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Liu XM, Yuan ZG, Rao S, Zhang WW, Ye JB, Cheng SY, Xu F. Identification, characterization, and expression analysis of WRKY transcription factors in Cardamine violifolia reveal the key genes involved in regulating selenium accumulation. BMC PLANT BIOLOGY 2024; 24:860. [PMID: 39266968 DOI: 10.1186/s12870-024-05562-y] [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: 06/03/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024]
Abstract
BACKGROUND Cardamine violifolia is a significant Brassicaceae plant known for its high selenium (Se) accumulation capacity, serving as an essential source of Se for both humans and animals. WRKY transcription factors play crucial roles in plant responses to various biotic and abiotic stresses, including cadmium stress, iron deficiency, and Se tolerance. However, the molecular mechanism of CvWRKY in Se accumulation is not completely clear. RESULTS In this study, 120 WRKYs with conserved domains were identified from C. violifolia and classified into three groups based on phylogenetic relationships, with Group II further subdivided into five subgroups. Gene structure analysis revealed WRKY variations and mutations within the CvWRKYs. Segmental duplication events were identified as the primary driving force behind the expansion of the CvWRKY family, with numerous stress-responsive cis-acting elements found in the promoters of CvWRKYs. Transcriptome analysis of plants treated with exogenous Se and determination of Se levels revealed a strong positive correlation between the expression levels of CvWRKY034 and the Se content. Moreover, CvWRKY021 and CvWRKY099 exhibited high homology with AtWRKY47, a gene involved in regulating Se accumulation in Arabidopsis thaliana. The WRKY domains of CvWRKY021 and AtWRKY47 were highly conserved, and transcriptome data analysis revealed that CvWRKY021 responded to Na2SeO4 induction, showing a positive correlation with the concentration of Na2SeO4 treatment. Under the induction of Na2SeO3, CvWRKY021 and CvWRKY034 were significantly upregulated in the roots but downregulated in the shoots, and the Se content in the roots increased significantly and was mainly concentrated in the roots. CvWRKY021 and CvWRKY034 may be involved in the accumulation of Se in roots. CONCLUSIONS The results of this study elucidate the evolution of CvWRKYs in the C. violifolia genome and provide valuable resources for further understanding the functional characteristics of WRKYs related to Se hyperaccumulation in C. violifolia.
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Affiliation(s)
- Xiao-Meng Liu
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430048, China
| | - Zhi-Gang Yuan
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430048, China
| | - Shen Rao
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430048, China
| | - Wei-Wei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Jia-Bao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Shui-Yuan Cheng
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430048, China
- National Selenium Rich Product Quality Supervision and Inspection Center, Enshi, Hubei, 445000, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China.
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Hao Y, Liu R, Mao Z, Yang Q, Zheng S, Lu X, Yang Y, Xie B, Zhao J, Li Y, Chen G, Ling J. Identification and Analysis of WRKY Transcription Factors in Response to Cowpea Fusarium Wilt in Cowpea. PLANTS (BASEL, SWITZERLAND) 2024; 13:2273. [PMID: 39204709 PMCID: PMC11360203 DOI: 10.3390/plants13162273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/10/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
In plants, WRKY transcription factors play a crucial role in plant growth, development, and response to abiotic and biotic stress. Cowpea (Vigna unguiculata) is an important legume crop. However, cowpea Fusarium wilt (CFW), caused by Fusarium oxysporum f. sp. tracheiphilum (Fot), poses a serious threat to its production. In this study, we systematically identified members of the cowpea WRKY (VuWRKY) gene family and analyzed their expression patterns under CFW stress. A total of 91 WRKY transcription factors were identified in the cowpea genome. Phylogenetic and synteny analyses indicated that the expansion of VuWRKY genes in cowpea is primarily due to recent duplication events. Transcriptome analysis of cowpea inoculated with Fo revealed 31 differentially expressed VuWRKY genes, underscoring their role in the response to CFW infection. Four differentially expressed WRKY genes were selected for validation. Subcellular localization and Western blot assays showed their nuclear localization and normal expression in N. benthamiana. Additionally, yeast one-hybrid assays demonstrated that VuWRKY2 can bind to the promoter region of the Catalase (CAT) gene, indicating its potential role in transcriptional regulation. This study establishes a foundation for further exploration of the role and regulatory mechanisms of VuWRKY genes in response to CFW stress.
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Affiliation(s)
- Yali Hao
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030810, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Rui Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Zhenchuan Mao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Qihong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Shijie Zheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Xiaofei Lu
- Institute of Zhongnong Tuba, Beijing 100081, China;
| | - Yuhong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Bingyan Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Jianlong Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Yan Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Guohua Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
| | - Jian Ling
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030810, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.L.); (Z.M.); (Q.Y.); (S.Z.); (Y.Y.); (B.X.); (J.Z.); (Y.L.)
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Zhou X, Lei Z, An P. Post-Translational Modification of WRKY Transcription Factors. PLANTS (BASEL, SWITZERLAND) 2024; 13:2040. [PMID: 39124158 PMCID: PMC11314200 DOI: 10.3390/plants13152040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/12/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024]
Abstract
Post-translational modifications (PTMs) of proteins are involved in numerous biological processes, including signal transduction, cell cycle regulation, growth and development, and stress responses. WRKY transcription factors (TFs) play significant roles in plant growth, development, and responses to both biotic and abiotic stresses, making them one of the largest and most vital TF families in plants. Recent studies have increasingly highlighted the importance of PTMs of WRKY TFs in various life processes. This review focuses on the recent advancements in understanding the phosphorylation and ubiquitination of WRKY TFs, particularly their roles in resistance to biotic and abiotic stresses and in plant growth and development. Future research directions and prospects in this field are also discussed.
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Affiliation(s)
- Xiangui Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zaojuan Lei
- Huanghua Port Business Department, Technical Center of Shijiazhuang Customs District, Cangzhou 061113, China; (Z.L.); (P.A.)
| | - Pengtian An
- Huanghua Port Business Department, Technical Center of Shijiazhuang Customs District, Cangzhou 061113, China; (Z.L.); (P.A.)
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Gu L, Chen X, Hou Y, Cao Y, Wang H, Zhu B, Du X, Wang H. ZmWRKY30 modulates drought tolerance in maize by influencing myo-inositol and reactive oxygen species homeostasis. PHYSIOLOGIA PLANTARUM 2024; 176:e14423. [PMID: 38945803 DOI: 10.1111/ppl.14423] [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: 03/22/2024] [Revised: 05/11/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
Maize (Zea mays L.) is an important food crop with a wide range of uses in both industry and agriculture. Drought stress during its growth cycle can greatly reduce maize crop yield and quality. However, the molecular mechanisms underlying maize responses to drought stress remain unclear. In this work, a WRKY transcription factor-encoding gene, ZmWRKY30, from drought-treated maize leaves was screened out and characterized. ZmWRKY30 gene expression was induced by dehydration treatments. The ZmWRKY30 protein localized to the nucleus and displayed transactivation activity in yeast. Compared with wild-type (WT) plants, Arabidopsis lines overexpressing ZmWRKY30 exhibited a significantly enhanced drought stress tolerance, as evidenced by the improved survival rate, increased antioxidant enzyme activity by superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), elevated proline content, and reduced lipid peroxidation recorded after drought stress treatment. In contrast, the mutator (Mu)-interrupted ZmWRKY30 homozygous mutant (zmwrky30) was more sensitive to drought stress than its null segregant (NS), characterized by the decreased survival rate, reduced antioxidant enzyme activity (SOD, POD, and CAT) and proline content, as well as increased malondialdehyde accumulation. RNA-Seq analysis further revealed that, under drought conditions, the knockout of the ZmWRKY30 gene in maize affected the expression of genes involved in reactive oxygen species (ROS), proline, and myo-inositol metabolism. Meanwhile, the zmwrky30 mutant exhibited significant downregulation of myo-inositol content in leaves under drought stress. Combined, our results suggest that ZmWRKY30 positively regulates maize responses to water scarcity. This work provides potential target genes for the breeding of drought-tolerant maize.
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Affiliation(s)
- Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xuanxuan Chen
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunyan Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yongyan Cao
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Huinan Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
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Yan X, Zhao J, Huang W, Liu C, Hao X, Gao C, Deng M, Wen J. Genome-Wide Identification of WRKY Transcription Factor Family in Chinese Rose and Response to Drought, Heat, and Salt Stress. Genes (Basel) 2024; 15:800. [PMID: 38927736 PMCID: PMC11203230 DOI: 10.3390/genes15060800] [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: 04/27/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The WRKY gene family is a key transcription factor family for plant development and the stress response. However, few studies have investigated the WRKY gene family in Chinese rose (Rosa chinensis). In this study, 68 RcWRKY genes were identified from the Chinese rose genome and classified into three primary groups and five subgroups based on the structural and phylogenetic characteristics. The analysis of the conserved domains, motifs, and gene structure revealed that the RcWRKY genes within the same group had the same exon-intron organization and composition. Chromosome mapping and gene duplication revealed that the RcWRKY genes were randomly dispersed across seven chromosomes. Fragment duplication and refined selection may have influenced the evolution of the WRKY gene family in Chinese rose. The cis-acting elements in the WRKY promoter region revealed that the RcWRKY genes contained numerous abiotic stress response elements. The results of qRT-PCR revealed that the expression of RcWRKY was tissue-specific, with high expression being observed under drought, heat, and salt stress. Notably, RcWRKY49's expression increased more than fivefold following salt stress, indicating that it is a crucial gene mediating the salt stress response of Chinese rose. These findings shed light on the regulatory role of RcWRKY in the growth and development of Chinese rose, and they serve as a foundation for future molecular breeding programs and gene discovery.
