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Han S, Han X, Li Y, Guo F, Qi C, Liu Y, Fang S, Yin J, Zhu Y. Genome-wide characterization and function analysis of ginger (Zingiber officinale Roscoe) ZoGRFs in responding to adverse stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108392. [PMID: 38301328 DOI: 10.1016/j.plaphy.2024.108392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024]
Abstract
Growth-regulating factors (GRFs) play crucial roles in plant growth, development, hormone signaling, and stress response. Despite their significance, the roles of GRFs in ginger remain largely unknown. Herein, 31 ginger ZoGRFs were identified and designated as ZoGRF1-ZoGRF31 according to their phylogenetic relationships. All ZoGRFs were characterized as unstable, hydrophilic proteins, with 29 predicted to be located in the nucleus. Functional cis-elements related to growth and development were enriched in ZoGRF's promoter regions. RNA-seq and RT-qPCR analysis revealed that ZoGRF12, ZoGRF24, and ZoGRF28 were highly induced in various growth and development stages, displaying differential regulation under waterlogging, chilling, drought, and salt stresses, indicating diverse expression patterns of ZoGRFs. Transient expression analysis in Nicotiana benthamiana indicated that overexpressing ZoGRF28 regulated the transcription levels of salicylic acid, jasmonic acid, and pattern-triggered immunity-related genes, increased chlorophyll content and contributed to reduced disease lesions and an increased net photosynthetic rate. This research lays the foundation for further understanding the biological roles of ZoGRFs.
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Affiliation(s)
- Shuo Han
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Xiaowen Han
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yiting Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Fengling Guo
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China.
| | - Chuandong Qi
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China.
| | - Yiqing Liu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Shengyou Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Junliang Yin
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yongxing Zhu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
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Park SJ, Park JS, Yang JH, Moon KB, Shin SY, Jeon JH, Kim HS, Lee HJ. MicroRNA396 negatively regulates shoot regeneration in tomato. HORTICULTURE RESEARCH 2024; 11:uhad291. [PMID: 38371631 PMCID: PMC10873581 DOI: 10.1093/hr/uhad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024]
Abstract
Numerous studies have been dedicated to genetically engineering crops to enhance their yield and quality. One of the key requirements for generating genetically modified plants is the reprogramming of cell fate. However, the efficiency of shoot regeneration during this process is highly dependent on genotypes, and the underlying molecular mechanisms remain poorly understood. Here, we identified microRNA396 (miR396) as a negative regulator of shoot regeneration in tomato. By selecting two genotypes with contrasting shoot regeneration efficiencies and analyzing their transcriptome profiles, we found that miR396 and its target transcripts, which encode GROWTH-REGULATING FACTORs (GRFs), exhibit differential abundance between high- and low-efficiency genotypes. Suppression of miR396 functions significantly improved shoot regeneration rates along with increased expression of GRFs in transformed T0 explants, suggesting that miR396 is a key molecule involved in the determination of regeneration efficiency. Notably, we also showed that co-expression of a miR396 suppressor with the gene-editing tool can be employed to generate gene-edited plants in the genotype with a low capacity for shoot regeneration. Our findings show the critical role of miR396 as a molecular barrier to shoot regeneration in tomato and suggest that regeneration efficiency can be improved by blocking this single microRNA.
