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Li JW, Zhou P, Hu ZH, Teng RM, Wang YX, Li T, Xiong AS, Li XH, Chen X, Zhuang J. CsPAT1, a GRAS transcription factor, promotes lignin accumulation by antagonistic interacting with CsWRKY13 in tea plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1312-1326. [PMID: 38319894 DOI: 10.1111/tpj.16670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/21/2024] [Accepted: 01/27/2024] [Indexed: 02/08/2024]
Abstract
Lignin is an important component of plant cell walls and plays crucial roles in the essential agronomic traits of tea quality and tenderness. However, the molecular mechanisms underlying the regulation of lignin biosynthesis in tea plants remain unclear. CsWRKY13 acts as a negative regulator of lignin biosynthesis in tea plants. In this study, we identified a GRAS transcription factor, phytochrome A signal transduction 1 (CsPAT1), that interacts with CsWRKY13. Silencing CsPAT1 expression in tea plants and heterologous overexpression in Arabidopsis demonstrated that CsPAT1 positively regulates lignin accumulation. Further investigation revealed that CsWRKY13 directly binds to the promoters of CsPAL and CsC4H and suppresses transcription of CsPAL and CsC4H. CsPAT1 indirectly affects the promoter activities of CsPAL and CsC4H by interacting with CsWRKY13, thereby facilitating lignin biosynthesis in tea plants. Compared with the expression of CsWRKY13 alone, the co-expression of CsPAT1 and CsWRKY13 in Oryza sativa significantly increased lignin biosynthesis. Conversely, compared with the expression of CsPAT1 alone, the co-expression of CsPAT1 and CsWRKY13 in O. sativa significantly reduced lignin accumulation. These results demonstrated the antagonistic regulation of the lignin biosynthesis pathway by CsPAT1 and CsWRKY13. These findings improve our understanding of lignin biosynthesis mechanisms in tea plants and provide insights into the role of the GRAS transcription factor family in lignin accumulation.
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Affiliation(s)
- Jing-Wen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ping Zhou
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Hang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Rui-Min Teng
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tong Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Xing-Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xuan Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Huerta-Venegas PI, Raya-González J, Ruíz-Herrera LF, López-Bucio J. PHYTOCHROME A controls the DNA damage response and cell death tolerance within the Arabidopsis root meristem. PLANT, CELL & ENVIRONMENT 2024; 47:1513-1525. [PMID: 38251425 DOI: 10.1111/pce.14831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/21/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
The DNA damage response avoids mutations into dividing cells. Here, we analysed the role of photoreceptors on the restriction of root growth imposed by genotoxic agents and its relationship with cell viability and performance of meristems. Comparison of root growth of Arabidopsis WT, phyA-211, phyB-9, and phyA-211phyB-9 double mutants unveiled a critical role for phytochrome A (PhyA) in protecting roots from genotoxic stress, regeneration and cell replenishment in the meristematic zone. PhyA was located on primary root tips, where it influences genes related to the repair of DNA, including ERF115 and RAD51. Interestingly, phyA-211 mutants treated with zeocin failed to induce the expression of the repressor of cell cycle MYB3R3, which correlated with expression of the mitotic cyclin CycB1, suggesting that PhyA is required for safeguarding the DNA integrity during cell division. Moreover, the growth of the primary roots of PhyA downstream component HY5 and root growth analyses in darkness suggest that cell viability and DNA damage responses within root meristems may act independently from light and photomorphogenesis. These data support novel roles for PhyA as a key player for stem cell niche maintenance and DNA damage responses, which are critical for proper root growth.
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Affiliation(s)
- Pedro Iván Huerta-Venegas
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Javier Raya-González
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - León Francisco Ruíz-Herrera
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - José López-Bucio
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
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Xue S, Huang H, Xu Y, Liu L, Meng Q, Zhu J, Zhou M, Du H, Yao C, Jin Q, Nie C, Zhong Y. Transcriptomic analysis reveals the molecular basis of photoperiod-regulated sex differentiation in tropical pumpkins (Cucurbita moschata Duch.). BMC PLANT BIOLOGY 2024; 24:90. [PMID: 38317069 PMCID: PMC10845594 DOI: 10.1186/s12870-024-04777-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Photoperiod, or the length of the day, has a significant impact on the flowering and sex differentiation of photoperiod-sensitive crops. The "miben" pumpkin (the main type of Cucurbita moschata Duch.) is well-known for its high yield and strong disease resistance. However, its cultivation has been limited due to its sensitivity to photoperiod. This sensitivity imposes challenges on its widespread cultivation and may result in suboptimal yields in regions with specific daylength conditions. As a consequence, efforts are being made to explore potential strategies or breeding techniques to enhance its adaptability to a broader range of photoperiods, thus unlocking its full cultivation potential and further promoting its valuable traits in agriculture. RESULTS This study aimed to identify photoperiod-insensitive germplasm exhibiting no difference in sex differentiation under different day-length conditions. The investigation involved a phenotypic analysis of photoperiod-sensitive (PPS) and photoperiod-insensitive (PPIS) pumpkin materials exposed to different day lengths, including long days (LDs) and short days (SDs). The results revealed that female flower differentiation was significantly inhibited in PPS_LD, while no differences were observed in the other three groups (PPS_SD, PPIS_LD, and PPIS_SD). Transcriptome analysis was carried out for these four groups to explore the main-effect genes of sex differentiation responsive to photoperiod. The main-effect gene subclusters were identified based on the principal component and hierarchical cluster analyses. Further, functional annotations and enrichment analysis revealed significant upregulation of photoreceptors (CmCRY1, F-box/kelch-repeat protein), circadian rhythm-related genes (CmGI, CmPRR9, etc.), and CONSTANS (CO) in PPS_LD. Conversely, a significant downregulation was observed in most Nuclear Factor Y (NF-Y) transcription factors. Regarding the gibberellic acid (GA) signal transduction pathway, positive regulators of GA signaling (CmSCL3, CmSCL13, and so forth) displayed higher expression levels, while the negative regulators of GA signaling, CmGAI, exhibited lower expression levels in PPS_LD. Notably, this effect was not observed in the synthetic pathway genes. Furthermore, genes associated with ethylene synthesis and signal transduction (CmACO3, CmACO1, CmERF118, CmERF118-like1,2, CmWIN1-like, and CmRAP2-7-like) showed significant downregulation. CONCLUSIONS This study offered a crucial theoretical and genetic basis for understanding how photoperiod influences the mechanism of female flower differentiation in pumpkins.
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Affiliation(s)
- Shudan Xue
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Hexun Huang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Yingchao Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Ling Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Qitao Meng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
- Department of Horticulture, College of Food Science and Engineering, Foshan University, Foshan, 528000, P. R. China
| | - Jitong Zhu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Meijiang Zhou
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Hu Du
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Chunpeng Yao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Qingmin Jin
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Chengrong Nie
- Department of Horticulture, College of Food Science and Engineering, Foshan University, Foshan, 528000, P. R. China
| | - Yujuan Zhong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P. R. China.
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Fan Y, Wan X, Zhang X, Zhang J, Zheng C, Yang Q, Yang L, Li X, Feng L, Zou L, Xiang D. GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses. BMC PLANT BIOLOGY 2024; 24:46. [PMID: 38216860 PMCID: PMC10787399 DOI: 10.1186/s12870-023-04674-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet. RESULTS In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement. CONCLUSIONS We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.
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Affiliation(s)
- Yu Fan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Xianqi Wan
- Sichuan Academy of Agricultural Machinery Science, Chengdu, 610011, P.R. China
| | - Xin Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Jieyu Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Chunyu Zheng
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, P.R. China
| | - Qiaohui Yang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Li Yang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Xiaolong Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610000, P.R. China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China.
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China.
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Tong N, Li D, Zhang S, Tang M, Chen Y, Zhang Z, Huang Y, Lin Y, Cheng Z, Lai Z. Genome-wide identification and expression analysis of the GRAS family under low-temperature stress in bananas. FRONTIERS IN PLANT SCIENCE 2023; 14:1216070. [PMID: 37719217 PMCID: PMC10502232 DOI: 10.3389/fpls.2023.1216070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
Introduction GRAS, named after GAI, RGA, and SCR, is a class of plant-specific transcription factors family that plays a crucial role in growth and development, signal transduction, and various stress responses. Methods To understand the biological functions of the banana GRAS gene family, a genome-wide identification and bioinformatics analysis of the banana GRAS gene family was performed based on information from the M. acuminata, M. balbisiana, and M. itinerans genomic databases. Result In the present study, we identified 73 MaGRAS, 59 MbGRAS, and 58 MiGRAS genes in bananas at the whole-genome scale, and 56 homologous genes were identified in the three banana genomes. Banana GRASs can be classified into 10 subfamilies, and their gene structures revealed that most banana GRAS gDNAs lack introns. The promoter sequences of GRASs had a large number of cis-acting elements related to plant growth and development, phytohormone, and adversity stress responsiveness. The expression pattern of seven key members of MaGRAS response to low-temperature stress and different tissues was also examined by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The microRNAs-MaGRASs target prediction showed perfect complementarity of seven GRAS genes with the five mac-miRNAs. The expression of all seven genes was lowest in roots, and the expression of five genes was highest in leaves during low-temperature stress. The expression of MaSCL27-2, MaSCL27-3, and MaSCL6-1 was significantly lower under low-temperature stress compared to the control, except for MaSCL27-2, which was slightly higher than the 28°C control at 4 h. The expression of MaSCL27-2, MaSCL27-3, and MaSCL6-1 dropped to the lowest levels at 24 h, 12 h, and 4 h, respectively. The MaSCL27-4 and MaSCL6-2 expression was intermittently upregulated, rising to the highest expression at 24h, while the expression of MaSCL22 was less variable, remaining at the control level with small changes. Discussion In summary, it is tentatively hypothesized that the GRAS family has an important function in low-temperature stress in bananas. This study provides a theoretical basis for further analyzing the function of the banana GRAS gene and the resistance of bananas to cold temperatures.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
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Shor E, Ravid J, Sharon E, Skaliter O, Masci T, Vainstein A. SCARECROW-like GRAS protein PES positively regulates petunia floral scent production. PLANT PHYSIOLOGY 2023; 192:409-425. [PMID: 36760164 PMCID: PMC10152688 DOI: 10.1093/plphys/kiad081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 05/03/2023]
Abstract
Emission of scent volatiles by flowers is important for successful pollination and consequently, reproduction. Petunia (Petunia hybrida) floral scent is formed mainly by volatile products of the phenylpropanoid pathway. We identified and characterized a regulator of petunia scent production: the GRAS protein PHENYLPROPANOID EMISSION-REGULATING SCARECROW-LIKE (PES). Its expression increased in petals during bud development and was highest in open flowers. Overexpression of PES increased the production of floral volatiles, while its suppression resulted in scent reduction. We showed that PES upregulates the expression of genes encoding enzymes of the phenylpropanoid and shikimate pathways in petals, and of the core regulator of volatile biosynthesis ODORANT1 by activating its promoter. PES is an ortholog of Arabidopsis (Arabidopsis thaliana) PHYTOCHROME A SIGNAL TRANSDUCTION 1, involved in physiological responses to far-red (FR) light. Analyses of the effect of nonphotosynthetic irradiation (low-intensity FR light) on petunia floral volatiles revealed FR light as a scent-activating factor. While PHYTOCHROME A regulated scent-related gene expression and floral scent production under FR light, the influence of PES on volatile production was not limited by FR light conditions.