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Affiliation(s)
- Xinyu Yan
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Jiahui Zhao
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Wei Huang
- College of Agronomy and Life Sciences, Kunming University, Kunming 650021, China;
| | - Cheng Liu
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Xuan Hao
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Chengye Gao
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Minghua Deng
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Jinfen Wen
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
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Guo X, Yan X, Li Y. Genome-wide identification and expression analysis of the WRKY gene family in Rhododendron henanense subsp. lingbaoense. PeerJ 2024; 12:e17435. [PMID: 38827309 PMCID: PMC11143974 DOI: 10.7717/peerj.17435] [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: 01/24/2024] [Accepted: 04/30/2024] [Indexed: 06/04/2024] Open
Abstract
Background This work explored the characteristics of the WRKY transcription factor family in Rhododendron henanense subsp. lingbaoense (Rhl) and the expression patterns of these genes under abiotic stress by conducting bioinformatics and expression analyses. Methods RhlWRKY genes were identified from a gene library of Rhl. Various aspects of these genes were analyzed, including genetic structures, conserved sequences, physicochemical properties, cis-acting elements, and chromosomal location. RNA-seq was employed to analyze gene expression in five different tissues of Rhl: roots, stems, leaves, flowers, and hypocotyls. Additionally, qRT-PCR was used to detect changes in the expression of five RhlWRKY genes under abiotic stress. Result A total of 65 RhlWRKY genes were identified and categorized into three subfamilies based on their structural characteristics: Groups I, II, and III. Group II was further divided into five subtribes, with shared similar genetic structures and conserved motifs among members of the same subtribe. The physicochemical properties of these proteins varied, but the proteins are generally predicted to be hydrophilic. Most proteins are predicted to be in the cell nucleus, and distributed across 12 chromosomes. A total of 84 cis-acting elements were discovered, with many related to responses to biotic stress. Among the identified RhlWRKY genes, there were eight tandem duplicates and 97 segmental duplicates. The majority of duplicate gene pairs exhibited Ka/Ks values <1, indicating purification under environmental pressure. GO annotation analysis indicated that WRKY genes regulate biological processes and participate in a variety of molecular functions. Transcriptome data revealed varying expression levels of 66.15% of WRKY family genes in all five tissue types (roots, stems, leaves, flowers, and hypocotyls). Five RhlWRKY genes were selected for further characterization and there were changes in expression levels for these genes in response to various stresses. Conclusion The analysis identified 65 RhlWRKY genes, among which the expression of WRKY_42 and WRKY_17 were mainly modulated by the drought and MeJA, and WRKY_19 was regulated by the low-temperature and high-salinity conditions. This insight into the potential functions of certain genes contributes to understanding the growth regulatory capabilities of Rhl.
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Affiliation(s)
- Xiangmeng Guo
- School of Life Sciences, Luoyang Normal University, Luoyang, Henan, China
| | - Xinyu Yan
- School of Life Sciences, Luoyang Normal University, Luoyang, Henan, China
| | - Yonghui Li
- School of Life Sciences, Luoyang Normal University, Luoyang, Henan, China
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Rehman A, Alwutayd KM, Alshehri D, Alsudays IM, Azeem F, Rahman S, Abid M, Shah AA. Regulatory role of AGC genes in heat stress adaptation in maize ( Zea mays). FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23282. [PMID: 38758970 DOI: 10.1071/fp23282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/19/2024] [Indexed: 05/19/2024]
Abstract
Heat stress represents a significant environmental challenge that restricts maize (Zea mays ) growth and yield on a global scale. Within the plant kingdom, the AGC gene family, encoding a group of protein kinases, has emerged as crucial players in various stress responses. Nevertheless, a comprehensive understanding of AGC genes in Z. mays under heat-stress conditions remains elusive. A genome-wide analysis was done using bioinformatics techniques to identify 39 AGC genes in Z. mays , categorising them into three subfamilies based on their conserved domains. We investigated their phylogenetic relationships, gene structures (including intron-exon configurations), and expression patterns. These genes are likely involved in diverse signalling pathways, fulfilling distinct roles when exposed to heat stress conditions. Notably, most ZmAGC1.5, ZmAGC1.9, ZmNDR3, ZmNDR5 and ZmIRE3 exhibited significant changes in expression levels under heat stress, featuring a high G-box ratio. Furthermore, we pinpointed a subset of AGC genes displaying highly coordinated expression, implying their potential involvement in the heat stress response pathway. Our study offers valuable insights into the contribution of AGC genes to Z. mays 's heat stress response, thus facilitating the development of heat-tolerant Z. mays varieties.
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Affiliation(s)
- Abdul Rehman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Dikhnah Alshehri
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | | | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shahroz Rahman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Abid
- Department of Plant Pathology, Bahauddin Zakariya University, Multan, Pakistan
| | - Asad Ali Shah
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
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Chen J, Tao F, Xue Y, Xu B, Li X. Genome-Wide Identification of the WRKY Gene Family and Functional Characterization of CpWRKY5 in Cucurbita pepo. Int J Mol Sci 2024; 25:4177. [PMID: 38673762 PMCID: PMC11049939 DOI: 10.3390/ijms25084177] [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: 02/29/2024] [Revised: 03/27/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The WRKY gene family is crucial for regulating plant growth and development. However, the WRKY gene is rarely studied in naked kernel formation in hull-less Cucurbita pepo L. (HLCP), a natural mutant that lacks the seed coat. In this research, 76 WRKY genes were identified through bioinformatics-based methods in C. pepo, and their phylogenetics, conserved motifs, synteny, collinearity, and temporal expression during seed coat development were analyzed. The results showed that 76 CpWRKYs were identified and categorized into three main groups (I-III), with Group II further divided into five subgroups (IIa-IIe). Moreover, 31 segmental duplication events were identified in 49 CpWRKY genes. A synteny analysis revealed that C. pepo shared more collinear regions with cucumber than with melon. Furthermore, quantitative RT-PCR (qRT-PCR) results indicated the differential expression of CpWRKYs across different varieties, with notable variations in seed coat development between HLCP and CP being attributed to differences in CpWRKY5 expression. To investigate this further, CpWRKY5-overexpression tobacco plants were generated, resulting in increased lignin content and an upregulation of related genes, as confirmed by qRT-PCR. This study offers valuable insights for future functional investigations of CpWRKY genes and presents novel information for understanding the regulation mechanism of lignin synthesis.
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Affiliation(s)
- Junhong Chen
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Fei Tao
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Yingyu Xue
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Bingliang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaowei Li
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
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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.
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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.
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Huang L, Ökmen B, Stolze SC, Kastl M, Khan M, Hilbig D, Nakagami H, Djamei A, Doehlemann G. The fungal pathogen Ustilago maydis targets the maize corepressor RELK2 to modulate host transcription for tumorigenesis. THE NEW PHYTOLOGIST 2024; 241:1747-1762. [PMID: 38037456 DOI: 10.1111/nph.19448] [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: 06/14/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
Ustilago maydis is a biotrophic fungus that causes tumor formation on all aerial parts of maize. U. maydis secretes effector proteins during penetration and colonization to successfully overcome the plant immune response and reprogram host physiology to promote infection. In this study, we functionally characterized the U. maydis effector protein Topless (TPL) interacting protein 6 (Tip6). We found that Tip6 interacts with the N-terminus of RELK2 through its two Ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. We show that the EAR motifs are essential for the virulence function of Tip6 and critical for altering the nuclear distribution pattern of RELK2. We propose that Tip6 mimics the recruitment of RELK2 by plant repressor proteins, thus disrupting host transcriptional regulation. We show that a large group of AP2/ERF B1 subfamily transcription factors are misregulated in the presence of Tip6. Our study suggests a regulatory mechanism where the U. maydis effector Tip6 utilizes repressive domains to recruit the corepressor RELK2 to disrupt the transcriptional networks of the host plant.