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Affiliation(s)
- Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Jin Ho Yang
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Seung Yong Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Korea
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Cheng Z, Wen S, Wu Y, Shang L, Wu L, Lyu D, Yu H, Wang J, Jian H. Comparatively Evolution and Expression Analysis of GRF Transcription Factor Genes in Seven Plant Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:2790. [PMID: 37570944 PMCID: PMC10421444 DOI: 10.3390/plants12152790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023]
Abstract
Growth regulatory factors (GRF) are plant-specific transcription factors that play pivotal roles in growth and various abiotic stresses regulation. However, adaptive evolution of GRF gene family in land plants are still being elucidated. Here, we performed the evolutionary and expression analysis of GRF gene family from seven representative species. Extensive phylogenetic analyses and gene structure analysis revealed that the number of genes, QLQ domain and WRC domain identified in higher plants was significantly greater than those identified in lower plants. Besides, dispersed duplication and WGD/segmental duplication effectively promoted expansion of the GRF gene family. The expression patterns of GRF gene family and target genes were found in multiple floral organs and abundant in actively growing tissues. They were also found to be particularly expressed in response to various abiotic stresses, with stress-related elements in promoters, implying potential roles in floral development and abiotic stress. Our analysis in GRF gene family interaction network indicated the similar results that GRFs resist to abiotic stresses with the cooperation of other transcription factors like GIFs. This study provides insights into evolution in the GRF gene family, together with expression patterns valuable for future functional researches of plant abiotic stress biology.
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Affiliation(s)
- Zhihan Cheng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yuke Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lin Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Hongtao Yu
- Suihua Branch of Heilongjiang Academy of Agriculture Sciences, Suihua 152052, China;
| | - Jichun Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
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Liu Y, Guo P, Wang J, Xu ZY. Growth-regulating factors: conserved and divergent roles in plant growth and development and potential value for crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1122-1145. [PMID: 36582168 DOI: 10.1111/tpj.16090] [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: 09/29/2022] [Revised: 12/13/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
High yield and stress resistance are the major prerequisites for successful crop cultivation, and can be achieved by modifying plant architecture. Evolutionarily conserved growth-regulating factors (GRFs) control the growth of different tissues and organs of plants. Here, we provide a systematic overview of the expression patterns of GRF genes and the structural features of GRF proteins in different plant species. Moreover, we illustrate the conserved and divergent roles of GRFs, microRNA396 (miR396), and GRF-interacting factors (GIFs) in leaf, root, and flower development. We also describe the molecular networks involving the miR396-GRF-GIF module, and illustrate how this module coordinates with different signaling molecules and transcriptional regulators to control development of different plant species. GRFs promote leaf growth, accelerate grain filling, and increase grain size and weight. We also provide some molecular insight into how coordination between GRFs and other signaling modules enhances crop productivity; for instance, how the GRF-DELLA interaction confers yield-enhancing dwarfism while increasing grain yield. Finally, we discuss how the GRF-GIF chimera substantially improves plant transformation efficiency by accelerating shoot formation. Overall, we systematically review the conserved and divergent roles of GRFs and the miR396-GRF-GIF module in growth regulation, and also provide insights into how GRFs can be utilized to improve the productivity and nutrient content of crop plants.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Huang J, Chen GZ, Ahmad S, Hao Y, Chen JL, Zhou YZ, Lan SR, Liu ZJ, Peng DH. Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum. Int J Mol Sci 2023; 24:ijms24021261. [PMID: 36674776 PMCID: PMC9863823 DOI: 10.3390/ijms24021261] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the GRF gene family in M. dodecandrum can help to improve their character of flavor and continuous flowering. The members of the GRF gene family were identified from the M. dodecandrum genome, and their bioinformatics, selective pressure, and expression patterns were analyzed. The results showed that there were 20 GRF genes in M. dodecandrum. Phylogenetic analysis showed that the 71 GRF genes from M. dodecandrum, Arabidopsis thaliana, Camellia sinensis, and Oryza sativa can be divided into three clades and six subclades. The 20 GRF genes of M. dodecandrum were distributed in twelve chromosomes and one contig. Furthermore, the gene structure and motif analysis showed that the intron and motif within each clade were very similar, but there were great differences among different clades. The promoter contained cis-acting elements related to hormone induction, stress, and growth and development. Different transcriptomic expression of MdGRFs indicated that MdGRFs may be involved in regulating the growth and development of M. dodecandrum. The results laid a foundation for further study on the function and molecular mechanism of the M. dodecandrum GRF gene family.