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Affiliation(s)
- Ekaterina Shor
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Jasmin Ravid
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Elad Sharon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Oded Skaliter
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Tania Masci
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Alexander Vainstein
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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Bisht A, Eekhout T, Canher B, Lu R, Vercauteren I, De Jaeger G, Heyman J, De Veylder L. PAT1-type GRAS-domain proteins control regeneration by activating DOF3.4 to drive cell proliferation in Arabidopsis roots. THE PLANT CELL 2023; 35:1513-1531. [PMID: 36747478 PMCID: PMC10118276 DOI: 10.1093/plcell/koad028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 05/22/2023]
Abstract
Plant roots possess remarkable regenerative potential owing to their ability to replenish damaged or lost stem cells. ETHYLENE RESPONSE FACTOR 115 (ERF115), one of the key molecular elements linked to this potential, plays a predominant role in the activation of regenerative cell divisions. However, the downstream operating molecular machinery driving wound-activated cell division is largely unknown. Here, we biochemically and genetically identified the GRAS-domain transcription factor SCARECROW-LIKE 5 (SCL5) as an interaction partner of ERF115 in Arabidopsis thaliana. Although nonessential under control growth conditions, SCL5 acts redundantly with the related PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) and SCL21 transcription factors to activate the expression of the DNA-BINDING ONE FINGER 3.4 (DOF3.4) transcription factor gene. DOF3.4 expression is wound-inducible in an ERF115-dependent manner and, in turn, activates D3-type cyclin expression. Accordingly, ectopic DOF3.4 expression drives periclinal cell division, while its downstream D3-type cyclins are essential for the regeneration of a damaged root. Our data highlight the importance and redundant roles of the SCL5, SCL21, and PAT1 transcription factors in wound-activated regeneration processes and pinpoint DOF3.4 as a key downstream element driving regenerative cell division.
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Affiliation(s)
- Anchal Bisht
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Balkan Canher
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
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Chen C, Lu LL, Ma SY, Zhao YP, Wu N, Li WJ, Ma L, Kong XH, Xie ZM, Hou YX. Analysis of PAT1 subfamily members in the GRAS family of upland cotton and functional characterization of GhSCL13-2A in Verticillium dahliae resistance. PLANT CELL REPORTS 2023; 42:487-504. [PMID: 36680639 DOI: 10.1007/s00299-022-02971-x] [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: 09/08/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
GhSCL13-2A, a member of the PAT1 subfamily in the GRAS family, positively regulates cotton resistance to Verticillium dahliae by mediating the jasmonic acid and salicylic acid signaling pathways and accumulation of reactive oxygen species. Verticillium wilt (VW) is a devastating disease of upland cotton (Gossypium hirsutum) that is primarily caused by the soil-borne fungus Verticillium dahliae. Scarecrow-like (SCL) proteins are known to be involved in plant abiotic and biotic stress responses, but their roles in cotton defense responses are still unclear. In this study, a total of 25 GhPAT1 subfamily members in the GRAS family were identified in upland cotton. Gene organization and protein domain analysis showed that GhPAT1 members were highly conserved. GhPAT1 genes were widely expressed in various tissues and at multiple developmental stages, and they were responsive to jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signals. Furthermore, GhSCL13-2A was induced by V. dahliae infection. V. dahliae resistance was enhanced in Arabidopsis thaliana by ectopic overexpression of GhSCL13-2A, whereas cotton GhSCL13-2A knockdowns showed increased susceptibility. Levels of reactive oxygen species (ROS) and JA were also increased and SA content was decreased in GhSCL13-2A knockdowns. At the gene expression level, PR genes and SA signaling marker genes were down-regulated and JA signaling marker genes were upregulated in GhSCL13-2A knockdowns. GhSCL13-2A was shown to be localized to the cell membrane and the nucleus. Yeast two-hybrid and luciferase complementation assays indicated that GhSCL13-2A interacted with GhERF5. In Arabidopsis, V. dahliae resistance was enhanced by GhERF5 overexpression; in cotton, resistance was reduced in GhERF5 knockdowns. This study revealed a positive role of GhSCL13-2A in V. dahliae resistance, establishing it as a strong candidate gene for future breeding of V. dahliae-resistant cotton cultivars.
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Affiliation(s)
- Chen Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Li-Li Lu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National NanfanResearch Institute (Sanya), Chinese Academy ofAgricultural Sciences, Sanya, 572024, Hainan, China
| | - Shu-Ya Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yan-Peng Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Na Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wen-Jie Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Li Ma
- Agricultural Science Institute of the Third Division of Xinjiang Production and Construction Corps, Tumushuke, 843901, Xinjiang, China
| | - Xian-Hui Kong
- Agricultural Science Institute of the Third Division of Xinjiang Production and Construction Corps, Tumushuke, 843901, Xinjiang, China
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Zong-Ming Xie
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Yu-Xia Hou
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- College of Science, China Agricultural University, Beijing, 100193, China.
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9
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Bai Y, Liu H, Zhu K, Cheng ZM. Evolution and functional analysis of the GRAS family genes in six Rosaceae species. BMC PLANT BIOLOGY 2022; 22:569. [PMID: 36471247 PMCID: PMC9724429 DOI: 10.1186/s12870-022-03925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND GRAS genes formed one of the important transcription factor gene families in plants, had been identified in several plant species. The family genes were involved in plant growth, development, and stress resistance. However, the comparative analysis of GRAS genes in Rosaceae species was insufficient. RESULTS In this study, a total of 333 GRAS genes were identified in six Rosaceae species, including 51 in strawberry (Fragaria vesca), 78 in apple (Malus domestica), 41 in black raspberry (Rubus occidentalis), 59 in European pear (Pyrus communis), 56 in Chinese rose (Rosa chinensis), and 48 in peach (Prunus persica). Motif analysis showed the VHIID domain, SAW motif, LR I region, and PFYRE motif were considerably conserved in the six Rosaceae species. All GRAS genes were divided into 10 subgroups according to phylogenetic analysis. A total of 15 species-specific duplicated clades and 3 lineage-specific duplicated clades were identified in six Rosaceae species. Chromosomal localization presented the uneven distribution of GRAS genes in six Rosaceae species. Duplication events contributed to the expression of the GRAS genes, and Ka/Ks analysis suggested the purification selection as a major force during the evolution process in six Rosaceae species. Cis-acting elements and GO analysis revealed that most of the GRAS genes were associated with various environmental stress in six Rosaceae species. Coexpression network analysis showed the mutual regulatory relationship between GRAS and bZIP genes, suggesting the ability of the GRAS gene to regulate abiotic stress in woodland strawberry. The expression pattern elucidated the transcriptional levels of FvGRAS genes in various tissues and the drought and salt stress in woodland strawberry, which were verified by RT-qPCR analysis. CONCLUSIONS The evolution and functional analysis of GRAS genes provided insights into the further understanding of GRAS genes on the abiotic stress of Rosaceae species.
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Affiliation(s)
- Yibo Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Kaikai Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zong-Ming Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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10
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Fei X, Wang Y, Zheng Y, Shen X, E L, Ding J, Lai J, Song W, Zhao H. Identification of two new QTLs of maize (Zea mays L.) underlying kernel row number using the HNAU-NAM1 population. BMC Genomics 2022; 23:593. [PMID: 35971070 PMCID: PMC9380338 DOI: 10.1186/s12864-022-08793-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maize kernel row number (KRN) is one of the most important yield traits and has changed greatly during maize domestication and selection. Elucidating the genetic basis of KRN will be helpful to improve grain yield in maize. RESULTS Here, we measured KRN in four environments using a nested association mapping (NAM) population named HNAU-NAM1 with 1,617 recombinant inbred lines (RILs) that were derived from 12 maize inbred lines with a common parent, GEMS41. Then, five consensus quantitative trait loci (QTLs) distributing on four chromosomes were identified in at least three environments along with the best linear unbiased prediction (BLUP) values by the joint linkage mapping (JLM) method. These QTLs were further validated by the separate linkage mapping (SLM) and genome-wide association study (GWAS) methods. Three KRN genes cloned through the QTL assay were found in three of the five consensus QTLs, including qKRN1.1, qKRN2.1 and qKRN4.1. Two new QTLs of KRN, qKRN4.2 and qKRN9.1, were also identified. On the basis of public RNA-seq and genome annotation data, five genes highly expressed in ear tissue were considered candidate genes contributing to KRN. CONCLUSIONS This study carried out a comprehensive analysis of the genetic architecture of KRN by using a new NAM population under multiple environments. The present results provide solid information for understanding the genetic components underlying KRN and candidate genes in qKRN4.2 and qKRN9.1. Single-nucleotide polymorphisms (SNPs) closely linked to qKRN4.2 and qKRN9.1 could be used to improve inbred yield during molecular breeding in maize.
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Affiliation(s)
- Xiaohong Fei
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.,Longping Agriculture Science Co. Ltd, Beijing, 100004, People's Republic of China
| | - Yifei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunxiao Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xiaomeng Shen
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lizhu E
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Junqiang Ding
- State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China. .,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Haiming Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China. .,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.
