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Pang Y, Cao L, Ye F, Ma C, Liang X, Song Y, Lu X. Identification of the Maize PP2C Gene Family and Functional Studies on the Role of ZmPP2C15 in Drought Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:340. [PMID: 38337873 PMCID: PMC10856965 DOI: 10.3390/plants13030340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
The protein phosphatase PP2C plays an important role in plant responses to stress. Therefore, the identification of maize PP2C genes that respond to drought stress is particularly important for the improvement and creation of new drought-resistant assortments of maize. In this study, we identified 102 ZmPP2C genes in maize at the genome-wide level. We analyzed the physicochemical properties of 102 ZmPP2Cs and constructed a phylogenetic tree with Arabidopsis. By analyzing the gene structure, conserved protein motifs, and synteny, the ZmPP2Cs were found to be strongly conserved during evolution. Sixteen core genes involved in drought stress and rewatering were screened using gene co-expression network mapping and expression profiling. The qRT-PCR results showed 16 genes were induced by abscisic acid (ABA), drought, and NaCl treatments. Notably, ZmPP2C15 exhibited a substantial expression difference. Through genetic transformation, we overexpressed ZmPP2C15 and generated the CRISPR/Cas9 knockout maize mutant zmpp2c15. Overexpressing ZmPP2C15 in Arabidopsis under drought stress enhanced growth and survival compared with WT plants. The leaves exhibited heightened superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), and catalase (CAT) activities, elevated proline (Pro) content, and reduced malondialdehyde (MDA) content. Conversely, zmpp2c15 mutant plants displayed severe leaf dryness, curling, and wilting under drought stress. Their leaf activities of SOD, POD, APX, and CAT were lower than those in B104, while MDA was higher. This suggests that ZmPP2C15 positively regulates drought tolerance in maize by affecting the antioxidant enzyme activity and osmoregulatory substance content. Subcellular localization revealed that ZmPP2C15 was localized in the nucleus and cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) experiments demonstrated ZmPP2C15's interaction with ZmWIN1, ZmADT2, ZmsodC, Zmcab, and ZmLHC2. These findings establish a foundation for understanding maize PP2C gene functions, offering genetic resources and insights for molecular design breeding for drought tolerance.
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Affiliation(s)
- Yunyun Pang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (Y.P.); (L.C.); (F.Y.); (C.M.); (X.L.); (Y.S.)
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450002, China
| | - Liru Cao
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (Y.P.); (L.C.); (F.Y.); (C.M.); (X.L.); (Y.S.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Feiyu Ye
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (Y.P.); (L.C.); (F.Y.); (C.M.); (X.L.); (Y.S.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Chenchen Ma
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (Y.P.); (L.C.); (F.Y.); (C.M.); (X.L.); (Y.S.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Xiaohan Liang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (Y.P.); (L.C.); (F.Y.); (C.M.); (X.L.); (Y.S.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Yinghui Song
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (Y.P.); (L.C.); (F.Y.); (C.M.); (X.L.); (Y.S.)
| | - Xiaomin Lu
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (Y.P.); (L.C.); (F.Y.); (C.M.); (X.L.); (Y.S.)
- The Shennong Laboratory, Zhengzhou 450002, China
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Zhang P, Liu D, Ma J, Sun C, Wang Z, Zhu Y, Zhang X, Liu Y. Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe. BMC Genomics 2024; 25:83. [PMID: 38245685 PMCID: PMC10799369 DOI: 10.1186/s12864-024-09966-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. RESULTS In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress. CONCLUSIONS Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.
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Affiliation(s)
- Pan Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Deqi Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiawei Ma
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Chong Sun
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Zhaofei Wang
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Yongxing Zhu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xuemei Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yiqing Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
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Zeng J, Wu C, Ye X, Zhou J, Chen Y, Li L, Lin M, Wang S, Liu S, Yan Y, Tie W, Yang J, Yan F, Zeng L, Liu Y, Hu W. MePP2C24, a cassava (Manihot esculenta) gene encoding protein phosphatase 2C, negatively regulates drought stress and abscisic acid responses in transgenic Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108291. [PMID: 38141400 DOI: 10.1016/j.plaphy.2023.108291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Abscisic acid (ABA) signaling plays a crucial role in plant development and response to abiotic/biotic stress. However, the function and regulation of protein phosphatase 2C (PP2C), a key component of abscisic acid signaling, under abiotic stress are still unknown in cassava, a drought-tolerant crop. In this study, a cassava PP2C gene (MePP2C24) was cloned and characterized. The MePP2C24 transcripts increased in response to mannitol, NaCl, and ABA. Overexpression of MePP2C24 in Arabidopsis resulted in increased sensitivity to drought stress and decreased sensitivity to exogenous ABA. This was demonstrated by transgenic lines having higher levels of malondialdehyde (MDA), ion leakage (IL), and reactive oxygen species (ROS), lower activities of catalase (CAT) and peroxidase (POD), and lower proline content than wild type (WT) under drought stress. Moreover, MePP2C24 overexpression caused decrease in expression of drought-responsive genes related to ABA signaling pathway. In addition, MePP2C24 was localized in the cell nucleus and showed self-activation. Furthermore, many MePYLs (MePYL1, MePYL4, MePYL7-9, and MePYL11-13) could interact with MePP2C24 in the presence of ABA, and MePYL1 interacted with MePP2C24 in both the presence and absence of ABA. Additionally, MebZIP11 interacted with the promoter of MePP2C24 and exerted a suppressive effect. Taken together, our results suggest that MePP2C24 acts as a negative regulator of drought tolerance and ABA response.
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Affiliation(s)
- Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China.
| | - Chunlai Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, 430074, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Xiaoxue Ye
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Jiewei Zhou
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Yingtong Chen
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Lizhen Li
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Man Lin
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Shuting Wang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Siwen Liu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yan Yan
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Weiwei Tie
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Jinghao Yang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Fei Yan
- Shaanxi Provincial Bioresource Key Laboratory, College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Liwang Zeng
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China.
| | - Yujia Liu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China.
| | - Wei Hu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China.
