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Meher PK, Sahu TK, Gupta A, Kumar A, Rustgi S. ASRpro: A machine-learning computational model for identifying proteins associated with multiple abiotic stress in plants. THE PLANT GENOME 2024; 17:e20259. [PMID: 36098562 DOI: 10.1002/tpg2.20259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
One of the thrust areas of research in plant breeding is to develop crop cultivars with enhanced tolerance to abiotic stresses. