1
|
Wang Z, You L, Gong N, Li C, Li Z, Shen J, Wan L, Luo K, Su X, Feng L, Chen S, Lin W. Comprehensive Expression Analysis of the WRKY Gene Family in Phoebe bournei under Drought and Waterlogging Stresses. Int J Mol Sci 2024; 25:7280. [PMID: 39000387 PMCID: PMC11242546 DOI: 10.3390/ijms25137280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/26/2024] [Accepted: 06/30/2024] [Indexed: 07/16/2024] Open
Abstract
In response to biotic and abiotic stresses, the WRKY gene family plays a crucial role in plant growth and development. This study focused on Phoebe bournei and involved genome-wide identification of WRKY gene family members, clarification of their molecular evolutionary characteristics, and comprehensive mapping of their expression profiles under diverse abiotic stress conditions. A total of 60 WRKY gene family members were identified, and their phylogenetic classification revealed three distinct groups. A conserved motif analysis underscored the significant conservation of motif 1 and motif 2 among the majority of PbWRKY proteins, with proteins within the same class sharing analogous gene structures. Furthermore, an examination of cis-acting elements and protein interaction networks revealed several genes implicated in abiotic stress responses in P. bournei. Transcriptomic data were utilized to analyze the expression patterns of WRKY family members under drought and waterlogged conditions, with subsequent validation by quantitative real-time PCR (RT-qPCR) experiments. Notably, PbWRKY55 exhibited significant expression modulation under drought stress; PbWRKY36 responded prominently to waterlogging stress; and PbWRKY18, PbWRKY38, and PbWRKY57 demonstrated altered expression under both drought and waterlogging stresses. This study revealed the PbWRKY candidate genes that potentially play a pivotal role in enhancing abiotic stress resilience in P. bournei. The findings have provided valuable insights and knowledge that can guide further research aimed at understanding and addressing the impacts of abiotic stress within this species.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.W.); (L.Y.); (N.G.); (C.L.); (Z.L.); (J.S.); (L.W.); (K.L.); (X.S.); (L.F.)
| | - Wenjun Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.W.); (L.Y.); (N.G.); (C.L.); (Z.L.); (J.S.); (L.W.); (K.L.); (X.S.); (L.F.)
| |
Collapse
|
2
|
Gelaw TA, Sanan-Mishra N. Molecular priming with H 2O 2 and proline triggers antioxidant enzyme signals in maize seedlings during drought stress. Biochim Biophys Acta Gen Subj 2024; 1868:130633. [PMID: 38762030 DOI: 10.1016/j.bbagen.2024.130633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Drought and water stress impose major limitations to crops, including Maize, as they affect the plant biology at multiple levels. Drought activates the cellular signalling machinery to maintain the osmotic and ROS homeostasis for controlling plant response and adaptation to stress. Molecular priming of seeds plays a significant role in imparting stress tolerance by helping plants to remember the stress, which improves their response when they encounter stress again. METHODS In this study, we examined the effect of priming maize seeds with H2O2 and proline, individually or in combination, on response to drought stress. We investigated the role of molecular priming on the physiological, biochemical and molecular response of maize seedlings during drought stress. RESULTS We observed that seed-priming played a significant role in mediating stress tolerance of seedlings under drought stress as indicated by changes in growth, biochemical properties, pigment and osmolyte accumulation, antioxidant enzyme activities, gas exchange parameters and gene expression. Seed-priming resulted in reduced expression of specific miRNAs to increase target transcripts associated with synthesis of osmolytes and maintenance of ROS homeostasis for reducing potential damage to the cellular components. CONCLUSIONS Seed-priming induced changes in the growth, biochemical properties, pigment and osmolyte accumulation, antioxidant enzyme activities, gas exchange parameters and gene expression, though the response was dependent on the genotype, as well as concentration and combination of the priming agents.
