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Lei P, Jiang Y, Zhao Y, Jiang M, Ji X, Ma L, Jin G, Li J, Zhang S, Kong D, Zhao X, Meng F. Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review. J Agric Food Chem 2024; 72:10692-10709. [PMID: 38712500 DOI: 10.1021/acs.jafc.3c09665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.
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Affiliation(s)
- Pei Lei
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Yaxuan Jiang
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Yong Zhao
- College of Life Sciences, Baicheng Normal University, Baicheng 137099, China
| | - Mingquan Jiang
- Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130022, China
| | - Ximei Ji
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Le Ma
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Guangze Jin
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Jianxin Li
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Subin Zhang
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Dexin Kong
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Xiyang Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Fanjuan Meng
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
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Zhao X, Qi G, Liu J, Chen K, Miao X, Hussain J, Liu S, Ren H. Genome-wide identification of WRKY transcription factors in Casuarina equisetifolia and the function analysis of CeqWRKY11 in response to NaCl/NaHCO 3 stresses. BMC Plant Biol 2024; 24:376. [PMID: 38714947 PMCID: PMC11077731 DOI: 10.1186/s12870-024-04889-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/07/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Casuarina equisetifolia (C. equisetifolia) is a woody species with many excellent features. It has natural resistance against drought, salt and saline-alkali stresses. WRKY transcription factors (TFs) play significant roles in plant response to abiotic stresses, therefore, molecular characterization of WRKY gene family under abiotic stresses holds great significance for improvement of forest trees through molecular biological tools. At present, WRKY TFs from C. equisetifolia have not been thoroughly studied with respect to their role in salt and saline-alkali stresses response. The current study was conducted to bridge the same knowledge gap. RESULTS A total of 64 WRKYs were identified in C. equisetifolia and divided into three major groups i.e. group I, II and III, consisting of 10, 42 and 12 WRKY members, respectively. The WRKY members in group II were further divided into 5 subgroups according to their homology with Arabidopsis counterparts. WRKYs belonging to the same group exhibited higher similarities in gene structure and the presence of conserved motifs. Promoter analysis data showed the presence of various response elements, especially those related to hormone signaling and abiotic stresses, such as ABRE (ABA), TGACG (MeJA), W-box ((C/T) TGAC (T/C)) and TC-rich motif. Tissue specific expression data showed that CeqWRKYs were mainly expressed in root under normal growth conditions. Furthermore, most of the CeqWRKYs were up-regulated by NaCl and NaHCO3 stresses with few of WRKYs showing early responsiveness to both stresses while few others exhibiting late response. Although the expressions of CeqWRKYs were also induced by cold stress, the response was delayed compared with other stresses. Transgenic C. equisetifolia plants overexpressing CeqWRKY11 displayed lower electrolyte leakage, higher chlorophyll content, and enhanced tolerance to both stresses. The higher expression of abiotic stress related genes, especially CeqHKT1 and CeqPOD7, in overexpression lines points to the maintenance of optimum Na+/K+ ratio, and ROS scavenging as possible key molecular mechanisms underlying salt stress tolerance. CONCLUSIONS Our results show that CeqWRKYs might be key regulators of NaCl and NaHCO3 stresses response in C. equisetifolia. In addition, positive correlation of CeqWRKY11 expression with increased stress tolerance in C. equisetifolia encourages further research on other WRKY family members through functional genomic tools. The best candidates could be incorporated in other woody plant species for improving stress tolerance.
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Affiliation(s)
- Xiaohong Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China
| | - Guoning Qi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China
| | - Jinhong Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China
| | - Kui Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China
| | - Xinxin Miao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China
| | - Jamshaid Hussain
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, University Road, Tobe Camp, Abbottabad, 22060, Pakistan
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China.
| | - Huimin Ren
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China.
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Lu Y, Hu L, Yu L, Liang S, Qu H, Wang M, Hao Z, Yang L, Shi J, Chen J. Physiological and transcriptomic analysis revealed that the accumulation of reactive oxygen species caused the low temperature sensitivity of Liriodendron × sinoamericanum. Plant Sci 2024; 342:112020. [PMID: 38311251 DOI: 10.1016/j.plantsci.2024.112020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Liriodendron × sinoamericanum is widely cultivated in southern China as an excellent wood and garden ornamental trees. However, its intolerance to low temperature limits its application to high latitudes. Understanding the molecular mechanism of low temperature sensitivity of Liriodendron × sinoamericanum is very important for its further application. In this study, combined with physiological and transcriptomic analysis, it was revealed that low temperature stress can lead to water loss and decreased photosynthetic capacity of Liriodendron × sinoamericanum leaves. The accelerated accumulation of reactive oxygen species (ROS) caused by the imbalance of cell REDOX homeostasis is one of the important reasons for the low temperature sensitivity. Further analysis showed that several transcription factors could be involved in regulating the synthesis and degradation of ROS, among which LsNAC72 and LsNAC73a could regulate the accumulation of O2- and H2O2 in leaves by affecting the expression level of LsAPX, LsSOD, LsPAO, and LsPOD.