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Liu Q, Qin B, Zhang D, Liang X, Yang Y, Wang L, Wang M, Zhang Y. Identification and Characterization of the HbPP2C Gene Family and Its Expression in Response to Biotic and Abiotic Stresses in Rubber Tree. Int J Mol Sci 2023; 24:16061. [PMID: 38003251 PMCID: PMC10671201 DOI: 10.3390/ijms242216061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Plant PP2C genes are crucial for various biological processes. To elucidate the potential functions of these genes in rubber tree (Hevea brasiliensis), we conducted a comprehensive analysis of these genes using bioinformatics methods. The 60 members of the PP2C family in rubber tree were identified and categorized into 13 subfamilies. The PP2C proteins were conserved across different plant species. The results revealed that the HbPP2C genes contained multiple elements responsive to phytohormones and stresses in their promoters, suggesting their involvement in these pathways. Expression analysis indicated that 40 HbPP2C genes exhibited the highest expression levels in branches and the lowest expression in latex. Additionally, the expression of A subfamily members significantly increased in response to abscisic acid, drought, and glyphosate treatments, whereas the expression of A, B, D, and F1 subfamily members notably increased under temperature stress conditions. Furthermore, the expression of A and F1 subfamily members was significantly upregulated upon powdery mildew infection, with the expression of the HbPP2C6 gene displaying a remarkable 33-fold increase. These findings suggest that different HbPP2C subgroups may have distinct roles in the regulation of phytohormones and the response to abiotic and biotic stresses in rubber tree. This study provides a valuable reference for further investigations into the functions of the HbPP2C gene family in rubber tree.
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Affiliation(s)
- Qifeng Liu
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Bi Qin
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (B.Q.); (L.W.)
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture and Rural Affairs, Danzhou 571737, China
| | - Dong Zhang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Xiaoyu Liang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Ye Yang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Lifeng Wang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (B.Q.); (L.W.)
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture and Rural Affairs, Danzhou 571737, China
| | - Meng Wang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Yu Zhang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
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Wang J, Li C, Li L, Gao L, Hu G, Zhang Y, Reynolds MP, Zhang X, Jia J, Mao X, Jing R. DIW1 encoding a clade I PP2C phosphatase negatively regulates drought tolerance by de-phosphorylating TaSnRK1.1 in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1918-1936. [PMID: 37158049 DOI: 10.1111/jipb.13504] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/05/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
Drought seriously impacts wheat production (Triticum aestivum L.), while the exploitation and utilization of genes for drought tolerance are insufficient. Leaf wilting is a direct reflection of drought tolerance in plants. Clade A PP2Cs are abscisic acid (ABA) co-receptors playing vital roles in the ABA signaling pathway, regulating drought response. However, the roles of other clade PP2Cs in drought tolerance, especially in wheat, remain largely unknown. Here, we identified a gain-of-function drought-induced wilting 1 (DIW1) gene from the wheat Aikang 58 mutant library by map-based cloning, which encodes a clade I protein phosphatase 2C (TaPP2C158) with enhanced protein phosphatase activity. Phenotypic analysis of overexpression and CRISPR/Cas9 mutant lines demonstrated that DIW1/TaPP2C158 is a negative regulator responsible for drought resistance. We found that TaPP2C158 directly interacts with TaSnRK1.1 and de-phosphorylates it, thus inactivating the TaSnRK1.1-TaAREB3 pathway. TaPP2C158 protein phosphatase activity is negatively correlated with ABA signaling. Association analysis suggested that C-terminal variation of TaPP2C158 changing protein phosphatase activity is highly correlated with the canopy temperature, and seedling survival rate under drought stress. Our data suggest that the favorable allele with lower phosphatase activity of TaPP2C158 has been positively selected in Chinese breeding history. This work benefits us in understanding the molecular mechanism of wheat drought tolerance, and provides elite genetic resources and molecular markers for improving wheat drought tolerance.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ge Hu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanfei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Matthew P Reynolds
- International Maize and Wheat Improvement Center, Texcoco, 56237, Mexico
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Née G, Krüger T. Dry side of the core: a meta-analysis addressing the original nature of the ABA signalosome at the onset of seed imbibition. FRONTIERS IN PLANT SCIENCE 2023; 14:1192652. [PMID: 37476171 PMCID: PMC10354442 DOI: 10.3389/fpls.2023.1192652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023]
Abstract
The timing of seedling emergence is a major agricultural and ecological fitness trait, and seed germination is controlled by a complex molecular network including phytohormone signalling. One such phytohormone, abscisic acid (ABA), controls a large array of stress and developmental processes, and researchers have long known it plays a crucial role in repressing germination. Although the main molecular components of the ABA signalling pathway have now been identified, the molecular mechanisms through which ABA elicits specific responses in distinct organs is still enigmatic. To address the fundamental characteristics of ABA signalling during germination, we performed a meta-analysis focusing on the Arabidopsis dry seed proteome as a reflexion basis. We combined cutting-edge proteome studies, comparative functional analyses, and protein interaction information with genetic and physiological data to redefine the singular composition and operation of the ABA core signalosome from the onset of seed imbibition. In addition, we performed a literature survey to integrate peripheral regulators present in seeds that directly regulate core component function. Although this may only be the tip of the iceberg, this extended model of ABA signalling in seeds already depicts a highly flexible system able to integrate a multitude of information to fine-tune the progression of germination.
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Huang X, Liang Y, Zhang R, Zhang B, Song X, Liu J, Lu M, Qin Z, Li D, Li S, Li Y. Genome-Wide Identification of the PP2C Gene Family and Analyses with Their Expression Profiling in Response to Cold Stress in Wild Sugarcane. PLANTS (BASEL, SWITZERLAND) 2023; 12:2418. [PMID: 37446979 DOI: 10.3390/plants12132418] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Type 2C protein phosphatases (PP2Cs) represent a major group of protein phosphatases in plants, some of which have already been confirmed to play important roles in diverse plant processes. In this study, analyses of the phylogenetics, gene structure, protein domain, chromosome localization, and collinearity, as well as an identification of the expression profile, protein-protein interaction, and subcellular location, were carried out on the PP2C family in wild sugarcane (Saccharum spontaneum). The results showed that 145 PP2C proteins were classified into 13 clades. Phylogenetic analysis suggested that SsPP2Cs are evolutionarily closer to those of sorghum, and the number of SsPP2Cs is the highest. There were 124 pairs of SsPP2C genes expanding via segmental duplications. Half of the SsPP2C proteins were predicted to be localized in the chloroplast (73), with the next most common predicted localizations being in the cytoplasm (37) and nucleus (17). Analysis of the promoter revealed that SsPP2Cs might be photosensitive, responsive to abiotic stresses, and hormone-stimulated. A total of 27 SsPP2Cs showed cold-stress-induced expressions, and SsPP2C27 (Sspon.01G0007840-2D) and SsPP2C64 (Sspon.03G0002800-3D) were the potential hubs involved in ABA signal transduction. Our study presents a comprehensive analysis of the SsPP2C gene family, which can play a vital role in the further study of phosphatases in wild sugarcane. The results suggest that the PP2C family is evolutionarily conserved, and that it functions in various developmental processes in wild sugarcane.