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Sun Y, Li H, Wu J, Zhang K, Tang W, Cong L, Xie H, Wang ZY, Chai M. Genome-wide identification of growth-regulating factor transcription factor family related to leaf and stem development in alfalfa. FRONTIERS IN PLANT SCIENCE 2022; 13:964604. [PMID: 36082290 PMCID: PMC9445573 DOI: 10.3389/fpls.2022.964604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Growth-regulating factors (GRFs) play crucial roles in plant growth and stress response. To date, there have been no reports of the analysis and identification of the GRF transcription factor family in alfalfa. In this study, we identified 27 GRF family members from alfalfa (Medicago sativa L.) "Xinjiang Daye", and analyzed their physicochemical properties. Based on phylogenetic analysis, these MsGRFs were divided into five subgroups, each with a similar gene structure and conserved motifs. MsGRFs genes are distributed on 23 chromosomes, and all contain QLQ and WRC conserved domains. The results of the collinearity analysis showed that all MsGRFs are involved in gene duplication, including multiple whole-genome duplication or segmental duplication and a set of tandem duplication, indicating that large-scale duplication is important for the expansion of the GRF family in alfalfa. Several hormone-related and stress-related cis-acting elements have been found in the promoter regions of MsGRFs. Some MsGRFs were highly expressed in young leaves and stems, and their expression decreased during development. In addition, the leaf size of different varieties was found to vary, and MsGRF1 to 4, MsGRF18 to 20, and MsGRF22 to 23 were differentially expressed in large and small leaf alfalfa varieties, suggesting that they are critical in the regulation of leaf size. The results of this study can benefit further exploration of the regulatory functions of MsGRFs in growth and development, and can identify candidate genes that control leaf size development.
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Genome-Wide Identification and Analysis of the Growth-Regulating Factor Family in Zanthoxylum armatum DC and Functional Analysis of ZaGRF6 in Leaf Size and Longevity Regulation. Int J Mol Sci 2022; 23:ijms23169043. [PMID: 36012309 PMCID: PMC9409285 DOI: 10.3390/ijms23169043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that play an important role in plant growth and development. In this study, fifteen GRF gene members containing QLQ and WRC domains were identified in Zanthoxylum armatum. Phylogenetic and collinearity analysis showed that ZaGRFs were closely related to CsGRFs and AtGRFs, and distantly related to OsGRFs. There are a large number of cis-acting elements related to hormone response and stress induction in the GRF gene promoter region of Z. armatum. Tissue-specific expression analysis showed that except for ZaGRF7, all the ZaGRFs were highly expressed in young parts with active growth and development, including terminal buds, seeds, and young flowers, suggesting their key roles in Z. armatum growth and development. Eight ZaGRFs were selected to investigate the transcriptional response to auxin, gibberellin and drought treatments. A total of six ZaGRFs in the NAA treatment, four ZaGRFs in the GA3 treatment, and six ZaGRFs in the PEG treatment were induced and significantly up-regulated. Overexpression of ZaGRF6 increased branching and chlorophyll content and delayed senescence of transgenic Nicotiana benthamiana. ZaGRF6 increased the expression of CRF2 and suppressed the expression of ARR4 and CKX1, indicating that ZaGRF6 is involved in cytokinin metabolism and signal transduction. These research results lay a foundation for further analysis of the GRF gene function of Z. armatum and provide candidate genes for growth, development, and stress resistance breeding of Z. armatum.