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Affiliation(s)
- Ye Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Lingfeng Hu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Long Yu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Shuang Liang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Haoxian Qu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Mingqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
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Lang X, Zhao X, Zhao J, Ren T, Nie L, Zhao W. MicroRNA Profiling Revealed the Mechanism of Enhanced Cold Resistance by Grafting in Melon ( Cucumis melo L.). Plants (Basel) 2024; 13:1016. [PMID: 38611545 PMCID: PMC11013280 DOI: 10.3390/plants13071016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Grafting is widely used to improve the resistance to abiotic stresses in cucurbit plants, but the effect and molecular mechanism of grafting on cold stress are still unknown in melon. In this study, phenotypic characteristics, physiological indexes, small-RNA sequencing and expression analyses were performed on grafted plants with pumpkin rootstock (PG) and self-grafted plants (SG) to explore the mechanism of changed cold tolerance by grafting in melon. Compared with SG plants, the cold tolerance was obviously enhanced, the malondialdehyde (MDA) content was significantly decreased and the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; peroxidase, POD) were significantly increased in PG plants. Depend on differentially expressed miRNA (DEM) identification and expression pattern analyses, cme-miR156b, cme-miR156f and chr07_30026 were thought to play a key role in enhancing low-temperature resistance resulting from grafting. Subsequently, 24, 37 and 17 target genes of cme-miR156b, cme-miR156f and chr07_30026 were respectively predicted, and 21 target genes were co-regulated by cme-miR156b and cme-miR156f. Among these 57 unique target genes, the putative promoter of 13 target genes contained the low-temperature responsive (LTR) cis-acting element. The results of qRT-PCR indicated that six target genes (MELO3C002370, MELO3C009217, MELO3C018972, MELO3C016713, MELO3C012858 and MELO3C000732) displayed the opposite expression pattern to their corresponding miRNAs. Furthermore, MELO3C002370, MELO3C016713 and MELO3C012858 were significantly downregulated in cold-resistant cultivars and upregulated in cold-sensitive varieties after cold stimulus, and they acted as the key negative regulators of low-temperature response in melon. This study revealed three key miRNAs and three putative target genes involved in the cold tolerance of melon and provided a molecular basis underlying how grafting improved the low-temperature resistance of melon plants.
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Affiliation(s)
- Xinmei Lang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Xuan Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Jiateng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Tiantian Ren
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Lanchun Nie
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding 071000, China
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding 071000, China
| | - Wensheng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding 071000, China
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding 071000, China
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Li R, Song Y, Wang X, Zheng C, Liu B, Zhang H, Ke J, Wu X, Wu L, Yang R, Jiang M. OsNAC5 orchestrates OsABI5 to fine-tune cold tolerance in rice. J Integr Plant Biol 2024; 66:660-682. [PMID: 37968901 DOI: 10.1111/jipb.13585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023]
Abstract
Due to its tropical origins, rice (Oryza sativa) is susceptible to cold stress, which poses severe threats to production. OsNAC5, a NAC-type transcription factor, participates in the cold stress response of rice, but the detailed mechanisms remain poorly understood. Here, we demonstrate that OsNAC5 positively regulates cold tolerance at germination and in seedlings by directly activating the expression of ABSCISIC ACID INSENSITIVE 5 (OsABI5). Haplotype analysis indicated that single nucleotide polymorphisms in a NAC-binding site in the OsABI5 promoter are strongly associated with cold tolerance. OsNAC5 also enhanced OsABI5 stability, thus regulating the expression of cold-responsive (COR) genes, enabling fine-tuned control of OsABI5 action for rapid, precise plant responses to cold stress. DNA affinity purification sequencing coupled with transcriptome deep sequencing identified several OsABI5 target genes involved in COR expression, including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1A (OsDREB1A), OsMYB20, and PEROXIDASE 70 (OsPRX70). In vivo and in vitro analyses suggested that OsABI5 positively regulates COR gene transcription, with marked COR upregulation in OsNAC5-overexpressing lines and downregulation in osnac5 and/or osabi5 knockout mutants. This study extends our understanding of cold tolerance regulation via OsNAC5 through the OsABI5-CORs transcription module, which may be used to ameliorate cold tolerance in rice via advanced breeding.
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Affiliation(s)
- Ruiqing Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Yue Song
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| | - Xueqiang Wang
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| | - Chenfan Zheng
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| | - Bo Liu
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Jian Ke
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Xuejing Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Liquan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Ruifang Yang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Meng Jiang
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
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He L, Wu Z, Wang X, Zhao C, Cheng D, Du C, Wang H, Gao Y, Zhang R, Han J, Xu J. A novel maize F-bZIP member, ZmbZIP76, functions as a positive regulator in ABA-mediated abiotic stress tolerance by binding to ACGT-containing elements. Plant Sci 2024; 341:111952. [PMID: 38072329 DOI: 10.1016/j.plantsci.2023.111952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/31/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
The group F-bZIP transcription factors (TFs) in Arabidopsis are involved in nutrient deficiency or salt stress responses. Nevertheless, our learning about the functions of group F-bZIP genes in maize remains limited. Here, we cloned a new F-bZIP gene (ZmbZIP76) from maize inbred line He344. The expression of ZmbZIP76 in maize was dramatically induced by high salt, osmotic stress and abscisic acid. Accordingly, overexpression of ZmbZIP76 increased tolerance of transgenic plants to salt and osmotic stress. In addition, ZmbZIP76 functions as a nuclear transcription factor and upregulates the expression of a range of abiotic stress-responsive genes by binding to the ACGT-containing elements, leading to enhanced reactive oxygen species (ROS) scavenging capability, increased abscisic acid level, proline content, and ratio of K+/Na+, reduced water loss rate, and membrane damage. These physiological changes caused by ZmbZIP76 ultimately enhanced tolerance of transgenic plants to salt and osmotic stress.
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Affiliation(s)
- Lin He
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Zixuan Wu
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Xueheyuan Wang
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Changjiang Zhao
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Dianjun Cheng
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Chuhuai Du
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Haoyu Wang
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Yuan Gao
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Ruijia Zhang
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing 100081, PR China.
| | - Jingyu Xu
- Key Laboratory of Low Carbon Green Agriculture in Northeast Plain, Ministry of Agriculture and Rural Affairs, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PRChina.