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11
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Jaiswal V, Kakkar M, Kumari P, Zinta G, Gahlaut V, Kumar S. Multifaceted Roles of GRAS Transcription Factors in Growth and Stress Responses in Plants. iScience 2022; 25:105026. [PMID: 36117995 PMCID: PMC9474926 DOI: 10.1016/j.isci.2022.105026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mrinalini Kakkar
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Priya Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Corresponding author
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
- Corresponding author
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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12
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Luo Z, Zhou Z, Li Y, Tao S, Hu ZR, Yang JS, Cheng X, Hu R, Zhang W. Transcriptome-based gene regulatory network analyses of differential cold tolerance of two tobacco cultivars. BMC PLANT BIOLOGY 2022; 22:369. [PMID: 35879667 PMCID: PMC9316383 DOI: 10.1186/s12870-022-03767-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 07/20/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cold is one of the main abiotic stresses that severely affect plant growth and development, and crop productivity as well. Transcriptional changes during cold stress have already been intensively studied in various plant species. However, the gene networks involved in the regulation of differential cold tolerance between tobacco varieties with contrasting cold resistance are quite limited. RESULTS Here, we conducted multiple time-point transcriptomic analyses using Tai tobacco (TT, cold susceptibility) and Yan tobacco (YT, cold resistance) with contrasting cold responses. We identified similar DEGs in both cultivars after comparing with the corresponding control (without cold treatment), which were mainly involved in response to abiotic stimuli, metabolic processes, kinase activities. Through comparison of the two cultivars at each time point, in contrast to TT, YT had higher expression levels of the genes responsible for environmental stresses. By applying Weighted Gene Co-Expression Network Analysis (WGCNA), we identified two main modules: the pink module was similar while the brown module was distinct between the two cultivars. Moreover, we obtained 100 hub genes, including 11 important transcription factors (TFs) potentially involved in cold stress, 3 key TFs in the brown module and 8 key TFs in the pink module. More importantly, according to the genetic regulatory networks (GRNs) between TFs and other genes or TFs by using GENIE3, we identified 3 TFs (ABI3/VP1, ARR-B and WRKY) mainly functioning in differential cold responses between two cultivars, and 3 key TFs (GRAS, AP2-EREBP and C2H2) primarily involved in cold responses. CONCLUSION Collectively, our study provides valuable resources for transcriptome- based gene network studies of cold responses in tobacco. It helps to reveal how key cold responsive TFs or other genes are regulated through network. It also helps to identify the potential key cold responsive genes for the genetic manipulation of tobacco cultivars with enhanced cold tolerance in the future.
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Affiliation(s)
- Zhenyu Luo
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Zhicheng Zhou
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Yangyang Li
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Zheng-Rong Hu
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Jia-Shuo Yang
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China.
| | - Risheng Hu
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China.
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China.
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13
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Sillo F, Brunetti C, Marroni F, Vita F, Dos Santos Nascimento LB, Vizzini A, Mello A, Balestrini R. Systemic effects of Tuber melanosporum inoculation in two Corylus avellana genotypes. TREE PHYSIOLOGY 2022; 42:1463-1480. [PMID: 35137225 DOI: 10.1093/treephys/tpac012] [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: 09/26/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Roots of the European hazelnut (Corylus avellana L.), i.e., one of the most economically important nut species, form symbiosis with ectomycorrhizal (ECM) fungi, including truffles. Although physical interactions only occur in roots, the presence of mycorrhizal fungi can lead to metabolic changes at a systemic level, i.e., in leaves. However, how root colonization by ECM fungi modifies these processes in the host plant has so far not been widely studied. This work aimed to investigate the response in two C. avellana genotypes, focusing on leaves from plants inoculated with the black truffle Tuber melanosporum Vittad. Transcriptomic profiles of leaves of colonized plants were compared with those of non-colonized plants, as well as sugar and polyphenolic content. Results suggested that T. melanosporum has the potential to support plants in stressed conditions, leading to the systemic regulation of several genes involved in signaling and defense responses. Although further confirmation is needed, our results open new perspectives for future research aimed to highlight novel aspects in ECM symbiosis.
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Affiliation(s)
- Fabiano Sillo
- National Research Council - Institute for Sustainable Plant Protection (CNR-IPSP), Strada della Cacce 73, 10135 Torino, Italy
| | - Cecilia Brunetti
- National Research Council - Institute for Sustainable Plant Protection (CNR-IPSP), Via Madonna del Piano 10, 50019 Firenze, Italy
| | - Fabio Marroni
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Federico Vita
- Department of Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | | | - Alfredo Vizzini
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
- National Research Council - Institute for Sustainable Plant Protection (CNR-IPSP), Viale Mattioli 25, 10125 Torino, Italy
| | - Antonietta Mello
- National Research Council - Institute for Sustainable Plant Protection (CNR-IPSP), Viale Mattioli 25, 10125 Torino, Italy
| | - Raffaella Balestrini
- National Research Council - Institute for Sustainable Plant Protection (CNR-IPSP), Strada della Cacce 73, 10135 Torino, Italy
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14
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Waseem M, Nkurikiyimfura O, Niyitanga S, Jakada BH, Shaheen I, Aslam MM. GRAS transcription factors emerging regulator in plants growth, development, and multiple stresses. Mol Biol Rep 2022; 49:9673-9685. [PMID: 35713799 DOI: 10.1007/s11033-022-07425-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
GRAS transcription factors play multifunctional roles in plant growth, development, and resistance to various biotic and abiotic stresses. The structural and functional features of GRAS TFs have been unveiled in the last two decades. A typical GRAS protein contained a C-terminal GRAS domain with a highly variable N-terminal region. Studies on these TFs increase in numbers and are reported to be involved in various important developmental processes such as flowering, root formation, and stress responses. The GRAS TFs and hormone signaling crosstalk can be implicated in plant development and to stress responses. There are relatively few reports about GRAS TFs roles in plants, and no related reviews have been published. In this review, we summarized the features of GRAS TFs, their targets, and the roles these GRAS TFs playing in plant development and multiple stresses.
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Affiliation(s)
- Muhammad Waseem
- Department of Botany, University of Narowal, Narowal, Punjab, Pakistan. .,College of Life Science, Hainan University, Hainan, P.R. China.
| | - Oswald Nkurikiyimfura
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Sylvain Niyitanga
- Department of Plant Pathology, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Bello Hassan Jakada
- College of Life Science, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Iffat Shaheen
- Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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15
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Zhang H, Tao H, Yang H, Zhang L, Feng G, An Y, Wang L. MdSCL8 as a Negative Regulator Participates in ALA-Induced FLS1 to Promote Flavonol Accumulation in Apples. Int J Mol Sci 2022; 23:ijms23042033. [PMID: 35216148 PMCID: PMC8875840 DOI: 10.3390/ijms23042033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 01/11/2023] Open
Abstract
Apples (Malus domestica) are rich in flavonols, and 5-aminolevulinic acid (ALA) plays an important role in the regulation of plant flavonoid metabolism. To date, the underlying mechanism of ALA promoting flavonol accumulation is unclear. Flavonol synthase (FLS) is a key enzyme in flavonol biosynthesis. In this study, we found that ALA could enhance the promoter activity of MdFLS1 in the ‘Fuji’ apple and improve its expression. With MdFLS1 as bait, we screened a novel transcription factor MdSCL8 by the Yeast One-Hybrid (Y1H) system from the apple cDNA library which we previously constructed. Using luciferase reporter assay and transient GUS activity assay, we verified that MdSCL8 inhibits the activity of MdFLS1 promoter and hinders MdFLS1 expression, thus reducing flavonol accumulation in apple. ALA significantly inhibited MdSCL8 expression. Therefore, ALA promoted the expression of MdFLS1 and the consequent flavonol accumulation probably by down-regulating MdSCL8. We also found that ALA significantly enhanced the gene expression of MdMYB22 and MdHY5, two positive regulators of MdFLS. We further demonstrated that MdMYB22 interacts with MdHY5, but neither of them interacts with MdSCL8. Taken together, our data suggest MdSCL8 as a novel regulator of MdFLS1 and provide important insights into mechanisms of ALA-induced flavonol accumulation in apples.
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16
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Beheshti H, Strotbek C, Arif MA, Klingl A, Top O, Frank W. PpGRAS12 acts as a positive regulator of meristem formation in Physcomitrium patens. PLANT MOLECULAR BIOLOGY 2021; 107:293-305. [PMID: 33598827 PMCID: PMC8648639 DOI: 10.1007/s11103-021-01125-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/01/2021] [Indexed: 05/29/2023]
Abstract
This study focused on the key regulatory function of Physcomitrium patens GRAS12 gene underlying an increasing plant complexity, an important step in plant terrestrialization and the evolutionary history of life. The miR171-GRAS module has been identified as a key player in meristem maintenance in angiosperms. PpGRAS12 is a member of the GRAS family and a validated target for miR171 in Physcomitrium (Physcomitrella) patens. Here we show a regulatory function of miR171 at the gametophytic vegetative growth stage and targeted deletion of the PpGRAS12 gene adversely affects sporophyte production since fewer sporophytes were produced in ΔPpGRAS12 knockout lines compared to wild type moss. Furthermore, highly specific and distinct growth arrests were observed in inducible PpGRAS12 overexpression lines at the protonema stage. Prominent phenotypic aberrations including the formation of multiple apical meristems at the gametophytic vegetative stage in response to elevated PpGRAS12 transcript levels were discovered via scanning electron microscopy. The production of multiple buds in the PpGRAS12 overexpression lines similar to ΔPpCLV1a/1b disruption mutants is accompanied by an upregulation of PpCLE and downregulation of PpCLV1, PpAPB, PpNOG1, PpDEK1, PpRPK2 suggesting that PpGRAS12 acts upstream of these genes and negatively regulates the proposed pathway to specify simplex meristem formation. As CLV signaling pathway components are not present in the chlorophytic or charophytic algae and arose with the earliest land plants, we identified a key regulatory function of PpGRAS12 underlying an increasing plant complexity, an important step in plant terrestrialization and the evolutionary history of life.
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Affiliation(s)
- Hossein Beheshti
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - Christoph Strotbek
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - M Asif Arif
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - Andreas Klingl
- Plant Developmental Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - Oguz Top
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany.