Collapse
Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, 110067 New Delhi, India; Department of Biotechnology, College of Agriculture and Natural Resource Sciences, Debre Birhan University, 445 Debre Birhan, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, 110067 New Delhi, India.
| |
Collapse
|
3
|
Qu J, Xiao P, Zhao ZQ, Wang YL, Zeng YK, Zeng X, Liu JH. Genome-wide identification, expression analysis of WRKY transcription factors in Citrus ichangensis and functional validation of CiWRKY31 in response to cold stress. BMC PLANT BIOLOGY 2024; 24:617. [PMID: 38937686 PMCID: PMC11212357 DOI: 10.1186/s12870-024-05320-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Ichang papeda (Citrus ichangensis), a wild perennial plant of the Rutaceae family, is a cold-hardy plant. WRKY transcription factors are crucial regulators of plant growth and development as well as abiotic stress responses. However, the WRKY genes in C. ichangensis (CiWRKY) and their expression patterns under cold stress have not been thoroughly investigated, hindering our understanding of their role in cold tolerance. RESULTS In this study, a total of 52 CiWRKY genes identified in the genome of C. ichangensis were classified into three main groups and five subgroups based on phylogenetic analysis. Comprehensive analyses of motif features, conserved domains, and gene structures were performed. Segmental duplication plays a significant role in the CiWRKY gene family expansion. Cis-acting element analysis revealed the presence of various stress-responsive elements in the promoters of the majority of CiWRKYs. Gene ontology (GO) analysis and protein-protein interaction predictions indicate that the CiWRKYs exhibit crucial roles in regulation of both development and stress response. Expression profiling analysis demonstrates that 14 CiWRKYs were substantially induced under cold stress. Virus-induced gene silencing (VIGS) assay confirmed that CiWRKY31, one of the cold-induced WRKYs, functions positively in regulation of cold tolerance. CONCLUSION Sequence and protein properties of CiWRKYs were systematically analyzed. Among the 52 CiWRKY genes 14 members exhibited cold-responsive expression patterns, and CiWRKY31 was verified to be a positive regulator of cold tolerance. These findings pave way for future investigations to understand the molecular functions of CiWRKYs in cold tolerance and contribute to unravelling WRKYs that may be used for engineering cold tolerance in citrus.
Collapse
Affiliation(s)
- Jing Qu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Xiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ze-Qi Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yi-Lei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yi-Ke Zeng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xi Zeng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ji-Hong Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
4
|
Vodiasova E, Sinchenko A, Khvatkov P, Dolgov S. Genome-Wide Identification, Characterisation, and Evolution of the Transcription Factor WRKY in Grapevine ( Vitis vinifera): New View and Update. Int J Mol Sci 2024; 25:6241. [PMID: 38892428 PMCID: PMC11172563 DOI: 10.3390/ijms25116241] [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: 05/03/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
WRKYs are a multigenic family of transcription factors that are plant-specific and involved in the regulation of plant development and various stress response processes. However, the evolution of WRKY genes is not fully understood. This family has also been incompletely studied in grapevine, and WRKY genes have been named with different numbers in different studies, leading to great confusion. In this work, 62 Vitis vinifera WRKY genes were identified based on six genomes of different cultivars. All WRKY genes were numbered according to their chromosomal location, and a complete revision of the numbering was performed. Amino acid variability between different cultivars was assessed for the first time and was greater than 5% for some WRKYs. According to the gene structure, all WRKYs could be divided into two groups: more exons/long length and fewer exons/short length. For the first time, some chimeric WRKY genes were found in grapevine, which may play a specific role in the regulation of different processes: VvWRKY17 (an N-terminal signal peptide region followed by a non-cytoplasmic domain) and VvWRKY61 (Frigida-like domain). Five phylogenetic clades A-E were revealed and correlated with the WRKY groups (I, II, III). The evolution of WRKY was studied, and we proposed a WRKY evolution model where there were two dynamic phases of complexity and simplification in the evolution of WRKY.
