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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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Xie Z, Yang D, Zhou Z, Li K, Yi P, Liu A, Zhou Z, Tu X. A genome-wide analysis of the GRAS gene family in upland cotton and a functional study of the role of the GhGRAS55 gene in regulating early maturity in cotton. Biotechnol J 2023; 18:e2300201. [PMID: 37575005 DOI: 10.1002/biot.202300201] [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: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/15/2023]
Abstract
The members of the GRAS gene family play important roles in regulating plant growth and development, but their functions in regulating early plant maturity traits are still unknown. In this study, we used a series of bioinformatics tools to identify GRAS gene family members and investigate the function of the gene family (GhGRAS55) using a genome-wide database of upland cotton samples. A total of 58 members of the GRAS gene family were identified and screened, which were distributed on 21 chromosomes within the whole cotton genome. The results of the phylogenetic analysis showed that the genes of upland cotton, island cotton, African cotton, Raymond cotton, and Arabidopsis were distributed in subfamilies I-VIII, although subfamily II did not contain any upland cotton or Arabidopsis GRAS family members. The structures and other characteristics of the genes in this family were clarified using bioinformatics technology. The transcriptomic sequencing results for early and late maturing cotton species showed that the expression of most GRAS family genes, such as GhGRAS10, GhGRAS5511, and GhGRAS55, was lower in early maturing species than late maturing species. We also found that cotton plants with GhGRAS55 genes that were silenced by virus-induced gene silencing (VIGS) technology showed early bud emergence phenotypes, so it could be speculated that the GhGRAS55 gene has the function of regulating early maturity in cotton.
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Affiliation(s)
- Zhangshu Xie
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
| | - Dan Yang
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
- Agriculture and Rural Bureau of Jingzhou County, Jingzhou, China
| | - Zhenzhong Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Kan Li
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
| | - Penghui Yi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Aiyu Liu
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
| | - Zhonghua Zhou
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
| | - Xiaoju Tu
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
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Tian S, Wan Y, Jiang D, Gong M, Lin J, Xia M, Shi C, Xing H, Li HL. Genome-Wide Identification, Characterization, and Expression Analysis of GRAS Gene Family in Ginger ( Zingiber officinale Roscoe). Genes (Basel) 2022; 14:96. [PMID: 36672837 PMCID: PMC9859583 DOI: 10.3390/genes14010096] [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: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
GRAS family proteins are one of the most abundant transcription factors in plants; they play crucial roles in plant development, metabolism, and biotic- and abiotic-stress responses. The GRAS family has been identified and functionally characterized in some plant species. However, this family in ginger (Zingiber officinale Roscoe), a medicinal crop and non-prescription drug, remains unknown to date. In the present study, 66 GRAS genes were identified by searching the complete genome sequence of ginger. The GRAS family is divided into nine subfamilies based on the phylogenetic analyses. The GRAS genes are distributed unevenly across 11 chromosomes. By analyzing the gene structure and motif distribution of GRAS members in ginger, we found that the GRAS genes have more than one cis-acting element. Chromosomal location and duplication analysis indicated that whole-genome duplication, tandem duplication, and segmental duplication may be responsible for the expansion of the GRAS family in ginger. The expression levels of GRAS family genes are different in ginger roots and stems, indicating that these genes may have an impact on ginger development. In addition, the GRAS genes in ginger showed extensive expression patterns under different abiotic stresses, suggesting that they may play important roles in the stress response. Our study provides a comprehensive analysis of GRAS members in ginger for the first time, which will help to better explore the function of GRAS genes in the regulation of tissue development and response to stress in ginger.
