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Huang Y, Zheng Q, Zhang MM, He X, Zhao X, Wang L, Lan S, Liu ZJ. Genome-Wide Identification and Expression Analysis of the GRAS Gene Family and Their Responses to Heat Stress in Cymbidium goeringii. Int J Mol Sci 2024; 25:6363. [PMID: 38928070 PMCID: PMC11204107 DOI: 10.3390/ijms25126363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The GRAS gene family, responsible for encoding transcription factors, serves pivotal functions in plant development, growth, and responses to stress. The exploration of the GRAS gene family within the Orchidaceae has been comparatively limited, despite its identification and functional description in various plant species. This study aimed to conduct a thorough examination of the GRAS gene family in Cymbidum goeringii, focusing on its physicochemical attributes, phylogenetic associations, gene structure, cis-acting elements, and expression profiles under heat stress. The results show that a total of 54 CgGRASs were pinpointed from the genome repository and categorized into ten subfamilies via phylogenetic associations. Assessment of gene sequence and structure disclosed the prevalent existence of the VHIID domain in most CgGRASs, with around 57.41% (31/54) CgGRASs lacking introns. The Ka/Ks ratios of all CgGRASs were below one, indicating purifying selection across all CgGRASs. Examination of cis-acting elements unveiled the presence of numerous elements linked to light response, plant hormone signaling, and stress responsiveness. Furthermore, CgGRAS5 contained the highest quantity of cis-acting elements linked to stress response. Experimental results from RT-qPCR demonstrated notable variations in the expression levels of eight CgGRASs after heat stress conditions, particularly within the LAS, HAM, and SCL4/7 subfamilies. In conclusion, this study revealed the expression pattern of CgGRASs under heat stress, providing reference for further exploration into the roles of CgGRAS transcription factors in stress adaptation.
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Affiliation(s)
- Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Linying Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
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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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Zhu L, Yin T, Zhang M, Yang X, Wu J, Cai H, Yang N, Li X, Wen K, Chen D, Zhang H, Liu X. Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress. BMC Genomics 2024; 25:12. [PMID: 38166720 PMCID: PMC10759511 DOI: 10.1186/s12864-023-09915-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported. RESULTS In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55, AcGRAS69, AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants. CONCLUSIONS These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.
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Affiliation(s)
- Ling Zhu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Mengjie Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Jiexin Wu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Hanbing Cai
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Na Yang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Xulin Li
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Ke Wen
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Daming Chen
- Research Institute of Agriculture Ecological in Hot Areas, Yunnan Academy of Agricultural Science, Yuan Mou, Yunnan, 651300, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
| | - Xiaozhen Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China.
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Neves C, Ribeiro B, Amaro R, Expósito J, Grimplet J, Fortes AM. Network of GRAS transcription factors in plant development, fruit ripening and stress responses. HORTICULTURE RESEARCH 2023; 10:uhad220. [PMID: 38077496 PMCID: PMC10699852 DOI: 10.1093/hr/uhad220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/20/2023] [Indexed: 06/23/2024]
Abstract
The plant-specific family of GRAS transcription factors has been wide implicated in the regulation of transcriptional reprogramming associated with a diversity of biological functions ranging from plant development processes to stress responses. Functional analyses of GRAS transcription factors supported by in silico structural and comparative analyses are emerging and clarifying the regulatory networks associated with their biological roles. In this review, a detailed analysis of GRAS proteins' structure and biochemical features as revealed by recent discoveries indicated how these characteristics may impact subcellular location, molecular mechanisms, and function. Nomenclature issues associated with GRAS classification into different subfamilies in diverse plant species even in the presence of robust genomic resources are discussed, in particular how it affects assumptions of biological function. Insights into the mechanisms driving evolution of this gene family and how genetic and epigenetic regulation of GRAS contributes to subfunctionalization are provided. Finally, this review debates challenges and future perspectives on the application of this complex but promising gene family for crop improvement to cope with challenges of environmental transition.
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Affiliation(s)
- Catarina Neves
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Beatriz Ribeiro
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Rute Amaro
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Jesús Expósito
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Jérôme Grimplet
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Gobierno de Aragón, Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón—IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet 177, 50013 Zaragoza, Spain
| | - Ana Margarida Fortes
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
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Rana D, Sharma P, Arpita K, Srivastava H, Sharma S, Gaikwad K. Genome-wide identification and characterization of GRAS gene family in pigeonpea ( Cajanus cajan (L.) Millspaugh). 3 Biotech 2023; 13:363. [PMID: 37840881 PMCID: PMC10570252 DOI: 10.1007/s13205-023-03782-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03782-x.