Collapse
Affiliation(s)
- Ekaterina Vodiasova
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 299011 Sevastopol, Russia
| | - Anastasiya Sinchenko
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
| | - Pavel Khvatkov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
| | - Sergey Dolgov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 142290 Puschino, Russia
| |
Collapse
|
5
|
Yu H, Li J, Chang X, Dong N, Chen B, Wang J, Zha L, Gui S. Genome-wide identification and expression profiling of the WRKY gene family reveals abiotic stress response mechanisms in Platycodon grandiflorus. Int J Biol Macromol 2024; 257:128617. [PMID: 38070802 DOI: 10.1016/j.ijbiomac.2023.128617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 01/26/2024]
Abstract
The WRKY family of transcription factors (TFs) is an important gene family involved in abiotic stress responses. Although the roles of WRKY TFs in plant abiotic stress responses are well studied, little is known about the stress-induced changes in WRKY family in Platycodon grandiflorus. 42 PgWRKY genes in seven subgroups were identified in the P. grandiflorus genome. The content of eight platycodins in P. grandiflorus was investigated under cold, heat, and drought stresses. Platycodin D levels significantly increased under three abiotic stresses, while the content changes of other platycodins varied. Transcriptome analysis showed that different WRKY family members exhibited varied expression patterns under different abiotic stresses. PgWRKY20, PgWRKY26, and PgWRKY39 were identified as three key candidates for temperature and drought stress responses, and were cloned and analysed for sequence characteristics, gene structure, subcellular localisation, and expression patterns. The RT-qPCR results showed that PgWRKY26 expression significantly increased after heat stress for 48 h, cold stress for 6 h, and drought stress for 2 d (DS_2 d). The PgWRKY39 expression level significantly increased at DS_2 d. This study provides a theoretical basis for clarifying the molecular mechanism of the abiotic stress responses of the WRKY gene family in P. grandiflorus.
Collapse
Affiliation(s)
- Hanwen Yu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Jing Li
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Xiangwei Chang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Nan Dong
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Bowen Chen
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Jutao Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Liangping Zha
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Institute of Conservation and Development of Traditional Chinese Medicine Resources, Anhui Academy of Chinese Medicine, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei 230012, China.
| | - Shuangying Gui
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Institute of Pharmaceutics, Anhui Academy of Chinese Medicine, Hefei, China; Anhui Province Key Laboratory of Pharmaceutical Technology and Application, Anhui University of Chinese Medicine, Hefei, China; MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Wang N, Song G, Zhang F, Shu X, Cheng G, Zhuang W, Wang T, Li Y, Wang Z. Characterization of the WRKY Gene Family Related to Anthocyanin Biosynthesis and the Regulation Mechanism under Drought Stress and Methyl Jasmonate Treatment in Lycoris radiata. Int J Mol Sci 2023; 24:ijms24032423. [PMID: 36768747 PMCID: PMC9917153 DOI: 10.3390/ijms24032423] [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: 12/07/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/28/2023] Open
Abstract
Lycoris radiata, belonging to the Amaryllidaceae family, is a well-known Chinese traditional medicinal plant and susceptible to many stresses. WRKY proteins are one of the largest families of transcription factors (TFs) in plants and play significant functions in regulating physiological metabolisms and abiotic stress responses. The WRKY TF family has been identified and investigated in many medicinal plants, but its members and functions are not identified in L. radiata. In this study, a total of 31 L. radiata WRKY (LrWRKY) genes were identified based on the transcriptome-sequencing data. Next, the LrWRKYs were divided into three major clades (Group I-III) based on the WRKY domains. A motif analysis showed the members within same group shared a similar motif component, indicating a conservational function. Furthermore, subcellular localization analysis exhibited that most LrWRKYs were localized in the nucleus. The expression pattern of the LrWRKY genes differed across tissues and might be important for Lycoris growth and flower development. There were large differences among the LrWRKYs based on the transcriptional levels under drought stress and MeJA treatments. Moreover, a total of 18 anthocyanin components were characterized using an ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis and pelargonidin-3-O-glucoside-5-O-arabinoside as well as cyanidin-3-O-sambubioside were identified as the major anthocyanin aglycones responsible for the coloration of the red petals in L. radiata. We further established a gene-to-metabolite correlation network and identified LrWRKY3 and LrWRKY27 significant association with the accumulation of pelargonidin-3-O-glucoside-5-O-arabinoside in the Lycoris red petals. These results provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in anthocyanin biosynthesis and in response to drought stress and MeJA treatment.