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Affiliation(s)
- Xing Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Yongsheng Liang
- Nanning Institute of Agricultural Sciences, Nanning 530021, China
| | - Ronghua Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Baoqing Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Xiupeng Song
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Junxian Liu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Manman Lu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Zhenqiang Qin
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Dewei Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Song Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Yangrui Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
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Wang L, Zhou Y, Ding Y, Chen C, Chen X, Su N, Zhang X, Pan Y, Li J. Novel flavin-containing monooxygenase protein FMO1 interacts with CAT2 to negatively regulate drought tolerance through ROS homeostasis and ABA signaling pathway in tomato. HORTICULTURE RESEARCH 2023; 10:uhad037. [PMID: 37101513 PMCID: PMC10124749 DOI: 10.1093/hr/uhad037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
Drought stress is the major abiotic factor that can seriously affect plant growth and crop production. The functions of flavin-containing monooxygenases (FMOs) are known in animals. They add molecular oxygen to lipophilic compounds or produce reactive oxygen species (ROS). However, little information on FMOs in plants is available. Here, we characterized a tomato drought-responsive gene that showed homology to FMO, and it was designated as FMO1. FMO1 was downregulated promptly by drought and ABA treatments. Transgenic functional analysis indicated that RNAi suppression of the expression of FMO1 (FMO1-Ri) improved drought tolerance relative to wild-type (WT) plants, whereas overexpression of FMO1 (FMO1-OE) reduced drought tolerance. The FMO1-Ri plants exhibited lower ABA accumulation, higher levels of antioxidant enzyme activities, and less ROS generation compared with the WT and FMO1-OE plants under drought stress. RNA-seq transcriptional analysis revealed the differential expression levels of many drought-responsive genes that were co-expressed with FMO1, including PP2Cs, PYLs, WRKY, and LEA. Using Y2H screening, we found that FMO1 physically interacted with catalase 2 (CAT2), which is an antioxidant enzyme and confers drought resistance. Our findings suggest that tomato FMO1 negatively regulates tomato drought tolerance in the ABA-dependent pathway and modulates ROS homeostasis by directly binding to SlCAT2.
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Affiliation(s)
| | | | - Yin Ding
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Chunrui Chen
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Xueting Chen
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Nini Su
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Xingguo Zhang
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Yu Pan
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
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9
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Pan C, Yao L, Yu L, Qiao Z, Tang M, Wei F, Huang X, Zhou Y. Transcriptome and proteome analyses reveal the potential mechanism of seed dormancy release in Amomum tsaoko during warm stratification. BMC Genomics 2023; 24:99. [PMID: 36864423 PMCID: PMC9983222 DOI: 10.1186/s12864-023-09202-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND In Amomum tsaoko breeding, the low germination rate is the major limitation for their large-scale reproduction. We found that warm stratification was an effective treatment to break the seed dormancy of A. tsaoko prior to sowing and could be an important component of improving breeding programs. The mechanism of seed dormancy release during warm stratification remains unclear. Therefore, we studied the differences between transcripts and proteomes at 0, 30, 60, and 90 days of warm stratification, to identify some regulatory genes and functional proteins that may cause seed dormancy release in A. tsaoko and reveal their regulatory mechanism. RESULTS RNA-seq was performed for the seed dormancy release process, and the number of differentially expressed genes (DEGs) was 3196 in three dormancy release periods. Using TMT-labelling quantitative proteome analysis, a total of 1414 proteins were defined as differentially expressed proteins (DEPs). Functional enrichment analyses revealed that the DEGs and DEPs were mainly involved in signal transduction pathways (MAPK signaling, hormone) and metabolism processes (cell wall, storage and energy reserves), suggesting that these differentially expressed genes and proteins are somehow involved in response to seed dormancy release process, including MAPK, PYR/PYL, PP2C, GID1, GH3, ARF, AUX/IAA, TPS, SPS, and SS. In addition, transcription factors ARF, bHLH, bZIP, MYB, SBP, and WRKY showed differential expression during the warm stratification stage, which may relate to dormancy release. Noteworthy, XTH, EXP, HSP and ASPG proteins may be involved in a complex network to regulate cell division and differentiation, chilling response and the seed germination status in A. tsaoko seed during warm stratification. CONCLUSION Our transcriptomic and proteomic analysis highlighted specific genes and proteins that warrant further study in fully grasping the precise molecular mechanisms that control the seed dormancy and germination of A. tsaoko. A hypothetical model of the genetic regulatory network provides a theoretical basis for overcoming the physiological dormancy in A. tsaoko in the future.
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Affiliation(s)
- Chunliu Pan
- Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lixiang Yao
- Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Liying Yu
- Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhu Qiao
- Guangxi Medicinal Resources Conservation and Genetic Improvement Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Meiqiong Tang
- Guangxi Medicinal Resources Conservation and Genetic Improvement Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Fan Wei
- Guangxi Medicinal Resources Conservation and Genetic Improvement Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Xueyan Huang
- Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Yunyi Zhou
- Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
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10
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Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads. Gene 2023; 852:147065. [PMID: 36435508 DOI: 10.1016/j.gene.2022.147065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are common mechanisms in eukaryotes to increase the complexity of transcriptomes and subsequently proteomes. Analysis of long reads transcriptomics data can result in the discovery of novel transcripts, splice sites, AS or APA events. Gossypium arboreum is an important cultivated cotton species and a putative contributor of the A sub-genome to the modern tetraploid cotton; and inherently tolerant to several biotic and abiotic stresses. Specifically, its variety 'FDH228' is considered to be an important resistance source. In this study, we sequenced the G. arboreum (var. FDH228) transcriptome using PacBio IsoSeq and illumina short read sequencing under three different conditions i.e. untreated/healthy, treated with biotic stress through whitefly infestation, and treated with abiotic stress via water deprivation, for the discovery and surveying of canonical and non-canonical AS, APA and transcript fusion events. We were able to obtain 15,419 unique transcripts from all samples representing 11,343 genes, out of which 10,832 were annotated and 520 were novel with respect to the published reference genome. These transcripts were grouped into different structural categories including 60 Antisense, 11,959 having a full-splice match, 999 with incomplete-splice match, 30 fusion transcripts, 177 genic, 479 intergenic, 771 novels in the catalog, and 944 Novel but not found in the catalog. Subsequently, randomly selected candidate transcripts were experimentally validated using qRT-PCR. Our comprehensive identification of canonical and non-canonical splicing events, and novel and fusion transcripts aids in the understanding of the resistance mechanisms for this specific germplasm.