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Affiliation(s)
- Luyao Huang
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
| | - Bilal Ökmen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Tübingen, 72076, Germany
| | - Sara Christina Stolze
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Melanie Kastl
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, 53127, Germany
| | - Mamoona Khan
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Daniel Hilbig
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, 53127, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Basic Immune System of Plants, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Armin Djamei
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
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11
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Gu L, Hou Y, Sun Y, Chen X, Wang G, Wang H, Zhu B, Du X. The maize WRKY transcription factor ZmWRKY64 confers cadmium tolerance in Arabidopsis and maize (Zea mays L.). PLANT CELL REPORTS 2024; 43:44. [PMID: 38246890 DOI: 10.1007/s00299-023-03112-8] [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: 09/12/2023] [Accepted: 11/10/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE ZmWRKY64 positively regulates Arabidopsis and maize Cd stress through modulating Cd uptake, translocation, and ROS scavenging genes expression. Cadmium (Cd) is a highly toxic heavy metal with severe impacts on crops growth and development. The WRKY transcription factor is a significant regulator influencing plant stress response. Nevertheless, the function of the WRKY protein in maize Cd stress response remains unclear. Here, we identified a maize WRKY gene, ZmWRKY64, the expression of which was enhanced in maize roots and leaves under Cd stress. ZmWRKY64 was localized in the nucleus and displayed transcriptional activity in yeast. Heterologous expression of ZmWRKY64 in Arabidopsis diminished Cd accumulation in plants by negatively regulating the expression of AtIRT1, AtZIP1, AtHMA2, AtNRAMP3, and AtNRAMP4, which are involved in Cd uptake and transport, resulting in Cd stress tolerance. Knockdown of ZmWRKY64 in maize led to excessive Cd accumulation in leaf cells and in the cytosol of the root cells, resulting in a Cd hypersensitive phenotype. Further analysis confirmed that ZmWRKY64 positively regulated ZmABCC4, ZmHMA3, ZmNRAMP5, ZmPIN2, ZmABCG51, ZmABCB13/32, and ZmABCB10, which may influence Cd translocation and auxin transport, thus mitigating Cd toxicity in maize. Moreover, ZmWRKY64 could directly enhance the transcription of ZmSRG7, a reported key gene regulating reactive oxygen species homeostasis under abiotic stress. Our results indicate that ZmWRKY64 is important in maize Cd stress response. This work provides new insights into the WRKY transcription factor regulatory mechanism under a Cd-polluted environment and may lead to the genetic improvement of Cd tolerance in maize.
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Affiliation(s)
- Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Yunyan Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Yiyue Sun
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Xuanxuan Chen
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Guangyi Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
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12
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Su J, Zhan N, Cheng X, Song S, Dong T, Ge X, Duan H. Genome-Wide Analysis of Cotton MYB Transcription Factors and the Functional Validation of GhMYB in Response to Drought Stress. PLANT & CELL PHYSIOLOGY 2024; 65:79-94. [PMID: 37847105 DOI: 10.1093/pcp/pcad125] [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: 06/29/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
MYB transcription factors play important roles during abiotic stress responses in plants. However, little is known about the accurate systematic analysis of MYB genes in the four cotton species, Gossypium hirsutum, G. barbadense, G. arboreum and G. raimondii. Herein, we performed phylogenetic analysis and showed that cotton MYBs and Arabidopsis MYBs were clustered in the same subfamilies for each species. The identified cotton MYBs were distributed unevenly on chromosomes in various densities for each species, wherein genome-wide tandem and segment duplications were the main driving force of MYB family expansion. Synteny analysis suggested that the abundant collinearity pairs of MYBs were identified between G. hirsutum and the other three species, and that they might have undergone strong purification selection. Characteristics of conserved motifs, along with their consensus sequence, promoter cis elements and gene structure, revealed that MYB proteins might be highly conserved in the same subgroups for each species. Subsequent analysis of differentially expressed genes and expression patterns indicated that most GhMYBs might be involved in response to drought (especially) and salt stress, which was supported by the expression levels of nine GhMYBs using real-time quantitative PCR. Finally, we performed a workflow that combined virus-induced gene silencing and the heterologous transformation of Arabidopsis, which confirmed the positive roles of GhMYBs under drought conditions, as validated by determining the drought-tolerant phenotypes, damage index and/or water loss rate. Collectively, our findings not only expand our understanding of the relationships between evolution and function of MYB genes, but they also provide candidate genes for cotton breeding.
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Affiliation(s)
- Jiuchang Su
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Na Zhan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiaoru Cheng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Shanglin Song
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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13
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Qin X, Li Y, Li C, Li X, Wu Y, Wu Q, Wen H, Jiang D, Liu S, Nan W, Liang Y, Zhang H. A Rapid and Simplified Method to Isolate Specific Regulators Based on Biotin-Avidin Binding Affinities in Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:883-893. [PMID: 38118073 DOI: 10.1021/acs.jafc.3c05638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Transcription factors (TFs) are indispensable components of transcriptional regulatory pathways involved in crop growth and development. Herein, we developed a new method for the identification of upstream TFs specific to genes in crops based on the binding affinities of biotin and avidin. First, we constructed and verified the new biotin and avidin system (BAS) by a coprecipitation assay. Subsequently, the feasibility of DNA-based BAS (DBAS) was further proved by in vivo and in vitro assays. Furthermore, we cloned the promoter of rice OsNRT1.1B and the possible regulators were screened and identified. Additionally, partial candidates were validated by the electrophoresis mobility shift assay (EMSA), yeast one-hybrid, and luciferase activity assays. Remarkably, the results showed that the candidates PIP3 and PIP19 both responded to nitrate immediately and overexpression of PIP3 caused retard growth, which indicates that the candidates are functional and the new DBAS method is useful to isolate regulators in crops.
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Affiliation(s)
- Xiaojian Qin
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Yuntong Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Cuiping Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Xiaowei Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yuanyuan Wu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Qian Wu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Huan Wen
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Dan Jiang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Shifeng Liu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Wenbin Nan
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Yongshu Liang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Hanma Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
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14
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Kumari A, Sharma P, Rani M, Laxmi V, Sahil, Sahi C, Satturu V, Katiyar-Agarwal S, Agarwal M. Meta-QTL and ortho analysis unravels the genetic architecture and key candidate genes for cold tolerance at seedling stage in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:93-108. [PMID: 38435852 PMCID: PMC10902255 DOI: 10.1007/s12298-024-01412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/13/2023] [Accepted: 01/10/2024] [Indexed: 03/05/2024]
Abstract
Rice, a critical cereal crop, grapples with productivity challenges due to its inherent sensitivity to low temperatures, primarily during the seedling and booting stages. Recognizing the polygenic complexity of cold stress signaling in rice, a meta-analysis was undertaken, focusing on 20 physiological traits integral to cold tolerance. This initiative allowed the consolidation of genetic data from 242 QTLs into 58 meta-QTLs, thereby significantly constricting the genetic and physical intervals, with 84% of meta-QTLs (MQTLs) being reduced to less than 2 Mb. The list of 10,505 genes within these MQTLs, was further refined utilizing expression datasets to pinpoint 46 pivotal genes exhibiting noteworthy differential regulation during cold stress. The study underscored the presence of several TFs such as WRKY, NAC, CBF/DREB, MYB, and bHLH, known for their roles in cold stress response. Further, ortho-analysis involving maize, barley, and Arabidopsis identified OsWRKY71, among others, as a prospective candidate for enhancing cold tolerance in diverse crop plants. In conclusion, our study delineates the intricate genetic architecture underpinning cold tolerance in rice and propounds significant candidate genes, offering crucial insights for further research and breeding strategies focused on fortifying crops against cold stress, thereby bolstering global food resilience. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01412-1.
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Affiliation(s)
- Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Mamta Rani
- Department of Botany, University of Delhi, Delhi, India
| | - Vijay Laxmi
- Department of Botany, University of Delhi, Delhi, India
| | - Sahil
- Department of Botany, University of Delhi, Delhi, India
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066 India
| | - Vanisree Satturu
- Professor Jayashankar, Telangana State Agricultural University, Hyderabad, India
| | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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15
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Gu L, Hou Y, Sun Y, Chen X, Wang H, Zhu B, Du X. ZmB12D, a target of transcription factor ZmWRKY70, enhances the tolerance of Arabidopsis to submergence. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108322. [PMID: 38169225 DOI: 10.1016/j.plaphy.2023.108322] [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: 09/07/2023] [Revised: 12/07/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024]
Abstract
Submergence stress represents a serious threat to the yield and quality of maize because it can lead to oxygen deficiency and the accumulation of toxic metabolites. However, the mechanisms by which maize resists the adverse effects of submergence stress have yet to be fully elucidated. Here, we cloned a gene from maize Balem (Barley aleurone and embryo), ZmB12D, which was expressed at significant levels in seed embryos during imbibition and in leaves under submergence stress. Subcellular localization analysis indicated that the ZmB12D protein was localized in the mitochondria. The overexpression of ZmB12D in increased the tolerance of Arabidopsis to submergence stress, probably due to a reduction in the levels of malonaldehyde (MDA), the increased activity of antioxidant enzymes (SOD, POD and CAT), enhanced electron transport by coordinating the expression of non-symbiotic hemoglobin-2 (AHb2) and Fe transport-related (AtNAS3) genes (mediating Fe and oxygen availability) and also modulated the anaerobic respiration rates through upregulated the AtPDC1, AtADH1, AtSUS4 genes under submergence. Yeast one-hybrid (Y1H) and transient transactivation assays demonstrated that ZmWRKY70 bound to the ZmB12D promoter and activated ZmB12D. Collectively, out findings indicate that ZmB12D plays an important role in the tolerance of maize to submergence stress. This research provides new insights into the genetic improvement of maize with regards to submergence tolerance.
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Affiliation(s)
- Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Yunyan Hou
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Yiyue Sun
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Xuanxuan Chen
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China.