Collapse
Affiliation(s)
- Ning Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
| | - Guowei Song
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
| | - Xiaochun Shu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
| | - Guanghao Cheng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
| | - Weibing Zhuang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
| | - Tao Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
| | - Yuhang Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
| | - Zhong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), 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
- Correspondence:
| |
Collapse
|
8
|
Genome-Wide Identification and Expression Pattern of the GRAS Gene Family in Pitaya ( Selenicereus undatus L.). BIOLOGY 2022; 12:biology12010011. [PMID: 36671704 PMCID: PMC9854919 DOI: 10.3390/biology12010011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
The GRAS gene family is one of the most important families of transcriptional factors that have diverse functions in plant growth and developmental processes including axillary meristem patterning, signal-transduction, cell maintenance, phytohormone and light signaling. Despite their importance, the function of GRAS genes in pitaya fruit (Selenicereus undatus L.) remains unknown. Here, 45 members of the HuGRAS gene family were identified in the pitaya genome, which was distributed on 11 chromosomes. All 45 members of HuGRAS were grouped into nine subfamilies using phylogenetic analysis with six other species: maize, rice, soybeans, tomatoes, Medicago truncatula and Arabidopsis. Among the 45 genes, 12 genes were selected from RNA-Seq data due to their higher expression in different plant tissues of pitaya. In order to verify the RNA-Seq data, these 12 HuGRAS genes were subjected for qRT-PCR validation. Nine HuGRAS genes exhibited higher relative expression in different tissues of the plant. These nine genes which were categorized into six subfamilies inlcuding DELLA (HuGRAS-1), SCL-3 (HuGRAS-7), PAT1 (HuGRAS-34, HuGRAS-35, HuGRAS-41), HAM (HuGRAS-37), SCR (HuGRAS-12) and LISCL (HuGRAS-18, HuGRAS-25) might regulate growth and development in the pitaya plant. The results of the present study provide valuable information to improve tropical pitaya through a molecular and conventional breeding program.
Collapse
|
9
|
Luo T, Song Y, Gao H, Wang M, Cui H, Ji C, Wang J, Yuan L, Li R. Genome-wide identification and functional analysis of Dof transcription factor family in Camelina sativa. BMC Genomics 2022; 23:812. [PMID: 36476342 PMCID: PMC9730592 DOI: 10.1186/s12864-022-09056-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Dof transcription factors (TFs) containing C2-C2 zinc finger domains are plant-specific regulatory proteins, playing crucial roles in a variety of biological processes. However, little is known about Dof in Camelina sativa, an important oil crop worldwide, with high stress tolerance. In this study, a genome-wide characterization of Dof proteins is performed to examine their basic structural characteristics, phylogenetics, expression patterns, and functions to identify the regulatory mechanism underlying lipid/oil accumulation and the candidate Dofs mediating stress resistance regulation in C. sativa. RESULTS Total of 103 CsDof genes unevenly distributed on 20 chromosomes were identified from the C. sativa genome, and they were classified into four groups (A, B, C and D) based on the classification of Arabidopsis Dof gene family. All of the CsDof proteins contained the highly-conserved typic CX2C-X21-CX2C structure. Segmental duplication and purifying selection were detected for CsDof genes. 61 CsDof genes were expressed in multiple tissues, and 20 of them showed tissue-specific expression patterns, suggesting that CsDof genes functioned differentially in different tissues of C. sativa. Remarkably, a set of CsDof members were detected to be possible involved in regulation of oil/lipid biosynthesis in C. sativa. Six CsDof genes exhibited significant expression changes in seedlings under salt stress treatment. CONCLUSIONS The present data reveals that segmental duplication is the key force responsible for the expansion of CsDof gene family, and a strong purifying pressure plays a crucial role in CsDofs' evolution. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Collectively, our findings provide a foundation for deep understanding the roles of CsDofs and genetic improvements of oil yield and salt stress tolerance in this species and the related crops.
Collapse
Affiliation(s)
- Tao Luo
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Yanan Song
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Huiling Gao
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Meng Wang
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Hongli Cui
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Chunli Ji
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Jiping Wang
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Lixia Yuan
- grid.495248.60000 0004 1778 6134College of Biological Science and Technology, Jinzhong University, Jinzhong, 030600 Shanxi China
| | - Runzhi Li
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| |
Collapse
|
10
|
Du Z, You S, Yang D, Tao Y, Zhu Y, Sun W, Chen Z, Li J. Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1048822. [PMID: 36466244 PMCID: PMC9714628 DOI: 10.3389/fpls.2022.1048822] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Kandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied. METHODS The KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis. RESULTS A total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated. CONCLUSIONS Seventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress.