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Wang H, Jia Y, Bai X, Wang J, Liu G, Wang H, Wu Y, Xin J, Ma H, Liu Z, Zou D, Zhao H. Whole-transcriptome profiling and identification of cold tolerance-related ceRNA networks in japonica rice varieties. Front Plant Sci 2024; 15:1260591. [PMID: 38567126 PMCID: PMC10985246 DOI: 10.3389/fpls.2024.1260591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/02/2024] [Indexed: 04/04/2024]
Abstract
Introduction Low-temperature stress negatively impacts rice yield, posing a significant risk to food security. While previous studies have explored the physiological and linear gene expression alterations in rice under low-temperature conditions, the changes in competing endogenous RNA (ceRNA) networks remain largely unexamined. Methods We conducted RNA sequencing on two japonica rice varieties with differing cold-tolerance capabilities to establish ceRNA networks. This enabled us to investigate the transcriptional regulatory network and molecular mechanisms that rice employs in response to low-temperature stress. Results We identified 364 differentially expressed circular RNAs (circRNAs), 224 differentially expressed microRNAs (miRNAs), and 12,183 differentially expressed messenger RNAs (mRNAs). WRKY family was the most prominent transcription factor family involved in cold tolerance. Based on the expression patterns and targeted relationships of these differentially expressed RNAs, we discerned five potential ceRNA networks related to low-temperature stress in rice: osa-miR166j-5p from the miR166 family was associated with cold tolerance; osa-miR528-3p and osa-miR156j-3p were linked to stress response; and osa-miR156j-3p was involved in the antioxidant system. In addition, Os03g0152000 in the antioxidant system, as well as Os12g0491800 and Os05g0381400, correlated with the corresponding stress response and circRNAs in the network. A gene sequence difference analysis and phenotypic validation of Os11g0685700 (OsWRKY61) within the WRKY family suggested its potential role in regulating cold tolerance in rice. Discussion and conclusion We identified Os11g0685700 (OsWRKY61) as a promising candidate gene for enhancing cold tolerance in japonica rice. The candidate miRNAs, mRNAs, and circRNAs uncovered in this study are valuable targets for researchers and breeders. Our findings will facilitate the development of cold-tolerant rice varieties from multiple angles and provide critical directions for future research into the functions of cold-tolerance-related miRNAs, mRNAs, and circRNAs in rice.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yan Jia
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xu Bai
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jin Wang
- Bei Da Huang Kenfeng Seed Limited Company, Research and Breeding Center, Harbin, China
| | - Ge Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Haixing Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yulong Wu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Junying Xin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Huimiao Ma
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Zhenyu Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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8
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Cheng YS, Sun YD, Xing JY, Zhan L, Li XJ, Huang J, Zhao MH, Guo ZF. Transcriptomic and functional analyzes reveal that the brassinosteroid insensitive 1 receptor (OsBRI1) regulates cold tolerance in rice. Plant Physiol Biochem 2024; 208:108472. [PMID: 38442627 DOI: 10.1016/j.plaphy.2024.108472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024]
Abstract
Brassinosteroids (BR) play crucial roles in plant development and abiotic stresses in plants. Exogenous application of BR can significantly enhance cold tolerance in rice. However, the regulatory relationship between cold tolerance and the BR signaling pathway in rice remains largely unknown. Here, we characterized functions of the BR receptor OsBRI1 in response to cold tolerance in rice using its loss-of-function mutant (d61-1). Our results showed that mutant d61-1 was less tolerant to cold stress than wild-type (WT). Besides, d61-1 had lower levels than WT for some physiological parameters, including catalase activity (CAT), superoxide dismutase activity (SOD), peroxidase activity (POD), peroxidase activity (PRO), soluble protein, and soluble sugar content, while malondialdehyde content (MDA) and relative electrical conductivity (REC) levels in d61-1 were higher than those in WT plants. These results indicated that the loss of OsBRI1 function resulted in decreased cold tolerance in rice. In addition, we performed RNA sequencing (RNA-seq) of WT and d61-1 mutant under cold stress. Numerous common and unique differentially expressed genes (DEGs) with up- and down-regulation were observed in WT and d61-1 mutant. Some DEGs were expressed to various degrees, even opposite, between CK1 vs. T1 (WT) and CK2 vs. T2 (d61-1). Among these specific DEGs, some typical genes are involved in plant tolerance to cold stress. Through weighted correlation network analysis (WGCNA), 50 hub genes were screened in the turquoise and blue module. Many genes were involved in cold stress and plant hormone, such as Os01g0279800 (BRI1-associated receptor kinase 1 precursor), Os10g0513200 (Dwarf and tiller-enhancing 1, DTE1), Os02g0706400 (MYB-related transcription factor, OsRL3), etc. Differential expression levels of some genes were verified in WT and d61-1 under cold stress using qRT-PCR. These valuable findings and gene resources will be critical for understanding the regulatory relationships between cold stress tolerance and the BR signaling pathways in rice.
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Affiliation(s)
- Yi-Shan Cheng
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Ye-Dong Sun
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Jia-Ying Xing
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Lu Zhan
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Xiu-Jie Li
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Jing Huang
- Department of Agronomy, College of Agriculture, Purdue University, West Lafayette, IN, 47907, United States
| | - Ming-Hui Zhao
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang, 110161, China.
| | - Zhi-Fu Guo
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China.
