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Rehman S, Bahadur S, Xia W. Unlocking nature's secrets: The pivotal role of WRKY transcription factors in plant flowering and fruit development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112150. [PMID: 38857658 DOI: 10.1016/j.plantsci.2024.112150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
The WRKY transcription factor family is a key player in the regulatory mechanisms of flowering plants, significantly influencing both their biotic and abiotic response systems as well as being vital to numerous physiological and biological functions. Over the past two decades, the functionality of WRKY proteins has been the subject of extensive research in over 50 plant species, with a strong focus on their roles in responding to various stresses. Despite this extensive research, there remains a notable gap in comprehensive studies aimed at understanding how specific WRKY genes directly influence the timing of flowering and fruit development. This review offers an up-to-date look at WRKY family genes and provides insights into the key genes of WRKY to control flowering, enhance fruit ripening and secondary metabolism synthesis, and maintain fruit quality of various plants, including annuals, perennials, medicinal, and crop plants. The WRKY transcription factors serve as critical regulators within the transcriptional regulatory network, playing a crucial role in the precise enhancement of flowering processes. It is also involved in the up-regulation of fruit ripening was strongly demonstrated by combined transcriptomics and metabolomic investigation. Therefore, we speculated that the WRKY family is known to be a key regulator of flowering and fruiting in plants. This detailed insight will enable the identification of the series of molecular occurrences featuring WRKY proteins throughout the stages of flowering and fruiting.
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Affiliation(s)
- Shazia Rehman
- Sanya Nanfan Research Institution, Hainan University, Sanya, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Saraj Bahadur
- College of Forestry, Hainan University, Haikou 570228, China; College of Life and Health Sciences, Hainan University, Haikou 570228, China.
| | - Wei Xia
- Sanya Nanfan Research Institution, Hainan University, Sanya, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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Goyal P, Devi R, Verma B, Hussain S, Arora P, Tabassum R, Gupta S. WRKY transcription factors: evolution, regulation, and functional diversity in plants. PROTOPLASMA 2023; 260:331-348. [PMID: 35829836 DOI: 10.1007/s00709-022-01794-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.
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Affiliation(s)
- Pooja Goyal
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Registered from Guru Nanak Dev University, Amritsar, India
| | - Ritu Devi
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhawana Verma
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahnawaz Hussain
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Palak Arora
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Rubeena Tabassum
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Suphla Gupta
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India.
- Faculty, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Yuan H, Guo W, Zhao L, Yu Y, Chen S, Tao L, Cheng L, Kang Q, Song X, Wu J, Yao Y, Huang W, Wu Y, Liu Y, Yang X, Wu G. Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.). BMC Genomics 2021; 22:375. [PMID: 34022792 PMCID: PMC8141250 DOI: 10.1186/s12864-021-07697-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Members of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, little information is available about WRKY transcription factors in flax (Linum usitatissimum L.). RESULTS In this study, comprehensive genome-wide characterization of the flax WRKY gene family was conducted that led to prediction of 102 LuWRKY genes. Based on bioinformatics-based predictions of structural and phylogenetic features of encoded LuWRKY proteins, 95 LuWRKYs were classified into three main groups (Group I, II, and III); Group II LuWRKYs were further assigned to five subgroups (IIa-e), while seven unique LuWRKYs (LuWRKYs 96-102) could not be assigned to any group. Most LuWRKY proteins within a given subgroup shared similar motif compositions, while a high degree of motif composition variability was apparent between subgroups. Using RNA-seq data, expression patterns of the 102 predicted LuWRKY genes were also investigated. Expression profiling data demonstrated that most genes associated with cellulose, hemicellulose, or lignin content were predominantly expressed in stems, roots, and less in leaves. However, most genes associated with stress responses were predominantly expressed in leaves and exhibited distinctly higher expression levels in developmental stages 1 and 8 than during other stages. CONCLUSIONS Ultimately, the present study provides a comprehensive analysis of predicted flax WRKY family genes to guide future investigations to reveal functions of LuWRKY proteins during plant growth, development, and stress responses.