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16
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Zhang X, Sun J, Zhang Y, Li J, Liu M, Li L, Li S, Wang T, Shaw RK, Jiang F, Fan X. Hotspot Regions of Quantitative Trait Loci and Candidate Genes for Ear-Related Traits in Maize: A Literature Review. Genes (Basel) 2023; 15:15. [PMID: 38275597 PMCID: PMC10815758 DOI: 10.3390/genes15010015] [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: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
In this study, hotspot regions, QTL clusters, and candidate genes for eight ear-related traits of maize (ear length, ear diameter, kernel row number, kernel number per row, kernel length, kernel width, kernel thickness, and 100-kernel weight) were summarized and analyzed over the past three decades. This review aims to (1) comprehensively summarize and analyze previous studies on QTLs associated with these eight ear-related traits and identify hotspot bin regions located on maize chromosomes and key candidate genes associated with the ear-related traits and (2) compile major and stable QTLs and QTL clusters from various mapping populations and mapping methods and techniques providing valuable insights for fine mapping, gene cloning, and breeding for high-yield and high-quality maize. Previous research has demonstrated that QTLs for ear-related traits are distributed across all ten chromosomes in maize, and the phenotypic variation explained by a single QTL ranged from 0.40% to 36.76%. In total, 23 QTL hotspot bins for ear-related traits were identified across all ten chromosomes. The most prominent hotspot region is bin 4.08 on chromosome 4 with 15 QTLs related to eight ear-related traits. Additionally, this study identified 48 candidate genes associated with ear-related traits. Out of these, five have been cloned and validated, while twenty-eight candidate genes located in the QTL hotspots were defined by this study. This review offers a deeper understanding of the advancements in QTL mapping and the identification of key candidates associated with eight ear-related traits. These insights will undoubtedly assist maize breeders in formulating strategies to develop higher-yield maize varieties, contributing to global food security.
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Affiliation(s)
- Xingjie Zhang
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Jiachen Sun
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.S.); (T.W.)
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Jinfeng Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Meichen Liu
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Linzhuo Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Shaoxiong Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Tingzhao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.S.); (T.W.)
| | - Ranjan Kumar Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
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17
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Yuan G, Zhang N, Zou Y, Hao Y, Pan J, Liu Y, Zhang W, Li B. Genome-wide identification and expression analysis of WRKY gene family members in red clover ( Trifolium pratense L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1289507. [PMID: 38130488 PMCID: PMC10733489 DOI: 10.3389/fpls.2023.1289507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Trifolium pratense is an important legume forage grass and a key component of sustainable livestock development. Serving as an essential component, the WRKY gene family, a crucial group of regulatory transcription factors in plants, holds significant importance in their response to abiotic stresses. However, there has been no systematic analysis conducted on the WRKY gene family in Trifolium pratense. This study conducted a comprehensive genomic characterization of the WRKY gene family in Trifolium pratense, utilizing the latest genomic data, resulting in the identification of 59 TpWRKY genes. Based on their structural features, phylogenetic characteristics, and conserved motif composition, the WRKY proteins were classified into three groups, with group II further subdivided into five subgroups (II-a, II-b, II-c, II-d, and II-e). The majority of the TpWRKYs in a group share a similar structure and motif composition. Intra-group syntenic analysis revealed eight pairs of duplicate segments. The expression patterns of 59 TpWRKY genes in roots, stems, leaves, and flowers were examined by analyzing RNA-seq data. The expression of 12 TpWRKY genes under drought, low-temperature (4°C), methyl jasmonate (MeJA) and abscisic acid (ABA) stresses was analyzed by RT-qPCR. The findings indicated that TpWRKY46 was highly induced by drought stress, and TpWRKY26 and TpWRKY41 were significantly induced by low temperature stress. In addition, TpWRKY29 and TpWRKY36 were greatly induced by MeJA stress treatment, and TpWRKY17 was significantly upregulated by ABA stress treatment. In this research, we identified and comprehensively analyzed the structural features of the WRKY gene family in T.pratense, along with determined the possible roles of WRKY candidate genes in abiotic stress. These discoveries deepen our understandings of how WRKY transcription factors contribute to species evolution and functional divergence, laying a solid molecular foundation for future exploration and study of stress resistance mechanisms in T.pratense.
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Affiliation(s)
| | | | | | | | | | | | - Weiguo Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Beibei Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
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18
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Yang R, Huang T, Song W, An Z, Lai Z, Liu S. Identification of WRKY gene family members in amaranth based on a transcriptome database and functional analysis of AtrWRKY42-2 in betalain metabolism. FRONTIERS IN PLANT SCIENCE 2023; 14:1300522. [PMID: 38130485 PMCID: PMC10734031 DOI: 10.3389/fpls.2023.1300522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Introduction WRKY TFs (WRKY transcription factors) contribute to the synthesis of secondary metabolites in plants. Betalains are natural pigments that do not coexist with anthocyanins within the same plant. Amaranthus tricolor ('Suxian No.1') is an important leaf vegetable rich in betalains. However, the WRKY family members in amaranth and their roles in betalain synthesis and metabolism are still unclear. Methods To elucidate the molecular characteristics of the amaranth WRKY gene family and its role in betalain synthesis, WRKY gene family members were screened and identified using amaranth transcriptome data, and their physicochemical properties, conserved domains, phylogenetic relationships, and conserved motifs were analyzed using bioinformatics methods. Results In total, 72 WRKY family members were identified from the amaranth transcriptome. Three WRKY genes involved in betalain synthesis were screened in the phylogenetic analysis of WRKY TFs. RT-qPCR showed that the expression levels of these three genes in red amaranth 'Suxian No.1' were higher than those in green amaranth 'Suxian No.2' and also showed that the expression level of AtrWRKY42 gene short-spliced transcript AtrWRKY42-2 in Amaranth 'Suxian No.1' was higher than that of the complete sequence AtrWRKY42-1, so the short-spliced transcript AtrWRKY42-2 was mainly expressed in 'Suxian No.2' amaranth. Moreover, the total expression levels of AtrWRKY42-1 and AtrWRKY42-2 were down-regulated after GA3 treatment, so AtrWRKY42-2 was identified as a candidate gene. Therefore, the short splice variant AtrWRKY42-2 cDNA sequence, gDNA sequence, and promoter sequence of AtrWRKY42 were cloned, and the PRI 101-AN-AtrWRKY42-2-EGFP vector was constructed to evaluate subcellular localization, revealing that AtrWRKY42-2 is located in the nucleus. The overexpression vector pRI 101-AN-AtrWRKY42-2-EGFP and VIGS (virus-induced gene silencing) vector pTRV2-AtrWRKY42-2 were transferred into leaves of 'Suxian No.1' by an Agrobacterium-mediated method. The results showed that AtrWRKY42-2 overexpression could promote the expression of AtrCYP76AD1 and increase betalain synthesis. A yeast one-hybrid assay demonstrated that AtrWRKY42-2 could bind to the AtrCYP76AD1 promoter to regulate betalain synthesis. Discussion This study lays a foundation for further exploring the function of AtrWRKY42-2 in betalain metabolism.
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Affiliation(s)
| | | | | | | | | | - Shengcai Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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19
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Chu W, Zhu X, Jiang T, Wang S, Ni W. Genome-wide identification of peanut IGT family genes and their potential roles in the development of plant architecture. Sci Rep 2023; 13:20400. [PMID: 37990054 PMCID: PMC10663514 DOI: 10.1038/s41598-023-47722-4] [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: 06/02/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
IGT family genes play essential roles in shaping plant architecture. However, limited amount of information is available about IGT family genes in peanuts (Arachis hypogaea). In the current study, 13 AhIGT genes were identified and classified into three groups based on their phylogenetic relationship. Gene structure, conserved domain analyses indicated all AhIGTs were observed to share a similar exon-intron distribution pattern. AhIGTs within the same subfamily maintained a consistent motif composition. Chromosomal localization and synteny analyses showed that AhIGTs were unevenly localized on 9 chromosomes and that segmental duplication and purifying selection may have played important roles in the evolution of AhIGT genes. The analysis of conserved motifs, GO annotation, and transcript profile suggested that AhLAZY1-3 may play roles in gravity sensing and shaping peanut plant architecture. Transcript profile analysis suggested that AhTAC1 could potentially be involved gynophore ('peg') penetration into the soil. The cis-element analysis revealed that the light-responsive elements accounted for most of all cis-acting elements. Furthermore, qRT-PCR analysis showed that the expression of several AhIGT genes, like AhTAC1-2/4, was light-dependent, indicating that these genes may regulate plant architecture in response to light signals. This study may facilitate functional studies of the IGT genes in peanut.
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Affiliation(s)
- Wen Chu
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaofeng Zhu
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Tao Jiang
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Song Wang
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wanli Ni
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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20
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Song X, Hou X, Zeng Y, Jia D, Li Q, Gu Y, Miao H. Genome-wide identification and comprehensive analysis of WRKY transcription factor family in safflower during drought stress. Sci Rep 2023; 13:16955. [PMID: 37805641 PMCID: PMC10560227 DOI: 10.1038/s41598-023-44340-y] [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: 05/19/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023] Open
Abstract
The WRKY family is an important family of transcription factors in plant development and stress response. Currently, there are few reports on the WRKY gene family in safflower (Carthamus tinctorius L.). In this study, a total of 82 CtWRKY genes were identified from the safflower genome and could be classified into 3 major groups and 5 subgroups based on their structural and phylogenetic characteristics. The results of gene structure, conserved domain and motif analyses indicated that CtWRKYs within the same subfamily maintained a consistent exon/intron organization and composition. Chromosomal localization and gene duplication analysis results showed that CtWRKYs were randomly localized on 12 chromosomes and that fragment duplication and purification selection may have played an important role in the evolution of the WRKY gene family in safflower. Promoter cis-acting element analysis revealed that the CtWRKYs contain many abiotic stress response elements and hormone response elements. Transcriptome data and qRT-PCR analyses revealed that the expression of CtWRKYs showed tissue specificity and a strong response to drought stress. Notably, the expression level of the CtWRKY55 gene rapidly increased more than eightfold under drought treatment and rehydration, indicating that it may be a key gene in response to drought stress. These results provide useful insights for investigating the regulatory function of the CtWRKY gene in safflower growth and development, as well as identifying key genes for future molecular breeding programmes.