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9
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Liu J, Peng L, Cao C, Bai C, Wang Y, Li Z, Zhu H, Wen Q, He S. Identification of WRKY Family Members and Characterization of the Low-Temperature-Stress-Responsive WRKY Genes in Luffa ( Luffa cylindrica L.). Plants (Basel) 2024; 13:676. [PMID: 38475522 DOI: 10.3390/plants13050676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
The plant-specific WRKY transcription factor family members have diverse regulatory effects on the genes associated with many plant processes. Although the WRKY proteins in Arabidopsis thaliana and other species have been thoroughly investigated, there has been relatively little research on the WRKY family in Luffa cylindrica, which is one of the most widely grown vegetables in China. In this study, we performed a genome-wide analysis to identify L. cylindrica WRKY genes, which were subsequently classified and examined in terms of their gene structures, chromosomal locations, promoter cis-acting elements, and responses to abiotic stress. A total of 62 LcWRKY genes (471-2238 bp) were identified and divided into three phylogenetic groups (I, II, and III), with group II further divided into five subgroups (IIa, IIb, IIc, IId, and IIe) in accordance with the classification in other plants. The LcWRKY genes were unevenly distributed across 13 chromosomes. The gene structure analysis indicated that the LcWRKY genes contained 0-11 introns (average of 4.4). Moreover, 20 motifs were detected in the LcWRKY proteins with conserved motifs among the different phylogenetic groups. Two subgroup IIc members (LcWRKY16 and LcWRKY31) contained the WRKY sequence variant WRKYGKK. Additionally, nine cis-acting elements related to diverse responses to environmental stimuli were identified in the LcWRKY promoters. The subcellular localization analysis indicated that three LcWRKY proteins (LcWRKY43, LcWRKY7, and LcWRKY23) are localized in the nucleus. The tissue-specific LcWRKY expression profiles reflected the diversity in LcWRKY expression. The RNA-seq data revealed the effects of low-temperature stress on LcWRKY expression. The cold-induced changes in expression were verified via a qRT-PCR analysis of 24 differentially expressed WRKY genes. Both LcWRKY7 and LcWRKY12 were highly responsive to the low-temperature treatment (approximately 110-fold increase in expression). Furthermore, the LcWRKY8, LcWRKY12, and LcWRKY59 expression levels increased by more than 25-fold under cold conditions. Our findings will help clarify the evolution of the luffa WRKY family while also providing valuable insights for future studies on WRKY functions.
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Affiliation(s)
- Jianting Liu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Lijuan Peng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengjuan Cao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changhui Bai
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Yuqian Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zuliang Li
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Haisheng Zhu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Qingfang Wen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013, China
| | - Shuilin He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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10
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Wang H, Jia Y, Bai X, Gong W, Liu G, Wang H, Xin J, Wu Y, Zheng H, Liu H, Wang J, Zou D, Zhao H. Whole-Transcriptome Profiling and Functional Prediction of Long Non-Coding RNAs Associated with Cold Tolerance in Japonica Rice Varieties. Int J Mol Sci 2024; 25:2310. [PMID: 38396991 PMCID: PMC10889138 DOI: 10.3390/ijms25042310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, the competitive endogenous RNA mechanism in rice at low temperatures has not been reported. Therefore, in this study, antioxidant physiological indices were combined with whole-transcriptome data through weighted correlation network analysis, which found that the gene modules had the highest correlation with the key antioxidant enzymes superoxide dismutase and peroxidase. The hub genes of the superoxide dismutase-related module included the UDP-glucosyltransferase family protein, sesquiterpene synthase and indole-3-glycerophosphatase gene. The hub genes of the peroxidase-related module included the WRKY transcription factor, abscisic acid signal transduction pathway-related gene plasma membrane hydrogen-ATPase and receptor-like kinase. Therefore, we selected the modular hub genes and significantly enriched the metabolic pathway genes to construct the key competitive endogenous RNA networks, resulting in three competitive endogenous RNA networks of seven long non-coding RNAs regulating three co-expressed messenger RNAs via four microRNAs. Finally, the negative regulatory function of the WRKY transcription factor OsWRKY61 was determined via subcellular localization and validation of the physiological indices in the mutant.
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Affiliation(s)
| | - Yan Jia
- Correspondence: (Y.J.); (H.Z.)
| | | | | | | | | | | | | | | | | | | | | | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (H.W.); (X.B.); (W.G.); (G.L.); (H.W.); (J.X.); (Y.W.); (H.Z.); (H.L.); (J.W.); (D.Z.)
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11
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Deng H, Cao S, Zhang G, Xiao Y, Liu X, Wang F, Tang W, Lu X. OsVPE2, a Member of Vacuolar Processing Enzyme Family, Decreases Chilling Tolerance of Rice. Rice (N Y) 2024; 17:5. [PMID: 38194166 PMCID: PMC10776553 DOI: 10.1186/s12284-023-00682-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024]
Abstract
Chilling is a major abiotic stress affecting rice growth, development and geographical distribution. Plant vacuolar processing enzymes (VPEs) contribute to the seed storage protein processing and mediate the programmed cell death by abiotic and biotic stresses. However, little is known about the roles of plant VPEs in cold stress responses and tolerance regulation. Here, we found that OsVPE2 was a chilling-responsive gene. The early-indica rice variety Xiangzaoxian31 overexpressing OsVPE2 was more sensitive to chilling stress, whereas the OsVPE2-knockout mutants generated by the CRISPR-Cas9 technology exhibited significantly enhanced chilling tolerance at the seedling stage without causing yield loss. Deficiency of OsVPE2 reduces relative electrolyte leakage, accumulation of toxic compounds such as reactive oxygen species and malondialdehyde, and promotes antioxidant enzyme activities under chilling stress conditions. It was indicated that OsVPE2 mediated the disintegration of vacuoles under chilling stress, accompanied by the entry of swollen mitochondria into vacuoles. OsVPE2 suppressed the expression of genes that have a positive regulatory role in antioxidant process. Moreover, haplotype analysis suggested that the natural variation in the OsVPE2 non-coding region may endow OsVPE2 with different expression levels, thereby probably conferring differences in cold tolerance between japonica and indica sub-population. Our results thus reveal a new biological function of the VPE family in regulating cold resistance, and suggest that the gene editing or natural variations of OsVPE2 can be used to create cold tolerant rice varieties with stable yield.