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Affiliation(s)
- Divyansh Rana
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313 India
| | - Priya Sharma
- Department of Biotechnology, Jamia Hamdard, New Delhi, Delhi 110062 India
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kumari Arpita
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Harsha Srivastava
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Sandhya Sharma
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kishor Gaikwad
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
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Mishra S, Chaudhary R, Pandey B, Singh G, Sharma P. Genome-wide identification and expression analysis of the GRAS gene family under abiotic stresses in wheat (Triticum aestivum L.). Sci Rep 2023; 13:18705. [PMID: 37907517 PMCID: PMC10618205 DOI: 10.1038/s41598-023-45051-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/15/2023] [Indexed: 11/02/2023] Open
Abstract
The GRAS transcription factors are multifunctional proteins involved in various biological processes, encompassing plant growth, metabolism, and responses to both abiotic and biotic stresses. Wheat is an important cereal crop cultivated worldwide. However, no systematic study of the GRAS gene family and their functions under heat, drought, and salt stress tolerance and molecular dynamics modeling in wheat has been reported. In the present study, we identified the GRAS gene in Triticum aestivum through systematically performing gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 177 GRAS genes were identified within the wheat genome. Based on phylogenetic analysis, these genes were categorically placed into 14 distinct subfamilies. Detailed analysis of the genetic architecture revealed that the majority of TaGRAS genes had no intronic regions. The expansion of the wheat GRAS gene family was proven to be influenced by both segmental and tandem duplication events. The study of collinearity events between TaGRAS and analogous orthologs from other plant species provided valuable insights into the evolution of the GRAS gene family in wheat. It is noteworthy that the promoter regions of TaGRAS genes consistently displayed an array of cis-acting elements that are associated with stress responses and hormone regulation. Additionally, we discovered 14 miRNAs that target key genes involved in three stress-responsive pathways in our study. Moreover, an assessment of RNA-seq data and qRT-PCR results revealed a significant increase in the expression of TaGRAS genes during abiotic stress. These findings highlight the crucial role of TaGRAS genes in mediating responses to different environmental stresses. Our research delved into the molecular dynamics and structural aspects of GRAS domain-DNA interactions, marking the first instance of such information being generated. Overall, the current findings contribute to our understanding of the organization of the GRAS genes in the wheat genome. Furthermore, we identified TaGRAS27 as a candidate gene for functional research, and to improve abiotic stress tolerance in the wheat by molecular breeding.
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Affiliation(s)
- Shefali Mishra
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India
- ICAR-Indian Institute of Wheat and Barley Research, Agrasain Marg, PO BOX-158, Karnal, Haryana, India
| | - Reeti Chaudhary
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India
| | - Bharti Pandey
- ICAR-National Dairy Research Institute, Karnal, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Agrasain Marg, PO BOX-158, Karnal, Haryana, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Agrasain Marg, PO BOX-158, Karnal, Haryana, India.