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Affiliation(s)
- Shuming Tian
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404020, China
| | - Yuepeng Wan
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Dongzhu Jiang
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Min Gong
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404020, China
| | - Junyao Lin
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Maoqin Xia
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Cuiping Shi
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Haitao Xing
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Hong-Lei Li
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
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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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Ni L, Wang Z, Liu X, Wu S, Hua J, Liu L, Yin Y, Li H, Gu C. Genome-wide study of the GRAS gene family in Hibiscus hamabo Sieb. et Zucc and analysis of HhGRAS14-induced drought and salt stress tolerance in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111260. [PMID: 35487668 DOI: 10.1016/j.plantsci.2022.111260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 05/24/2023]
Abstract
GRAS proteins are widely distributed plant-specific transcription factors. In this study, we identified 59 GRAS proteins (HhGRASs) from the genomic and transcriptomic datasets of Hibiscus hamabo Sieb. et Zucc. These proteins were phylogenetically divided into nine subfamilies. RNA-seq analysis revealed that most HhGRASs were expressed in response to abiotic stresses. Results from quantitative real-time PCR analysis of nine selected HhGRASs suggested that HhGRAS14 was significantly upregulated under multiple abiotic stresses; therefore, this gene was selected for further study. Silencing HhGRAS14 in H. hamabo reduced the tolerance to drought and salt stress, while overexpression in Arabidopsis thaliana significantly increased the tolerance to drought and salt and reduced the sensitivity to abscisic acid (ABA). In summary, we analyzed the GRAS family of proteins in semi-mangrove plants for the first time and identified a gene that responds to drought and salt stress, which provided the basis for a comprehensive analysis of GRAS genes and insight into the abiotic stress response mechanism in H. hamabo.
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Affiliation(s)
- Longjie Ni
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Xiangdong Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Shuting Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Liangqin Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Huogen Li
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China.
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Tang Z, Song N, Peng W, Yang Y, Qiu T, Huang C, Dai L, Wang B. Genome Identification and Expression Analysis of GRAS Family Related to Development, Hormone and Pathogen Stress in Brachypodium distachyon. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.675177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
GRAS transcription factors are widely present in the plant kingdom and play important roles in regulating multiple plant physiological processes. Brachypodium distachyon is a model for grasses for researching plant-pathogen interactions. However, little is known about the BdGRAS family genes involved in plant response to biotic stress. In this study, we identified 63 genes of the GRAS family in B. distachyon. The phylogenetic analysis showed that BdGRAS genes were divided into ten subfamilies and unevenly distributed on five chromosomes. qRT-PCR results showed that the BdGRAS family genes were involved in the growth and development of B. distachyon. Moreover, the expression of the HAM subfamily genes of BdGRAS changed during the interaction between B. distachyon and Magnaporthe oryzae. Interestingly, BdGRAS31 in the HAM subfamily was regulated by miR171 after inoculation with M. oryzae. These results provide insight into the potential functions of the BdGRAS family in disease resistance.
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Shan Z, Luo X, Wu M, Wei L, Fan Z, Zhu Y. Genome-wide identification and expression of GRAS gene family members in cassava. BMC PLANT BIOLOGY 2020; 20:46. [PMID: 31996133 PMCID: PMC6990482 DOI: 10.1186/s12870-020-2242-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/08/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Cassava is highly tolerant to stressful conditions, especially drought stress conditions; however, the mechanisms underlying this tolerance are poorly understood. The GRAS gene family is a large family of transcription factors that are involved in regulating the growth, development, and stress responses of plants. Currently, GRAS transcription factors have not been systematically studied in cassava, which is the sixth most important crop in the world. RESULTS Seventy-seven MeGRAS genes were identified from the cassava genome database. Phylogenetic analysis revealed that the MeGRAS proteins could be divided into 14 subfamilies. The gene structure and motif compositions of the proteins were considerably conserved within the same subfamily. Duplication events, particularly segmental duplication, were identified as the main driving force for GRAS gene expansion in cassava. Global expression analysis revealed that MeGRAS genes exhibited similar or distinct expression profiles within different tissues among different varieties. Moreover, qRT-PCR analysis revealed the expression patterns of MeGRAS genes in response to abiotic stress (drought, salt, cold, and H2O2), and the results suggest that these genes may have multiple functions. CONCLUSION This study is the first to provide comprehensive information on GRAS gene family members in cassava. The data will increase our understanding of both the molecular basis and the effects of GRAS genes. In addition, the results will contribute further to identifying the responses to various environmental conditions and provide insights into the potential functions of GRAS genes.