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Affiliation(s)
- Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Sai Cao
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Feng Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Wenbang Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- Yuelushan Laboratory, Changsha, 410128, China.
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Yuelushan Laboratory, Changsha, 410128, China.
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12
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Zhang J, Zhao H, Chen L, Lin J, Wang Z, Pan J, Yang F, Ni X, Wang Y, Wang Y, Li R, Pi E, Wang S. Multifaceted roles of WRKY transcription factors in abiotic stress and flavonoid biosynthesis. Front Plant Sci 2023; 14:1303667. [PMID: 38169626 PMCID: PMC10758500 DOI: 10.3389/fpls.2023.1303667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Increasing biotic and abiotic stresses are seriously impeding the growth and yield of staple crops and threatening global food security. As one of the largest classes of regulators in vascular plants, WRKY transcription factors play critical roles governing flavonoid biosynthesis during stress responses. By binding major W-box cis-elements (TGACCA/T) in target promoters, WRKYs modulate diverse signaling pathways. In this review, we optimized existing WRKY phylogenetic trees by incorporating additional plant species with WRKY proteins implicated in stress tolerance and flavonoid regulation. Based on the improved frameworks and documented results, we aim to deduce unifying themes of distinct WRKY subfamilies governing specific stress responses and flavonoid metabolism. These analyses will generate experimentally testable hypotheses regarding the putative functions of uncharacterized WRKY homologs in tuning flavonoid accumulation to enhance stress resilience.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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13
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Zhang X, Yu F, Lyu X, Chen J, Zeng H, Xu N, Wu Y, Zhu Q. Transcriptome profiling of Bergenia purpurascens under cold stress. BMC Genomics 2023; 24:754. [PMID: 38062379 PMCID: PMC10702111 DOI: 10.1186/s12864-023-09850-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Bergenia purpurascens is an important medicinal, edible and ornamental plant. It generally grows in high-altitude areas with complex climates. There have been no reports about how B. purpurascens survives under cold stress. Here, the B. purpurascens under low temperature were subjected to transcriptomics analysis to explore the candidate genes and pathways that involved in the cold tolerance of B. purpurascens. Compared with the control treatment, we found 9,600 up-regulated differentially expressed genes (DEGs) and 7,055 down-regulated DEGs. A significant number of DEGs were involved in the Ca2+ signaling pathway, mitogen-activated protein kinase (MAPK) cascade, plant hormone signaling pathway, and lipid metabolism. A total of 400 transcription factors were found to respond to cold stress, most of which belonged to the MYB and AP2/ERF families. Five novel genes were found to be potential candidate genes involved in the cold tolerance of B. purpurascens. The study provide insights into further investigation of the molecular mechanism of how B. purpurascens survives under cold stress.
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Affiliation(s)
- Xuebin Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Fang Yu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xin Lyu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Jingyu Chen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Hongyan Zeng
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Nuomei Xu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yufeng Wu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Qiankun Zhu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
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14
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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15
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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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16
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Zhou Z, Liu J, Meng W, Sun Z, Tan Y, Liu Y, Tan M, Wang B, Yang J. Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Mechanisms of Rice with Different Salinity Tolerances. Plants (Basel) 2023; 12:3359. [PMID: 37836098 PMCID: PMC10574619 DOI: 10.3390/plants12193359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Rice is a crucial global food crop, but it lacks a natural tolerance to high salt levels, resulting in significant yield reductions. To gain a comprehensive understanding of the molecular mechanisms underlying rice's salt tolerance, further research is required. In this study, the transcriptomic and metabolomic differences between the salt-tolerant rice variety Lianjian5 (TLJIAN) and the salt-sensitive rice variety Huajing5 (HJING) were examined. Transcriptome analysis revealed 1518 differentially expressed genes (DEGs), including 46 previously reported salt-tolerance-related genes. Notably, most of the differentially expressed transcription factors, such as NAC, WRKY, MYB, and EREBP, were upregulated in the salt-tolerant rice. Metabolome analysis identified 42 differentially accumulated metabolites (DAMs) that were upregulated in TLJIAN, including flavonoids, pyrocatechol, lignans, lipids, and trehalose-6-phosphate, whereas the majority of organic acids were downregulated in TLJIAN. The interaction network of 29 differentially expressed transporter genes and 19 upregulated metabolites showed a positive correlation between the upregulated calcium/cation exchange protein genes (OsCCX2 and CCX5_Ath) and ABC transporter gene AB2E_Ath with multiple upregulated DAMs in the salt-tolerant rice variety. Similarly, in the interaction network of differentially expressed transcription factors and 19 upregulated metabolites in TLJIAN, 6 NACs, 13 AP2/ERFs, and the upregulated WRKY transcription factors were positively correlated with 3 flavonoids, 3 lignans, and the lipid oleamide. These results suggested that the combined effects of differentially expressed transcription factors, transporter genes, and DAMs contribute to the enhancement of salt tolerance in TLJIAN. Moreover, this study provides a valuable gene-metabolite network reference for understanding the salt tolerance mechanism in rice.