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Sun S, Ma W, Mao P. Analysis of MsTERT Gene Expression Profile in Alfalfa ( Medicago sativa) Indicates Their Response to Abiotic Stress and Seed Aging. PLANTS (BASEL, SWITZERLAND) 2023; 12:2036. [PMID: 37653953 PMCID: PMC10221914 DOI: 10.3390/plants12102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Seed aging is always taken as a crucial factor for vigor loss due to delayed seed germination and seedling growth, which limits hay production. Many studies have found that telomeres are closely related to abiotic stress and seed vigor. However, the molecular mechanism of telomeres' response to abiotic stress, seed vigor, and the maintenance mechanism of plant telomere homeostasis still remain unclear. Alfalfa (Medicago sativa) enjoys the title of "King of Forage", and is an important protein forage for the dairy industry as planted in the world. This comprehensive investigation was performed to explore the molecular characterization, phylogenetic relationship, and gene expression analysis of MsTERT under abiotic stress and during seed aging in alfalfa. In this study, MsTERT was identified from the 'Zhongmu 1' alfalfa genome and encoded a coding sequence (CDS) of 3615 bp in length, consisting of telomerase- RNA-Binding Domain (RBD) and Reverse Transcriptase (RT) domains, 1024 amino acids, an isoelectric point of 9.58, and a relative molecular mass of 138.94 kD. Subcellular localization showed that MsTERT was mainly localized in the nucleus and mitochondria. The results of the expression profile showed that MsTERT was observed to respond to various stress conditions such as salt (100 mmol/L NaCl) and drought (20% PEG 6000). Furthermore, exogenous hormones IAA, ABA, and GA3 showed the potential to affect MsTERT expression. Additionally, MsTERT also responded to seed aging. Our results revealed a marginal but significant association between relative telomere length, MsTERT expression, and seed germination percentage, suggesting that the length of telomeres was shortened, and expression of MsTERT decreased with alfalfa seed aged. These results provide some evidence for the hypothesis of relative telomere length and/or TERT expression serving as biomarkers of seed aging. Although this finding is helpful to offer a new way to elucidate the molecular mechanism of vigor loss in alfalfa seed, further investigation is required to elucidate the molecular mechanism by which the MsTERT gene regulates seed vigor.
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Affiliation(s)
| | | | - Peisheng Mao
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (S.S.); (W.M.)
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Liu C, Wang K, Yun Z, Liu W, Zhao M, Wang Y, Hu J, Liu T, Wang N, Wang Y, Zhang M. Functional Study of PgGRAS68-01 Gene Involved in the Regulation of Ginsenoside Biosynthesis in Panax ginseng. Int J Mol Sci 2023; 24:ijms24043347. [PMID: 36834759 PMCID: PMC9961673 DOI: 10.3390/ijms24043347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/11/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Ginseng (Panax ginseng C. A. Meyer) is a perennial herb from the genus Panax in the family Araliaceae. It is famous in China and abroad. The biosynthesis of ginsenosides is controlled by structural genes and regulated by transcription factors. GRAS transcription factors are widely found in plants. They can be used as tools to modify plant metabolic pathways by interacting with promoters or regulatory elements of target genes to regulate the expression of target genes, thereby activating the synergistic interaction of multiple genes in metabolic pathways and effectively improving the accumulation of secondary metabolites. However, there are no reports on the involvement of the GRAS gene family in ginsenoside biosynthesis. In this study, the GRAS gene family was located on chromosome 24 pairs in ginseng. Tandem replication and fragment replication also played a key role in the expansion of the GRAS gene family. The PgGRAS68-01 gene closely related to ginsenoside biosynthesis was screened out, and the sequence and expression pattern of the gene were analyzed. The results showed that the expression of PgGRAS68-01 gene was spatio-temporal specific. The full-length sequence of PgGRAS68-01 gene was cloned, and the overexpression vector pBI121-PgGRAS68-01 was constructed. The ginseng seedlings were transformed by Agrobacterium rhifaciens-mediated method. The saponin content in the single root of positive hair root was detected, and the inhibitory role of PgGRAS68-01 in ginsenoside synthesis is reported.
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Affiliation(s)
- Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.W.); (M.Z.)
| | - Ziyi Yun
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Wenbo Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Yanfang Wang
- Laboratory for Cultivation and Breeding of Medicinal Plants of National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China
| | - Jian Hu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Tao Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Nan Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.W.); (M.Z.)
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9
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Ling L, Li M, Chen N, Ren G, Qu L, Yue H, Wu X, Zhao J. Genome-Wide Analysis and Expression of the GRAS Transcription Factor Family in Avena sativa. Genes (Basel) 2023; 14:genes14010164. [PMID: 36672905 PMCID: PMC9858933 DOI: 10.3390/genes14010164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The GRAS transcription factor is an important transcription factor in plants. In recent years, more GRAS genes have been identified in many plant species. However, the GRAS gene family has not yet been studied in Avena sativa. We identified 100 members of the GRAS gene family in A. sativa (Avena sativa), named them AsGRAS1~AsGRAS100 according to the positions of 21 chromosomes, and classified them into 9 subfamilies. In this study, the motif and gene structures were also relatively conserved in the same subfamilies. At the same time, we found a great deal related to the stress of cis-acting promoter regulatory elements (MBS, ABRE, and TC-rich repeat elements). qRT-PCR suggested that the AsGRAS gene family (GRAS gene family in A. sativa) can regulate the response to salt, saline-alkali, and cold and freezing abiotic stresses. The current study provides original and detailed information about the AsGRAS gene family, which contributes to the functional characterization of GRAS proteins in other plants.