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Affiliation(s)
- Xianming Song
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Urumqi, 830046, China
| | - Xianfei Hou
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Youling Zeng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Urumqi, 830046, China.
| | - Donghai Jia
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China.
| | - Qiang Li
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China.
| | - Yuanguo Gu
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Haocui Miao
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
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21
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Tang R, Zhu Y, Yang S, Wang F, Chen G, Chen J, Zhao K, Liu Z, Peng D. Genome-Wide Identification and Analysis of WRKY Gene Family in Melastoma dodecandrum. Int J Mol Sci 2023; 24:14904. [PMID: 37834352 PMCID: PMC10573167 DOI: 10.3390/ijms241914904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
WRKY is one of the largest transcription factor families in plants and plays an important role in plant growth and development as well as in abiotic and biological stresses. However, there is little information about the WRKY family in Melastoma dodecandrum. In this study, 126 WRKY members were identified in M. dodecandrum. According to phylogenetic analysis, they were divided into three major groups, and group II was further divided into five subgroups. MedWRKY genes were unevenly distributed on 12 chromosomes. Additionally, the gene structure and sequence composition were similar within the same group and differed between groups, suggesting their functional diversity. The promoter sequence analysis identified a number of cis-acting elements related to plant growth and development, stress response, and secondary metabolite synthesis in the WRKY gene family. The collinearity analysis showed that gene replication events were the main driving force of MedWRKY gene evolution. The transcriptome data and RT-qPCR analysis suggested that MedWRKY genes had higher expression in the roots and ripe fruit of M. dodecandrum. In short, this paper lays a foundation for further study of the functions and molecular mechanism of M. dodecandrum WRKY gene family.
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Affiliation(s)
- Ruonan Tang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
| | - Yunjun Zhu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
| | - Songmin Yang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
| | - Fei Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
| | - Guizhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
| | - Jinliao Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
| | - Kai Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
| | - Donghui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.T.); (Y.Z.); (S.Y.); (F.W.); (G.C.); (J.C.); (K.Z.); (Z.L.)
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22
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Wei N, Zhang Z, Yang H, Hu D, Wu Y, Xue J, Guo D, Xu S. Characterization of the Isocitrate Dehydrogenase Gene Family and Their Response to Drought Stress in Maize. PLANTS (BASEL, SWITZERLAND) 2023; 12:3466. [PMID: 37836206 PMCID: PMC10574653 DOI: 10.3390/plants12193466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Isocitrate dehydrogenase (IDH) is a key rate-limiting enzyme in the tricarboxylic acid cycle and acts in glutamine synthesis. IDH also participates in plant growth and development and in response to abiotic stresses. We identified 11 maize IDH genes (ZmIDH) and classified these genes into ZmNAD-IDH and ZmNADP-IDH groups based on their different coenzymes (NAD+ or NADP+). The ZmNAD-IDH group was further divided into two subgroups according to their catalytic and non-catalytic subunits, as in Arabidopsis. The ZmIDHs significantly differed in physicochemical properties, gene structure, conserved motifs, and protein tertiary structure. Promoter prediction analysis revealed that the promoters of these ZmIDHs contain cis-acting elements associated with light response, abscisic acid, phytohormones, and abiotic stresses. ZmIDH is predicted to interact with proteins involved in development and stress resistance. Expression analysis of public data revealed that most ZmIDHs are specifically expressed in anthers. Different types of ZmIDHs responded to abiotic stresses with different expression patterns, but all exhibited responses to abiotic stresses to some extent. In addition, analysis of the public sequence from transcription data in an association panel suggested that natural variation in ZmIDH1.4 will be associated with drought tolerance in maize. These results suggested that ZmIDHs respond differently and/or redundantly to abiotic stresses during plant growth and development, and this analysis provides a foundation to understand how ZmIDHs respond to drought stress in maize.
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Affiliation(s)
- Ningning Wei
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.W.); (Z.Z.); (H.Y.); (D.H.); (Y.W.); (J.X.)
- Maize Engineering Technology Research Centre, Yangling 712100, China
| | - Ziran Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.W.); (Z.Z.); (H.Y.); (D.H.); (Y.W.); (J.X.)
- Maize Engineering Technology Research Centre, Yangling 712100, China
| | - Haoxiang Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.W.); (Z.Z.); (H.Y.); (D.H.); (Y.W.); (J.X.)
- Maize Engineering Technology Research Centre, Yangling 712100, China
| | - Die Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.W.); (Z.Z.); (H.Y.); (D.H.); (Y.W.); (J.X.)
- Maize Engineering Technology Research Centre, Yangling 712100, China
| | - Ying Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.W.); (Z.Z.); (H.Y.); (D.H.); (Y.W.); (J.X.)
- Maize Engineering Technology Research Centre, Yangling 712100, China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.W.); (Z.Z.); (H.Y.); (D.H.); (Y.W.); (J.X.)
- Maize Engineering Technology Research Centre, Yangling 712100, China
| | - Dongwei Guo
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.W.); (Z.Z.); (H.Y.); (D.H.); (Y.W.); (J.X.)
- Maize Engineering Technology Research Centre, Yangling 712100, China
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.W.); (Z.Z.); (H.Y.); (D.H.); (Y.W.); (J.X.)
- Maize Engineering Technology Research Centre, Yangling 712100, China
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23
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Javed T, Gao SJ. WRKY transcription factors in plant defense. Trends Genet 2023; 39:787-801. [PMID: 37633768 DOI: 10.1016/j.tig.2023.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/28/2023]
Abstract
Environmental stressors caused by climate change are fundamental barriers to agricultural sustainability. Enhancing the stress resilience of crops is a key strategy in achieving global food security. Plants perceive adverse environmental conditions and initiate signaling pathways to activate precise responses that contribute to their survival. WRKY transcription factors (TFs) are essential players in several signaling cascades and regulatory networks that have crucial implications for defense responses in plants. This review summarizes advances in research concerning how WRKY TFs mediate various signaling cascades and metabolic adjustments as well as how epigenetic modifications involved in environmental stress responses in plants can modulate WRKYs and/or their downstream genes. Emerging research shows that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing of WRKYs could be used to improve crop resilience.
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Affiliation(s)
- Talha Javed
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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24
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Wang J, Zhao S, Zhang Y, Lu X, Du J, Wang C, Wen W, Guo X, Zhao C. Investigating the genetic basis of maize ear characteristics: a comprehensive genome-wide study utilizing high-throughput phenotypic measurement method and system. FRONTIERS IN PLANT SCIENCE 2023; 14:1248446. [PMID: 37701799 PMCID: PMC10493325 DOI: 10.3389/fpls.2023.1248446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023]
Abstract
The morphology of maize ears plays a critical role in the breeding of new varieties and increasing yield. However, the study of traditional ear-related traits alone can no longer meet the requirements of breeding. In this study, 20 ear-related traits, including size, shape, number, and color, were obtained in 407 maize inbred lines at two sites using a high-throughput phenotypic measurement method and system. Significant correlations were found among these traits, particularly the novel trait ear shape (ES), which was correlated with traditional traits: kernel number per row and kernel number per ear. Pairwise comparison tests revealed that the inbred lines of tropical-subtropical were significantly different from other subpopulations in row numbers per ear, kernel numbers per ear, and ear color. A genome-wide association study identified 275, 434, and 362 Single nucleotide polymorphisms (SNPs) for Beijing, Sanya, and best linear unbiased prediction scenarios, respectively, explaining 3.78% to 24.17% of the phenotypic variance. Furthermore, 58 candidate genes with detailed functional descriptions common to more than two scenarios were discovered, with 40 genes being associated with color traits on chromosome 1. After analysis of haplotypes, gene expression, and annotated information, several candidate genes with high reliability were identified, including Zm00001d051328 for ear perimeter and width, zma-MIR159f for ear shape, Zm00001d053080 for kernel width and row number per ear, and Zm00001d048373 for the blue color channel of maize kernels in the red-green-blue color model. This study emphasizes the importance of researching novel phenotypic traits in maize by utilizing high-throughput phenotypic measurements. The identified genetic loci enrich the existing genetic studies related to maize ears.