Collapse
Affiliation(s)
- Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Shixian You
- Section of Maritime Space and Island Management, Yuhuan Municipal Bureau of Natural Resources and Planning, Yuhuan, China
| | - Dang Yang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Yutian Tao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Yunxiao Zhu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Wen Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Zhengman Chen
- Department of Security Production Management, Taizhou Circular Economy Development Co., Ltd., Taizhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| |
Collapse
|
11
|
Identification of the WRKY Gene Family and Characterization of Stress-Responsive Genes in Taraxacum kok-saghyz Rodin. Int J Mol Sci 2022; 23:ijms231810270. [PMID: 36142183 PMCID: PMC9499643 DOI: 10.3390/ijms231810270] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
WRKY transcription factors present unusual research value because of their critical roles in plant physiological processes and stress responses. Taraxacum kok-saghyz Rodin (TKS) is a perennial herb of dandelion in the Asteraceae family. However, the research on TKS WRKY TFs is limited. In this study, 72 TKS WRKY TFs were identified and named. Further comparison of the core motifs and the structure of the WRKY motif was analyzed. These TFs were divided into three groups through phylogenetic analysis. Genes in the same group of TkWRKY usually exhibit a similar exon-intron structure and motif composition. In addition, virtually all the TKS WRKY genes contained several cis-elements related to stress response. Expression profiling of the TkWRKY genes was assessed using transcriptome data sets and Real-Time RT-PCR data in tissues during physiological development, under abiotic stress and hormonal treatments. For instance, the TkWRKY18, TkWRKY23, and TkWRKY38 genes were significantly upregulated during cold stress, whereas the TkWRKY21 gene was upregulated under heat-stress conditions. These results could provide a basis for further studies on the function of the TKS WRKY gene family and genetic amelioration of TKS germplasm.
Collapse
|
12
|
Xu X, Tian Z, Xing A, Wu Z, Li X, Dai L, Yang Y, Yin J, Wang Y. Nitric Oxide Participates in Aluminum-Stress-Induced Pollen Tube Growth Inhibition in Tea (Camelliasinensis) by Regulating CsALMTs. PLANTS 2022; 11:plants11172233. [PMID: 36079615 PMCID: PMC9460577 DOI: 10.3390/plants11172233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022]
Abstract
Nitric oxide (NO), as a signal molecule, is involved in the mediation of heavy-metal-stress-induced physiological responses in plants. In this study, we investigated the effect of NO on Camellia sinensis pollen tubes exposed to aluminum (Al) stress. Exogenous application of the NO donor decreased the pollen germination rate and pollen tube length and increased the malondialdehyde (MDA) content and antioxidant enzyme activities under Al stress. Simultaneously, the NO donor effectively increased NO content in pollen tube of C. sinensis under Al stress and could aggravate the damage of Al3+ to C. sinensis pollen tubes by promoting the uptake of Al3+. In addition, application of the NO-specific scavenger significantly alleviated stress damage in C. sinensis pollen tube under Al stress. Moreover, 18 CsALMT members from a key Al-transporting gene family were identified, which could be divided into four subclasses. Pearson correlation analysis showed the expression level of CsALMT8 showed significant positive correlation with the Al3+ concentration gradient and NO levels, but a significant negative correlation with pollen germination rate and pollen tube length. The expression level of CsALMT5 was negatively correlated with the Al3+ concentration gradient and NO level, and positively correlated with pollen germination rate and pollen tube length. The expression level of CsALMT17 showed a significant negative correlation with Al3+ concentration and NO content in pollen tubes, but significant positive correlation with pollen germination rate and pollen tube length. In conclusion, a complex signal network regulated by NO-mediated CsALMTs revealed that CsALMT8 was regulated by environmental Al3+ and NO to assist Al3+ entry into pollen tubes; CsALMT5 might be influenced by the Al3+ signal, stimulate malate efflux in vacuoles and chelate with Al3+ to detoxify Al in C. sinensis pollen tube.
