1
|
Chen L, Qin Y, Fan S. Genome-Wide Identification and Characterization of the GRAS Gene Family in Lettuce Revealed That Silencing LsGRAS13 Delayed Bolting. PLANTS (BASEL, SWITZERLAND) 2024; 13:1360. [PMID: 38794431 PMCID: PMC11124801 DOI: 10.3390/plants13101360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Lettuce is susceptible to high-temperature stress during cultivation, leading to bolting and affecting yield. Plant-specific transcription factors, known as GRAS proteins, play a crucial role in regulating plant growth, development, and abiotic stress responses. In this study, the entire lettuce LsGRAS gene family was identified. The results show that 59 LsGRAS genes are unevenly distributed across the nine chromosomes. Additionally, all LsGRAS proteins showed 100% nuclear localization based on the predicted subcellular localization and were phylogenetically classified into nine conserved subfamilies. To investigate the expression profiles of these genes in lettuce, we analyzed the transcription levels of all 59 LsGRAS genes in the publicly available RNA-seq data under the high-temperature treatment conducted in the presence of exogenous melatonin. The findings indicate that the transcript levels of the LsGRAS13 gene were higher on days 6, 9, 15, 18, and 27 under the high-temperature (35/30 °C) treatment with melatonin than on the same treatment days without melatonin. The functional studies demonstrate that silencing LsGRAS13 accelerated bolting in lettuce. Furthermore, the paraffin sectioning results showed that flower bud differentiation in LsGRAS13-silenced plants occurred significantly faster than in control plants. In this study, the LsGRAS genes were annotated and analyzed, and the expression pattern of the LsGRAS gene following melatonin treatment under high-temperature conditions was explored. This exploration provides valuable information and identifies candidate genes associated with the response mechanism of lettuce plants high-temperature stress.
Collapse
Affiliation(s)
- Li Chen
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
| | - Yong Qin
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
| | - Shuangxi Fan
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
- Plant Science and Technology College, Beijing Vocational College of Agriculture, Beijing 102442, China
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Zhang C, Liu S, Liu D, Guo F, Yang Y, Dong T, Zhang Y, Ma C, Tang Z, Li F, Meng X, Zhu M. Genome-wide survey and expression analysis of GRAS transcription factor family in sweetpotato provides insights into their potential roles in stress response. BMC PLANT BIOLOGY 2022; 22:232. [PMID: 35524176 PMCID: PMC9074257 DOI: 10.1186/s12870-022-03618-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The plant-specific GRAS transcription factors play pivotal roles in various adverse environmental conditions. Numerous GRAS genes have been explored and characterized in different plants, however, comprehensive survey on GRASs in sweetpotato is lagging. RESULTS In this study, 72 putative sweetpotato IbGRAS genes with uneven distribution were isolated on 15 chromosomes and classified into 12 subfamilies supported by gene structures and motif compositions. Moreover, both tandem duplication and segmental duplication events played critical roles in the expansion of sweetpotato GRAS genes, and the collinearity between IbGRAS genes and the related orthologs from nine other plants further depicted evolutionary insights into GRAS gene family. RNA-seq analysis under salt stress and qRT-PCR detection of 12 selected IbGRAS genes demonstrated their significant and varying inductions under multiple abiotic stresses (salt, drought, heat and cold) and hormone treatments (ABA, ACC and JA). Consistently, the promoter regions of IbGRAS genes harbored a series of stress- and hormone-associated cis-acting elements. Among them, IbGRAS71, the potential candidate for breeding tolerant plants, was characterized as having transactivation activity in yeasts, while IbGRAS-2/-4/-9 did not. Moreover, a complex interaction relationship between IbGRASs was observed through the interaction network analysis and yeast two-hybrid assays. CONCLUSIONS Our results laid a foundation for further functional identifications of IbGRAS genes, and multiple members may serve as potential regulators for molecular breeding of tolerant sweetpotato.
