Y, Song P, Gao H, Guan Y. Genome-wide identification and characterization of the Lateral Organ Boundaries Domain ( LBD) gene family in polyploid wheat and related species. PeerJ 2021; 9:e11811. [PMID: 34447619 PMCID: PMC8364319 DOI: 10.7717/peerj.11811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/27/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. METHODS Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a-e, II a and II b). RESULTS The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.
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Affiliation(s)
- Jun Xu
- Henan Institute of Science and Technology, Xinxiang, China
| | - Ping Hu
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Ye Tao
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Puwen Song
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Huanting Gao
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Yuanyuan Guan
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
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Zhao J, Zhang H, Zhang X, Wang Z, Niu Y, Chen Y, Sun L, Wang H, Wang X, Xiao J. The Exocyst Complex Subunit EXO70E1-V From Haynaldia villosa Interacts With Wheat Powdery Mildew Resistance Gene CMPG1-V. FRONTIERS IN PLANT SCIENCE 2021; 12:652337. [PMID: 34305961 PMCID: PMC8295898 DOI: 10.3389/fpls.2021.652337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/08/2021] [Indexed: 06/03/2023]
Abstract
EXO70 belongs to the exocyst complex subunit that plays a critical role in regulating plant cell polarity establishment and defense response. A previous study proved that the E3 ligase CMPG1-V from Haynaldia villosa, a diploid wheat relative, positively regulates the resistance to wheat powdery mildew (Pm), caused by fungus Blumeria graminis f.sp tritici (Bgt). In this study, a member of EXO70 superfamily named EXO70E1-V was isolated from H. villosa, and EXO70E1-V interacted with CMPG1-V were shown by yeast two-hybrid (Y2H), pull-down assay, bimolecular fluorescence complementation (BiFC) assay, and luciferase complementation imaging (LCI) assay. It is localized in various subcellular organs, i.e., plasma membrane (PM) and endoplasmic reticulum. Co-expression of EXO70E1-V and CMPG1-V showed dot-like structure fluorescence signals that were mainly in PM and nucleus. Expression of EXO70E1-V was relatively higher in leaf and was significantly induced by Bgt infection and exogenous application of hormones such as salicylic acid. Transient or stable overexpression of EXO70E1-V could not enhance/decrease the Pm resistance level, suggesting overexpression of EXO70E1-V alone has no impact on Pm resistance in wheat.
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Affiliation(s)
- Jia Zhao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Heng Zhang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xu Zhang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Zongkuan Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Ying Niu
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Yiming Chen
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Li Sun
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Haiyan Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Xiue Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Jin Xiao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
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Wang H, Ma ZH, Mao J, Chen BH. Genome-wide identification and expression analysis of the EXO70 gene family in grape ( Vitis vinifera L). PeerJ 2021; 9:e11176. [PMID: 33976971 PMCID: PMC8067907 DOI: 10.7717/peerj.11176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
EXO70 is the pivotal protein subunit of exocyst, which has a very crucial role in enhancing the shielding effect of the cell wall, resisting abiotic and hormonal stresses. This experiment aims to identify family members of the EXO70 gene family in grape and predict the characteristics of this gene family, so as to lay the foundation of further exploring the mechanism of resisting abiotic and hormone stresses of VvEXO70s. Therefore, the Vitis vinifera ‘Red Globe’ tube plantlet were used as materials. Bioinformatics was used to inquire VvEXO70 genes family members, gene structure, system evolution, cis-acting elements, subcellular and chromosomal localization, collinearity, selective pressure, codon bias and tissue expression. All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. Microarray analysis suggested that most genes expressed to varying degrees in tendrils, leaves, seeds, buds, roots and stems. Quantitative Real-Time PCR (qRT-PCR) showed that the expression levels of all genes with 5 mM salicylic acid (SA), 0.1 mM methy jasmonate (MeJA), 20% PEG6000 and 4 °C for 24 h were higher than for 12 h. With 20% PEG6000 treatment about 24 h, the relative expression of VvEXO70-02 was significantly up-regulated and 361 times higher than CK. All genes’ relative expression was higher at 12 h than that at 24 h after treatment with 7 mM hydrogen peroxide (H2O2) and 0.1 mM ethylene (ETH). In conclusion, the expression levels of 14 VvEXO70 genes are distinguishing under these treatments, which play an important role in the regulation of anti-stress signals in grape. All of these test results provide a reference for the future research on the potential function analysis and plant breeding of VvEXO70 genes.