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17
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Laskar P, Bhattacharya S, Chaudhuri A, Kundu A. Exploring the GRAS gene family in common bean (Phaseolus vulgaris L.): characterization, evolutionary relationships, and expression analyses in response to abiotic stresses. PLANTA 2021; 254:84. [PMID: 34561734 DOI: 10.1007/s00425-021-03725-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Genome-wide identification reveals 55 PvuGRAS genes belonging to 16 subfamilies and their gene structures and evolutionary relationships were characterized. Expression analyses highlight their prominence in plant growth, development and abiotic stress responses. GRAS proteins comprise a plant-specific transcription factor family involved in multiple growth regulatory pathways and environmental cues including abiotic/biotic stresses. Despite its crucial importance, characterization of this gene family is still elusive in common bean. A systematic genome-wide scan identified 55 PvuGRAS genes unevenly anchored to the 11 common bean chromosomes. Segmental duplication appeared to be the key driving force behind expansion of this gene family that underwent purifying selection during evolution. Computational investigation unraveled their intronless organization and identified similar motif composition within the same subfamily. Phylogenetic analyses clustered the PvuGRAS proteins into 16 phylogenetic clades and established extensive orthologous relationships with Arabidopsis and rice. Analysis of the upstream promoter region uncovered cis-elements responsive to growth, development, and abiotic stresses that may account for their differential expression. The identified SSRs could serve as putative molecular markers facilitating future breeding programs. 37 PvuGRAS transcripts were post-transcriptionally regulated by different miRNA families, miR171 being the major player preferentially targeting members of the HAM subfamily. Global expression profile based on RNA-seq data indicates a clade specific expression pattern in various tissues and developmental stages. Additionally, nine PvuGRAS genes were chosen for further qPCR analyses under drought, salt, and cold stress suggesting their involvement in acclimation to environmental stimuli. Combined, the present results significantly contribute to the current understanding of the complexity and biological function of the PvuGRAS gene family. The resources generated will provide a solid foundation in future endeavors for genetic improvement in common bean.
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Affiliation(s)
- Parbej Laskar
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India
| | - Saswati Bhattacharya
- Department of Botany, Dr. A.P.J. Abdul Kalam Government College, New Town, Rajarhat, India
| | - Atreyee Chaudhuri
- Aquatic Bioresource Research Laboratory, Department of Zoology , University of Calcutta, Kolkata, India
| | - Anirban Kundu
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India.
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18
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Yang C, Marillonnet S, Tissier A. The scarecrow-like transcription factor SlSCL3 regulates volatile terpene biosynthesis and glandular trichome size in tomato (Solanum lycopersicum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1102-1118. [PMID: 34143914 DOI: 10.1111/tpj.15371] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 05/20/2023]
Abstract
Tomato (Solanum lycopersicum L.) type VI glandular trichomes that occur on the surface of leaves, stems, young fruits and flowers produce and store a blend of volatile monoterpenes and sesquiterpenes. These compounds play important roles in the interaction with pathogens and herbivorous insects. Although the function of terpene synthases in the biosynthesis of volatile terpenes in tomato has been comprehensively investigated, the deciphering of their transcriptional regulation is only just emerging. We selected transcription factors that are over-expressed in trichomes based on existing transcriptome data and silenced them individually by virus-induced gene silencing. Of these, SlSCL3, a scarecrow-like (SCL) subfamily transcription factor, led to a significant decrease in volatile terpene content and expression of the corresponding terpene synthase genes when its transcription level was downregulated. Overexpression of SlSCL3 dramatically increased both the volatile terpene content and glandular trichome size, whereas its homozygous mutants showed reduced terpene biosynthesis. However, its heterozygous mutants also showed a significantly elevated volatile terpene content and enlarged glandular trichomes, similar to the overexpression plants. SlSCL3 modulates the expression of terpene biosynthetic pathway genes by transcriptional activation, but neither direct protein-DNA binding nor interaction with known regulators was observed. Moreover, transcript levels of the endogenous copy of SlSCL3 were decreased in the overexpression plants but increased in the heterozygous and homozygous mutants, suggesting feedback repression of its own promoter. Taken together, our results provide new insights into the role of SlSCL3 in the complex regulation of volatile terpene biosynthesis and glandular trichome development in tomato.
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Affiliation(s)
- Changqing Yang
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, 266100, China
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
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Fan Y, Yan J, Lai D, Yang H, Xue G, He A, Guo T, Chen L, Cheng XB, Xiang DB, Ruan J, Cheng J. Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. BMC Genomics 2021; 22:509. [PMID: 34229611 PMCID: PMC8259154 DOI: 10.1186/s12864-021-07848-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of the sorghum genome, a plethora of genetic studies were mainly focused on the genomic information. The indepth identification or genome-wide analysis of GRAS family genes, especially in Sorghum bicolor, have rarely been studied. Results A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. We found that the contribution of tandem repeats to the increase in sorghum GRAS members was slightly greater than that of fragment repeats. By quantitative (q) RT-PCR, the expression of 13 SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. We further investigated the relationship between DELLA genes, GAs and grain development in S. bicolor. The paclobutrazol treatment significantly increased grain weight, and affected the expression levels of all DELLA subfamily genes. SbGRAS03 is the most sensitive to paclobutrazol treatment, but also has a high response to abiotic stresses. Conclusions Collectively, SbGRAs play an important role in plant development and response to abiotic stress. This systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07848-z.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, 610106, Chengdu, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Tianrong Guo
- Chengdu Institute of Food Inspection, 610030, Chengdu, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, 618200, Mianzhu, People's Republic of China
| | - Xiao-Bin Cheng
- Department of Environmental and Life Sciences, Sichuan MinZu College, 626001, Kangding, People's Republic of China
| | - Da-Bing Xiang
- School of Food and Biological engineering, Chengdu University, 610106, Chengdu, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China.
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20
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Lv G, Zheng X, Duan Y, Wen Y, Zeng B, Ai M, He B. The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations. PeerJ 2021; 9:e11526. [PMID: 34123598 PMCID: PMC8164414 DOI: 10.7717/peerj.11526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/06/2021] [Indexed: 01/22/2023] Open
Abstract
The family of GRAS plant-specific transcription factor plays diverse roles in numerous biological processes. Despite the identification and characterization of GRAS genes family in dozens of plant species, until now, GRAS members in watermelon (Citrullus lanatus) have not been investigated comprehensively. In this study, using bioinformatic analysis, we identified 37 GRAS genes in the watermelon genome (ClGRAS). These genes are classified into 10 distinct subfamilies based on previous research, and unevenly distributed on 11 chromosomes. Furthermore, a complete analysis was conducted to characterize conserved motifs and gene structures, which revealed the members within same subfamily that have analogous conserved gene structure and motif composition. Additionally, the expression pattern of ClGRAS genes was characterized in fruit flesh and rind tissues during watermelon fruit development and under red light (RL) as well as root knot nematode infestation. Finally, for verification of the availability of public transcriptome data, we also evaluated the expression levels of randomly selected four ClGRAS genes under RL and nematode infection by using qRT-PCR. The qRT-PCR results indicated that several ClGRAS genes were differentially expressed, implying their vital role in RL induction of watermelon resistance against root-knot nematodes. The results obtained in this study could be useful in improving the quality of watermelon.
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Affiliation(s)
- Gongbo Lv
- College of Life Sciences, Jiangxi Science & Technology Normal University, Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, Nanchang, Jiangxi, China
| | - Xing Zheng
- College of Life Sciences, Jiangxi Science & Technology Normal University, Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, Nanchang, Jiangxi, China
| | - Yitian Duan
- Renmin University of China, School of Information, Beijing, China
| | - Yunyong Wen
- College of Life Sciences, Jiangxi Science & Technology Normal University, Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, Nanchang, Jiangxi, China
| | - Bin Zeng
- College of Life Sciences, Jiangxi Science & Technology Normal University, Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, Nanchang, Jiangxi, China.,Shenzhen Technology University, College of Pharmacy, Shenzhen, Guangdong, China
| | - Mingqiang Ai
- College of Life Sciences, Jiangxi Science & Technology Normal University, Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, Nanchang, Jiangxi, China
| | - Bin He
- College of Life Sciences, Jiangxi Science & Technology Normal University, Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, Nanchang, Jiangxi, China
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21
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Kumar B, Bhalothia P. Evolutionary analysis of GRAS gene family for functional and structural insights into hexaploid bread wheat (Triticum aestivum). J Biosci 2021. [DOI: 10.1007/s12038-021-00163-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses. HORTICULTURAE 2020. [DOI: 10.3390/horticulturae6040110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) proteins are a family of plant-specific transcription factors that regulate plant growth, development, and stress response. Currently, the role of GRAS transcription factors in various abiotic stress responses has not been systematically studied in cucumber (Cucumis sativus L.), a popular vegetable crop. Here, we provide a comprehensive bioinformatics analysis of the 35 GRAS genes identified in the cucumber genome. In this study, cucumber genotypes, i.e., “CG104”, which is stress-tolerant, and genotype “CG37”, which is stress-sensitive, were examined to provide insight on potential differences in the GRAS-regulated abiotic stress pathways. Transcriptional analysis by RNA-seq or qRT-PCR of these two genotypes revealed common and divergent functions of CsGRAS genes regulated by low and high temperatures, salinity, and by exposure to the phytohormones gibberellin (GA) and abscisic acid (ABA). Notably, CsGRAS2 (DELLA) and CsGRAS26 (LISCL) were regulated by all abiotic stresses and hormone treatments, suggesting that they may function in the biological cross-talk between multiple signaling pathways. This study provides candidate genes for improving cucumber tolerance to various environmental stresses.
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23
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Lu X, Liu W, Xiang C, Li X, Wang Q, Wang T, Liu Z, Zhang J, Gao L, Zhang W. Genome-Wide Characterization of GRAS Family and Their Potential Roles in Cold Tolerance of Cucumber ( Cucumis sativus L.). Int J Mol Sci 2020; 21:E3857. [PMID: 32485801 PMCID: PMC7312588 DOI: 10.3390/ijms21113857] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cucumber (Cucumis sativus L.) is one of the most important cucurbit vegetables but is often subjected to stress during cultivation. GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) genes encode a family of transcriptional factors that regulate plant growth and development. In the model plant Arabidopsis thaliana, GRAS family genes function in formation of axillary meristem and root radial structure, phytohormone (gibberellin) signal transduction, light signal transduction and abiotic/biological stress. In this study, a gene family was comprehensively analyzed from the aspects of evolutionary tree, gene structure, chromosome location, evolutionary and expression pattern by means of bioinformatics; 37 GRAS gene family members have been screened from cucumber. We reconstructed an evolutionary tree based on multiple sequence alignment of the typical GRAS domain and conserved motif sequences with those of other species (A. thaliana and Solanum lycopersicum). Cucumber GRAS family was divided into 10 groups according to the classification of Arabidopsis and tomato genes. We conclude that tandem and segmental duplication have played important roles in the expansion and evolution of the cucumber GRAS (CsaGRAS) family. Expression patterns of CsaGRAS genes in different tissues and under cold treatment, combined with gene ontology annotation and interaction network analysis, revealed potentially different functions for CsaGRAS genes in response to cold tolerance, with members of the SHR, SCR and DELLA subfamilies likely playing important roles. In conclusion, this study provides valuable information and candidate genes for improving cucumber tolerance to cold stress.