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11
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Gao S, Li C, Chen X, Li S, Liang N, Wang H, Zhan Y, Zeng F. Basic helix-loop-helix transcription factor PxbHLH02 enhances drought tolerance in Populus (Populus simonii × P. nigra). TREE PHYSIOLOGY 2023; 43:185-202. [PMID: 36054366 DOI: 10.1093/treephys/tpac107] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
The basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in plant morphogenesis and various abiotic and biotic stress responses. However, further exploration is required of drought-responsive bHLH family members and their detailed regulatory mechanisms in Populus. Two bHLH TF genes, PxbHLH01/02, were identified in Populus simonii × P. nigra and cloned. The aim of this study was to examine the role of bHLH TFs in drought tolerance in P. simonii × P. nigra. The results showed that the amino acid sequences of the two genes were homologous to Arabidopsis thaliana UPBEAT1 (AtUPB1) and overexpression of PxbHLH01/02 restored normal root length in the AtUPB1 insertional mutant (upb1-1). The PxbHLH01/02 gene promoter activity analysis suggested that they were involved in stress responses and hormone signaling. Furthermore, Arabidopsis transgenic lines overexpressing PxbHLH01/02 exhibited higher stress tolerance compared with the wild-type. Populus simonii × P. nigra overexpressing PxbHLH02 increased drought tolerance and exhibited higher superoxide dismutase and peroxidase activities, lower H2O2 and malondialdehyde content, and lower relative conductivity. The results of transcriptome sequencing (RNA-seq) and quantitative real-time PCR suggested that the response of PxbHLH02 to drought stress was related to abscisic acid (ABA) signal transduction. Overall, the findings of this study suggest that PxbHLH02 from P. simonii × P. nigra functions as a positive regulator of drought stress responses by regulating stomatal aperture and promoting ABA signal transduction.
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Affiliation(s)
- Shangzhu Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Caihua Li
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050041, China
| | - Xiaohui Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Sida Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Nansong Liang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Hengtao Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yaguang Zhan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fansuo Zeng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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12
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Study on ZmRPN10 Regulating Leaf Angle in Maize by RNA-Seq. Int J Mol Sci 2022; 24:ijms24010189. [PMID: 36613631 PMCID: PMC9820655 DOI: 10.3390/ijms24010189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin/proteasome-mediated proteolysis (UPP) plays a crucial role in almost all aspects of plant growth and development, proteasome subunit RPN10 mediates ubiquitination substrate recognition in the UPP process. The recognition pathway of ubiquitinated UPP substrate is different in different species, which indicates that the mechanism and function of RPN10 are different in different species. However, the homologous ZmRPN10 in maize has not been studied. In this study, the changing of leaf angle and gene expression in leaves in maize wild-type B73 and mutant rpn10 under exogenous brassinosteroids (BRs) were investigated. The regulation effect of BR on the leaf angle of rpn10 was significantly stronger than that of B73. Transcriptome analysis showed that among the differentially expressed genes, CRE1, A-ARR and SnRK2 were significantly up-regulated, and PP2C, BRI1 AUX/IAA, JAZ and MYC2 were significantly down-regulated. This study revealed the regulation mechanism of ZmRPN10 on maize leaf angle and provided a promising gene resource for maize breeding.
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MdPP2C24/37, Protein Phosphatase Type 2Cs from Apple, Interact with MdPYL2/12 to Negatively Regulate ABA Signaling in Transgenic Arabidopsis. Int J Mol Sci 2022; 23:ijms232214375. [PMID: 36430851 PMCID: PMC9696740 DOI: 10.3390/ijms232214375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
The phytohormone abscisic acid (ABA) plays an important role in the ability of plants to cope with drought stress. As core members of the ABA signaling pathway, protein phosphatase type 2Cs (PP2Cs) have been reported in many species. However, the functions of MdPP2Cs in apple (Malus domestica) are unclear. In this study, we identified two PP2C-encoding genes, MdPP2C24/37, with conserved PP2C catalytic domains, using sequence alignment. The nucleus-located MdPP2C24/37 genes were induced by ABA or mannitol in apple. Genetic analysis revealed that overexpression of MdPP2C24/37 in Arabidopsis thaliana led to plant insensitivity to ABA or mannitol treatment, in terms of inhibiting seed germination and overall seedling establishment. The expression of stress marker genes was upregulated in MdPP2C24/37 transgenic lines. At the same time, MdPP2C24/37 transgenic lines displayed inhibited ABA-mediated stomatal closure, which led to higher water loss rates. Moreover, when exposed to drought stress, chlorophyll levels decreased and MDA and H2O2 levels accumulated in the MdPP2C24/37 transgenic lines. Further, MdPP2C24/37 interacted with MdPYL2/12 in vitro and vivo. The results indicate that MdPP2C24/37 act as negative regulators in response to ABA-mediated drought resistance.
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14
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Sisi C, Jieru D, Peidong C, Zhaolong Z, Yihang W, Shuwen C, Yan T, Tianyu W, Guiyan Y. Transcriptome-wide identification of walnut PP2C family genes in response to external stimulus. BMC Genomics 2022; 23:640. [PMID: 36076184 PMCID: PMC9461273 DOI: 10.1186/s12864-022-08856-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 11/11/2022] Open
Abstract
Walnut is an important economic tree species while confronting with global environmental stress, resulting in decline in quality and yield. Therefore, it is urgent to elucidate the molecular mechanism for the regulation of walnut response to adversity. The protein phosphatase 2C (PP2C) gene family participates in cellular processes in eukaryotes through reversible phosphorylation of proteins and signal transduction regulation. However, the stress response function of PP2C genes was far to be clarified. Therefore, to understand the stress response mechanism of walnut tree, in this study, a total of 41 PP2C genes with complete ORFs were identified from Juglans regia, whose basic bio-information and expression patterns in response to multiple stresses and ABA were confirmed. The results showed that the ORFs of JrPP2Cs were 495 ~ 3231 bp in length, the predicted JrPP2C proteins contained 164 to 1076 amino acids and the molecular weights were 18,581.96 ~ 118,853.34 Da, the pI was 4.55 ~ 9.58. These JrPP2C genes were unevenly distributed on 14 chromosomes, among which Chr11 and Chr13 contained the most genes. Phylogenetic analysis found that these JrPP2C proteins were classed into 9 subfamilies, among which group F covered most JrPP2Cs. The JrPP2Cs in the same subfamily exhibited similarities in the composition of conserved domains, amino acid sequences of motifs and exon/intron organization in DNA sequences. Each JrPP2C includes 4 ~ 10 motifs and each motif contained 15 ~ 37 amino acids. Among the motifs, motif1, motif2, motif3 and motif8 were most abundant. Most of the JrPP2C genes diversely response to osmotic, cadmium, and Colletotrichum gloeosporioide stress as well as ABA treatments, among which JrPP2C28, JrPP2C17, JrPP2C09, JrPP2C36 were more obvious and deserves further attention. All these results indicated that JrPP2C genes play potential vital roles in plant response to multiple stimulus, and are possibly involved in ABA-dependent signaling pathway.