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Pan J, Zhou Q, Wang H, Chen Y, Wang Z, Zhang J. Genome-wide identification and characterization of abiotic stress responsive GRAS family genes in oat ( Avena sativa). PeerJ 2023; 11:e15370. [PMID: 37187518 PMCID: PMC10178225 DOI: 10.7717/peerj.15370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Background GRAS transcription factors play a variety of functions in plant growth and development and are named after the first three transcription factors GAI (GIBBERRELLICACIDINSENSITIVE), RGA (REPRESSOROFGAI), and SCR (SCARECROW) found in this family. Oat (Avena sativa) is one of the most important forage grasses in the world. However, there are few reports on the GRAS gene family in oat. Methods In order to understand the information and expression pattern of oat GRAS family members, we identified the GRAS members and analyzed their phylogenetic relationship, gene structure, and expression pattern in oat by bioinformatics technology. Results The results showed that the oat GRAS family consists of 30 members, and most of the AsGRAS proteins were neutral or acidic proteins. The phylogenetic tree divided the oat GRAS members into four subfamilies, and each subfamily has different conservative domains and functions. Chromosome location analysis suggested that 30 GRAS genes were unevenly distributed on five chromosomes of oat. The results of real-time quantitative reverse transcription-PCR (qRT-PCR) showed that some AsGRAS genes (AsGRAS12, AsGRAS14, AsGRAS21, and AsGRAS24) were all up-regulated with increasing stress treatment time.The results of this study provide a theoretical basis for further research into the corresponding stress of oat. Therefore, further studies concentrating on these AsGRAS genes might reveal the many roles played by GRAS genes in oat.
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Affiliation(s)
- Jing Pan
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Qingping Zhou
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Hui Wang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Youjun Chen
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Zhiqiang Wang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Junchao Zhang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
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Genome-Wide Identification and Expression Pattern of the GRAS Gene Family in Pitaya ( Selenicereus undatus L.). BIOLOGY 2022; 12:biology12010011. [PMID: 36671704 PMCID: PMC9854919 DOI: 10.3390/biology12010011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
The GRAS gene family is one of the most important families of transcriptional factors that have diverse functions in plant growth and developmental processes including axillary meristem patterning, signal-transduction, cell maintenance, phytohormone and light signaling. Despite their importance, the function of GRAS genes in pitaya fruit (Selenicereus undatus L.) remains unknown. Here, 45 members of the HuGRAS gene family were identified in the pitaya genome, which was distributed on 11 chromosomes. All 45 members of HuGRAS were grouped into nine subfamilies using phylogenetic analysis with six other species: maize, rice, soybeans, tomatoes, Medicago truncatula and Arabidopsis. Among the 45 genes, 12 genes were selected from RNA-Seq data due to their higher expression in different plant tissues of pitaya. In order to verify the RNA-Seq data, these 12 HuGRAS genes were subjected for qRT-PCR validation. Nine HuGRAS genes exhibited higher relative expression in different tissues of the plant. These nine genes which were categorized into six subfamilies inlcuding DELLA (HuGRAS-1), SCL-3 (HuGRAS-7), PAT1 (HuGRAS-34, HuGRAS-35, HuGRAS-41), HAM (HuGRAS-37), SCR (HuGRAS-12) and LISCL (HuGRAS-18, HuGRAS-25) might regulate growth and development in the pitaya plant. The results of the present study provide valuable information to improve tropical pitaya through a molecular and conventional breeding program.