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Affiliation(s)
- Han Wang
- Department of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zong-Huan Ma
- Department of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Juan Mao
- Department of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Bai-Hong Chen
- Department of Horticulture, Gansu Agricultural University, Lanzhou, China
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15
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Muhammad I, Li K, Shuaib M, Inamullah, Ayub M, Shafqat N, Alam B, Romman M, Azam N. Identification of biotic stress tolerant wheat germplasm using morphological and molecular approaches. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Pradhan AK, Kumar S, Singh AK, Budhlakoti N, Mishra DC, Chauhan D, Mittal S, Grover M, Kumar S, Gangwar OP, Kumar S, Gupta A, Bhardwaj SC, Rai A, Singh K. Identification of QTLs/Defense Genes Effective at Seedling Stage Against Prevailing Races of Wheat Stripe Rust in India. Front Genet 2020; 11:572975. [PMID: 33329711 PMCID: PMC7728992 DOI: 10.3389/fgene.2020.572975] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
Resistance in modern wheat cultivars for stripe rust is not long lasting due to the narrow genetic base and periodical evolution of new pathogenic races. Though nearly 83 Yr genes conferring resistance to stripe rust have been cataloged so far, few of them have been mapped and utilized in breeding programs. Characterization of wheat germplasm for novel sources of resistance and their incorporation into elite cultivars is required to achieve durable resistance and thus to minimize the yield losses. Here, a genome-wide association study (GWAS) was performed on a set of 391 germplasm lines with the aim to identify quantitative trait loci (QTL) using 35K Axiom® array. Phenotypic evaluation disease severity against four stripe rust pathotypes, i.e., 46S119, 110S119, 238S119, and 47S103 (T) at the seedling stage in a greenhouse providing optimal conditions was carried out consecutively for 2 years (2018 and 2019 winter season). We identified, a total of 17 promising QTl which passed FDR criteria. Moreover these 17 QTL identified in the current study were mapped at different genomic locations i.e. 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5B and 6B. These 17 QTLs identified in the present study might play a key role in marker-assisted breeding for developing stripe rust resistant wheat cultivars.
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Affiliation(s)
- Anjan Kumar Pradhan
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Amit Kumar Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Neeraj Budhlakoti
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dwijesh C Mishra
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Divya Chauhan
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shikha Mittal
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Monendra Grover
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Suneel Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Om P Gangwar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Subodh Kumar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Arun Gupta
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Subhash C Bhardwaj
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Anil Rai
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kuldeep Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
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17
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Comprehensive analysis of polygalacturonase genes offers new insights into their origin and functional evolution in land plants. Genomics 2020; 113:1096-1108. [PMID: 33171205 DOI: 10.1016/j.ygeno.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/22/2020] [Accepted: 11/04/2020] [Indexed: 11/21/2022]
Abstract
Polygalacturonase (PG) is a hydrolase that participates in pectin degradation, pod shattering and fruit softening. Here, we identified 2786 PG genes across 54 plants, which could be divided into three groups. Evolutionary analysis suggested that PG family originated from the charophyte green algae, and Subgroups A2-A4 evolved from the Subgroup A1 after the tracheophyte-angiosperm split. Whole-genome duplication was the major force leading to PG gene expansion. Interestingly, the PG genes continuously expanded in eudicots, whereas it contracted in monocots after the eudicot-monocot split. PG genes in Group A are expressed at high levels in floral organs, whereas genes in Groups B and C are expressed at high levels in various tissues. Moreover, three BnaPG15 members were found for their potential possibility in pod shattering in Brassica napus. Our results provide new insight into the evolutionary history of PG family, and their potentially functional role in plants.
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18
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OsExo70B1 Positively Regulates Disease Resistance to Magnaporthe oryzae in Rice. Int J Mol Sci 2020; 21:ijms21197049. [PMID: 32992695 PMCID: PMC7582735 DOI: 10.3390/ijms21197049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 01/21/2023] Open
Abstract
The exocyst, an evolutionarily conserved octameric protein complex, mediates tethering of vesicles to the plasma membrane in the early stage of exocytosis. Arabidopsis Exo70, a subunit of the exocyst complex, has been found to be involved in plant immunity. Here, we characterize the function of OsExo70B1 in rice. OsExo70B1 mainly expresses in leaf and shoot and its expression is induced by pathogen-associated molecular patterns (PAMPs) and rice blast fungus Magnaporthe oryzae (M. oryzae). Knocking out OsExo70B1 results in significantly decreased resistance and defense responses to M. oryzae compared to the wild type, including more disease lesions and enhanced fungal growth, downregulated expression of pathogenesis-related (PR) genes, and decreased reactive oxygen species accumulation. In contrast, the exo70B1 mutant does not show any defects in growth and development. Furthermore, OsExo70B1 can interact with the receptor-like kinase OsCERK1, an essential component for chitin reception in rice. Taken together, our data demonstrate that OsExo70B1 functions as an important regulator in rice immunity.