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Affiliation(s)
- Chen Sisi
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Deng Jieru
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Cheng Peidong
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Zhang Zhaolong
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Wang Yihang
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Chen Shuwen
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Tang Yan
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Wang Tianyu
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yang Guiyan
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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15
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A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize. Int J Mol Sci 2022; 23:ijms23179755. [PMID: 36077153 PMCID: PMC9456493 DOI: 10.3390/ijms23179755] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Salinization seriously threatens the normal growth of maize, especially at the seedling stage. Recent studies have demonstrated that circular RNAs (circRNAs) play vital roles in the regulation of plant stress resistance. Here, we performed a genome-wide association study (GWAS) on the survival rate of 300 maize accessions under a salt stress treatment. A total of 5 trait-associated SNPs and 86 candidate genes were obtained by the GWAS. We performed RNA sequencing for 28 transcriptome libraries derived from 2 maize lines with contrasting salt tolerance under normal and salt treatment conditions. A total of 1217 highly expressed circRNAs were identified, of which 371 were responsive to a salt treatment. Using PCR and Sanger sequencing, we verified the reliability of these differentially expressed circRNAs. An integration of the GWAS and RNA-Seq analyses uncovered two differentially expressed hub genes (Zm00001eb013650 and Zm00001eb198930), which were regulated by four circRNAs. Based on these results, we constructed a regulation model of circRNA/miRNA/mRNA that mediated salt stress tolerance in maize. By conducting hub gene-based association analyses, we detected a favorable haplotype in Zm00001eb198930, which was responsible for high salt tolerance. These results help to clarify the regulatory relationship between circRNAs and their target genes as well as to develop salt-tolerant lines for maize breeding.
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16
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Shen Y, Fan K, Wang Y, Wang H, Ding S, Song D, Shen J, Li H, Song Y, Han X, Qian W, Ma Q, Ding Z. Red and Blue Light Affect the Formation of Adventitious Roots of Tea Cuttings ( Camellia sinensis) by Regulating Hormone Synthesis and Signal Transduction Pathways of Mature Leaves. FRONTIERS IN PLANT SCIENCE 2022; 13:943662. [PMID: 35873958 PMCID: PMC9301306 DOI: 10.3389/fpls.2022.943662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Light is an important environmental factor which affects plant growth, through changes of intensity and quality. In this study, monochromatic white (control), red (660 nm), and blue (430 nm) light-emitting diodes (LEDs) were used to treat tea short cuttings. The results showed the most adventitious roots in blue light treated tea cuttings, but the lowest roots in that treated by red light. In order to explore the molecular mechanism of light quality affecting adventitious root formation, we performed full-length transcriptome and metabolome analyses of mature leaves under three light qualities, and then conducted weighted gene co-expression network analysis (WGCNA). Phytohormone analysis showed that Indole-3-carboxylic acid (ICA), Abscisic acid (ABA), ABA-glucosyl ester (ABA-GE), trans-Zeatin (tZ), and Jasmonic acid (JA) contents in mature leaves under blue light were significantly higher than those under white and red light. A crosstalk regulatory network comprising 23 co-expression modules was successfully constructed. Among them, the "MEblue" module which had a highly positive correlation with ICA (R = 0.92, P = 4e-04). KEGG analysis showed that related genes were significantly enriched in the "Plant hormone signal transduction (ko04075)" pathway. YUC (a flavin-containing monooxygenase), AUX1, AUX/IAA, and ARF were identified as hub genes, and gene expression analysis showed that the expression levels of these hub genes under blue light were higher than those under white and red light. In addition, we also identified 6 auxin transport-related genes, including PIN1, PIN3, PIN4, PILS5, PILS6, and PILS7. Except PILS5, all of these genes showed the highest expression level under blue light. In conclusion, this study elucidated the molecular mechanism of light quality regulating adventitious root formation of tea short cutting through WGCNA analysis, which provided an innovation for "rapid seedling" of tea plants.
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Affiliation(s)
- Yaozong Shen
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Kai Fan
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Hui Wang
- Rizhao Tea Research Institute, Rizhao, China
| | - Shibo Ding
- Rizhao Tea Research Institute, Rizhao, China
| | - Dapeng Song
- Rizhao Tea Research Institute, Rizhao, China
| | - Jiazhi Shen
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Rizhao, China
| | - He Li
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Yujie Song
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Xiao Han
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Wenjun Qian
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Qingping Ma
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Rizhao, China
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17
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Liu Q, Ding J, Huang W, Yu H, Wu S, Li W, Mao X, Chen W, Xing J, Li C, Yan S. OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice. RICE (NEW YORK, N.Y.) 2022; 15:34. [PMID: 35779169 PMCID: PMC9250576 DOI: 10.1186/s12284-022-00581-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Although type 2C protein phosphatases (PP2Cs) have been demonstrated to play important roles in regulating plant development and various stress responses, their specific roles in rice abiotic stress tolerance are still largely unknown. In this study, the functions of OsPP65 in rice osmotic and salt stress tolerance were investigated. Here, we report that OsPP65 is responsive to multiple stresses and is remarkably induced by osmotic and salt stress treatments. OsPP65 was highly expressed in rice seedlings and leaves and localized in the nucleus and cytoplasm. OsPP65 knockout rice plants showed enhanced tolerance to osmotic and salt stresses. Significantly higher induction of genes involved in jasmonic acid (JA) and abscisic acid (ABA) biosynthesis or signaling, as well as higher contents of endogenous JA and ABA, were observed in the OsPP65 knockout plants compared with the wild-type plants after osmotic stress treatment. Further analysis indicated that JA and ABA function independently in osmotic stress tolerance conferred by loss of OsPP65. Moreover, metabolomics analysis revealed higher endogenous levels of galactose and galactinol but a lower content of raffinose in the OsPP65 knockout plants than in the wild-type plants after osmotic stress treatment. These results together suggest that OsPP65 negatively regulates osmotic and salt stress tolerance through regulation of the JA and ABA signaling pathways and modulation of the raffinose family oligosaccharide metabolism pathway in rice. OsPP65 is a promising target for improvement of rice stress tolerance using gene editing.