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Zhao X, Liu DK, Wang QQ, Ke S, Li Y, Zhang D, Zheng Q, Zhang C, Liu ZJ, Lan S. Genome-wide identification and expression analysis of the GRAS gene family in Dendrobium chrysotoxum. FRONTIERS IN PLANT SCIENCE 2022; 13:1058287. [PMID: 36518517 PMCID: PMC9742484 DOI: 10.3389/fpls.2022.1058287] [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: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
The GRAS gene family encodes transcription factors that participate in plant growth and development phases. They are crucial in regulating light signal transduction, plant hormone (e.g. gibberellin) signaling, meristem growth, root radial development, response to abiotic stress, etc. However, little is known about the features and functions of GRAS genes in Orchidaceae, the largest and most diverse angiosperm lineage. In this study, genome-wide analysis of the GRAS gene family was conducted in Dendrobium chrysotoxum (Epidendroideae, Orchidaceae) to investigate its physicochemical properties, phylogenetic relationships, gene structure, and expression patterns under abiotic stress in orchids. Forty-six DchGRAS genes were identified from the D. chrysotoxum genome and divided into ten subfamilies according to their phylogenetic relationships. Sequence analysis showed that most DchGRAS proteins contained conserved VHIID and SAW domains. Gene structure analysis showed that intronless genes accounted for approximately 70% of the DchGRAS genes, the gene structures of the same subfamily were the same, and the conserved motifs were also similar. The Ka/Ks ratios of 12 pairs of DchGRAS genes were all less than 1, indicating that DchGRAS genes underwent negative selection. The results of cis-acting element analysis showed that the 46 DchGRAS genes contained a large number of hormone-regulated and light-responsive elements as well as environmental stress-related elements. In addition, the real-time reverse transcription quantitative PCR (RT-qPCR) experimental results showed significant differences in the expression levels of 12 genes under high temperature, drought and salt treatment, among which two members of the LISCL subfamily (DchGRAS13 and DchGRAS15) were most sensitive to stress. Taken together, this paper provides insights into the regulatory roles of the GRAS gene family in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian-Qian Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijie Ke
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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Genome-Wide Characterization and Expression Profiling of the GRAS Gene Family in Salt and Alkali Stresses in Miscanthus sinensis. Int J Mol Sci 2022; 23:ijms232314521. [PMID: 36498850 PMCID: PMC9737823 DOI: 10.3390/ijms232314521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
The GRAS family genes encode plant-specific transcription factors that play important roles in a diverse range of developmental processes and abiotic stress responses. However, the information of GRAS gene family in the bioenergy crop Miscanthus has not been available. Here, we report the genome-wide identification of GRAS gene family in Micanthus sinensis. A total of 123 MsGRAS genes were identified, which were divided into ten subfamilies based on the phylogenetic analysis. The co-linearity analysis revealed that 59 MsGRAS genes experienced segmental duplication, forming 35 paralogous pairs. The expression of six MsGRAS genes in responding to salt, alkali, and mixed salt-alkali stresses was analyzed by transcriptome and real-time quantitative PCR (RT-qPCR) assays. Furthermore, the role of MsGRAS60 in salt and alkali stress response was characterized in transgenic Arabidopsis. The MsGRAS60 overexpression lines exhibited hyposensitivity to abscisic acid (ABA) treatment and resulted in compromised tolerance to salt and alkali stresses, suggesting that MsGRAS60 is a negative regulator of salt and alkali tolerance via an ABA-dependent signaling pathway. The salt and alkali stress-inducible MsGRAS genes identified serve as candidates for the improvement of abiotic stress tolerance in Miscanthus.
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He Z, Tian Z, Zhang Q, Wang Z, Huang R, Xu X, Wang Y, Ji X. Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla. FRONTIERS IN PLANT SCIENCE 2022; 13:1022076. [PMID: 36352865 PMCID: PMC9638169 DOI: 10.3389/fpls.2022.1022076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The GRAS gene family is a plant-specific family of transcription factors and play a vital role in many plant growth processes and abiotic stress responses. Nevertheless, the functions of the GRAS gene family in woody plants, especially in Betula platyphylla (birch), are hardly known. In this study, we performed a genome-wide analysis of 40 BpGRAS genes (BpGRASs) and identified typical GRAS domains of most BpGRASs. The BpGRASs were unevenly distributed on 14 chromosomes of birch and the phylogenetic analysis of six species facilitated the clustering of 265 GRAS proteins into 17 subfamilies. We observed that closely related GRAS homologs had similar conserved motifs according to motif analysis. Besides, an analysis of the expression patterns of 26 BpGRASs showed that most BpGRASs were highly expressed in the leaves and responded to salt stress. Six BpGRASs were selected for cis-acting element analysis because of their significant upregulation under salt treatment, indicating that many elements were involved in the response to abiotic stress. This result further confirmed that these BpGRASs might participate in response to abiotic stress. Transiently transfected birch plants with transiently overexpressed 6 BpGRASs and RNAi-silenced 6 BpGRASs were generated for gain- and loss-of-function analysis, respectively. In addition, overexpression of BpGRAS34 showed phenotype resistant to salt stress, decreased the cell death and enhanced the reactive oxygen species (ROS) scavenging capabilities and proline content under salt treatment, consistent with the results in transiently transformed birch plants. This study is a systematic analysis of the GRAS gene family in birch plants, and the results provide insight into the molecular mechanism of the GRAS gene family responding to abiotic stress in birch plants.