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Affiliation(s)
- Zhongying Shan
- Agricultural College, Guangxi University, Nanning, 530005 China
- College of Ecology and Garden Architecture, Dezhou University, Dezhou, 253023 China
| | - Xinglu Luo
- Agricultural College, Guangxi University, Nanning, 530005 China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Nanning, 530004 China
| | - Meiyan Wu
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Limei Wei
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Zhupeng Fan
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Yanmei Zhu
- Agricultural College, Guangxi University, Nanning, 530005 China
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Genome-wide Identification, Classification, Expression and Duplication Analysis of GRAS Family Genes in Juglans regia L. Sci Rep 2019; 9:11643. [PMID: 31406208 PMCID: PMC6691012 DOI: 10.1038/s41598-019-48287-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/01/2019] [Indexed: 12/01/2022] Open
Abstract
Fifty-two GRAS genes are identified in walnut genome. Based on the evolutionary relationship and motif analysis, the walnut GRAS gene family was divided into eight subfamilies, and the sequence features analysis of JrGRAS proteins showed that the JrGRAS protein sequences were both conserved and altered during the evolutionary process. Gene duplication analysis indicated that seven GRAS genes in walnut have orthologous genes in other species, and five of them occurred duplicated events in walnut genome. Expression pattern analysis of the GRAS family genes in walnut showed that two JrGRAS genes (JrCIGRa-b and JrSCL28a) were differentially expressed between flower bud and leaf bud (p < 0.01), and two JrGRAS genes (JrCIGRa-b and JrSCL13b-d) were differentially expressed between the different development stages of flower buds transition (p < 0.01), besides, three hub genes (JrGAIa, JrSCL3f and JrSHRc) were identified by co-expression analysis, which suggested these GRAS genes may play an important role in regulating the development of apical meristem in walnut. This study laid a foundation for further understanding of the function of GRAS family genes in walnut.
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Zhang H, Mi L, Xu L, Yu C, Li C, Chen C. Genome-wide identification, characterization, interaction network and expression profile of GRAS gene family in sweet orange (Citrus sinensis). Sci Rep 2019; 9:2156. [PMID: 30770885 PMCID: PMC6377710 DOI: 10.1038/s41598-018-38185-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/16/2018] [Indexed: 12/31/2022] Open
Abstract
GRAS genes are suggested to be grouped into plant-specific transcriptional regulatory families that have been reported to participate in multiple processes, including plant development, phytohormone signaling, the formation of symbiotic relationships, and response to environmental signals. GRAS genes have been characterized in a number of plant species, but little is known about this gene family in Citrus sinensis. In this study, we identified a total of 50 GRAS genes and characterized the gene structures, conserved motifs, genome localizations and cis-elements within their promoter regions. According to their structural and phylogenetic features, the identified sweet orange GRAS members were divided into 11 subgroups, of which subfamily CsGRAS34 was sweet orange-specific. Based on publicly available RNA-seq data generated from callus, flower, leaf and fruit in sweet orange, we found that some sweet orange GRAS genes exhibited tissue-specific expression patterning. Three of the six members of subfamily AtSHR, particularly CsGRAS9, and two of the six members of subfamily AtPAT1 were preferentially expressed in leaf. Moreover, protein-protein interactions with CsGRAS were predicted. Gene expression analysis was performed under conditions of phosphate deficiency, and GA3 and NaCl treatment to identify the potential functions of GRAS members in regulating stress and hormone responses. This study provides the first comprehensive understanding of the GRAS gene family in the sweet orange genome. As such, the study generates valuable information for further gene function analysis and identifying candidate genes to improve abiotic stress tolerance in citrus plants.