Collapse
Affiliation(s)
- Chengbin Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Siyuan Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Delong Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Fen Guo
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Yiyu Yang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Yi Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Chen Ma
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Zixuan Tang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Feifan Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
| |
Collapse
|
4
|
Li M, Li B, Yang M, Wang L, Hou G, Lin Y, Zhang Y, Zhang Y, Chen Q, Wang Y, He W, Wang X, Tang H, Yang G, Luo Y. Genome-Wide Identification and Expression of MAPK Gene Family in Cultivated Strawberry and Their Involvement in Fruit Developing and Ripening. Int J Mol Sci 2022; 23:ijms23095201. [PMID: 35563593 PMCID: PMC9104773 DOI: 10.3390/ijms23095201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 12/10/2022] Open
Abstract
Studies on many plants have shown that mitogen-activated protein kinases (MAPKs) are key proteins involved in regulating plant responses to biotic and abiotic stresses. However, their involvement in cultivated strawberry development and ripening remains unclear. In this study, 43 FaMAPK gene family members were identified in the genome of cultivated strawberry (Fragaria × ananassa), phylogenetic analysis indicated that FaMAPKs could be classified into four groups. Systematic analysis of the conserved motif, exon-intron structure showed that there were significant varieties between different groups in structure, but in the same group they were similar. Multiple cis-regulatory elements associated with phytohormone response, and abiotic and biotic stresses were predicted in the promoter regions of FaMAPK genes. Transcriptional analysis showed that all FaMAPK genes were expressed at all developmental stages. Meanwhile, the effect of exogenous ABA and sucrose on the expression profile of FaMAPKs was investigated. Exogenous ABA, sucrose, and ABA plus sucrose treatments upregulated the expression of FaMAPK genes and increased the content of endogenous ABA, sucrose, and anthocyanin in strawberry fruits, suggesting that ABA and sucrose might be involved in the FaMAPK-mediated regulation of strawberry fruit ripening. Based on the obtained results, MAPK genes closely related to the ripening of strawberries were screened to provide a theoretical basis and support for future research on strawberries.
Collapse
Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Binghua Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Min Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Liangxin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoyan Hou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Guichuan Yang
- Departmental and Municipal Co-Construction of Crops Genetic Improvement of Hill Land Key Laboratory of Sichuan, Nanchong 637000, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
5
|
Khan Y, Xiong Z, Zhang H, Liu S, Yaseen T, Hui T. Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:404-416. [PMID: 34854195 DOI: 10.1111/plb.13364] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.
Collapse
Affiliation(s)
- Y Khan
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Z Xiong
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - H Zhang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - S Liu
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - T Yaseen
- Department of Botany, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - T Hui
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
6
|
Jiang L, Sun Q, Wang Y, Chang P, Kong H, Luo C, He X. Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida. PeerJ 2021; 9:e11212. [PMID: 33996278 PMCID: PMC8106399 DOI: 10.7717/peerj.11212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/15/2021] [Indexed: 01/05/2023] Open
Abstract
Background NAC (NAM, ATAF1/2, and CUC2) transcription factors play an important role in plant growth and development. However, in tumorous stem mustard (Brassica juncea var. tumida), one of the economically important crops cultivated in southwest China and some southeast Asian countries, reports on the identification of NAC family genes are lacking. In this study, we conducted a genome-wide investigation of the NAC family genes in B. juncea var. tumida, based on its recently published genome sequence data. Methods The NAC genes were identified in B. juncea var. tumida using the bioinformatics approach on the whole genome level. Additionally, the expression of BjuNAC genes was analyzed under high- and low-temperature stresses by quantitative real-time PCR (qRT-PCR). Results A total of 300 BjuNAC genes were identified, of which 278 were mapped to specific chromosomes. Phylogenetic analysis of B. juncea var. tumida, Brassica rapa, Brassica nigra, rice and Arabidopsis thaliana NAC proteins revealed that all NAC genes were divided into 18 subgroups. Furthermore, gene structure analysis showed that most of the NAC genes contained two or three exons. Conserved motif analysis revealed that BjuNAC genes contain a conserved NAM domain. Additionally, qRT-PCR data indicated that thirteen BjuNAC genes with a varying degree of up-regulation during high-temperature stress. Conversely, four BjuNAC genes (BjuNAC006, BjuNAC083, BjuNAC170 and BjuNAC223) were up-regulated and two BjuNAC genes (BjuNAC074 and BjuNAC295) down-regulated under low temperature, respectively. Together, the results of this study provide a strong foundation for future investigation of the biological function of NAC genes in B. juncea var. tumida.