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Affiliation(s)
- Xiaohong Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Chenggang Xiang
- College of Life Science and Technology, HongHe University, Mengzi 661100, China;
| | - Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Qing Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Tao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Zixi Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Jiali Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
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24
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Genome-Wide Analysis of the GRAS Gene Family in Barley ( Hordeum vulgare L.). Genes (Basel) 2020; 11:genes11050553. [PMID: 32423019 PMCID: PMC7290968 DOI: 10.3390/genes11050553] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 11/16/2022] Open
Abstract
The GRAS (named after first three identified proteins within this family, GAI, RGA, and SCR) family contains plant-specific genes encoding transcriptional regulators that play a key role in gibberellin (GA) signaling, which regulates plant growth and development. Even though GRAS genes have been characterized in some plant species, little research is known about the GRAS genes in barley (Hordeum vulgare L.). In this study, we observed 62 GRAS members from barley genome, which were grouped into 12 subgroups by using phylogenomic analysis together with the GRAS genes from Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). Chromosome localization and gene structure analysis suggested that duplication events and abundant presence of intronless genes might account for the massive expansion of GRAS gene family in barley. The analysis of RNA-seq data indicates the expression pattern of GRAS genes in various tissues at different stages in barley. Noteworthy, our qRT-PCR analysis showed the expression of 18 candidate GRAS genes abundantly in the developing inflorescence, indicating their potential roles in the barley inflorescence development and reproduction. Collectively, our evolutionary and expression analysis of GRAS family are useful for future functional characterization of GA signaling in barley and agricultural improvement.
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25
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Wang N, Wang K, Li S, Jiang Y, Li L, Zhao M, Jiang Y, Zhu L, Wang Y, Su Y, Wang Y, Zhang M. Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer. PLANTS 2020; 9:plants9020190. [PMID: 32033157 PMCID: PMC7076401 DOI: 10.3390/plants9020190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 11/22/2022]
Abstract
GRAS transcription factors are a kind of plant-specific transcription factor that have been found in a variety of plants. According to previous studies, GRAS proteins are widely involved in the physiological processes of plant signal transduction, stress, growth and development. The Jilin ginseng (Panax ginseng C.A. Meyer) is a heterogeneous tetraploid perennial herb of the Araliaceae family, ginseng genus. Important information regarding the GRAS transcription factors has not been reported in ginseng. In this study, 59 Panax ginseng GRAS (PgGRAS) genes were obtained from the Jilin ginseng transcriptome data and divided into 13 sub-families according to the classification of Arabidopsis thaliana. Through systematic evolution, structural variation, function and gene expression analysis, we further reveal GRAS’s potential function in plant growth processes and its stress response. The expression of PgGRAS genes responding to gibberellin acids (GAs) suggests that these genes could be activated after application concentration of GA. The qPCR analysis result shows that four PgGRAS genes belonging to the DELLA sub-family potentially have important roles in the GA stress response of ginseng hairy roots. This study provides not only a preliminary exploration of the potential functions of the GRAS genes in ginseng, but also valuable data for further exploration of the candidate PgGRAS genes of GA signaling in Jilin ginseng, especially their roles in ginseng hairy root development and GA stress response.
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Affiliation(s)
- Nan Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Shaokun Li
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Yang Jiang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Li Li
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Lei Zhu
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Yanfang Wang
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yingjie Su
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
- Correspondence: (Y.W.); (M.Z.)
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
- Correspondence: (Y.W.); (M.Z.)
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Interaction between the Circadian Clock and Regulators of Heat Stress Responses in Plants. Genes (Basel) 2020; 11:genes11020156. [PMID: 32024106 PMCID: PMC7074488 DOI: 10.3390/genes11020156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
The circadian clock is found ubiquitously in nature, and helps organisms coordinate internal biological processes with environmental cues that inform the time of the day or year. Both temperature stress and the clock affect many important biological processes in plants. Specifically, clock-controlled gene regulation and growth are impacted by a compromised clock or heat stress. The interactions linking these two regulatory pathways include several rhythmic transcription factors that are important for coordinating the appropriate response to temperature stress. Here we review the current understanding of clock control of the regulators involved in heat stress responses in plants.
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27
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Shan Z, Luo X, Wu M, Wei L, Fan Z, Zhu Y. Genome-wide identification and expression of GRAS gene family members in cassava. BMC PLANT BIOLOGY 2020; 20:46. [PMID: 31996133 PMCID: PMC6990482 DOI: 10.1186/s12870-020-2242-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/08/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Cassava is highly tolerant to stressful conditions, especially drought stress conditions; however, the mechanisms underlying this tolerance are poorly understood. The GRAS gene family is a large family of transcription factors that are involved in regulating the growth, development, and stress responses of plants. Currently, GRAS transcription factors have not been systematically studied in cassava, which is the sixth most important crop in the world. RESULTS Seventy-seven MeGRAS genes were identified from the cassava genome database. Phylogenetic analysis revealed that the MeGRAS proteins could be divided into 14 subfamilies. The gene structure and motif compositions of the proteins were considerably conserved within the same subfamily. Duplication events, particularly segmental duplication, were identified as the main driving force for GRAS gene expansion in cassava. Global expression analysis revealed that MeGRAS genes exhibited similar or distinct expression profiles within different tissues among different varieties. Moreover, qRT-PCR analysis revealed the expression patterns of MeGRAS genes in response to abiotic stress (drought, salt, cold, and H2O2), and the results suggest that these genes may have multiple functions. CONCLUSION This study is the first to provide comprehensive information on GRAS gene family members in cassava. The data will increase our understanding of both the molecular basis and the effects of GRAS genes. In addition, the results will contribute further to identifying the responses to various environmental conditions and provide insights into the potential functions of GRAS genes.
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Affiliation(s)
- Zhongying Shan
- Agricultural College, Guangxi University, Nanning, 530005 China
- College of Ecology and Garden Architecture, Dezhou University, Dezhou, 253023 China
| | - Xinglu Luo
- Agricultural College, Guangxi University, Nanning, 530005 China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Nanning, 530004 China
| | - Meiyan Wu
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Limei Wei
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Zhupeng Fan
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Yanmei Zhu
- Agricultural College, Guangxi University, Nanning, 530005 China
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28
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Teng K, Teng W, Wen H, Yue Y, Guo W, Wu J, Fan X. PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome. BMC Genomics 2019; 20:789. [PMID: 31664898 PMCID: PMC6821003 DOI: 10.1186/s12864-019-6163-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 10/09/2019] [Indexed: 12/19/2022] Open
Abstract
Background Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts. Results In this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing. Conclusions This study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis.
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Affiliation(s)
- Ke Teng
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Wenjun Teng
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Haifeng Wen
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Yuesen Yue
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Weier Guo
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Juying Wu
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Xifeng Fan
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
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Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry ( Fragaria vesca). Int J Mol Sci 2019; 20:ijms20184593. [PMID: 31533278 PMCID: PMC6770801 DOI: 10.3390/ijms20184593] [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] [Received: 08/25/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/17/2022] Open
Abstract
The cultivated strawberry (Fragaria × ananassa), an allo-octoploid with non-climacteric fleshy fruits, is a popular Rosaceae horticultural crop worldwide that is mainly propagated via stolons during cultivation. Woodland strawberry (Fragaria vesca), one of the four diploid progenitor species of cultivated strawberry, is widely used as a model plant in the study of Rosaceae fruit trees, non-climacteric fruits and stolons. One GRAS transcription factor has been shown to regulate stolon formation; the other GRAS proteins in woodland strawberry remain unknown. In this study, we identified 54 FveGRAS proteins in woodland strawberry, and divided them into 14 subfamilies. Conserved motif analysis revealed that the motif composition of FveGRAS proteins was conserved within each subfamily, but diverged widely among subfamilies. We found 56 orthologous pairs of GRAS proteins between woodland strawberry and Arabidopsis thaliana, 47 orthologous pairs between woodland strawberry and rice and 92 paralogous pairs within woodland strawberry. The expression patterns of FveGRAS genes in various organs and tissues, and changes therein under cold, heat and GA3 treatments, were characterized using transcriptomic analysis. The results showed that 34 FveGRAS genes were expressed with different degrees in at least four organs, including stolons; only a few genes displayed organ-specific expression. The expression levels of 16 genes decreased, while that of four genes increased during fruit ripening; FveGRAS54 showed the largest increase in expression. Under cold, heat and GA3 treatments, around half of the FveGRAS genes displayed increased or decreased expression to some extent, suggesting differing functions of these FveGRAS genes in the responses to cold, heat and GAs. This study provides insight into the potential functions of FveGRAS genes in woodland strawberry. A few FveGRAS genes were identified as candidate genes for further study, in terms of their functions in stolon formation, fruit ripening and abiotic stresses.
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Genome-wide Identification, Classification, Expression and Duplication Analysis of GRAS Family Genes in Juglans regia L. Sci Rep 2019; 9:11643. [PMID: 31406208 PMCID: PMC6691012 DOI: 10.1038/s41598-019-48287-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/01/2019] [Indexed: 12/01/2022] Open
Abstract
Fifty-two GRAS genes are identified in walnut genome. Based on the evolutionary relationship and motif analysis, the walnut GRAS gene family was divided into eight subfamilies, and the sequence features analysis of JrGRAS proteins showed that the JrGRAS protein sequences were both conserved and altered during the evolutionary process. Gene duplication analysis indicated that seven GRAS genes in walnut have orthologous genes in other species, and five of them occurred duplicated events in walnut genome. Expression pattern analysis of the GRAS family genes in walnut showed that two JrGRAS genes (JrCIGRa-b and JrSCL28a) were differentially expressed between flower bud and leaf bud (p < 0.01), and two JrGRAS genes (JrCIGRa-b and JrSCL13b-d) were differentially expressed between the different development stages of flower buds transition (p < 0.01), besides, three hub genes (JrGAIa, JrSCL3f and JrSHRc) were identified by co-expression analysis, which suggested these GRAS genes may play an important role in regulating the development of apical meristem in walnut. This study laid a foundation for further understanding of the function of GRAS family genes in walnut.