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Miao S, Li F, Han Y, Yao Z, Xu Z, Chen X, Liu J, Zhang Y, Wang A. Identification of OSCA gene family in Solanum habrochaites and its function analysis under stress. BMC Genomics 2022; 23:547. [PMID: 35915415 PMCID: PMC9341080 DOI: 10.1186/s12864-022-08675-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022] Open
Abstract
Background OSCA (hyperosmolality-gated calcium-permeable channel) is a calcium permeable cation channel protein that plays an important role in regulating plant signal transduction. It is involved in sensing changes in extracellular osmotic potential and an increase in Ca2+ concentration. S. habrochaites is a good genetic material for crop improvement against cold, late blight, planthopper and other diseases. Till date, there is no report on OSCA in S. habrochaites. Thus, in this study, we performed a genome-wide screen to identify OSCA genes in S. habrochaites and characterized their responses to biotic and abiotic stresses. Results A total of 11 ShOSCA genes distributed on 8 chromosomes were identified. Subcellular localization analysis showed that all members of ShOSCA localized on the plasma membrane and contained multiple stress-related cis acting elements. We observed that genome-wide duplication (WGD) occurred in the genetic evolution of ShOSCA5 (Solhab04g250600) and ShOSCA11 (Solhab12g051500). In addition, repeat events play an important role in the expansion of OSCA gene family. OSCA gene family of S. habrochaites used the time lines of expression studies by qRT-PCR, do indicate OSCAs responded to biotic stress (Botrytis cinerea) and abiotic stress (drought, low temperature and abscisic acid (ABA)). Among them, the expression of ShOSCAs changed significantly under four stresses. The resistance of silencing ShOSCA3 plants to the four stresses was reduced. Conclusion This study identified the OSCA gene family of S. habrochaites for the first time and analyzed ShOSCA3 has stronger resistance to low temperature, ABA and Botrytis cinerea stress. This study provides a theoretical basis for clarifying the biological function of OSCA, and lays a foundation for tomato crop improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08675-6.
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Affiliation(s)
- Shuang Miao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Fengshuo Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Han
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zhongtong Yao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Zeqian Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiuling Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Jiayin Liu
- College of Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Yao Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
| | - Aoxue Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China. .,College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
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Liu K, Kabir N, Wei Z, Sun Z, Wang J, Qi J, Liu M, Liu J, Zhou K. Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L.. PeerJ 2022; 10:e13372. [PMID: 35586135 PMCID: PMC9109687 DOI: 10.7717/peerj.13372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/12/2022] [Indexed: 01/13/2023] Open
Abstract
Background Cotton is the primary source of renewable natural fiber in the textile industry and an important biodiesel crop. Growth regulating factors (GRFs) are involved in regulating plant growth and development. Methods Using genome-wide analysis, we identified 35 GRF genes in Gossypium hirsutum. Results Chromosomal location information revealed an uneven distribution of GhGRF genes, with maximum genes on chromosomes A02, A05, and A12 from the At sub-genome and their corresponding D05 and D12 from the Dt sub-genome. In the phylogenetic tree, 35 GRF genes were divided into five groups, including G1, G2, G3, G4, and G5. The majority of GhGRF genes have two to three introns and three to four exons, and their deduced proteins contained conserved QLQ and WRC domains in the N-terminal end of GRFs in Arabidopsis and rice. Sequence logos revealed that GRF genes were highly conserved during the long-term evolutionary process. The CDS of the GhGRF gene can complement MiRNA396a. Moreover, most GhGRF genes transcripts developed high levels of ovules and fibers. Analyses of promoter cis-elements and expression patterns indicated that GhGRF genes play an essential role in regulating plant growth and development by coordinating the internal and external environment and multiple hormone signaling pathways. Our analysis indicated that GhGRFs are ideal target genes with significant potential for improving the molecular structure of cotton.