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Affiliation(s)
- Zihang He
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zengzhi Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qun Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhibo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruikun Huang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xin Xu
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yucheng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xiaoyu Ji
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Fan K, Sze CC, Li MW, Lam HM. Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2022; 13:997037. [PMID: 36330261 PMCID: PMC9623164 DOI: 10.3389/fpls.2022.997037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.
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Qi J, Yu X, Wang X, Zhang F, Ma C. Differentially expressed genes related to plant height and yield in two alfalfa cultivars based on RNA-seq. PeerJ 2022; 10:e14096. [PMID: 36248707 PMCID: PMC9558622 DOI: 10.7717/peerj.14096] [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: 04/08/2022] [Accepted: 08/30/2022] [Indexed: 01/21/2023] Open
Abstract
Background Alfalfa (Medicago sativa L.) is a kind of forage with high relative feeding value in farming and livestock breeding, and is of great significance to the development of animal husbandry. The growth of the aboveground part of alfalfa is an important factor that limits crop yield. Clarifying the molecular mechanisms that maintain vigorous growth in alfalfa may contribute to the development of molecular breeding for this crop. Methods Here, we evaluated the growth phenotypes of five cultivars of alfalfa (WL 712, WL 525HQ, Victoria, Knight 2, and Aohan). Then RNA-seq was performed on the stems of WL 712, chosen as a fast growing cultivar, and Aohan, chosen as a slow growing cultivar. GO enrichment analysis was conducted on all differentially expressed genes (DEGs). Result Among the differentially expressed genes that were up-regulated in the fast growing cultivar, GO analysis revealed enrichment in the following seven categories: formation of water-conducting tissue in vascular plants, biosynthesis and degradation of lignin, formation of the primary or secondary cell wall, cell enlargement and plant growth, cell division and shoot initiation, stem growth and induced germination, and cell elongation. KEGG analysis showed that differentially expressed genes were annotated as being involved in plant hormone signal transduction, photosynthesis, and phenylpropanoid biosynthesis. KEGG analysis also showed that up-regulated in the fast growing cultivar were members of the WRKY family of transcription factors related to plant growth and development, members of the NAC and MYB gene families related to the synthesis of cellulose and hemicellulose, and the development of secondary cell wall fibres, and finally, MYB family members that are involved in plant growth regulation. Our research results not only enrich the transcriptome database of alfalfa, but also provide valuable information for explaining the molecular mechanism of fast growth, and can provide reference for the production of alfalfa.
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Affiliation(s)
- Jiangjiao Qi
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Xue Yu
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Xuzhe Wang
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Fanfan Zhang
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Chunhui Ma
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
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Yu A, Jiang X, Sun Y, Hu Q, Zhu X, Kang J, Chen L, Liu L, Hao L, Yang Q, Long R, Li M. Genome-wide identification, characterization, and expression analysis of UDP-glycosyltransferase genes associated with secondary metabolism in alfalfa ( Medicago sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1001206. [PMID: 36254261 PMCID: PMC9568668 DOI: 10.3389/fpls.2022.1001206] [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: 07/23/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Uridine diphosphate glycosyltransferases (UGTs) are enzymes that catalyze glycosylation modifications and play an essential role in regulating plant metabolism. Alfalfa (Medicago sativa L.) is the most important legume in the world due to its high yields and protein content; however, the UGT genes in alfalfa have not yet been studied. Identifying UGT genes with metabolic roles in alfalfa is essential for identifying and modifying genetic traits that are relevant to yield and quality. In this study, 90 of the 239 UGT genes identified from the alfalfa "Zhongmu No. 1" genome database were found to be related to secondary metabolism, and a series of gene family characterization analyses were conducted on each. The results demonstrated that all 90 UGT genes were unevenly distributed on eight chromosomes with few introns and that tandem duplications were the crucial driving force expanding the UGT family in alfalfa. Notably, the 90 UGT genes can be clustered into ten evolutionary groups which contain specific PSPG motifs, and genes in these ten groups have specific tissue expressions. This suggests that the UGT genes in each group could have similar glycosylation roles corresponding to analogous secondary metabolites in alfalfa. Additionally, multiple cis-acting elements found in MsUGT promoter regions, such as phytohormone and flavonoids, indicate that 90 UGT members could be induced by these features, which are also related to secondary metabolism. Therefore, our study identified 90 UGT members inten evolutionary groups that are likely related to glycosylation modifications with secondary metabolites in alfalfa. These findings help uncover pivotal regulatory mechanisms associated with secondary metabolism in plant yield and quality and contribute to genetic modification and breeding in alfalfa and other plant species.