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Niu X, Chen S, Li J, Liu Y, Ji W, Li H. Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1. BMC Genomics 2019; 20:635. [PMID: 31387534 PMCID: PMC6683515 DOI: 10.1186/s12864-019-5985-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background As one of the most important transcription factor families, GRAS proteins are involved in numerous regulatory processes, especially plant growth and development. However, they have not been systematically analyzed in Brachypodium distachyon, a new model grass. Results In this study, 48 BdGRAS genes were identified. Duplicated genes account for 41.7% of them and contribute to the expansion of this gene family. 33, 39, 35 and 35 BdGRAS genes were identified by synteny with their orthologs in rice, sorghum, maize and wheat genome, respectively, indicating close relationships among these species. Based on their phylogenic relationships to GRAS genes in rice and maize, BdGRAS genes can be divided into ten subfamilies in which members of the same subfamily showed similar protein sequences, conserved motifs and gene structures, suggesting possible conserved functions. Although expression variation is high, some BdGRAS genes are tissue-specific, phytohormones- or abiotic stresses-responsive, and they may play key roles in development, signal transduction pathways and stress responses. In addition, DELLA genes BdSLR1 and BdSLRL1 were functionally characterized to play a role in plant growth via the GA signal pathway, consistent with GO annotations and KEGG pathway analyses. Conclusions Systematic analyses of BdGRAS genes indicated that members of the same subfamily may play similar roles. This was supported by the conserved functions of BdSLR1 and BdSLRL1 in GA pathway. These results laid a foundation for further functional elucidation of BdGRAS genes, especially, BdSLR1 and BdSLRL1. Electronic supplementary material The online version of this article (10.1186/s12864-019-5985-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Jiawei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
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Muntha ST, Zhang L, Zhou Y, Zhao X, Hu Z, Yang J, Zhang M. Phytochrome A signal transduction 1 and CONSTANS-LIKE 13 coordinately orchestrate shoot branching and flowering in leafy Brassica juncea. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1333-1343. [PMID: 30578711 PMCID: PMC6576096 DOI: 10.1111/pbi.13057] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/22/2018] [Accepted: 12/04/2018] [Indexed: 05/21/2023]
Abstract
Branching is a major determinant of crop yield, and enables vigorous shoot growth and the production of a dense canopy. Phytochrome A signal transduction 1 (PAT1) positively regulates phytochrome A signal transduction in response to light, but its effects on branching remain unknown. In this study, we mapped PAT1, and revealed a previously unknown role related to branching and flowering in leafy Brassica juncea. Earlier and increased branching was observed when PAT1 expression was down-regulated, implying that PAT1 negatively regulates shoot branching. Additionally, down-regulated PAT1 expression reversed the inhibited branching induced by far-red light, suggesting PAT1 is involved in the shade avoidance response. PAT1 negatively regulated branching only after bud initiation. The observed interaction between PAT1 and BRC1 implied that PAT1 influences bud outgrowth in a BRC1-dependent manner. Biochemical and genetic evidence indicate that PAT1 directly interacts with CONSTANS-LIKE 13 (COL13), which negatively regulates flowering, with the resulting PAT1-COL13 complex mediating shoot branching and flowering. Our findings reveal a new crosstalk modality between phytochrome signalling and flowering pathways during the regulation of shoot branching and flowering. The data presented herein may be useful for future studies involving the editing of the GRAS family transcription factor PAT1 gene to enhance crop productivity and enable earlier harvesting.
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Affiliation(s)
- Sidra Tul Muntha
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable SciencesZhejiang UniversityHangzhouChina
| | - Lili Zhang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable SciencesZhejiang UniversityHangzhouChina
| | - Yufeng Zhou
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable SciencesZhejiang UniversityHangzhouChina
| | - Xuan Zhao
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable SciencesZhejiang UniversityHangzhouChina
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable SciencesZhejiang UniversityHangzhouChina
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Horticultural Plant Growth, Development & Quality ImprovementMinistry of AgricultureHangzhouChina
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhouChina
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Horticultural Plant Growth, Development & Quality ImprovementMinistry of AgricultureHangzhouChina
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhouChina
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Genome-wide identification, phylogeny and function analysis of GRAS gene family in Dendrobium catenatum (Orchidaceae). Gene 2019; 705:5-15. [PMID: 30999026 DOI: 10.1016/j.gene.2019.04.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND In recent years, the molecular mechanism of plant growth and development has been reported in detail. GRAS genes, a plant-specific family of transcription factor, play critical roles in the process. GRAS transcription factors are associated with axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic or biotic stress. OBJECTIVE Here, we firstly investigated GRAS gene family in Dendrobium catenatum, an important medicinal and flowering orchid in China. METHODS The GRAS gene family in D. catenatum was cloned based on RNA-Seq data. Selected GRAS genes were introduced into Escherichia coli to express proteins. RESULTS Based on phylogenetic relationship with the Arabidopsis and Oryza GRAS family members, 47 GRAS genes from D. catenatum are identified and their deduced proteins are classified into 11 subgroups. Most of these GRAS genes contain one exon and closely related members in the phylogenetic tree have similar motif composition. Our result also reveals that GRAS genes in D. catenatum are widely distributed and expressed in different tissue. In addition, 35 GRAS genes are successfully cloned from different subgroups and 7 DoGRAS fusion proteins are induced using E. coli system. Moreover, 8 genes were up-regulated in different tissue following exposure to heat and salt stresses. CONCLUSION Our findings provide valuable information and candidate genes for future functional analysis for improving the resistance of D. catenatum growth.
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Wang S, Zhang N, Zhu X, Yang J, Li S, Che Y, Liu W, Si H. Identification and expression analysis of StGRAS gene family in potato (Solanum tuberosum L.). Comput Biol Chem 2019; 80:195-205. [PMID: 30978571 DOI: 10.1016/j.compbiolchem.2019.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 03/21/2019] [Accepted: 03/24/2019] [Indexed: 12/25/2022]
Abstract
The GRAS gene family is a class of plant-specific transcription factors which play pivotal roles in the regulation of plant growth and development. At present, the GRAS gene family has been completely identified in Arabidopsis thaliana, however, there are no systematic research reports in potato. In the present study, we obtained an overview of the GRAS gene family including gene structure, gene expression, chromosome mapping and phylogenetic analysis, and 52 StGRASs were identified in the potato by bioinformatics analysis, which could be divided into eight subfamilies based on phylogeny. More than 90% of genes do not contain introns and the StGRAS family major function is protein binding according to gene ontology analysis (GO).The tissue specific expression analysis showed that StGRAS3, StGRAS35 and StGRAS50 gene had the higher expression in roots, stems and leaves compared with other StGRAS, StGRAS9 and StGRAS28 genes were responded to plant hormones IAA, ABA and GA3 treatment. The result could provide a basis for further studying the function of GRAS genes and GRAS-mediated signal transduction pathways in potato.
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Affiliation(s)
- Shulin Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xi Zhu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangwei Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Shigui Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhang Che
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Weigang Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Huaijun Si
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China.
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Li M, Sun B, Xie F, Gong R, Luo Y, Zhang F, Yan Z, Tang H. Identification of the GRAS gene family in the Brassica juncea genome provides insight into its role in stem swelling in stem mustard. PeerJ 2019; 7:e6682. [PMID: 30972257 PMCID: PMC6448559 DOI: 10.7717/peerj.6682] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/12/2019] [Indexed: 12/18/2022] Open
Abstract
GRAS transcription factors are known to play important roles in plant signal transduction and development. A comprehensive study was conducted to explore the GRAS family in the Brassica juncea genome. A total of 88 GRAS genes were identified which were categorized into nine groups according to the phylogenetic analysis. Gene structure analysis showed a high group-specificity, which corroborated the gene grouping results. The chromosome distribution and sequence analysis suggested that gene duplication events are vital for the expansion of GRAS genes in the B. juncea genome. The changes in evolution rates and amino acid properties among groups might be responsible for their functional divergence. Interaction networks and cis-regulatory elements were analyzed including DELLA and eight interaction proteins (including four GID1, two SLY1, and two PIF3 proteins) that are primarily involved in light and hormone signaling. To understand their regulatory role in growth and development, the expression profiles of BjuGRASs and interaction genes were examined based on transcriptome data and qRT-PCR, and selected genes (BjuGRAS3, 5, 7, 8, 10, BjuB006276, BjuB037910, and BjuA021658) had distinct temporal expression patterns during stem swelling, indicating that they possessed diverse regulatory functions during the developmental process. These results contribute to our understanding on the GRAS gene family and provide the basis for further investigations on the evolution and functional characterization of GRAS genes.
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Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Fangjie Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ronggao Gong
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zesheng Yan
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
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Zhang H, Mi L, Xu L, Yu C, Li C, Chen C. Genome-wide identification, characterization, interaction network and expression profile of GRAS gene family in sweet orange (Citrus sinensis). Sci Rep 2019; 9:2156. [PMID: 30770885 PMCID: PMC6377710 DOI: 10.1038/s41598-018-38185-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/16/2018] [Indexed: 12/31/2022] Open
Abstract
GRAS genes are suggested to be grouped into plant-specific transcriptional regulatory families that have been reported to participate in multiple processes, including plant development, phytohormone signaling, the formation of symbiotic relationships, and response to environmental signals. GRAS genes have been characterized in a number of plant species, but little is known about this gene family in Citrus sinensis. In this study, we identified a total of 50 GRAS genes and characterized the gene structures, conserved motifs, genome localizations and cis-elements within their promoter regions. According to their structural and phylogenetic features, the identified sweet orange GRAS members were divided into 11 subgroups, of which subfamily CsGRAS34 was sweet orange-specific. Based on publicly available RNA-seq data generated from callus, flower, leaf and fruit in sweet orange, we found that some sweet orange GRAS genes exhibited tissue-specific expression patterning. Three of the six members of subfamily AtSHR, particularly CsGRAS9, and two of the six members of subfamily AtPAT1 were preferentially expressed in leaf. Moreover, protein-protein interactions with CsGRAS were predicted. Gene expression analysis was performed under conditions of phosphate deficiency, and GA3 and NaCl treatment to identify the potential functions of GRAS members in regulating stress and hormone responses. This study provides the first comprehensive understanding of the GRAS gene family in the sweet orange genome. As such, the study generates valuable information for further gene function analysis and identifying candidate genes to improve abiotic stress tolerance in citrus plants.
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Affiliation(s)
- Hua Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Limin Mi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Long Xu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changxiu Yu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chen Li
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. .,Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China.