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Zhang H, Zhang X, Liu J, Niu Y, Chen Y, Hao Y, Zhao J, Sun L, Wang H, Xiao J, Wang X. Characterization of the Heavy-Metal-Associated Isoprenylated Plant Protein ( HIPP) Gene Family from Triticeae Species. Int J Mol Sci 2020; 21:E6191. [PMID: 32867204 PMCID: PMC7504674 DOI: 10.3390/ijms21176191] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Heavy-metal-associated (HMA) isoprenylated plant proteins (HIPPs) only exist in vascular plants. They play important roles in responses to biotic/abiotic stresses, heavy-metal homeostasis, and detoxification. However, research on the distribution, diversification, and function of HIPPs in Triticeae species is limited. In this study, a total of 278 HIPPs were identified from a database from five Triticeae species, and 13 were cloned from Haynaldia villosa. These genes were classified into five groups by phylogenetic analysis. Most HIPPs had one HMA domain, while 51 from Clade I had two, and all HIPPs had good collinear relationships between species or subgenomes. In silico expression profiling revealed that 44 of the 114 wheat HIPPs were dominantly expressed in roots, 43 were upregulated under biotic stresses, and 29 were upregulated upon drought or heat treatment. Subcellular localization analysis of the cloned HIPPs from H. villosa showed that they were expressed on the plasma membrane. HIPP1-V was upregulated in H. villosa after Cd treatment, and transgenic wheat plants overexpressing HIPP1-V showed enhanced Cd tolerance, as shown by the recovery of seed-germination and root-growth inhibition by supplementary Cd. This research provides a genome-wide overview of the Triticeae HIPP genes and proved that HIPP1-V positively regulates Cd tolerance in common wheat.
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Affiliation(s)
- Heng Zhang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Xu Zhang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Jia Liu
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Ying Niu
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Yiming Chen
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Yongli Hao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Jia Zhao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
- College of Agriculture, South China Agriculture University, Guangzhou 510642, China
| | - Li Sun
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Haiyan Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Jin Xiao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
| | - Xiue Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (H.Z.); (X.Z.); (J.L.); (Y.N.); (Y.C.); (Y.H.); (J.Z.); (L.S.); (H.W.)
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Žárský V, Sekereš J, Kubátová Z, Pečenková T, Cvrčková F. Three subfamilies of exocyst EXO70 family subunits in land plants: early divergence and ongoing functional specialization. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:49-62. [PMID: 31647563 DOI: 10.1093/jxb/erz423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/10/2019] [Indexed: 05/27/2023]
Abstract
Localized delivery of plasma membrane and cell wall components is an essential process in all plant cells. The vesicle-tethering complex, the exocyst, an ancient eukaryotic hetero-octameric protein cellular module, assists in targeted delivery of exocytosis vesicles to specific plasma membrane domains. Analyses of Arabidopsis and later other land plant genomes led to the surprising prediction of multiple putative EXO70 exocyst subunit paralogues. All land plant EXO70 exocyst subunits (including those of Bryophytes) form three distinct subfamilies-EXO70.1, EXO70.2, and EXO70.3. Interestingly, while the basal well-conserved EXO70.1 subfamily consists of multiexon genes, the remaining two subfamilies contain mostly single exon genes. Published analyses as well as public transcriptomic and proteomic data clearly indicate that most cell types in plants express and also use several different EXO70 isoforms. Here we sum up recent advances in the characterization of the members of the family of plant EXO70 exocyst subunits and present evidence that members of the EXO70.2 subfamily are often recruited to non-canonical functions in plant membrane trafficking pathways. Engagement of the most evolutionarily dynamic EXO70.2 subfamily of EXO70s in biotic interactions and defence correlates well with massive proliferation and conservation of new protein variants in this subfamily.
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Affiliation(s)
- Viktor Žárský
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
- Institute of Experimental Botany, v.v.i., Czech Academy of Sciences, Rozvojová, Prague, Czech Republic
| | - Juraj Sekereš
- Institute of Experimental Botany, v.v.i., Czech Academy of Sciences, Rozvojová, Prague, Czech Republic
| | - Zdeňka Kubátová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Tamara Pečenková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
- Institute of Experimental Botany, v.v.i., Czech Academy of Sciences, Rozvojová, Prague, Czech Republic
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
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