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Affiliation(s)
- Andong Yu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xueqian Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Qiannan Hu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xiaoxi Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Liu
- Bayannur Institute of Agricultural and Animal Husbandry Sciences, Inner Mongolia, China
| | - Linfeng Hao
- Bayannur Institute of Agricultural and Animal Husbandry Sciences, Inner Mongolia, China
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhang D, Zhang Z, Li C, Xing Y, Luo Y, Wang X, Li D, Ma Z, Cai H. Overexpression of MsRCI2D and MsRCI2E Enhances Salt Tolerance in Alfalfa (Medicago sativa L.) by Stabilizing Antioxidant Activity and Regulating Ion Homeostasis. Int J Mol Sci 2022; 23:ijms23179810. [PMID: 36077224 PMCID: PMC9456006 DOI: 10.3390/ijms23179810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/30/2022] Open
Abstract
Rare cold-inducible 2 (RCI2) genes from alfalfa (Medicago sativa L.) are part of a multigene family whose members respond to a variety of abiotic stresses by regulating ion homeostasis and stabilizing membranes. In this study, salt, alkali, and ABA treatments were used to induce MsRCI2D and MsRCI2E expression in alfalfa, but the response time and the expression intensity of the MsRCI2D,-E genes were different under specific treatments. The expression intensity of the MsRCI2D gene was the highest in salt- and alkali-stressed leaves, while the MsRCI2E gene more rapidly responded to salt and ABA treatment. In addition to differences in gene expression, MsRCI2D and MsRCI2E differ in their subcellular localization. Akin to MtRCI2D from Medicago truncatula, MsRCI2D is also localized in the cell membrane, while MsRCI2E is different from MtRCI2E, localized in the cell membrane and the inner membrane. This difference might be related to an extra 20 amino acids in the C-terminal tail of MsRCI2E. We investigated the function of MsRCI2D and MsRCI2E proteins in alfalfa by generating transgenic alfalfa chimeras. Compared with the MsRCI2E-overexpressing chimera, under high-salinity stress (200 mmol·L−1 NaCl), the MsRCI2D-overexpressing chimera exhibited a better phenotype, manifested as a higher chlorophyll content and a lower MDA content. After salt treatment, the enzyme activities of SOD, POD, CAT, and GR in MsRCI2D- and -E-overexpressing roots were significantly higher than those in the control. In addition, after salt stress, the Na+ content in MsRCI2D- and -E-transformed roots was lower than that in the control; K+ was higher than that in the control; and the Na+/K+ ratio was lower than that in the control. Correspondingly, H+-ATPase, SOS1, and NHX1 genes were significantly up-regulated, and the HKT gene was significantly down-regulated after 6 h of salt treatment. MsRCI2D was also found to regulate the expression of the MsRCI2B and MsRCI2E genes, and the MsRCI2E gene could alter the expression of the MsRCI2A, MsRCI2B, and MsRCI2D genes. MsRCI2D- and -E-overexpressing alfalfa was found to have higher salt tolerance, manifested as improved activity of antioxidant enzymes, reduced content of reactive oxygen species, and sustained Na+ and K+ ion balance by regulating the expression of the H+-ATPase, SOS1, NHX1, HKT, and MsRCI2 genes.