Collapse
Affiliation(s)
- Xiaohan Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiqiang Tian
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Anqi Xing
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zichen Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuyan Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingcong Dai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyang Yang
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Juan Yin
- Jiangsu Maoshan Tea Resorts Company Limited, Changzhou 213200, China
| | - Yuhua Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: ; Tel.: +86-133-7609-2013
| |
Collapse
|
13
|
Ayoub Khan M, Dongru K, Yifei W, Ying W, Penghui A, Zicheng W. Characterization of WRKY Gene Family in Whole-Genome and Exploration of Flowering Improvement Genes in Chrysanthemum lavandulifolium. FRONTIERS IN PLANT SCIENCE 2022; 13:861193. [PMID: 35557735 PMCID: PMC9087852 DOI: 10.3389/fpls.2022.861193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/02/2022] [Indexed: 05/27/2023]
Abstract
Chrysanthemum is a well-known ornamental plant with numerous uses. WRKY is a large family of transcription factors known for a variety of functions ranging from stress resistance to plant growth and development. Due to the limited research on the WRKY family in chrysanthemums, we examined them for the first time in Chrysanthemum lavandulifolium. A total of 138 ClWRKY genes were identified, which were classified into three groups. Group III in C. lavandulifolium contains 53 members, which is larger than group III of Arabidopsis. The number of introns varied from one to nine in the ClWRKY gene family. The "WRKYGQK" motif is conserved in 118 members, while other members showed slight variations. AuR and GRE responsive cis-acting elements were located in the promoter region of WRKY members, which are important for plant development and flowering induction. In addition, the W box was present in most genes; the recognition site for the WRKY gene may play a role in autoregulation and cross-regulation. The expression of the most variable 19 genes in terms of different parameters was observed at different stages. Among them, 10 genes were selected due to the presence of CpG islands, while nine genes were selected based on their close association with important Arabidopsis genes related to floral traits. ClWRKY36 and ClWRKY45 exhibit differential expression at flowering stages in the capitulum, while methylation is detected in three genes, including ClWRKY31, ClWRKY100, and ClWRKY129. Our results provide a basis for further exploration of WRKY members to find their functions in plant growth and development, especially in flowering traits.
Collapse
|
14
|
Du Z, You S, Zhao X, Xiong L, Li J. Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata. Front Genet 2022; 13:875316. [PMID: 35432463 PMCID: PMC9008847 DOI: 10.3389/fgene.2022.875316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/11/2022] [Indexed: 11/25/2022] Open
Abstract
Background:Kandelia obovata, a dominant mangrove species, is widely distributed in tropical and subtropical areas. Low temperature is the major abiotic stress that seriously limits the survival and growth of mangroves. WRKY transcription factors (TFs) play vital roles in responses to biotic and abiotic stresses. However, genome-wide analysis of WRKY genes in K. obovata and their responses to chilling stress have not been reported. Methods: Bioinformatic analysis was used to identify and characterize the K. obovata WRKY (KoWRKY) gene family, RNA-seq and qRT–PCR analyses were employed to screen KoWRKYs that respond to chilling stress. Results: Sixty-four KoWRKYs were identified and they were unevenly distributed across all 18 K. obovata chromosomes. Many orthologous WRKY gene pairs were identified between Arabidopsis thaliana and K. obovata, showing high synteny between the two genomes. Segmental duplication events were found to be the major force driving the expansion for the KoWRKY gene family. Most of the KoWRKY genes contained several kinds of hormone- and stress-responsive cis-elements in their promoter. KoWRKY proteins belonged to three groups (I, II, III) according to their conserved WRKY domains and zinc-finger structure. Expression patterns derived from the RNA-seq and qRT–PCR analyses revealed that 9 KoWRKYs were significantly upregulated during chilling acclimation in the leaves. KEGG pathway enrichment analysis showed that the target genes of KoWRKYs were significantly involved in 11 pathways, and coexpression network analysis showed that 315 coexpressed pairs (KoWRKYs and mRNAs) were positively correlated. Conclusion: Sixty-four KoWRKYs from the K. obovata genome were identified, 9 of which exhibited chilling stress-induced expression patterns. These genes represent candidates for future functional analysis of KoWRKYs involved in chilling stress related signaling pathways in K. obovata. Our results provide a basis for further analysis of KoWRKY genes to determine their functions and molecular mechanisms in K. obovata in response to chilling stress.