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Affiliation(s)
- Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jierong Ding
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Hang Yu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Shaowen Wu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Wenyan Li
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xingxue Mao
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Wenfeng Chen
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Junlian Xing
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Chen Li
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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Molecular Cloning and Characterization of MbMYB108, a Malus baccata MYB Transcription Factor Gene, with Functions in Tolerance to Cold and Drought Stress in Transgenic Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23094846. [PMID: 35563237 PMCID: PMC9099687 DOI: 10.3390/ijms23094846] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 02/07/2023] Open
Abstract
The MYB transcription factor (TF) family is one of the largest transcription families in plants, which is widely involved in the responses of plants to biotic and abiotic stresses, as well as plant growth, development, and metabolic regulation. In the present study, a new MYB TF gene, MbMYB108, from Malus baccata (L.) Borkh, was identified and characterized. The open reading frame (ORF) of MbMYB108 was found to be 903 bp, encoding 300 amino acids. Sequence alignment results and predictions of the protein structure indicated that the MbMYB108 protein contained the conserved MYB domain. Subcellular localization showed that MbMYB108 was localized to the nucleus. The expression of MbMYB108 was enriched in young and mature leaves, and was highly affected by cold and drought treatments in M. baccata seedlings. When MbMYB108 was introduced into Arabidopsis thaliana, it greatly increased the cold and drought tolerances in the transgenic plant. Increased expression of MbMYB108 in transgenic A. thaliana also resulted in higher activities of peroxidase (POD) and catalase (CAT), higher contents of proline and chlorophyll, while malondialdehyde (MDA) content and relative conductivity were lower, especially in response to cold and drought stresses. Therefore, these results suggest that MbMYB108 probably plays an important role in the response to cold and drought stresses in A. thaliana by enhancing the scavenging capability for reactive oxygen species (ROS).
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Nie L, Xu Z, Wu L, Chen X, Cui Y, Wang Y, Song J, Yao H. Genome-wide identification of protein phosphatase 2C family members in Glycyrrhiza uralensis Fisch. and their response to abscisic acid and polyethylene glycol stress. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2022. [DOI: 10.1080/16583655.2022.2027650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Liping Nie
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Liwei Wu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Xinlian Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Yingxian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
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20
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Liang Y, Ma F, Li B, Guo C, Hu T, Zhang M, Liang Y, Zhu J, Zhan X. A bHLH transcription factor, SlbHLH96, promotes drought tolerance in tomato. HORTICULTURE RESEARCH 2022; 9:uhac198. [PMID: 36467272 PMCID: PMC9714257 DOI: 10.1093/hr/uhac198] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 09/01/2022] [Indexed: 05/10/2023]
Abstract
Drought stress caused by water deficit reduces plant productivity in many regions of the world. In plants, basic helix-loop-helix (bHLH) transcription factors regulate a wide range of cellular activities related to growth, development and stress response; however, the role of tomato SlbHLHs in drought stress responses remains elusive. Here, we used reverse genetics approaches to reveal the function of SlbHLH96, which is induced by drought and abscisic acid (ABA) treatment. We found that SlbHLH96 functions as a positive regulator of drought tolerance in tomato. Overexpression of SlbHLH96 in tomato improves drought tolerance by stimulating the expression of genes encoding antioxidants, ABA signaling molecules and stress-related proteins. In contrast, silencing of SlbHLH96 in tomato reduces drought tolerance. SlbHLH96 physically interacts with an ethylene-responsive factor, SlERF4, and silencing of SlERF4 in tomato also decreases drought tolerance. Furthermore, SlbHLH96 can repress the expression of the ABA catabolic gene, SlCYP707A2, through direct binding to its promoter. Our results uncover a novel mechanism of SlbHLH96-mediated drought tolerance in tomato plants, which can be exploited for breeding drought-resilient crops.
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Affiliation(s)
| | | | - Boyu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Cong Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Tixu Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Mingke Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Yan Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, China
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Francki MG, Stainer GS, Walker E, Rebetzke GJ, Stefanova KT, French RJ. Phenotypic Evaluation and Genetic Analysis of Seedling Emergence in a Global Collection of Wheat Genotypes ( Triticum aestivum L.) Under Limited Water Availability. FRONTIERS IN PLANT SCIENCE 2021; 12:796176. [PMID: 35003185 PMCID: PMC8739788 DOI: 10.3389/fpls.2021.796176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P < 0.001) environment and genotype-by-environment interactions within and between field and GH experiments, eight genotypes that included five cultivars, two landraces, and one inbred line had consistently high seedling emergence (mean value > 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues.
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Affiliation(s)
- Michael G. Francki
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Grantley S. Stainer
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gregory J. Rebetzke
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Katia T. Stefanova
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Robert J. French
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
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Abhilasha A, Roy Choudhury S. Molecular and Physiological Perspectives of Abscisic Acid Mediated Drought Adjustment Strategies. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122769. [PMID: 34961239 PMCID: PMC8708728 DOI: 10.3390/plants10122769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 05/15/2023]
Abstract
Drought is the most prevalent unfavorable condition that impairs plant growth and development by altering morphological, physiological, and biochemical functions, thereby impeding plant biomass production. To survive the adverse effects, water limiting condition triggers a sophisticated adjustment mechanism orchestrated mainly by hormones that directly protect plants via the stimulation of several signaling cascades. Predominantly, water deficit signals cause the increase in the level of endogenous ABA, which elicits signaling pathways involving transcription factors that enhance resistance mechanisms to combat drought-stimulated damage in plants. These responses mainly include stomatal closure, seed dormancy, cuticular wax deposition, leaf senescence, and alteration of the shoot and root growth. Unraveling how plants adjust to drought could provide valuable information, and a comprehensive understanding of the resistance mechanisms will help researchers design ways to improve crop performance under water limiting conditions. This review deals with the past and recent updates of ABA-mediated molecular mechanisms that plants can implement to cope with the challenges of drought stress.
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23
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Li L, Liu J, Liang Q, Feng Y, Wang C, Wu S, Li Y. Downregulation of lncRNA PpL-T31511 and Pp-miRn182 Promotes Hydrogen Cyanamide-Induced Endodormancy Release through the PP2C-H 2O 2 Pathway in Pear ( Pyrus pyrifolia). Int J Mol Sci 2021; 22:ijms222111842. [PMID: 34769273 PMCID: PMC8584160 DOI: 10.3390/ijms222111842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Bud endodormancy is an important, complex process subject to both genetic and epigenetic control, the mechanism of which is still unclear. The endogenous hormone abscisic acid (ABA) and its signaling pathway play important roles in the endodormancy process, in which the type 2C protein phosphatases (PP2Cs) is key to the ABA signal pathway. Due to its excellent effect on endodormancy release, hydrogen cyanamide (HC) treatment is considered an effective measure to study the mechanism of endodormancy release. In this study, RNA-Seq analysis was conducted on endodormant floral buds of pear (Pyrus pyrifolia) with HC treatment, and the HC-induced PP2C gene PpPP2C1 was identified. Next, software prediction, expression tests and transient assays revealed that lncRNA PpL-T31511-derived Pp-miRn182 targets PpPP2C1. The expression analysis showed that HC treatment upregulated the expression of PpPP2C1 and downregulated the expression of PpL-T31511 and Pp-miRn182. Moreover, HC treatment inhibited the accumulation of ABA signaling pathway-related genes and hydrogen peroxide (H2O2). Furthermore, overexpression of Pp-miRn182 reduced the inhibitory effect of PpPP2C1 on the H2O2 content. In summary, our study suggests that downregulation of PpL-T31511-derived Pp-miRn182 promotes HC-induced endodormancy release in pear plants through the PP2C-H2O2 pathway.