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Affiliation(s)
- Kun Liu
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhenzhen Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jian Wang
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jing Qi
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Miaoyang Liu
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Kehai Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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Liu X, Luo M, Li M, Wei J. Transcriptomic Analysis Reveals LncRNAs Associated with Flowering of Angelica sinensis during Vernalization. Curr Issues Mol Biol 2022; 44:1867-1888. [PMID: 35678657 PMCID: PMC9164074 DOI: 10.3390/cimb44050128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/16/2022] Open
Abstract
Angelica sinensis is a “low-temperature and long-day” perennial plant that produces bioactive compounds such as phthalides, organic acids, and polysaccharides for various types of clinical agents, including those with cardio-cerebrovascular, hepatoprotective, and immunomodulatory effects. To date, the regulatory mechanism of flowering under the photoperiod has been revealed, while the regulatory network of flowering genes during vernalization, especially in the role of lncRNAs, has yet to be identified. Here, lncRNAs associated with flowering were identified based on the full-length transcriptomic analysis of A. sinensis at vernalization and freezing temperatures, and the coexpressed mRNAs of lncRNAs were validated by qRT-PCR. We obtained a total of 2327 lncRNAs after assessing the protein-coding potential of coexpressed mRNAs, with 607 lncRNAs aligned against the TAIR database of model plant Arabidopsis, 345 lncRNAs identified, and 272 lncRNAs characterized on the SwissProt database. Based on the biological functions of coexpressed mRNAs, the 272 lncRNAs were divided into six categories: (1) chromatin, DNA/RNA and protein modification; (2) flowering; (3) stress response; (4) metabolism; (5) bio-signaling; and (6) energy and transport. The differential expression levels of representatively coexpressed mRNAs were almost consistent with the flowering of A. sinensis. It can be concluded that the flowering of A. sinensis is positively or negatively regulated by lncRNAs, which provides new insights into the regulation mechanism of the flowering of A. sinensis.
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Affiliation(s)
- Xiaoxia Liu
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
| | - Mimi Luo
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
- Correspondence: (M.L.); (J.W.)
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Correspondence: (M.L.); (J.W.)
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Chen H, Ge W. Identification, Molecular Characteristics, and Evolution of GRF Gene Family in Foxtail Millet (Setaria italica L.). Front Genet 2022; 12:727674. [PMID: 35185998 PMCID: PMC8851420 DOI: 10.3389/fgene.2021.727674] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Growth-regulating factor (GRF) is a multigene family that plays a vital role in the growth and development of plants. In the past, the GRF family of many plants has been studied. However, there is not a report about identification and evolution of GRF in foxtail millet (Setaria italia). Here, we identified 10 GRF genes in foxtail millet. Seven (70.00%) were regulated by Sit-miR396, and there were 19 optimal codons in GRFs of foxtail millet. Additionally, we found that WGD or segmental duplication have affected GRFs in foxtail millet between 15.07 and 45.97 million years ago. Regarding the GRF gene family of land plants, we identified a total of 157 GRF genes in 15 representative land plants. We found that GRF gene family originated from Group E, and the GRF gene family in monocots was gradually shrinking. Also, more loss resulted from the small number of GRF genes in lower plants. Exploring the evolution of GRF and functional analysis in the foxtail millet help us to understand GRF better and make a further study about the mechanism of GRF. These results provide a basis for the genetic improvement of foxtail millet and indicate an improvement of the yield.
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Identification and Expression Analyses of the Special 14-3-3 Gene Family in Papaya and its Involvement in Fruit Development, Ripening, and Abiotic Stress Responses. Biochem Genet 2021; 59:1599-1616. [PMID: 34009493 DOI: 10.1007/s10528-021-10077-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/29/2021] [Indexed: 10/21/2022]
Abstract
Plant 14-3-3 proteins play key roles in regulating growth, development, and stress responses. However, little is known about this gene family in papaya (Carica papaya L.). We characterized eight 14-3-3 genes from the papaya genome and designed them as CpGRF1-8. Based on phylogenetic, conserved motif, and gene structure analyses, papaya CpGRFs were divided into ε and non-ε groups. Expression analysis showed differential and class-specific transcription patterns in different organs. Quantitative real-time polymerase chain reaction analysis showed that most CpGRFs had large changes in expression during fruit development and ripening. This indicated that the CpGRFs were involved in regulating fruit development and ripening. Significant expression changes occurred after cold, salt, and drought treatments in papaya seedlings, indicating that CpGRFs were also involved in signaling responses to abiotic stress. These results provide a transcription profile of 14-3-3 genes in organs, during fruit development and ripening and in response to stress. Some highly expressed, fruit-specific, and stress-responsive candidate CpGRFs will be identified for further genetic improvement of papayas.