Collapse
Affiliation(s)
- Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Shixian You
- Yuhuan Municipal Bureau of Natural Resources and Planning, Yuhuan, China
| | - Xin Zhao
- Marine Academy of Zhejiang Province, Hangzhou, China
| | - Lihu Xiong
- Marine Academy of Zhejiang Province, Hangzhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- *Correspondence: Junmin Li,
| |
Collapse
|
15
|
Wu W, Zhu S, Xu L, Zhu L, Wang D, Liu Y, Liu S, Hao Z, Lu Y, Yang L, Shi J, Chen J. Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress. BMC PLANT BIOLOGY 2022; 22:25. [PMID: 35012508 PMCID: PMC8744262 DOI: 10.1186/s12870-021-03371-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Liriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions. RESULTS In this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus. CONCLUSIONS This study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree's response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.
Collapse
Affiliation(s)
- Weihuang Wu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Sheng Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Lin Xu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dandan Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yang Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Siqin Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
| |
Collapse
|
16
|
Yan L, Jin H, Raza A, Huang Y, Gu D, Zou X. WRKY genes provide novel insights into their role against Ralstonia solanacearum infection in cultivated peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2022; 13:986673. [PMID: 36204053 PMCID: PMC9531958 DOI: 10.3389/fpls.2022.986673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/16/2022] [Indexed: 05/11/2023]
Abstract
As one of the most important and largest transcription factors, WRKY plays a critical role in plant disease resistance. However, little is known regarding the functions of the WRKY family in cultivated peanuts (Arachis hypogaea L.). In this study, a total of 174 WRKY genes (AhWRKY) were identified from the genome of cultivated peanuts. Phylogenetic analysis revealed that AhWRKY proteins could be divided into four groups, including 35 (20.12%) in group I, 107 (61.49%) in group II, 31 (17.82%) in group III, and 1 (0.57%) in group IV. This division is further supported by the conserved motif compositions and intron/exon structures. All AhWRKY genes were unevenly located on all 20 chromosomes, among which 132 pairs of fragment duplication and seven pairs of tandem duplications existed. Eighteen miRNAs were found to be targeting 50 AhWRKY genes. Most AhWRKY genes from some groups showed tissue-specific expression. AhWRKY46, AhWRKY94, AhWRKY156, AhWRKY68, AhWRKY41, AhWRKY128, AhWRKY104, AhWRKY19, AhWRKY62, AhWRKY155, AhWRKY170, AhWRKY78, AhWRKY34, AhWRKY12, AhWRKY95, and AhWRKY76 were upregulated in ganhua18 and kainong313 genotypes after Ralstonia solanacearum infection. Ten AhWRKY genes (AhWRKY34, AhWRKY76, AhWRKY78, AhWRKY120, AhWRKY153, AhWRKY155, AhWRKY159, AhWRKY160, AhWRKY161, and AhWRKY162) from group III displayed different expression patterns in R. solanacearum sensitive and resistant peanut genotypes infected with the R. solanacearum. Two AhWRKY genes (AhWRKY76 and AhWRKY77) from group III obtained the LRR domain. AhWRKY77 downregulated in both genotypes; AhWRKY76 showed lower-higher expression in ganhua18 and higher expression in kainong313. Both AhWRKY76 and AhWRKY77 are targeted by ahy-miR3512, which may have an important function in peanut disease resistance. This study identified candidate WRKY genes with possible roles in peanut resistance against R. solanacearum infection. These findings not only contribute to our understanding of the novel role of WRKY family genes but also provide valuable information for disease resistance in A. hypogaea.