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Affiliation(s)
- Liang Li
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Jinan District, Fuzhou 350013, China
| | - Jinhang Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Qin Liang
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Yu Feng
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Chao Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Shaohua Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Yongyu Li
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
- Correspondence:
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Zang F, Ma Y, Tu X, Huang P, Wu Q, Li Z, Liu T, Lin F, Pei S, Zang D, Zhang X, Zheng Y, Yu Y. A high-quality chromosome-level genome of wild Rosa rugosa. DNA Res 2021; 28:6367774. [PMID: 34499118 DOI: 10.1093/dnares/dsab017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 01/01/2023] Open
Abstract
Rosa rugosa is an important shrub with economic, ecological, and pharmaceutical value. A high-quality chromosome-scale genome for R. rugosa sequences was assembled using PacBio and Hi-C technologies. The final assembly genome sequences size was about 407.1 Mb, the contig N50 size was 2.85 Mb, and the scaffold N50 size was 56.6 Mb. More than 98% of the assembled genome sequences were anchored to seven pseudochromosomes (402.9 Mb). The genome contained 37,512 protein-coding genes, with 37,016 genes (98.68%) that were functionally annotated, and 206.67 Mb (50.76%) of the assembled sequences are repetitive sequences. Phylogenetic analyses indicated that R. rugosa diverged from Rosa chinensis ∼6.6 million years ago, and no lineage-specific whole-genome duplication event occurred after divergence from R. chinensis. Chromosome synteny analysis demonstrated highly conserved synteny between R. rugosa and R. chinensis, between R. rugosa and Prunus persica as well. Comparative genome and transcriptome analysis revealed genes related to colour, scent, and environment adaptation. The chromosome-level reference genome provides important genomic resources for molecular-assisted breeding and horticultural comparative genomics research.
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Affiliation(s)
- Fengqi Zang
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P.R. China
| | - Yan Ma
- Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, P. R. China
| | - Xiaolong Tu
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, P. R. China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P.R. China
| | - Qichao Wu
- Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, P. R. China
| | - Zhimin Li
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, P. R. China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, P. R. China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P.R. China
| | - Surui Pei
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, P. R. China
| | - Dekui Zang
- Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, P. R. China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, P. R. China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P.R. China
| | - Yunyan Yu
- Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, P. R. China
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Overexpression of antisense phosphatase 2C affords cold resistance in hybrid Populus davidiana × Populus bolleana. Genes Genomics 2021; 43:1209-1222. [PMID: 34338987 DOI: 10.1007/s13258-021-01143-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Overexpression of the abiotic and biotic stress-resistance genes of the plant signaling pathway is well known for its significant role in the regulation of plant growth and enhancement of the productivity of agricultural land under changing climatic conditions. OBJECTIVES This research aimed to clone Populus davidiana × Populus bolleana PP2C (PdPP2C) gene and analyze its structure and function, and downregulate PdPP2C by overexpression of its antisense PdPP2C (AS-PdPP2C) gene for enhancing cold resistance in transgenic lines of hybrid P. davidiana × P. bolleana. METHODS PdPP2C was cloned and transformed to identify its function, and its antisense was overexpressed via downregulation to increase the cold resistance in transgenic lines of hybrid P. davidiana × P. bolleana. RESULTS Antisense inhibition of protein phosphatase 2C accelerates the cold acclimation of Poplar (P. davidiana × P. bolleana) gene in terms of antifreeze. CONCLUSION PdPP2C was expressed in the roots, stems, and leaves of P. davidiana × P. bolleana, and the expression was higher in the leaves. The expression of PdPP2C was also significantly downregulated at low-temperature (0 °C and 4 °C) stress. The relative conductivity and malondialdehyde content of non-transgenic lines were higher than those of AS-PdPP2C lines after 2 days of cold treatment at - 1 °C. The leaves of the transgenic lines were not wilted and showed no chlorosis compared with those of the non-transgenic lines. The AS-PdPP2C transgenic lines also showed higher freezing resistance than the non-transgenic lines. AS-PdPP2C participated in the regulation of freezing resistance.
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Tai L, Wang HJ, Xu XJ, Sun WH, Ju L, Liu WT, Li WQ, Sun J, Chen KM. Pre-harvest sprouting in cereals: genetic and biochemical mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2857-2876. [PMID: 33471899 DOI: 10.1093/jxb/erab024] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/18/2021] [Indexed: 05/22/2023]
Abstract
With the growth of the global population and the increasing frequency of natural disasters, crop yields must be steadily increased to enhance human adaptability to risks. Pre-harvest sprouting (PHS), a term mainly used to describe the phenomenon in which grains germinate on the mother plant directly before harvest, is a serious global problem for agricultural production. After domestication, the dormancy level of cultivated crops was generally lower than that of their wild ancestors. Although the shortened dormancy period likely improved the industrial performance of cereals such as wheat, barley, rice, and maize, the excessive germination rate has caused frequent PHS in areas with higher rainfall, resulting in great economic losses. Here, we systematically review the causes of PHS and its consequences, the major indicators and methods for PHS assessment, and emphasize the biological significance of PHS in crop production. Wheat quantitative trait loci functioning in the control of PHS are also comprehensively summarized in a meta-analysis. Finally, we use Arabidopsis as a model plant to develop more complete PHS regulatory networks for wheat. The integration of this information is conducive to the development of custom-made cultivated lines suitable for different demands and regions, and is of great significance for improving crop yields and economic benefits.