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13
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Piya S, Liu J, Burch-Smith T, Baum TJ, Hewezi T. A role for Arabidopsis growth-regulating factors 1 and 3 in growth-stress antagonism. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1402-1417. [PMID: 31701146 PMCID: PMC7031083 DOI: 10.1093/jxb/erz502] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/05/2019] [Indexed: 05/21/2023]
Abstract
Growth-regulating factors (GRFs) belong to a small family of transcription factors that are highly conserved in plants. GRFs regulate many developmental processes and plant responses to biotic and abiotic stimuli. Despite the importance of GRFs, a detailed mechanistic understanding of their regulatory functions is still lacking. In this study, we used ChIP sequencing (ChIP-seq) to identify genome-wide binding sites of Arabidopsis GRF1 and GRF3, and correspondingly their direct downstream target genes. RNA-sequencing (RNA-seq) analysis revealed that GRF1 and GRF3 regulate the expression of a significant number of the identified direct targets. The target genes unveiled broad regulatory functions of GRF1 and GRF3 in plant growth and development, phytohormone biosynthesis and signaling, and the cell cycle. Our analyses also revealed that clock core genes and genes with stress- and defense-related functions are most predominant among the GRF1- and GRF3-bound targets, providing insights into a possible role for these transcription factors in mediating growth-defense antagonism and integrating environmental stimuli into developmental programs. Additionally, GRF1 and GRF3 target molecular nodes of growth-defense antagonism and modulate the levels of defense- and development-related hormones in opposite directions. Taken together, our results point to GRF1 and GRF3 as potential key determinants of plant fitness under stress conditions.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Jinyi Liu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Present address: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Tessa Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Correspondence:
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Chen F, Yang Y, Luo X, Zhou W, Dai Y, Zheng C, Liu W, Yang W, Shu K. Genome-wide identification of GRF transcription factors in soybean and expression analysis of GmGRF family under shade stress. BMC PLANT BIOLOGY 2019; 19:269. [PMID: 31226949 PMCID: PMC6588917 DOI: 10.1186/s12870-019-1861-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/31/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND The Growth-regulating factor (GRF) family encodes plant-specific transcription factors which contain two conserved domains, QLQ and WRC. Members of this family play vital roles in plant development and stress response processes. Although GRFs have been identified in various plant species, we still know little about the GRF family in soybean (Glycine max). RESULTS In the present study, 22 GmGRFs distributed on 14 chromosomes and one scaffold were identified by searching soybean genome database and were clustered into five subgroups according to their phylogenetic relationships. GmGRFs belonging to the same subgroup shared a similar motif composition and gene structure. Synteny analysis revealed that large-scale duplications played key roles in the expansion of the GmGRF family. Tissue-specific expression data showed that GmGRFs were strongly expressed in growing tissues, including the shoot apical meristems, developing seeds and flowers, indicating that GmGRFs play critical roles in plant growth and development. On the basis of expression analysis of GmGRFs under shade conditions, we found that all GmGRFs responded to shade stress. Most GmGRFs were down-regulated in soybean leaves after shade treatment. CONCLUSIONS Taken together, this research systematically analyzed the characterization of the GmGRF family and its primary roles in soybean development and shade stress response. Further studies of the function of the GmGRFs in the growth, development and stress tolerance of soybean, especially under shade stress, will be valuable.
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Affiliation(s)
- Feng Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yingzeng Yang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaofeng Luo
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wenguan Zhou
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yujia Dai
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Chuan Zheng
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Weiguo Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wenyu Yang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Kai Shu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
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Wu C, Ding X, Ding Z, Tie W, Yan Y, Wang Y, Yang H, Hu W. The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression. Int J Mol Sci 2019; 20:ijms20112730. [PMID: 31163686 PMCID: PMC6600411 DOI: 10.3390/ijms20112730] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/27/2023] Open
Abstract
The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops.
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Affiliation(s)
- Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Xupo Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yu Wang
- Beijing Commerce and Trade School, Beijing 100162, China.
| | - Hai Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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