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Affiliation(s)
- Zhenling Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China;
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Juan Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (J.L.); (W.M.); (M.T.)
| | - Wenna Meng
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (J.L.); (W.M.); (M.T.)
| | - Zhiguang Sun
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Yiluo Tan
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Yan Liu
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Mingpu Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (J.L.); (W.M.); (M.T.)
| | - Baoxiang Wang
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China;
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Shaheen N, Ahmad S, Alghamdi SS, Rehman HM, Javed MA, Tabassum J, Shao G. CRISPR-Cas System, a Possible "Savior" of Rice Threatened by Climate Change: An Updated Review. Rice (N Y) 2023; 16:39. [PMID: 37688677 PMCID: PMC10492775 DOI: 10.1186/s12284-023-00652-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/04/2023] [Indexed: 09/11/2023]
Abstract
Climate change has significantly affected agriculture production, particularly the rice crop that is consumed by almost half of the world's population and contributes significantly to global food security. Rice is vulnerable to several abiotic and biotic stresses such as drought, heat, salinity, heavy metals, rice blast, and bacterial blight that cause huge yield losses in rice, thus threatening food security worldwide. In this regard, several plant breeding and biotechnological techniques have been used to raise such rice varieties that could tackle climate changes. Nowadays, gene editing (GE) technology has revolutionized crop improvement. Among GE technology, CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) system has emerged as one of the most convenient, robust, cost-effective, and less labor-intensive system due to which it has got more popularity among plant researchers, especially rice breeders and geneticists. Since 2013 (the year of first application of CRISPR/Cas-based GE system in rice), several trait-specific climate-resilient rice lines have been developed using CRISPR/Cas-based GE tools. Earlier, several reports have been published confirming the successful application of GE tools for rice improvement. However, this review particularly aims to provide an updated and well-synthesized brief discussion based on the recent studies (from 2020 to present) on the applications of GE tools, particularly CRISPR-based systems for developing CRISPR rice to tackle the current alarming situation of climate change, worldwide. Moreover, potential limitations and technical bottlenecks in the development of CRISPR rice, and prospects are also discussed.
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Affiliation(s)
- Nabeel Shaheen
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia.
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hafiz Mamoon Rehman
- Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, National Rice Research Institute, 310006, Hangzhou, China.
- Zhejiang Lab, 310006, Hangzhou, China.
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Tang Q, Wang X, Jin X, Peng J, Zhang H, Wang Y. CRISPR/Cas Technology Revolutionizes Crop Breeding. Plants (Basel) 2023; 12:3119. [PMID: 37687368 PMCID: PMC10489799 DOI: 10.3390/plants12173119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed.
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Affiliation(s)
- Qiaoling Tang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soi-Borne Diseases, Baoding University, Baoding 071000, China;
| | - Jun Peng
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
| | - Haiwen Zhang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Youhua Wang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
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Yan T, Sun M, Su R, Wang X, Lu X, Xiao Y, Deng H, Liu X, Tang W, Zhang G. Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of Indica Rice. Plants (Basel) 2023; 12:2675. [PMID: 37514289 PMCID: PMC10384097 DOI: 10.3390/plants12142675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/15/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the indica cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two indica cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including WRKY, NAC, bHLH, ERF, bZIP, MYB, C2H2, and GRAS, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the "response to cold" category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as "Pyruvate metabolism", "Glycolysis/Gluconeogenesis", and "Starch and sucrose metabolism", contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the indica cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible indica rice cultivars.
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Affiliation(s)
- Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Meng Sun
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Rui Su
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xiaozhong Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410128, China
- State Key Laboratory of Hybrid Rice, Changsha 410128, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
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Huang C, Wang J, Wang D, Chang J, Chen H, Chen D, Deng W, Tian C. Genome-Wide Identification and Analysis of OsSPXs Revealed Its Genetic Influence on Cold Tolerance of Dongxiang Wild Rice (DXWR). Int J Mol Sci 2023; 24:ijms24108755. [PMID: 37240100 DOI: 10.3390/ijms24108755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential functions of other SPX genes in cold stress are unknown. Therefore, in this study, we identified six OsSPXs from the whole genome of DXWR. The phylogeny of OsSPXs has a strong correlation with its motif. Transcriptome data analysis showed that OsSPXs were highly sensitive to cold stress, and real-time PCR verified that the levels of OsSPX1, OsSPX2, OsSPX4, and OsSPX6 in cold-tolerant materials (DXWR) during cold treatment were higher than that of cold-sensitive rice (GZX49). The promoter region of DXWR OsSPXs contains a large number of cis-acting elements related to abiotic stress tolerance and plant hormone response. At the same time, these genes have expression patterns that are highly similar to cold-tolerance genes. This study provides useful information about OsSPXs, which is helpful for the gene-function research of DXWR and genetic improvements during breeding.