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Affiliation(s)
- Li Tai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hong-Jin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiao-Jing Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei-Hang Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lan Ju
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
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Ni L, Wang Z, Guo J, Pei X, Liu L, Li H, Yuan H, Gu C. Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis. Genes (Basel) 2021; 12:434. [PMID: 33803672 PMCID: PMC8002972 DOI: 10.3390/genes12030434] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Iris lactea var. chinensis (I. lactea var. chinensis) is a perennial herb halophyte with salt and drought tolerance. In this study, full-length transcripts of I. lactea var. chinensis were sequenced using the PacBio RSII sequencing platform. Moreover, the transcriptome was investigated under NaCl or polyethylene glycol (PEG) stress. Approximately 30.89 G subreads were generated and 31,195 unigenes were obtained by clustering the same isoforms by the PacBio RSII platform. A total of 15,466 differentially expressed genes (DEGs) were obtained under the two stresses using the Illumina platform. Among them, 9266 and 8390 DEGs were obtained under high concentrations of NaCl and PEG, respectively. In total, 3897 DEGs with the same expression pattern under the two stresses were obtained. The transcriptome expression profiles of I. lactea var. chinensis under NaCl or PEG stress obtained in this study may provide a resource for the same and different response mechanisms against different types of abiotic stress. Furthermore, the stress-related genes found in this study can provide data for future molecular breeding.
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Affiliation(s)
- Longjie Ni
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China;
| | - Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Jinbo Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Xiaoxiao Pei
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Liangqin Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Huogen Li
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China;
| | - Haiyan Yuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China;
- Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
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Li Y, Song J, Zhu G, Hou Z, Wang L, Wu X, Fang Z, Liu Y, Gao C. Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat ( Triticum aestivum L.). PeerJ 2021; 9:e10963. [PMID: 33717696 PMCID: PMC7934654 DOI: 10.7717/peerj.10963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/27/2021] [Indexed: 12/27/2022] Open
Abstract
The ARF gene family plays important roles in intracellular transport in eukaryotes and is involved in conferring tolerance to biotic and abiotic stresses in plants. To explore the role of these genes in the development of wheat (Triticum aestivum L.), 74 wheat ARF genes (TaARFs; including 18 alternate transcripts) were identified and clustered into seven sub-groups. Phylogenetic analysis revealed that TaARFA1 sub-group genes were strongly conserved. Numerous cis-elements functionally associated with the stress response and hormones were identified in the TaARFA1 sub-group, implying that these TaARFs are induced in response to abiotic and biotic stresses in wheat. According to available transcriptome data and qRT-PCR analysis, the TaARFA1 genes displayed tissue-specific expression patterns and were regulated by biotic stress (powdery mildew and stripe rust) and abiotic stress (cold, heat, ABA, drought and NaCl). Protein interaction network analysis further indicated that TaARFA1 proteins may interact with protein phosphatase 2C (PP2C), which is a key protein in the ABA signaling pathway. This comprehensive analysis will be useful for further functional characterization of TaARF genes and the development of high-quality wheat varieties.
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Affiliation(s)
- Yaqian Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Jinghan Song
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Guang Zhu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
| | - Zehao Hou
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Lin Wang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Xiaoxue Wu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengwu Fang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yike Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Chunbao Gao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
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Ye H, Qiao L, Guo H, Guo L, Ren F, Bai J, Wang Y. Genome-Wide Identification of Wheat WRKY Gene Family Reveals That TaWRKY75-A Is Referred to Drought and Salt Resistances. FRONTIERS IN PLANT SCIENCE 2021; 12:663118. [PMID: 34149760 PMCID: PMC8212938 DOI: 10.3389/fpls.2021.663118] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 05/14/2023]
Abstract
It is well known that WRKY transcription factors play essential roles in plants' response to diverse stress responses, especially to drought and salt stresses. However, a full comprehensive analysis of this family in wheat is still missing. Here we used in silico analysis and identified 124 WRKY genes, including 294 homeologous copies from a high-quality reference genome of wheat (Triticum aestivum). We also found that the TaWRKY gene family did not undergo gene duplication rather than gene loss during the evolutionary process. The TaWRKY family members displayed different expression profiles under several abiotic stresses, indicating their unique functions in the mediation of particular responses. Furthermore, TaWRKY75-A was highly induced after polyethylene glycol and salt treatments. The ectopic expression of TaWRKY75-A in Arabidopsis enhanced drought and salt tolerance. A comparative transcriptome analysis demonstrated that TaWRKY75-A integrated jasmonic acid biosynthetic pathway and other potential metabolic pathways to increase drought and salt resistances in transgenic Arabidopsis. Our study provides valuable insights into the WRKY family in wheat and will generate a useful genetic resource for improving wheat breeding.
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Affiliation(s)
- Hong Ye
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Linyi Qiao
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Haoyu Guo
- College of Life Science, Capital Normal University, Beijing, China
| | - Liping Guo
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Fei Ren
- School of Agricultural Science and Engineering, Shaoguan University, Shaoguan, China
| | - Jianfang Bai
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Jianfang Bai,
| | - Yukun Wang
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- *Correspondence: Jianfang Bai,
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Khan ZH, Agarwal S, Rai A, Memaya MB, Mehrotra S, Mehrotra R. Co-expression network analysis of protein phosphatase 2A (PP2A) genes with stress-responsive genes in Arabidopsis thaliana reveals 13 key regulators. Sci Rep 2020; 10:21480. [PMID: 33293553 PMCID: PMC7722862 DOI: 10.1038/s41598-020-77746-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
Abiotic and biotic stresses adversely affect plant growth and development and eventually result in less yield and threaten food security worldwide. In plants, several studies have been carried out to understand molecular responses to abiotic and biotic stresses. However, the complete circuitry of stress-responsive genes that plants utilise in response to those environmental stresses are still unknown. The protein phosphatase 2A (PP2A) gene has been known to have a crucial role in abiotic and biotic stresses; but how it regulates the stress response in plants is still not known completely. In this study, we constructed gene co-expression networks of PP2A genes with stress-responsive gene datasets from cold, drought, heat, osmotic, genotoxic, salt, and wounding stresses to unveil their relationships with the PP2A under different conditions of stress. The graph analysis identified 13 hub genes and several influential genes based on closeness centrality score (CCS). Our findings also revealed the count of unique genes present in different settings of stresses and subunits. We also formed clusters of influential genes based on the stress, CCS, and co-expression value. Analysis of cis-regulatory elements (CREs), recurring in promoters of these genes was also performed. Our study has led to the identification of 16 conserved CREs.
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Affiliation(s)
- Zaiba Hasan Khan
- Department of Biological Sciences, K.K. Birla Goa Campus, BITS-Pilani, Goa, India
| | - Swati Agarwal
- Department of Computer Science and Information Systems, K.K. Birla Goa Campus, BITS-Pilani, Goa, India.
| | - Atul Rai
- Department of Computer Science and Information Systems, K.K. Birla Goa Campus, BITS-Pilani, Goa, India
| | - Mounil Binal Memaya
- Department of Computer Science and Information Systems, K.K. Birla Goa Campus, BITS-Pilani, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, K.K. Birla Goa Campus, BITS-Pilani, Goa, India
| | - Rajesh Mehrotra
- Department of Biological Sciences, K.K. Birla Goa Campus, BITS-Pilani, Goa, India.
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