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Affiliation(s)
- Hua Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Limin Mi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Long Xu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changxiu Yu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chen Li
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. .,Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China.
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10
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Zhang B, Liu J, Yang ZE, Chen EY, Zhang CJ, Zhang XY, Li FG. Genome-wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L. BMC Genomics 2018; 19:348. [PMID: 29743013 PMCID: PMC5944045 DOI: 10.1186/s12864-018-4722-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cotton is a major fiber and oil crop worldwide. Cotton production, however, is often threatened by abiotic environmental stresses. GRAS family proteins are among the most abundant transcription factors in plants and play important roles in regulating root and shoot development, which can improve plant resistance to abiotic stresses. However, few studies on the GRAS family have been conducted in cotton. Recently, the G. hirsutum genome sequences have been released, which provide us an opportunity to analyze the GRAS family in G. hirsutum. RESULTS In total, 150 GRAS proteins from G. hirsutum were identified. Phylogenetic analysis showed that these GRAS protins could be classified into 14 subfamilies including SCR, DLT, OS19, LAS, SCL4/7, OS4, OS43, DELLA, PAT1, SHR, HAM, SCL3, LISCL and G_GRAS. The gene structure and motif distribution analysis of the GRAS members in G. hirsutum revealed that many genes of the SHR subfamily have more than one intron, which maybe a kind of form in the evolution of plant by obtaining or losing introns. Chromosomal location and duplication analysis revealed that segment and tandem duplication maybe the reasons of the expension of the GRAS family in cotton. Gene expression analysis confirmed the expression level of GRAS members were up-regulated under different abiotic stresses, suggesting that their possible roles in response to stresses. What's more, higher expression level in root, stem, leaf and pistil also indicated these genes may have effect on the development and breeding of cotton. CONCLUSIONS This study firstly shows the comprehensive analysis of GRAS members in G. hirsutum. Our results provide important information about GRAS family and a framework for stress-resistant breeding in G. hirsutum.
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Affiliation(s)
- Bin Zhang
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - J Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhao E Yang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Er Y Chen
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chao J Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xue Y Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Fu G Li
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, China. .,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Wang Y, Shi S, Zhou Y, Zhou Y, Yang J, Tang X. Genome-wide identification and characterization of GRAS transcription factors in sacred lotus (Nelumbo nucifera). PeerJ 2016; 4:e2388. [PMID: 27635351 PMCID: PMC5012262 DOI: 10.7717/peerj.2388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/29/2016] [Indexed: 11/20/2022] Open
Abstract
The GRAS gene family is one of the most important plant-specific gene families, which encodes transcriptional regulators and plays an essential role in plant development and physiological processes. The GRAS gene family has been well characterized in many higher plants such as Arabidopsis, rice, Chinese cabbage, tomato and tobacco. In this study, we identified 38 GRAS genes in sacred lotus (Nelumbo nucifera), analyzed their physical and chemical characteristics and performed phylogenetic analysis using the GRAS genes from eight representative plant species to show the evolution of GRAS genes in Planta. In addition, the gene structures and motifs of the sacred lotus GRAS proteins were characterized in detail. Comparative analysis identified 42 orthologous and 9 co-orthologous gene pairs between sacred lotus and Arabidopsis, and 35 orthologous and 22 co-orthologous gene pairs between sacred lotus and rice. Based on publically available RNA-seq data generated from leaf, petiole, rhizome and root, we found that most of the sacred lotus GRAS genes exhibited a tissue-specific expression pattern. Eight of the ten PAT1-clade GRAS genes, particularly NnuGRAS-05, NnuGRAS-10 and NnuGRAS-25, were preferentially expressed in rhizome and root. In summary, this is the first in silico analysis of the GRAS gene family in sacred lotus, which will provide valuable information for further molecular and biological analyses of this important gene family.
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Affiliation(s)
- Yu Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Shenglu Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ying Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yu Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xiaoqing Tang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
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