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Affiliation(s)
- Cheng Huang
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jilin Wang
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Dianwen Wang
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Hongping Chen
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Dazhou Chen
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Wei Deng
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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Li C, Dong S, Beckles DM, Liu X, Guan J, Gu X, Miao H, Zhang S. GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber. Front Plant Sci 2023; 14:1116214. [PMID: 37235012 PMCID: PMC10208356 DOI: 10.3389/fpls.2023.1116214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/24/2023] [Indexed: 05/28/2023]
Abstract
Low temperatures (LTs) negatively affect the percentage and rate of cucumber (Cucumis sativus L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify the genetic loci underlying low temperature germination (LTG) in 151 cucumber accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative germination rate (RGR), relative germination energy (RGE), relative germination index (RGI) and relative radical length (RRL), were collected in two environments, and 17 of the 151 accessions were found to be highly cold tolerant using cluster analysis. A total of 1,522,847 significantly associated single-nucleotide polymorphism (SNP) were identified, and seven loci associated with LTG, on four chromosomes, were detected: gLTG1.1, gLTG1.2, gLTG1.3, gLTG4.1, gLTG5.1, gLTG5.2, and gLTG6.1 after resequencing of the accessions. Of the seven loci, three, i.e., gLTG1.2, gLTG4.1, and gLTG5.2, showed strong signals that were consistent over two years using the four germination indices, and are thus strong and stable for LTG. Eight candidate genes associated with abiotic stress were identified, and three of them were potentially causal to LTG: CsaV3_1G044080 (a pentatricopeptide repeat-containing protein) for gLTG1.2, CsaV3_4G013480 (a RING-type E3 ubiquitin transferase) for gLTG4.1, and CsaV3_5G029350 (a serine/threonine-protein kinase) for gLTG5.2. The function for CsPPR (CsaV3_1G044080) in regulating LTG was confirmed, as Arabidopsis lines ectopically expressing CsPPR showed higher germination and survival rates at 4°C compared to the wild-type, which preliminarily illustrates that CsPPR positively regulates cucumber cold tolerance at the germination stage. This study will provide insights into cucumber LT-tolerance mechanisms and further promote cucumber breeding development.
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Affiliation(s)
- Caixia Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Diane M. Beckles
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Huang P, Ding Z, Duan M, Xiong Y, Li X, Yuan X, Huang J. OsLUX Confers Rice Cold Tolerance as a Positive Regulatory Factor. Int J Mol Sci 2023; 24:ijms24076727. [PMID: 37047700 PMCID: PMC10094877 DOI: 10.3390/ijms24076727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
During the early seedling stage, rice (Oryza sativa L.) must overcome low-temperature stress. While a few cold-tolerance genes have been characterized, further excavation of cold-resistance genes is still needed. In this study, we identified a cold-induced transcription factor—LUX ARRHYTHMO (LUX)—in rice. OsLUX was found to be specifically expressed in leaf blades and upregulated by both cold stress and circadian rhythm. The full-length OsLUX showed autoactivation activity, and the OsLUX protein localized throughout the entire onion cell. Overexpressing OsLUX resulted in increased cold tolerance and reduced ion leakage under cold-stress conditions during the seedling stage. In contrast, the knockout of OsLUX decreased seedling cold tolerance and showed higher ion leakage compared to the wild type. Furthermore, overexpressing OsLUX upregulated the expression levels of oxidative stress-responsive genes, which improved reactive oxygen species (ROS) scavenging ability and enhanced tolerance to chilling stress. Promoter analysis showed that the OsLUX promoter contains two dehydration-responsive element binding (DREB) motifs at positions −510/−505 (GTCGGa) and −162/−170 (cCACCGccc), which indicated that OsDREB1s and OsDREB2s probably regulate OsLUX expression by binding to the motif to respond to cold stress. Thus, OsLUX may act as a downstream gene of the DREB pathway. These results demonstrate that OsLUX serves as a positive regulatory factor of cold stress and that overexpressing OsLUX could be used in rice breeding programs to enhance abiotic stress tolerance.
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Affiliation(s)
- Peng Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhengquan Ding
- Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Min Duan
- Taizhou Academy Agricultural of Sciences, Taizhou 317000, China
| | - Yi Xiong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xinxin Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xi Yuan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Zhang M, Zhao R, Wang H, Ren S, Shi L, Huang S, Wei Z, Guo B, Jin J, Zhong Y, Chen M, Jiang W, Wu T, Du X. OsWRKY28 positively regulates salinity tolerance by directly activating OsDREB1B expression in rice. Plant Cell Rep 2023; 42:223-234. [PMID: 36350394 DOI: 10.1007/s00299-022-02950-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
OsWRKY28 confers salinity tolerance by directly binding to OsDREB1B promoter and increasing its transcriptional activity, and negatively regulates abscisic acid mediated seedling establishment in rice. WRKY transcription factors have been reported to play a vital role in plants growth, development, abiotic and biotic stress responses. In this study, we explored the functions of a transcription factor OsWRKY28 in rice. The transcript level of OsWRKY28 was strikingly increased under drought, chilling, salt and abscisic acid treatments. The OsWRKY28 overexpression lines showed enhanced salinity stress tolerance, whereas the oswrky28 mutants displayed salt sensitivity compared to wild-type plants. Under salt stress treatment, the expression levels of OsbZIP05, OsHKT1;1 and OsDREB1B were significantly lower yet the level of OsHKT2;1 was significantly higher in oswrky28 mutants than those in wide type plants. Our data of yeast one-hybrid assay and dual-luciferase assay supported that OsWRKY28 could directly bind to the promoter of OsDREB1B to enhance salinity tolerance in rice. In addition, OsWRKY28 overexpression lines displayed hyposensitivity and the oswrky28 mutants showed hypersensitivity compared to wild-type plants under exogenous abscisic acid treatment. Based on the results of yeast two-hybrid assay and GAL4-dependent chimeric transactivation assay, OsWRKY28 physically interacts with OsMPK11 and its transcriptional activity could be regulated by OsMPK11. Together, OsWRKY28 confers salinity tolerance through directly targeting OsDREB1B promoter and further activating its transcription in rice.
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Affiliation(s)
- Mingxing Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Ranran Zhao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Haitao Wang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Shule Ren
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Liyuan Shi
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Shuangzhan Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Zhiqi Wei
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Boya Guo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Jiuyan Jin
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Yu Zhong
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Mojun Chen
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China
| | - Wenzhu Jiang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China.
| | - Tao Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China.
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, People's Republic of China.