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Affiliation(s)
- Jinglu Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shuaihao Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ying Zhang
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xianju Lu
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chuanyu Wang
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Weiliang Wen
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xinyu Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunjiang Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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25
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Gu L, Chen X, Hou Y, Wang H, Wang H, Zhu B, Du X. ZmWRKY70 activates the expression of hypoxic responsive genes in maize and enhances tolerance to submergence in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107861. [PMID: 37364509 DOI: 10.1016/j.plaphy.2023.107861] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/29/2023] [Accepted: 06/22/2023] [Indexed: 06/28/2023]
Abstract
Hypoxic stress due to submergence is a serious threat to the growth and development of maize. WRKY transcription factors are significant regulators of plant responses to various abiotic and biotic stresses. Nevertheless, their function and regulatory mechanisms in the resistance of maize to submergence stress remain unclear. Here we report the cloning of a maize WRKY transcription factor gene, ZmWRKY70, transcripts of which accumulate under submergence stress in maize seedlings. Subcellular localization analysis and yeast transcriptional activation assay indicated that ZmWRKY70 was localized in the nucleus and had transcriptional activation activity. Heterologous overexpression of ZmWRKY70 in Arabidopsis increased the tolerance of seeds and seedlings to submergence stress by upregulating the transcripts of several key genes involved in anaerobic respiration, such as group VII ethylene-responsive factor (ERFVII) (AtRAP2.2), alcohol dehydrogenase (AtADH1), pyruvate decarboxylase (AtPDC1/2), and sucrose synthase (AtSUS4), under submergence conditions. Moreover, the overexpression of ZmWRKY70 in maize mesophyll protoplasts enhanced the expression of ZmERFVII members (ZmERF148, ZmERF179, and ZmERF193), ZmADH1, ZmPDC2/3, and ZmSUS1. Yeast one-hybrid and dual-luciferase activity assays further confirmed that ZmWRKY70 enhanced the expression of ZmERF148 by binding to the W box motif located in the promoter region of ZmERF148. Together, these results indicate that ZmWRKY70 plays a significant role in tolerance of submergence stress. This work provides a theoretical basis, and suggests excellent genes, for biotechnological breeding to improve the tolerance of maize to submergence through the regulation of ZmWRKY genes.
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Affiliation(s)
- Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Xuanxuan Chen
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Yunyan Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Heyan Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
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26
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Wang C, Ye D, Li Y, Hu P, Xu R, Wang X. Genome-wide identification and bioinformatics analysis of the WRKY transcription factors and screening of candidate genes for anthocyanin biosynthesis in azalea ( Rhododendron simsii). Front Genet 2023; 14:1172321. [PMID: 37234867 PMCID: PMC10206045 DOI: 10.3389/fgene.2023.1172321] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
WRKY transcription factors have been demonstrated to influence the anthocyanin biosynthesis in many plant species. However, there is limited knowledge about the structure and function of WRKY genes in the major ornamental plant azalea (Rhododendron simsii). In this study, we identified 57 RsWRKY genes in the R. simsii genome and classified them into three main groups and several subgroups based on their structural and phylogenetic characteristics. Comparative genomic analysis suggested WRKY gene family has significantly expanded during plant evolution from lower to higher species. Gene duplication analysis indicated that the expansion of the RsWRKY gene family was primarily due to whole-genome duplication (WGD). Additionally, selective pressure analysis (Ka/Ks) suggested that all RsWRKY duplication gene pairs underwent purifying selection. Synteny analysis indicated that 63 and 24 pairs of RsWRKY genes were orthologous to Arabidopsis thaliana and Oryza sativa, respectively. Furthermore, RNA-seq data was used to investigate the expression patterns of RsWRKYs, revealing that 17 and 9 candidate genes may be associated with anthocyanin synthesis at the bud and full bloom stages, respectively. These findings provide valuable insights into the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species and lay the foundation for future functional studies of WRKY genes.
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Affiliation(s)
- Cheng Wang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Dan Ye
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai, China
| | - Peiling Hu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Run Xu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Xiaojing Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, China
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27
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Dong W, Xie Q, Liu Z, Han Y, Wang X, Xu R, Gao C. Genome-wide identification and expression profiling of the bZIP gene family in Betula platyphylla and the functional characterization of BpChr04G00610 under low-temperature stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107676. [PMID: 37060866 DOI: 10.1016/j.plaphy.2023.107676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
The basic leucine zipper (bZIP) gene, which plays a significant role in the regulation of tolerance to biotic/abiotic stresses, has been characterized in many plant species. Betula platyphylla is a significant afforestation species. To elucidate the stress resistance mechanism of birch, previous studies identified some stress resistance genes. However, the genome-wide identification and characterization of bZIP gene family in the birch have not been reported. Here, the 56 BpbZIP genes were identified and classified into 13 groups in birch. Cis-element analysis showed that the promoters of 56 family genes contained 108 elements, of which 16 were shared by 13 groups. There were 8 pairs of fragment repeats and 1 pair of tandem repeats, indicating that duplication may be the major reason for the amplification of the BpbZIP gene family. Tissue-specific of BpbZIP genes showed 18 genes with the highest expression in roots, 15 in flowers, 11 in xylem and 9 in leaves. In addition, five differentially expressed bZIP genes were identified from the RNA-seq data of birch under low-temperature stress, and the co-expressed differentially expressed genes were further screened. The analysis of gene ontology (GO) enrichment of each co-expression regulatory network showed that they were related to membrane lipids and cell walls. Furthermore, the transient overexpression of BpChr04G00610 decreased the ROS scavenging ability of birch under low-temperature stress, suggesting that it may be more sensitive to low-temperature. In conclusion, this study provides a basis for the study of the function of BpbZIP genes.
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Affiliation(s)
- Wenfang Dong
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Qingjun Xie
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Zhongyuan Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Yating Han
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Xinyu Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Ruiting Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China.
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Qian C, Li L, Guo H, Zhu G, Yang N, Tan X, Zhao H. Genome-Wide Analysis of DREB Family Genes and Characterization of Cold Stress Responses in the Woody Plant Prunus nana. Genes (Basel) 2023; 14:genes14040811. [PMID: 37107569 PMCID: PMC10137973 DOI: 10.3390/genes14040811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Dehydration response element binding factor (DREB) is a family of plant-specific transcription factors, whose members participate in the regulation of plant responses to various abiotic stresses. Prunus nana, also known as the wild almond, is a member of the Rosaceae family that is rare and found to grow in the wild in China. These wild almond trees are found in hilly regions in northern Xinjiang, and exhibit greater drought and cold stress resistance than cultivated almond varieties. However, the response of P. nana DREBs (PnaDREBs) under low temperature stress is still unclear. In this study, 46 DREB genes were identified in the wild almond genome, with this number being slightly lower than that in the sweet almond (Prunus dulcis cultivar ‘Nonpareil’). These DREB genes in wild almond were separated into two classes. All PnaDREB genes were located on six chromosomes. PnaDREB proteins that were classified in the same groups contained specific shared motifs, and promoter analyses revealed that PnaDREB genes harbored a range of stress-responsive elements associated with drought, low-temperature stress, light responsivity, and hormone-responsive cis-regulatory elements within their promoter regions. MicroRNA target site prediction analyses also suggested that 79 miRNAs may regulate the expression of 40 of these PnaDREB genes, with PnaDREB2. To examine if these identified PnaDREB genes responded to low temperature stress, 15 of these genes were selected including seven homologous to Arabidopsis C-repeat binding factor (CBFs), and their expression was assessed following incubation for 2 h at 25 °C, 5 °C, 0 °C, −5 °C, or −10 °C. In summary, this analysis provides an overview of the P. nana PnaDREB gene family and provides a foundation for further studies of the ability of different PnaDREB genes to regulate cold stress responses in almond plants.
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Affiliation(s)
- Cheng Qian
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Lulu Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Huanhuan Guo
- Zhengzhou Botanical Garden, Zhengzhou 450042, China
| | - Gaopu Zhu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450014, China
| | - Ning Yang
- Qingdao Landscape and Forestry Integrated Service Center, Qingdao 266003, China
| | - Xiaoyan Tan
- Qingdao Landscape and Forestry Integrated Service Center, Qingdao 266003, China
| | - Han Zhao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450014, China
- Correspondence:
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Pan H, Chen Y, Zhao J, Huang J, Shu N, Deng H, Song C. In-depth analysis of large-scale screening of WRKY members based on genome-wide identification. Front Genet 2023; 13:1104968. [PMID: 36699467 PMCID: PMC9868916 DOI: 10.3389/fgene.2022.1104968] [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: 11/28/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
With the rapid advancement of high-throughput sequencing technology, it is now possible to identify individual gene families from genomes on a large scale in order to study their functions. WRKY transcription factors are a key class of regulators that regulate plant growth and abiotic stresses. Here, a total of 74 WRKY genes were identified from Dendrobium officinale Kimura et Migo genome. Based on the genome-wide analysis, an in-depth analysis of gene structure and conserved motif was performed. The phylogenetic analysis indicated that DoWRKYs could be classified into three main groups: I, II, and III, with group II divided into five subgroups: II-a, II-b, II-c, II-d, and II-e. The sequence alignment indicated that these WRKY transcriptional factors contained a highly conserved WRKYGQK heptapeptide. The localization analysis of chromosomes showed that WRKY genes were irregularly distributed across several chromosomes of D. officinale. These genes comprised diverse patterns in both number and species, and there were certain distinguishing motifs among subfamilies. Moreover, the phylogenetic tree and chromosomal location results indicated that DoWRKYs may have undergone a widespread genome duplication event. Based on an evaluation of expression profiles, we proposed that DoWRKY5, 54, 57, 21, etc. may be involved in the transcriptional regulation of the JA signaling pathway. These results provide a scientific reference for the study of DoWRKY family genes.