Collapse
Affiliation(s)
- Lei Yan
- Institute of Crops, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Haotian Jin
- Institute of Crops, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Ali Raza
- College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Huang
- Institute of Crops, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Deping Gu
- Institute of Crops, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- Deping Gu
| | - Xiaoyun Zou
- Institute of Crops, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- *Correspondence: Xiaoyun Zou
| |
Collapse
|
17
|
Javed T, Zhou JR, Li J, Hu ZT, Wang QN, Gao SJ. Identification and Expression Profiling of WRKY Family Genes in Sugarcane in Response to Bacterial Pathogen Infection and Nitrogen Implantation Dosage. FRONTIERS IN PLANT SCIENCE 2022; 13:917953. [PMID: 35755708 PMCID: PMC9218642 DOI: 10.3389/fpls.2022.917953] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/03/2022] [Indexed: 05/11/2023]
Abstract
WRKY transcription factors (TFs) are essential players in different signaling cascades and regulatory networks involved in defense responses to various stressors. This study systematically analyzed and characterized WRKY family genes in the Saccharum spp. hybrid R570 and their expression in two sugarcane cultivars LCP85-384 (resistant to leaf scald) and ROC20 (susceptible to leaf scald) in response to bacterial pathogen infection and nitrogen implantation dosage. A total of 53 ShWRKY genes with 66 alleles were systematically identified in R570 based on the query sequence SsWRKY in S. spontaneum AP85-441. All ShRWKY alleles were further classified into four groups with 11 (16.7%) genes in group I, 36 (54.5%) genes in group II, 18 (27.3%) genes in group III, and 1 (1.5%) gene in group IV. Among them, 4 and 11 ShWRKY gene pairs displayed tandem and segmental duplication events, respectively. The ShWRKY genes exhibited conserved DNA-binding domains, which were accompanied by variations in introns, exons, and motifs. RT-qPCR analysis of two sugarcane cultivars triggered by Xanthomonas albilineans (Xa) revealed that four genes, ShWRKY13-2/39-1/49-3/125-3, exhibited significant upregulation in leaf scald-resistant LCP85-384. These WRKY genes were downregulated or unchanged in ROC20 at 24-72 h post-inoculation, suggesting that they play an important role in defense responses to Xa infection. Most of the 12 tested ShWRKYs, ShWRKY22-1/49-3/52-1 in particular, functioned as negative regulators in the two cultivars in response to a range of nitrogen (N) implantation doses. A total of 11 ShWRKY proteins were predicted to interact with each other. ShWRKY43 and ShWRKY49-3 are predicted to play core roles in the interaction network, as indicated by their interaction with six other ShWRKY proteins. Our results provide important candidate gene resources for the genetic improvement of sugarcane and lay the foundation for further functional characterization of ShWRKY genes in response to coupling effects of Xa infection and different N levels.
Collapse
Affiliation(s)
- Talha Javed
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing-Ru Zhou
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Li
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Ting Hu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qin-Nan Wang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
- Qin-Nan Wang,
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: San-Ji Gao,
| |
Collapse
|
18
|
Li F, Lu X, Duan P, Liang Y, Cui J. Integrating transcriptome and metabolome analyses of the response to cold stress in pumpkin (Cucurbita maxima). PLoS One 2021; 16:e0249108. [PMID: 33956796 PMCID: PMC8101736 DOI: 10.1371/journal.pone.0249108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/11/2021] [Indexed: 12/14/2022] Open
Abstract
Cucurbita maxima belong to the genus Cucurbita and are of nutritional and economic importance. Physiological activity, transcriptome, and metabolome analyses of leaf samples from the C. maxima inbreding line IL7 treated at 5 °C and 25 °C were performed. Cold stress resulted in a significant increase in the malondialdehyde content, relative electrical conductivity, soluble protein, sugar content, and catalase activity. A total of 5,553 differentially expressed genes were identified, of which 2,871 were up-regulated and 2,682 down-regulated. In addition, the transcription of differentially expressed genes in the plant hormone signal transduction pathway and transcription factor families of AP2/ERF, bHLH, WRKY, MYB, and HSF was activated. Moreover, 114 differentially expressed metabolites were identified by gas chromatography time-of-flight mass spectrometry, particularly through the analysis of carboxylic acids and derivatives, and organooxygen compounds. The demonstration of a series of potential metabolites and corresponding genes highlighted a comprehensive regulatory mechanism. These findings will provide novel insights into the molecular mechanisms associated with the response to cold stress in C. maxima.
Collapse
Affiliation(s)
- Fengmei Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, Shandong, China
| | - Xiuping Lu
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, Shandong, China
| | - Pengfei Duan
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, Shandong, China
| | - Yanjiao Liang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, Shandong, China
| | - Jian Cui
- Qingdao Institute of Agricultural Science Research, Qingdao, Shandong, China
| |
Collapse
|