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Zhou S, Hu Z, Li F, Yu X, Naeem M, Zhang Y, Chen G. Manipulation of plant architecture and flowering time by down-regulation of the GRAS transcription factor SlGRAS26 in Solanum lycopersicum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:81-93. [PMID: 29650160 DOI: 10.1016/j.plantsci.2018.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 05/03/2023]
Abstract
Previous studies suggest that GRAS transcription factors act as essential regulators, not only in plant growth and development but also in response to biotic and abiotic stresses. Recently, 53 GRAS proteins have been identified, but only a few of them have been functionally studied in tomato. Here, we isolated a novel GRAS transcription factor SlGRAS26, its down-regulation generated pleiotropic phenotypes, including reduced plant height with more lateral shoots, internode length, leaf size, even leaflets, accelerated flowering transition and decreased trichome number. Transcription analysis showed that down-regulation of SlGRAS26 altered vegetative growth by suppressing gibberellin (GA) biosynthesis genes and activating the GA inactivating genes, thereby reducing endogenous GA content in transgenic plants. SlGRAS26 may regulate the initiation of lateral buds by regulating the expression of Blind (BL) and BRC1b. The earlier initiation of flower buds in transgenic lines may be controlled by significant up-regulation of SFT, CO1, SBP3, SBP13, and SBP15 genes, related to flowering time. These results demonstrate that SlGRAS26 may play a vital role in the initiation of lateral and inflorescence meristems in tomato.
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Affiliation(s)
- Shengen Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Fenfen Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Xiaohui Yu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Muhammad Naeem
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Yanjie Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
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Li M, Wang X, Li C, Li H, Zhang J, Ye Z. Silencing GRAS2 reduces fruit weight in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:498-513. [PMID: 29359472 DOI: 10.1111/jipb.12636] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
GRAS family transcription factors are involved in multiple biological processes in plants. Here, we report that GRAS2 plays a vital role in regulating fruit weight in tomato (Solanum lycopersicum). We establish that the expression of GRAS2 was elevated in ovaries and maintained at a constant level in fertilized ovules. Reduction of GRAS2 expression in transgenic plants reduced fruit weight through modulating ovary growth and cell size. At the metabolic level, downregulation of GRAS2 decreased activities of the gibberellic acid biosynthesis and signal transduction pathways, leading to insufficient levels of active gibberellic acid during the initial ovary development of tomato. Moreover, genotypic diversity of GRAS2 was consistent with the molecular basis of fruit weight evolution, suggesting that GRAS2 contributes to the molecular basis of the evolution of fruit weight in tomato. Collectively, these findings enhance our understanding of GRAS2 functions, in fruit development of tomato, and demonstrate a strong association between the GRAS gene family and fruit development.
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Affiliation(s)
- Miao Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Changxing Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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Wang YX, Liu ZW, Wu ZJ, Li H, Wang WL, Cui X, Zhuang J. Genome-wide identification and expression analysis of GRAS family transcription factors in tea plant (Camellia sinensis). Sci Rep 2018; 8:3949. [PMID: 29500448 PMCID: PMC5834537 DOI: 10.1038/s41598-018-22275-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 02/20/2018] [Indexed: 12/16/2022] Open
Abstract
GRAS proteins are important transcription factors that play multifarious roles in regulating the growth and development as well as stress responses of plants. Tea plant is an economically important leaf -type beverage crop. Information concerning GRAS family transcription factors in tea plant is insufficient. In this study, 52 CsGRAS genes encoding GRAS proteins were identified from tea plant genome database. Phylogenetic analysis of the identified GRAS proteins from tea plant, Arabidopsis, and rice divided these proteins into at least 13 subgroups. Conserved motif analysis revealed that the gene structure and motif compositions of the proteins were considerably conserved among the same subgroup. Functional divergence analysis indicated that the shifted evolutionary rate might act as a major evolutionary force driving subfamily-specific functional diversification. Transcriptome analysis showed that the transcriptional levels of CsGRAS genes under non-stress conditions varied among different tea plant cultivars. qRT-PCR analysis revealed tissue and development stage-specific expression patterns of CsGRAS genes in tea plant. The expression patterns of CsGRAS genes in response to abiotic stresses and gibberellin treatment suggested the possible multiple functions of these genes. This study provides insights into the potential functions of GRAS genes.
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Affiliation(s)
- Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Jun Wu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen-Li Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Cui
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Heyman J, Canher B, Bisht A, Christiaens F, De Veylder L. Emerging role of the plant ERF transcription factors in coordinating wound defense responses and repair. J Cell Sci 2018; 131:jcs.208215. [PMID: 29242229 DOI: 10.1242/jcs.208215] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
Plants react to wounding through the activation of both defense and repair pathways, but how these two responses are coordinated is unclear. Here, we put forward the hypothesis that diverse members of the subfamily X of the plant-specific ethylene response factor (ERF) transcription factors coordinate stress signaling with the activation of wound repair mechanisms. Moreover, we highlight the observation that tissue repair is strongly boosted through the formation of a heterodimeric protein complex that comprises ERF and transcription factors of the GRAS domain type. This interaction turns ERFs into highly potent and stress-responsive activators of cell proliferation. The potency to induce stem cell identity suggests that these heterodimeric transcription factor complexes could become valuable tools to increase crop regeneration and transformation efficiency.
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Affiliation(s)
- Jefri Heyman
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Balkan Canher
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Anchal Bisht
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Fien Christiaens
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Lieven De Veylder
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
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41
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Li P, Zhang B, Su T, Li P, Xin X, Wang W, Zhao X, Yu Y, Zhang D, Yu S, Zhang F. BrLAS, a GRAS Transcription Factor From Brassica rapa, Is Involved in Drought Stress Tolerance in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1792. [PMID: 30574156 PMCID: PMC6291521 DOI: 10.3389/fpls.2018.01792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/19/2018] [Indexed: 05/20/2023]
Abstract
GRAS proteins belong to a plant-specific transcription factor family and play roles in diverse physiological processes and environmental signals. In this study, we identified and characterized a GRAS transcription factor gene in Brassica rapa, BrLAS, an ortholog of Arabidopsis AtLAS. BrLAS was primarily expressed in the roots and axillary meristems, and localized exclusively in the nucleus of B. rapa protoplast cells. qRT-PCR analysis indicated that BrLAS was upregulated by exogenous abscisic acid (ABA) and abiotic stress treatment [polyethylene glycol (PEG), NaCl, and H2O2]. BrLAS-overexpressing Arabidopsis plants exhibited pleiotropic characteristics, including morphological changes, delayed bolting and flowering time, reduced fertility and delayed senescence. Transgenic plants also displayed significantly enhanced drought resistance with decreased accumulation of ROS and increased antioxidant enzyme activity under drought treatment compared with the wild-type. Increased sensitivity to exogenous ABA was also observed in the transgenic plants. qRT-PCR analysis further showed that expression of several genes involved in stress responses and associated with leaf senescence were also modified. These findings suggest that BrLAS encodes a stress-responsive GRASs transcription factor that positively regulates drought stress tolerance, suggesting a role in breeding programs aimed at improving drought tolerance in plants.
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Affiliation(s)
- Pan Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Bin Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- *Correspondence: Shuancang Yu, Fenglan Zhang,
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- *Correspondence: Shuancang Yu, Fenglan Zhang,
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42
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Niu Y, Zhao T, Xu X, Li J. Genome-wide identification and characterization of GRAS transcription factors in tomato ( Solanum lycopersicum). PeerJ 2017; 5:e3955. [PMID: 29134140 PMCID: PMC5681854 DOI: 10.7717/peerj.3955] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/03/2017] [Indexed: 11/20/2022] Open
Abstract
Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time. The GRAS genes among tomato, Arabidopsis, rice, and grapevine were rebuilt to form a phylogenomic tree, which was divided into ten groups according to the previous classification of Arabidopsis and rice. A multiple sequence alignment exhibited the typical GRAS domain and conserved motifs similar to other gene families. Both the segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in tomato; the expression patterns across a variety of tissues and biotic conditions revealed potentially different functions of GRAS genes in tomato development and stress responses. Altogether, this study provides valuable information and robust candidate genes for future functional analysis for improving the resistance of tomato growth.
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Affiliation(s)
- Yiling Niu
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Tingting Zhao
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Xiangyang Xu
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Jingfu Li
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
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43
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Identification and expression of GRAS family genes in maize (Zea mays L.). PLoS One 2017; 12:e0185418. [PMID: 28957440 PMCID: PMC5619761 DOI: 10.1371/journal.pone.0185418] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 09/12/2017] [Indexed: 02/01/2023] Open
Abstract
GRAS transcriptional factors have diverse functions in plant growth and development, and are named after the first three transcription factors, namely, GAI (GIBBERELLIC ACID INSENSITIVE), RGA (REPRESSOR OF GAI) and SCR (SCARECROW) identified in this family. Knowledge of the GRAS gene family in maize remains was largely unknown, and their characterization is necessary to understand their importance in the maize life cycle. This study identified 86 GRAS genes in maize, and further characterized with phylogenetics, gene structural analysis, genomic loci, and expression patterns. The 86 GRAS genes were divided into 8 groups (SCL3, HAM, LS, SCR, DELLA, SHR, PAT1 and LISCL) by phylogenetic analysis. Most of the maize GRAS genes contain one exon (80.23%) and closely related members in the phylogenetic tree had similar structure and motif composition. Different motifs especially in the N-terminus might be the sources of their functional divergence. Segmental- and tandem-duplication occurred in this family leading to expansion of maize GRAS genes and the expression patterns of the duplicated genes in the heat map according to the published microarray data were very similar. Quantitative RT-PCR (qRT-PCR) results demonstrated that the expression level of genes in different tissues were different, suggesting their differential roles in plant growth and development. The data set expands our knowledge to understanding the function of GRAS genes in maize, an important crop plant in the world.