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Affiliation(s)
- Haoyu Pan
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China,School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China
| | - Jingyi Zhao
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China
| | - Jie Huang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China
| | - Nana Shu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China
| | - Hui Deng
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China,*Correspondence: Hui Deng, ; Cheng Song,
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China,*Correspondence: Hui Deng, ; Cheng Song,
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Li J, Yu H, Liu M, Chen B, Dong N, Chang X, Wang J, Xing S, Peng H, Zha L, Gui S. Transcriptome-wide identification of WRKY transcription factors and their expression profiles in response to methyl jasmonate in Platycodon grandiflorus. PLANT SIGNALING & BEHAVIOR 2022; 17:2089473. [PMID: 35730590 PMCID: PMC9225661 DOI: 10.1080/15592324.2022.2089473] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Platycodon grandiflorus, a perennial flowering plant widely distributed in China and South Korea, is an excellent resource for both food and medicine. The main active compounds of P. grandiflorus are triterpenoid saponins. WRKY transcription factors (TFs) are among the largest gene families in plants and play an important role in regulating plant terpenoid accumulation, physiological metabolism, and stress response. Numerous studies have been reported on other medicinal plants; however, little is known about WRKY genes in P. grandiflorus. In this study, 27 PgWRKYs were identified in the P. grandiflorus transcriptome. Phylogenetic analysis showed that PgWRKY genes were clustered into three main groups and five subgroups. Transcriptome analysis showed that the PgWRKY gene expression patterns in different tissues differed between those in Tongcheng City (Southern Anhui) and Taihe County (Northern Anhui). Gene expression analysis based on RNA sequencing and qRT-PCR analysis showed that most PgWRKY genes were expressed after induction with methyl jasmonate (MeJA). Co-expressing PgWRKY genes with triterpenoid biosynthesis pathway genes revealed four PgWRKY genes that may have functions in triterpenoid biosynthesis. Additionally, functional annotation and protein-protein interaction analysis of PgWRKY proteins were performed to predict their roles in potential regulatory networks. Thus, we systematically analyzed the structure, evolution, and expression patterns of PgWRKY genes to provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in triterpenoid biosynthesis.
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Affiliation(s)
- Jing Li
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Hanwen Yu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Mengli Liu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Bowen Chen
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Nan Dong
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiangwei Chang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jutao Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Huasheng Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesState Key Laboratory of Dao-Di, Beijing, Hebei, China
| | - Liangping Zha
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of traditional Chinese medicine resources, Anhui University of Chinese Medicine, Hefei, Anhui, China
- CONTACT Liangping Zha College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Shuangying Gui
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Anhui Province Key Laboratory of Pharmaceutical Technology and Application Anhui University of Chinese Medicine, Hefei, Anhui, China
- Shuangying Gui College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, Chinai
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Wan Z, Li X, Cheng H, Zhang J, Chen Y, Xu Y, Jin S. Comprehensive Genomic Survey, Structural Classification, and Expression Analysis of WRKY Transcription Factor Family in Rhododendron simsii. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212967. [PMID: 36365420 PMCID: PMC9654210 DOI: 10.3390/plants11212967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/12/2022] [Accepted: 11/01/2022] [Indexed: 06/01/2023]
Abstract
(1) Rhododendron is one of the top ten traditional flowers in China, with both high ornamental and economic values. However, with the change of the environment, Rhododendron suffers from various biological stresses. The WRKY transcription factor is a member of the most crucial transcription factor families, which plays an essential regulatory role in a variety of physiological processes and developmental stresses. (2) In this study, 57 RsWRKYs were identified using genome data and found to be randomly distributed on 13 chromosomes. Based on gene structure and phylogenetic relationships, 57 proteins were divided into three groups: I, II, and III. Multiple alignments of RsWRKYs with Arabidopsis thaliana homologous genes revealed that WRKY domains in different groups had different conserved sites. RsWRKYs have a highly conserved domain, WRKYGQK, with three variants, WRKYGKK, WRKYGEK, and WRKYGRK. Furthermore, cis-acting elements analysis revealed that all of the RsWRKYs had stress and plant hormone cis-elements, with figures varying by group. Finally, the expression patterns of nine WRKY genes treated with gibberellin acid (GA), methyl jasmonate (MeJA), heat, and drought in Rhododendron were also measured using quantitative real-time PCR (qRT-PCR). The results showed that the expression levels of the majority of RsWRKY genes changed in response to multiple phytohormones and abiotic stressors. (3) This current study establishes a theoretical basis for future studies on the response of RsWRKY transcription factors to various hormone and abiotic stresses as well as a significant foundation for the breeding of new stress-tolerant Rhododendron varieties.
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Affiliation(s)
- Ziyun Wan
- Jiyang College, Zhejiang A&F University, Zhuji 311800, China
| | - Xueqin Li
- Jiyang College, Zhejiang A&F University, Zhuji 311800, China
| | - Hefeng Cheng
- Jiyang College, Zhejiang A&F University, Zhuji 311800, China
| | - Jing Zhang
- Jiyang College, Zhejiang A&F University, Zhuji 311800, China
| | - Yujia Chen
- Jiyang College, Zhejiang A&F University, Zhuji 311800, China
| | - Yanxia Xu
- Jiyang College, Zhejiang A&F University, Zhuji 311800, China
| | - Songheng Jin
- Jiyang College, Zhejiang A&F University, Zhuji 311800, China
- School of Life Science and Health, Huzhou College, Huzhou 313000, China
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Xi Y, Ling Q, Zhou Y, Liu X, Qian Y. ZmNAC074, a maize stress-responsive NAC transcription factor, confers heat stress tolerance in transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:986628. [PMID: 36247610 PMCID: PMC9558894 DOI: 10.3389/fpls.2022.986628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
The harsh environment such as high temperature greatly limits the growth, development and production of crops worldwide. NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) play key regulatory roles in abiotic stress responses of plants. However, the functional roles of NAC TFs in heat stress response of maize remain elusive. In our present study, we identified and isolated a stress-responsive NAC transcription factor gene in maize, designated as ZmNAC074 and orthologous with rice OsNTL3. Further studies revealed that ZmNAC074 may encode a membrane-bound transcription factor (MTF) of NAC family in maize, which is comprised of 517 amino acid residues with a transmembrane domain at the C-terminus. Moreover, ZmNAC074 was highly expressed and induced by various abiotic stresses in maize seedlings, especially in leaf tissues under heat stress. Through generating ZmNAC074 transgenic plants, phenotypic and physiological analyses further displayed that overexpression of ZmNAC074 in transgenic Arabidopsis confers enhanced heat stress tolerance significantly through modulating the accumulation of a variety of stress metabolites, including reactive oxygen species (ROS), antioxidants, malondialdehyde (MDA), proline, soluble protein, chlorophyll and carotenoid. Further, quantitative real-time PCR analysis showed that the expression levels of most ROS scavenging and HSR- and UPR-associated genes in transgenic Arabidopsis were significantly up-regulated under heat stress treatments, suggesting that ZmNAC074 may encode a positive regulator that activates the expression of ROS-scavenging genes and HSR- and UPR-associated genes to enhance plant thermotolerance under heat stress conditions. Overall, our present study suggests that ZmNAC074 may play a crucial role in conferring heat stress tolerance in plants, providing a key candidate regulatory gene for heat stress tolerance regulation and genetic improvement in maize as well as in other crops.
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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.
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Zhang J, Huang D, Zhao X, Zhang M, Wang Q, Hou X, Di D, Su B, Wang S, Sun P. Drought-responsive WRKY transcription factor genes IgWRKY50 and IgWRKY32 from Iris germanica enhance drought resistance in transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:983600. [PMID: 36147225 PMCID: PMC9486095 DOI: 10.3389/fpls.2022.983600] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Drought greatly affects the growth and development of garden plants and affects their ornamental value. WRKY transcription factors make up one of the largest transcription factor families in plants and they play an important role in the plant response to drought stress. However, the function of the WRKY gene in response to drought stress in Iris germanica, which is commonly used in landscaping, has not been studied. In this study, we isolated two WRKY transcription factor genes from Iris germanica, IgWRKY50 and IgWRKY32, which belong to Group II and Group III of the WRKY family, respectively. IgWRKY50 and IgWRKY32 could be induced by PEG-6000, high temperature and ABA in Iris germanica. IgWRKY50 and IgWRKY32 could quickly respond to drought and they peaked at 3 h after PEG-6000 treatment (19.93- and 23.32-fold). The fusion proteins IgWRKY50-GFP and IgWRKY32-GFP were located in the nucleus of mesophyll protoplasts of Arabidopsis. The overexpression of the IgWRKY50 and IgWRKY32 genes improved the osmotic tolerance of transgenic Arabidopsis, mainly exhibited by the transgenic plants having a higher germination rate and a longer total root length on 1/2 MS medium containing mannitol. Under PEG-6000 stress, the transgenic plants had higher stomatal closure than the wild type (WT). Under natural drought stress, the water loss rate of the isolated leaves of transgenic Arabidopsis was lower than that of WT, the contents of proline (Pro) and soluble protein (SP) and the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in the transgenic plants were higher, but the content of malondialdehyde (MDA) was lower. Furthermore, the expression of several stress-related genes (RD29A, DREB2A, PP2CA, and ABA2) was significantly increased in IgWRKY50- and IgWRKY32- overexpressing transgenic Arabidposis plants after drought treatment. These results suggest that IgWRKY50 and IgWRKY32, as two positive regulators, enhance the drought resistance of transgenic Arabidopsis by mediating the ABA signal transduction pathway. IgWRKY50 and IgWRKY32 can be used as candidate genes for molecular breeding of drought resistance in Iris.