Collapse
Affiliation(s)
- Longxing Jiang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Quan Sun
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yu Wang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Pingan Chang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Haohuan Kong
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Changshu Luo
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Xiaohong He
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| |
Collapse
|
7
|
Li M, Xie F, Li Y, Gong L, Luo Y, Zhang Y, Chen Q, Wang Y, Lin Y, Zhang Y, Wang X, Tang H. Genome-Wide Analysis of the Heat Shock Transcription Factor Gene Family in Brassica juncea: Structure, Evolution, and Expression Profiles. DNA Cell Biol 2020; 39:1990-2004. [PMID: 32945687 DOI: 10.1089/dna.2020.5922] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Heat shock transcription factor (HSF) is ubiquitous in the whole biological world and plays an important role in regulating growth and development and responses to environment stress. In this study, a total of 60 HSF transcription factors in Brassica juncea genome were identified and analyzed. Phylogenetic analysis showed that HSF genes were divided into three groups namely: A, B, and C, of which group A was further divided into nine subgroups (A1-A9). The analysis of gene structure and conserved motifs showed that some homologous genes are highly conserved. There was strong conservative microcollinearity among Brassica rapa, B. juncea, and Brassica oleracea, which provides a basis for studying the replication of gene families. Moreover, the results revealed that the promoter regions of BjuHSF genes were rich in cis-elements related to growth and development, hormone signal, and stress response. The prediction of protein interaction results showed that HSFs could interact with multiple transcription factors and proteins in the genome, while functional annotation revealed that BjuHSF genes were involved in many biological processes. The expression patterns of BjuHSF genes were analyzed by qPCR, and the results showed that these genes were closely linked to stress response, hormones, and development process. These results are a foundation for further analysis of the regulation mechanism of HSF gene family.
Collapse
Affiliation(s)
- Mengyao Li
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
| | - Fangjie Xie
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
| | - Yanwen Li
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
| | - Li Gong
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
| | - Ya Luo
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
| | - Yong Zhang
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
| | - Qing Chen
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yuanxiu Lin
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yunting Zhang
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaorong Wang
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Haoru Tang
- College of Horticulture and Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
8
|
Li M, Xie F, Li J, Sun B, Luo Y, Zhang Y, Chen Q, Wang Y, Zhang F, Zhang Y, Lin Y, Wang X, Tang H. Tumorous Stem Development of Brassica Juncea: A Complex Regulatory Network of Stem Formation and Identification of Key Genes in Glucosinolate Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1006. [PMID: 32784853 PMCID: PMC7466272 DOI: 10.3390/plants9081006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 11/16/2022]
Abstract
Stem mustard is a stem variety of mustard, an important Brassica vegetable. The formation and development of the tumorous stem, which is the key organ for the direct yield and quality, is a complex biological process involving morphogenesis, material accumulation and gene regulation. In this study, we demonstrated through anatomical studies that stem swelling is mainly dependent on the increase in the number of cells and the volume of parenchyma cells in the cortex and pith. To further understand transcript and metabolic changes during stem swelling, we obtained 27,901 differentially expressed genes, of which 671 were specifically detected using transcriptome sequencing technology in all four stages of stem swelling. Functional annotation identified enrichment for genes involved in photosynthesis, energy metabolism, cell growth, sulfur metabolism and glucosinolate biosynthesis. Glucosinolates are a group of nitrogen- and sulfur-containing secondary metabolites, which largely exist in the Cruciferous vegetables. HPLC analysis of the contents and components of glucosinolates in four different stem development stages revealed eight glucosinolates, namely, three aliphatic glucosinolates (sinigrin, glucoalyssin and gluconapin), four indole glucosinolates (4-hydroxyglucobrassicin, glucobrassicin, 4-methoxyglucobrassicin and neoglucobrassicin) and one aromatic glucosinolate (gluconasturtiin). All these types of glucosinolates showed a significant downward trend during the stem swelling period. The content of aliphatic glucosinolates was the highest, with sinigrin being the main component. In addition, qPCR was used to validate the expression of nine genes involved in glucosinolate biosynthesis. Most of these genes were down-regulated during stem swelling in qPCR, which is consistent with transcriptome data. These data provide a basic resource for further molecular and genetic research on Brassica juncea.