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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: 11] [Impact Index Per Article: 5.5] [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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Ma L, An R, Jiang L, Zhang C, Li Z, Zou C, Yang C, Pan G, Lübberstedt T, Shen Y. Effects of ZmHIPP on lead tolerance in maize seedlings: Novel ideas for soil bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128457. [PMID: 35180524 DOI: 10.1016/j.jhazmat.2022.128457] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 05/19/2023]
Abstract
Extensive lead (Pb) absorption by plants affects their growth and development and causes damage to the human body by entering the food chain. In this study, we cloned ZmHIPP, a gene associated with Pb tolerance and accumulation in maize, using combined linkage mapping and weighted gene co-expression network analysis. We show that ZmHIPP, which encodes a heavy metal-associated isoprenylated plant protein, positively modulated Pb tolerance and accumulation in maize seedlings, Arabidopsis, and yeast. The genetic variation locus (A/G) in the promoter of ZmHIPP contributed to the phenotypic disparity in Pb tolerance among different maize inbred lines by altering the expression abundance of ZmHIPP. Knockdown of ZmHIPP significantly inhibited growth and decreased Pb accumulation in maize seedlings under Pb stress. ZmHIPP facilitated Pb deposition in the cell wall and prevented it from entering the intracellular organelles, thereby alleviating Pb toxicity in maize seedlings. Compared to that in the mutant zmhipp, the accumulated Pb in the wild-type line mainly consisted of the low-toxicity forms of Pb. Our study increases the understanding of the mechanism underlying Pb tolerance in maize and provides new insights into the bioremediation of Pb-polluted soil.
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Affiliation(s)
- Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Rong An
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chen Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhaoling Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Cong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | | | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
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21
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Wang X, Manzoor MA, Wang M, Zhao Y, Feng X, Alam P, Chi X, Cai Y. Integrative Analysis of the GRAS Genes From Chinese White Pear ( Pyrus bretschneideri): A Critical Role in Leaf Regeneration. FRONTIERS IN PLANT SCIENCE 2022; 13:898786. [PMID: 35734253 PMCID: PMC9208361 DOI: 10.3389/fpls.2022.898786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/27/2022] [Indexed: 05/16/2023]
Abstract
GRAS is a transcription regulator factor, which plays an important role in plant growth and development. Previous analyses found that several GRAS functions have been identified, such as axillary bud meristem formation, radial root elongation, gibberellin signaling, light signaling, and abiotic stress. The GRAS family has been comprehensively evaluated in several species. However, little finding is on the GRAS transcription factors (TFs) in Chinese white pear. In this study, 99 PbGRAS were systemically characterized and renamed PbGRAS1 to PbGRAS99 according to their chromosomal localizations. Phylogenetic analysis and structural features revealed that could be classified into eight subfamilies (LISCL, Ls, SHR, HAM, SCL, PAT, SCR, and DELLA). Further analysis of introns/exons and conserved motifs revealed that they are diverse and functionally differentiated in number and structure. Synteny analysis among Pyrus bretschenedri, Prunus mume, Prunus avium, Fragaria vesca, and Prunus persica showed that GRAS duplicated regions were more conserved. Dispersed duplication events are the most common mechanism and may play a crucial role in the expansion of the GRAS gene family. In addition, cis-acting elements of the PbGRAS gene were found in promoter regions associated with hormone and environmental stress responses. Notably, the expression pattern detected by qRT-PCR indicated that PbGRAS genes were differentially expressed under gibberellin (GA), abscisic acid (ABA), and auxin (IAA) conditions, which are responsive to abiotic stress. PbGRAS89 and PbGRAS99 were highly expressed at different stages of hormone treatment and may play important role in leaf development. Therefore, we selected PbGRAS89 and PbGRAS99 to clone and construct pCAMBIA1301-PbGRAS89, 99 and transferred them into Arabidopsis thaliana. Finally, we observed and compared the changes of overexpressed plants and wild-type plants during regeneration. This method was used to analyze their roles in leaf regeneration of Chinese white pear. In addition, we also constructed pCAMBIA1305-PbGRAS89, 99, and transferred them into onion cells to determine the subcellular localization. Subcellular localization experiments showed that PbGRAS89 and PbGRAS99 were localized in the nucleus. In summary, the results of this study indicate that PbGRAS89 and PbGRAS99 are mainly responsible for leaf regeneration of Chinese white pear, which plays a positive role in callus formation and provides rich resources for studying GRAS gene functions.
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Affiliation(s)
- Xinya Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | | | - Mengna Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yu Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaofeng Feng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Xujing Chi
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- *Correspondence: Yongping Cai
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