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Affiliation(s)
- Jingwei Zhang
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Dazhuang Huang
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Xiaojie Zhao
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Man Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Qian Wang
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Xueyan Hou
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Dongliu Di
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Beibei Su
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Shaokun Wang
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Pai Sun
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
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Xi Y, Hu W, Zhou Y, Liu X, Qian Y. Genome-Wide Identification and Functional Analysis of Polyamine Oxidase Genes in Maize Reveal Essential Roles in Abiotic Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:950064. [PMID: 35991458 PMCID: PMC9386529 DOI: 10.3389/fpls.2022.950064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Polyamines (PAs) play a critical role in growth and developmental processes and stress responses in plants. Polyamine oxidase (PAO) is a flavin adenine dinucleotide (FAD)-dependent enzyme that plays a major role in PA catabolism. Here, for the first time, PAO genes in maize were screened for the whole genome-wide and nine ZmPAO genes were identified in this study, named as ZmPAO1-9. Based on structural characteristics and a comparison of phylogenetic relationships of PAO gene families from seven representative species, all nine PAO proteins in maize were categorized into three distinct subfamilies. Further, chromosome location and schematic structure revealed an unevenly distribution on chromosomes and evolutionarily conserved structure features of ZmPAO genes in maize, respectively. Furthermore, transcriptome analysis demonstrated that ZmPAO genes showed differential expression patterns at diverse developmental stages of maize, suggesting that these genes may play functional developmental roles in multiple tissues. Further, through qRT-PCR validation, these genes were confirmed to be responsive to heat, drought and salinity stress treatments in three various tissues, indicating their potential roles in abiotic stress responses. Eventually, to verify the biological function of ZmPAO genes, the transgenic Arabidopsis plants overexpressing ZmPAO6 gene were constructed as a typical representative to explore functional roles in plants. The results demonstrated that overexpression of ZmPAO6 can confer enhanced heat tolerance through mediating polyamine catabolism in transgenic Arabidopsis, which might result in reduced H2O2 and MDA accumulation and alleviated chlorophyll degradation under heat stress treatment, indicating that ZmPAO6 may play a crucial role in enhancing heat tolerance of transgenic Arabidopsis through the involvement in various physiological processes. Further, the expression analysis of related genes of antioxidant enzymes including glutathione peroxidase (GPX) and ascorbate peroxidase (APX) demonstrated that ZmPAO6 can enhance heat resistance in transgenic Arabidopsis through modulating heat-induced H2O2 accumulation in polyamine catabolism. Taken together, our results are the first to report the ZmPAO6 gene response to heat stress in plants and will serve to present an important theoretical basis for further unraveling the function and regulatory mechanism of ZmPAO genes in growth, development and adaptation to abiotic stresses in maize.
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Wei YL, Jin JP, Liang D, Gao J, Li J, Xie Q, Lu CQ, Yang FX, Zhu GF. Genome-wide identification of Cymbidium sinense WRKY gene family and the importance of its Group III members in response to abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:969010. [PMID: 35968117 PMCID: PMC9365948 DOI: 10.3389/fpls.2022.969010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 05/13/2023]
Abstract
Transcription factors (TFs) of the WRKY family play pivotal roles in defense responses and secondary metabolism of plants. Although WRKY TFs are well documented in numerous plant species, no study has performed a genome-wide investigation of the WRKY gene family in Cymbidium sinense. In the present work, we found 64 C. sinense WRKY (CsWRKY) TFs, and they were further divided into eight subgroups. Chromosomal distribution of CsWRKYs revealed that the majority of these genes were localized on 16 chromosomes, especially on Chromosome 2. Syntenic analysis implied that 13 (20.31%) genes were derived from segmental duplication events, and 17 orthologous gene pairs were identified between Arabidopsis thaliana WRKY (AtWRKY) and CsWRKY genes. Moreover, 55 of the 64 CsWRKYs were detectable in different plant tissues in response to exposure to plant hormones. Among them, Group III members were strongly induced in response to various hormone treatments, indicating their potential essential roles in hormone signaling. We subsequently analyzed the function of CsWRKY18 in Group III. The CsWRKY18 was localized in the nucleus. The constitutive expression of CsWRKY18 in Arabidopsis led to enhanced sensitivity to ABA-mediated seed germination and root growth and elevated plant tolerance to abiotic stress within the ABA-dependent pathway. Overall, our study represented the first genome-wide characterization and functional analysis of WRKY TFs in C. sinense, which could provide useful clues about the evolution and functional description of CsWRKY genes.
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Affiliation(s)
| | | | | | | | | | | | | | - Feng-Xi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gen-Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Liu L, Pu Y, Niu Z, Wu J, Fang Y, Xu J, Xu F, Yue J, Ma L, Li X, Sun W. Transcriptomic Insights Into Root Development and Overwintering Transcriptional Memory of Brassica rapa L. Grown in the Field. FRONTIERS IN PLANT SCIENCE 2022; 13:900708. [PMID: 35937315 PMCID: PMC9355659 DOI: 10.3389/fpls.2022.900708] [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: 03/21/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
As the only overwintering oil crop in the north area of China, living through winter is the primary feature of winter rapeseed. Roots are the only survival organ during prolonged cold exposure during winter to guarantee flowering in spring. However, little is known about its root development and overwintering memory mechanism. In this study, root collar tissues (including the shoot apical meristem) of three winter rapeseed varieties with different cold resistance, i.e., Longyou-7 (strong cold tolerance), Tianyou-4 (middle cold tolerance), and Lenox (cold-sensitive), were sampled in the pre-winter period (S1), overwintering periods (S2-S5), and re-greening stage (S6), and were used to identify the root development and overwintering memory mechanisms and seek candidate overwintering memory genes by measuring root collar diameter and RNA sequencing. The results showed that the S1-S2 stages were the significant developmental stages of the roots as root collar diameter increased slowly in the S3-S5 stages, and the roots developed fast in the strong cold resistance variety than in the weak cold resistance variety. Subsequently, the RNA-seq analysis revealed that a total of 37,905, 45,102, and 39,276 differentially expressed genes (DEGs), compared to the S1 stage, were identified in Longyou-7, Tianyou-4, and Lenox, respectively. The function enrichment analysis showed that most of the DEGs are significantly involved in phenylpropanoid biosynthesis, plant hormone signal transduction, MAPK signaling pathway, starch and sucrose metabolism, photosynthesis, amino sugar and nucleotide sugar metabolism, and spliceosome, ribosome, proteasome, and protein processing in endoplasmic reticulum pathways. Furthermore, the phenylpropanoid biosynthesis and plant hormone signal transduction pathways were related to the difference in root development of the three varieties, DEGs involved in photosynthesis and carbohydrate metabolism processes may participate in overwintering memory of Longyou-7 and Tianyou-4, and the spliceosome pathway may contribute to the super winter resistance of Longyou-7. The transcription factor enrichment analysis showed that the WRKY family made up the majority in different stages and may play an important regulatory role in root development and overwintering memory. These results provide a comprehensive insight into winter rapeseed's complex overwintering memory mechanisms. The identified candidate overwintering memory genes may also serve as important genetic resources for breeding to further improve the cold resistance of winter rapeseed.
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Affiliation(s)
- Lijun Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Yuanyuan Pu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zaoxia Niu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Junyan Wu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Jun Xu
- Shanghai OE Biotech Co., Ltd.,Shanghai, China
| | - Fang Xu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jinli Yue
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Li Ma
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Xuecai Li
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
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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.
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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.
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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.
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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
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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.
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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,
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Genome-Wide Analysis of WRKY Gene Family and the Dynamic Responses of Key WRKY Genes Involved in Ostrinia furnacalis Attack in Zea mays. Int J Mol Sci 2021; 22:ijms222313045. [PMID: 34884854 PMCID: PMC8657575 DOI: 10.3390/ijms222313045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
WRKY transcription factors comprise one of the largest gene families and serve as key regulators of plant defenses against herbivore attack. However, studies related to the roles of WRKY genes in response to herbivory are limited in maize. In this study, a total of 128 putative maize WRKY genes (ZmWRKYs) were identified from the new maize genome (v4). These genes were divided into seven subgroups (groups I, IIa–e, and III) based on phylogenomic analysis, with distinct motif compositions in each subgroup. Syntenic analysis revealed that 72 (56.3%) of the genes were derived from either segmental or tandem duplication events (69 and 3, respectively), suggesting a pivotal role of segmental duplication in the expansion of the ZmWRKY family. Importantly, transcriptional regulation prediction showed that six key WRKY genes contribute to four major defense-related pathways: L-phenylalanine biosynthesis II and flavonoid, benzoxazinoid, and jasmonic acid (JA) biosynthesis. These key WRKY genes were strongly induced in commercial maize (Jingke968) infested with the Asian corn borer, Ostrinia furnacalis, for 0, 2, 4, 12 and 24 h in the field, and their expression levels were highly correlated with predicted target genes, suggesting that these genes have important functions in the response to O. furnacalis. Our results provide a comprehensive understanding of the WRKY gene family based on the new assembly of the maize genome and lay the foundation for further studies into functional characteristics of ZmWRKY genes in commercial maize defenses against O. furnacalis in the field.
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Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum. Genes (Basel) 2021; 12:genes12121867. [PMID: 34946815 PMCID: PMC8701280 DOI: 10.3390/genes12121867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.
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