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Affiliation(s)
- Hongmei Yuan
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
| | - Wendong Guo
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin, 150040, China
| | - Lijuan Zhao
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ying Yu
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Si Chen
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Lei Tao
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Lili Cheng
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Qinghua Kang
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xixia Song
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jianzhong Wu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yubo Yao
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wengong Huang
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ying Wu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yan Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xue Yang
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Guangwen Wu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
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Qu R, Cao Y, Tang X, Sun L, Wei L, Wang K. Identification and expression analysis of the WRKY gene family in Isatis indigotica. Gene 2021; 783:145561. [PMID: 33705810 DOI: 10.1016/j.gene.2021.145561] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 01/14/2021] [Accepted: 03/01/2021] [Indexed: 12/16/2022]
Abstract
The WRKY proteins, which represent one of the largest families of transcriptional regulators in plants, play pivotal roles in regulating multiple processes of growth and development, particularly in diverse stress responses. Isatis indigotica is widely used in Traditional Chinese Medicine and is famous for its use as a dye for the color indigo. However, reports of the WRKY gene family in I. indigotica are limited. In this study, 64 IiWRKY genes encoding proteins with the complete WRKY domain were identified from genome of I. indigotica. Based on their structure and phylogenetic relationships of this gene family in I. indigotica, the IiWRKY genes were classified into three groups: Group I (n = 13), Group II (n = 35) and Group III (n = 16). Sequence alignment revealed that IiWRKY proteins harbored two variants, WRKYRQK and WRKYGKK, of the highly conserved WRKYGQK motif. The number of exons in IiWRKY genes varied from two to 14, with most of IiWRKY genes containing three exons. Investigation of gene duplication demonstrated that 10 and 14 IiWRKY genes were incorporated in tandem and segmental duplication events, respectively. Finally, the expression profiles derived from transcriptome data and quantitative real-time PCR analysis showed distinct expression patterns of these IiWRKY gene in five different organs or in response to four abiotic stresses. Taken together, our results will contribute to functional analysis of IiWRKY genes, and also provide a basis for further clarification of the molecular mechanism of stress responses in this important herb.
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Affiliation(s)
- Renjun Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yiwen Cao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiaoqing Tang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Liqiong Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lian Wei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kangcai Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Bruznican S, De Clercq H, Eeckhaut T, Van Huylenbroeck J, Geelen D. Celery and Celeriac: A Critical View on Present and Future Breeding. FRONTIERS IN PLANT SCIENCE 2020; 10:1699. [PMID: 32038678 PMCID: PMC6987470 DOI: 10.3389/fpls.2019.01699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Cultivated for the crispy petioles and round, fleshy, and flavored hypocotyl celery and celeriac have over two centuries of breeding history in Europe. In this review paper we summarized the most recent advances touching when necessary the historical context of celery and celeriac breeding. In the post genomic era of research, the genome sequence of celery is only partially available. We comprised however in this paper the most important aspects of celery genetics that are available today and have applicability in celery modern cultivars development. We discussed the problems and traits that drive the main celery and celeriac breeding goals, like hybrid seed production, disease resistance, and interesting enlarged hypocotyl and petiole characteristics. Besides the classical breeding traits we covered the potential of integration of existing cultivars as sources for consumer oriented traits like nutraceuticals and health promoting substances. Sustainability is a subject that is continuously growing in popularity and we looked at the genetic base of celery and celeriac that makes them sources for abiotic stress resistance and candidates for phytoremediation. We explored the fundamental concepts gained in various fields of celery and related species research, as resources for future improvement of celery and celeriac germplasm. We forecast what the next years will bring to Apium breeding.
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Affiliation(s)
- Silvia Bruznican
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Production, Ghent University, Ghent, Belgium
| | - Hervé De Clercq
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Eeckhaut
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Johan Van Huylenbroeck
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Danny Geelen
- Department of Plant Production, Ghent University, Ghent, Belgium
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Iquebal MA, Sharma P, Jasrotia RS, Jaiswal S, Kaur A, Saroha M, Angadi UB, Sheoran S, Singh R, Singh GP, Rai A, Tiwari R, Kumar D. RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat. Sci Rep 2019; 9:13917. [PMID: 31558740 PMCID: PMC6763491 DOI: 10.1038/s41598-019-49915-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 01/08/2023] Open
Abstract
Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Amandeep Kaur
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Monika Saroha
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India.
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India.
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