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Wang H, Gong W, Wang Y, Ma Q. Contribution of a WRKY Transcription Factor, ShWRKY81, to Powdery Mildew Resistance in Wild Tomato. Int J Mol Sci 2023; 24. [PMID: 36768909 DOI: 10.3390/ijms24032583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/21/2023] [Accepted: 01/22/2023] [Indexed: 01/31/2023] Open
Abstract
Tomato powdery mildew, caused by Oidium neolycopersici, is a destructive fungal disease that damages almost all of the aerial parts of tomato, causing devastating losses in tomato production worldwide. WRKY transcription factors are key regulators of plant immunity, but the roles of ShWRKYs in wild tomato Solanum habrochaites LA1777 against O. neolycopersici still remain to be uncovered. Here, we show that ShWRKY81 is an important WRKY transcription factor from wild tomato Solanum habrochaites LA1777, contributing to plant resistance against O. neolycopersici. ShWRKY81 was isolated and identified to positively modulate tomato resistance against On-Lz. The transient overexpression of the ShWRKY81-GFP (green fluorescent protein) fusion protein in Nicotiana benthamiana cells revealed that ShWRKY81 was localized in the nucleus. ShWRKY81 responded differentially to abiotic and biotic stimuli, with ShWRKY81 mRNA accumulation in LA1777 seedlings upon On-Lz infection. The virus-induced gene silencing of ShWRKY81 led to host susceptibility to On-Lz in LA1777, and a loss of H2O2 formation and hypersensitive response (HR) induction. Furthermore, the transcripts of ShWRKY81 were induced by salicylic acid (SA), and ShWRKY81-silenced LA1777 seedlings displayed decreased levels of the defense hormone SA and SA-dependent PRs gene expression upon On-Lz infection. Together, these results demonstrate that ShWRKY81 acts as a positive player in tomato powdery mildew resistance.
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Wu B, Chen S, Cheng S, Li C, Li S, Chen J, Zha W, Liu K, Xu H, Li P, Shi S, Yang G, Chen Z, Liu K, You A, Zhou L. Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage. Int J Mol Sci 2023; 24:ijms24031914. [PMID: 36768236 PMCID: PMC9916315 DOI: 10.3390/ijms24031914] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Cold damage is one of the most important environmental factors influencing crop growth, development, and production. In this study, we generated a pair of near-isogenic lines (NILs), Towada and ZL31, and Towada showed more cold sensitivity than ZL31 in the rice seedling stage. To explore the transcriptional regulation mechanism and the reason for phenotypic divergence of the two lines in response to cold stress, an in-depth comparative transcriptome study under cold stress was carried out. Our analysis uncovered that rapid and high-amplitude transcriptional reprogramming occurred in the early stage of cold treatment. GO enrichment and KEGG pathway analysis indicated that genes of the response to stress, environmental adaptation, signal transduction, metabolism, photosynthesis, and the MAPK signaling pathway might form the main part of the engine for transcriptional reprogramming in response to cold stress. Furthermore, we identified four core genes, OsWRKY24, OsCAT2, OsJAZ9, and OsRR6, that were potential candidates affecting the cold sensitivity of Towada and ZL31. Genome re-sequencing analysis between the two lines revealed that only OsWRKY24 contained sequence variations which may change its transcript abundance. Our study not only provides novel insights into the cold-related transcriptional reprogramming process, but also highlights the potential candidates involved in cold stress.
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Affiliation(s)
- Bian Wu
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Siyuan Chen
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shiyuan Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Changyan Li
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Sanhe Li
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Junxiao Chen
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wenjun Zha
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Kai Liu
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Huashan Xu
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Peide Li
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shaojie Shi
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Guocai Yang
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhijun Chen
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Kai Liu
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Aiqing You
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence: (A.Y.); (L.Z.)
| | - Lei Zhou
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence: (A.Y.); (L.Z.)
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Zhang M, Zhao R, Huang K, Wei Z, Guo B, Huang S, Li Z, Jiang W, Wu T, Du X. OsWRKY76 positively regulates drought stress via OsbHLH148-mediated jasmonate signaling in rice. Front Plant Sci 2023; 14:1168723. [PMID: 37089644 PMCID: PMC10113545 DOI: 10.3389/fpls.2023.1168723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Drought stress is a major environmental threat that limits plant growth and crop productivity. Therefore, it is necessary to uncover the molecular mechanisms behind drought tolerance in crops. Here, OsWRKY76 positively regulated drought stress in rice. OsWRKY76 expression was induced by PEG treatment, dehydration stress, and exogenous MeJA rather than by no treatment. Notably, OsWRKY76 knockout weakened drought tolerance at the seedling stage and decreased MeJA sensitivity. OsJAZ12 was significantly induced by drought stress, and its expression was significantly higher in OsWRKY76-knockout mutants than in wild-type ZH11 under drought stress. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsWRKY76 interacted with OsJAZ12. OsWRKY76 weakened the interaction between OsbHLH148 and OsJAZ12 in yeast cells. The OsJAZ12 protein repressed the transactivation activity of OsbHLH148, and this repression was partly restored by OsWRKY76 in rice protoplasts. Moreover, OsDREB1E expression was lower in OsWRKY76-knockout mutants than in wild-type ZH11 under drought stress, but it was upregulated under normal growth conditions. Yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays showed that OsWRKY76 and OsbHLH148 bound directly to the OsDREB1E promoter and activated OsDREB1E expression in response to drought stress. These results suggest that OsWRKY76 confers drought tolerance through OsbHLH148-mediated jasmonate signaling in rice, offering a new clue to uncover the mechanisms behind drought tolerance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Tao Wu
- *Correspondence: Tao Wu, ; Xinglin Du,
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