Collapse
Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
| | - Fangjie Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
| | - Jie Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (Y.W.); (F.Z.); (Y.Z.); (Y.L.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
9
|
Lu X, Liu W, Xiang C, Li X, Wang Q, Wang T, Liu Z, Zhang J, Gao L, Zhang W. Genome-Wide Characterization of GRAS Family and Their Potential Roles in Cold Tolerance of Cucumber ( Cucumis sativus L.). Int J Mol Sci 2020; 21:E3857. [PMID: 32485801 PMCID: PMC7312588 DOI: 10.3390/ijms21113857] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cucumber (Cucumis sativus L.) is one of the most important cucurbit vegetables but is often subjected to stress during cultivation. GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) genes encode a family of transcriptional factors that regulate plant growth and development. In the model plant Arabidopsis thaliana, GRAS family genes function in formation of axillary meristem and root radial structure, phytohormone (gibberellin) signal transduction, light signal transduction and abiotic/biological stress. In this study, a gene family was comprehensively analyzed from the aspects of evolutionary tree, gene structure, chromosome location, evolutionary and expression pattern by means of bioinformatics; 37 GRAS gene family members have been screened from cucumber. We reconstructed an evolutionary tree based on multiple sequence alignment of the typical GRAS domain and conserved motif sequences with those of other species (A. thaliana and Solanum lycopersicum). Cucumber GRAS family was divided into 10 groups according to the classification of Arabidopsis and tomato genes. We conclude that tandem and segmental duplication have played important roles in the expansion and evolution of the cucumber GRAS (CsaGRAS) family. Expression patterns of CsaGRAS genes in different tissues and under cold treatment, combined with gene ontology annotation and interaction network analysis, revealed potentially different functions for CsaGRAS genes in response to cold tolerance, with members of the SHR, SCR and DELLA subfamilies likely playing important roles. In conclusion, this study provides valuable information and candidate genes for improving cucumber tolerance to cold stress.
Collapse
Affiliation(s)
- Xiaohong Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Chenggang Xiang
- College of Life Science and Technology, HongHe University, Mengzi 661100, China;
| | - Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Qing Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Tao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Zixi Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Jiali Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| |
Collapse
|
10
|
Xu X, Feng G, Huang L, Yang Z, Liu Q, Shuai Y, Zhang X. Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass. Mol Biol Rep 2020; 47:1845-1857. [PMID: 32026320 DOI: 10.1007/s11033-020-05279-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/24/2020] [Indexed: 11/24/2022]
Abstract
The GRAS gene family is a family of transcription factors that regulates plant growth and development. Despite being well-studied in many plant species, little is known about this gene family in orchardgrass (Dactylis glomerata L.), one of the top four economically important perennial forage grasses cultivated worldwide. We identified 46 GRAS genes in orchardgrass and analyzed their characteristics by phylogenetic, gene structural, motifs and expression patterns analysis. The phylogenetic analysis of eight species revealed that DgGRAS family had the evolutional conservation and closer homology relationship with the GRAS family of rice, barley and Brachypodium distachyon. Moreover, 46 DgGRAS proteins were divided into eight subfamilies based on the tree topology and rice or Arabidopsis classification, and LISCL subfamily was the largest one. Besides, we found that the motif 15 may be unique to the orchardgrass LISCL subfamily, and the motif 6 and motif 17 had indispensable functions in the orchardgrass LISCL subfamily. We further analyzed the expression profiles of DgGRAS genes at mature and seeding stage. And we found that DgGRAS17 played an important role in the growth and development no matter what stage it was at. DgGRAS5, DgGRAS28, DgGRAS31, DgGRAS42 and DgGRAS44 got involved in processes of the growth and development at seeding stage instead of mature stage. These results indicated that the major expression patterns and detailed functions of the DgGRAS genes varied with developmental stages. Taken together, this is the first systematic analysis of the GRAS gene family in the orchardgrass genome and the results provide insights into the potential functions of GRAS genes.
Collapse
Affiliation(s)
- Xiaoheng Xu
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guangyan Feng
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linkai Huang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongfu Yang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiuxu Liu
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yang Shuai
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinquan Zhang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China.
| |
Collapse
|
11
|
Revalska M, Radkova M, Zagorchev L, Iantcheva A. Functional GUSassay of GRAStranscription factor from Medicago truncatula. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1649096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Miglena Revalska
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Mariana Radkova
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Lyuben Zagorchev
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Anelia Iantcheva
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| |
Collapse
|