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44
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Bai Z, Xia P, Wang R, Jiao J, Ru M, Liu J, Liang Z. Molecular cloning and characterization of five SmGRAS genes associated with tanshinone biosynthesis in Salvia miltiorrhiza hairy roots. PLoS One 2017; 12:e0185322. [PMID: 28953930 PMCID: PMC5617194 DOI: 10.1371/journal.pone.0185322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/11/2017] [Indexed: 01/31/2023] Open
Abstract
The gibberellin-responsive element binding factor (GRAS) family of proteins plays an important role in the transcriptional regulation of plant development and hormone signaling. To date, there are no reports on GRAS family proteins expressed in Salvia miltiorrhiza. In this study, 28 ESTs that contained the GRAS domain were identified from a S. miltiorrhiza cDNA library. Of these, full-length sequences of five genes were cloned and sequence analysis indicated that all five proteins contain only one GRAS domain and therefore, belong to the GRAS family. The five genes were designated S. miltiorrhiza GRAS1-5 (SmGRAS1-5), which belong to groups I (SmGRAS2 and SmGRAS4), II (SmGRAS3), III (SmGRAS1), and VIII (SmGRAS5) respectively. Additionally, SmGRAS1-5 have different expression patterns in the reed head, stems, leaves, flowers, and roots of S. miltiorrhiza. In this study, the expression of SmGRAS1-5 was sensitive to Gibberellin (GA) stress and that of SmGRAS1, SmGRAS4 and SmGRAS5 was sensitive to Ethephon (Eth) stress respectively. Moreover, S. miltiorrhiza copalyl diphosphate synthases 1 (SmCPS1) and S. miltiorrhiza kaurene synthase like 1 (SmKSL1), which are two key enzymes gene in the diterpenoid biosynthesis pathway, were also response to GA and Eth stress. In addition, Dihydrotanshinone (DT-I) and Tanshinone I (T-I) content were enhanced by GA and Eth stress, Tanshinone IIA (T-IIA) content was increased by GA stress, and the accumulation of Cryptotanshinone (CT) was insensitive to both GA and Eth stress. Together, these results provide insights into functional conservation and diversification of SmGRASs and are useful information for further elucidating SmGRAS functions.
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Affiliation(s)
- Zhenqing Bai
- College of Life Science, Northwest A&F University, Yangling, China
| | - Pengguo Xia
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ruilin Wang
- College of Life Science, Northwest A&F University, Yangling, China
| | - Jie Jiao
- College of Life Science, Northwest A&F University, Yangling, China
| | - Mei Ru
- College of Life Science, Northwest A&F University, Yangling, China
| | - Jingling Liu
- College of Life Science, Northwest A&F University, Yangling, China
| | - Zongsuo Liang
- College of Life Science, Northwest A&F University, Yangling, China
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, China
- * E-mail:
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45
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Zhang H, Cao Y, Shang C, Li J, Wang J, Wu Z, Ma L, Qi T, Fu C, Bai Z, Hu B. Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification. PLoS One 2017; 12:e0185439. [PMID: 28945786 PMCID: PMC5612761 DOI: 10.1371/journal.pone.0185439] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/12/2017] [Indexed: 12/20/2022] Open
Abstract
The GRAS gene family is a large plant-specific family of transcription factors that are involved in diverse processes during plant development. Medicago truncatula is an ideal model plant for genetic research in legumes, and specifically for studying nodulation, which is crucial for nitrogen fixation. In this study, 59 MtGRAS genes were identified and classified into eight distinct subgroups based on phylogenetic relationships. Motifs located in the C-termini were conserved across the subgroups, while motifs in the N-termini were subfamily specific. Gene duplication was the main evolutionary force for MtGRAS expansion, especially proliferation of the LISCL subgroup. Seventeen duplicated genes showed strong effects of purifying selection and diverse expression patterns, highlighting their functional importance and diversification after duplication. Thirty MtGRAS genes, including NSP1 and NSP2, were preferentially expressed in nodules, indicating possible roles in the process of nodulation. A transcriptome study, combined with gene expression analysis under different stress conditions, suggested potential functions of MtGRAS genes in various biological pathways and stress responses. Taken together, these comprehensive analyses provide basic information for understanding the potential functions of GRAS genes, and will facilitate further discovery of MtGRAS gene functions.
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Affiliation(s)
- Hailing Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yingping Cao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chen Shang
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Jikai Li
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Jianli Wang
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Zhenying Wu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Lichao Ma
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Tianxiong Qi
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Zetao Bai
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- * E-mail: (ZB); (BH)
| | - Baozhong Hu
- College of Life Science, Northeast Agricultural University, Harbin, China
- Harbin University, Harbin, China
- * E-mail: (ZB); (BH)
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46
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Liu H, Qin J, Fan H, Cheng J, Li L, Liu Z. Genome-wide identification, phylogeny and expression analyses of SCARECROW- LIKE( SCL) genes in millet ( Setaria italica). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:629-640. [PMID: 28878501 PMCID: PMC5567716 DOI: 10.1007/s12298-017-0455-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/13/2017] [Accepted: 05/29/2017] [Indexed: 06/04/2023]
Abstract
As a member of the GRAS gene family, SCARECROW-LIKE (SCL) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6-8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes. Several putative millet orthologous genes in Arabidopsis, maize and rice were identified. High throughput RNA sequencing revealed that the expressions of millet SCL genes in root, stem, leaf, spica, and along leaf gradient varied greatly. Analyses combining the gene expression patterns, gene structures, motif compositions, promoter cis-elements identification, alternative splicing of transcripts and phylogenetic relationship of SCL genes indicate that the these genes may play diverse functions. Functionally characterized SCL genes in maize, rice and Arabidopsis would provide us some clues for future characterization of their homologues in millet. To the best of our knowledge, this is the first study of millet SCL genes at the genome wide level. Our work provides a useful platform for functional analysis of SCL genes in millet, a model crop for C4 photosynthesis and bioenergy studies.
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Affiliation(s)
- Hongyun Liu
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Jiajia Qin
- School of Physical Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Hui Fan
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Jinjin Cheng
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Lin Li
- College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Zheng Liu
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
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47
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Wang G, Weng L, Li M, Xiao H. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato. Int J Mol Sci 2017; 18:E475. [PMID: 28257093 PMCID: PMC5372491 DOI: 10.3390/ijms18030475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/07/2017] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops.
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Affiliation(s)
- Guixiang Wang
- University of Chinese Academy of Sciences, 19A Yuquan Rd., Beijing 100049, China.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Lin Weng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Meng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Han Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
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48
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Computational identification and systematic classification of novel GRAS genes in Isatis indigotica. Chin J Nat Med 2016; 14:161-76. [PMID: 27025363 DOI: 10.1016/s1875-5364(16)30013-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 12/20/2022]
Abstract
Isatis indigotica Fort., belonging to Cruciferae, is one of the most commonly used plants in traditional Chinese medicine. The accumulation of the effective components of I. indigotica is related with its growth conditions. The GRAS genes are members of a multigene family of transcriptional regulators that play a crucial role in plant growth. Although the activities of many GRAS genes have long been recognized, only in recent years were some of them identified and functionally characterized in detail. In the present study, 41 GRAS genes were identified from I. indigotica through bioinformatics methods for the first time. They were classified into ten groups according to the classification of Arabidopsis and rice. The characterization, gene structure, conserved motifs, disordered N-terminal domains, and phylogenetic reconstruction of these GRASs were analyzed. Forty-three orthologous gene pairs were shared by I. indigotica and Arabidopsis, and interaction networks of these orthologous genes were constructed. Furthermore, gene expression patterns were investigated by analysis in methyl jasmonate (MeJA)-treated I. indigotica hairy roots based on RNA-seq data. In conclusion, this comprehensive analysis would provide rich resources for further studies of GRAS protein functions in this plant.
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49
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Heyman J, Cools T, Canher B, Shavialenka S, Traas J, Vercauteren I, Van den Daele H, Persiau G, De Jaeger G, Sugimoto K, De Veylder L. The heterodimeric transcription factor complex ERF115-PAT1 grants regeneration competence. NATURE PLANTS 2016; 2:16165. [PMID: 27797356 DOI: 10.1038/nplants.2016.165] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/28/2016] [Indexed: 05/17/2023]
Abstract
Regeneration of a tissue damaged by injury represents a physiological response for organ recovery1-3. Although this regeneration process is conserved across multicellular taxa, plants appear to display extremely high regenerative capacities, a feature widely used in tissue culture for clonal propagation and grafting4,5. Regenerated cells arise predominantly from pre-existing populations of division-competent cells6,7; however, the mechanisms by which these cells are triggered to divide in response to injury remain largely elusive8. Here, we demonstrate that the heterodimeric transcription factor complex ETHYLENE RESPONSE FACTOR115 (ERF115)-PHYTOCHROME A SIGNAL TRANSDUCTION1 (PAT1) sustains meristem function by promoting cell renewal after stem cell loss. High-resolution time-lapse imaging revealed that cell death promotes ERF115 activity in cells that are in direct contact with damaged cells, triggering divisions that replenish the collapsed stem cells. Correspondingly, the ERF115-PAT1 complex plays an important role in full stem cell niche recovery upon root tip excision, whereas its ectopic expression triggers neoplastic growth, correlated with activation of the putative target gene WOUND INDUCED DEDIFFERENTIATION1 (WIND1)9. We conclude that the ERF115-PAT1 complex accounts for the high regenerative potential of plants, granting them the ability to efficiently replace damaged cells with new ones.
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Affiliation(s)
- Jefri Heyman
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Toon Cools
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Balkan Canher
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Sviatlana Shavialenka
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jan Traas
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Ilse Vercauteren
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Hilde Van den Daele
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Keiko Sugimoto
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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50
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Grimplet J, Agudelo-Romero P, Teixeira RT, Martinez-Zapater JM, Fortes AM. Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses. FRONTIERS IN PLANT SCIENCE 2016; 7:353. [PMID: 27065316 PMCID: PMC4811876 DOI: 10.3389/fpls.2016.00353] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/07/2016] [Indexed: 05/18/2023]
Abstract
GRAS transcription factors are involved in many processes of plant growth and development (e.g., axillary shoot meristem formation, root radial patterning, nodule morphogenesis, arbuscular development) as well as in plant disease resistance and abiotic stress responses. However, little information is available concerning this gene family in grapevine (Vitis vinifera L.), an economically important woody crop. We performed a model curation of GRAS genes identified in the latest genome annotation leading to the identification of 52 genes. Gene models were improved and three new genes were identified that could be grapevine- or woody-plant specific. Phylogenetic analysis showed that GRAS genes could be classified into 13 groups that mapped on the 19 V. vinifera chromosomes. Five new subfamilies, previously not characterized in other species, were identified. Multiple sequence alignment showed typical GRAS domain in the proteins and new motifs were also described. As observed in other species, both segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in grapevine. Expression patterns across a variety of tissues and upon abiotic and biotic conditions revealed possible divergent functions of GRAS genes in grapevine development and stress responses. By comparing the information available for tomato and grapevine GRAS genes, we identified candidate genes that might constitute conserved transcriptional regulators of both climacteric and non-climacteric fruit ripening. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits.
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | | | - Rita T. Teixeira
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
| | - Jose M. Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | - Ana M. Fortes
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
- Instituto de Tecnologia de Química Biológica, Biotecnologia de Células VegetaisOeiras, Portugal
- *Correspondence: Ana M. Fortes
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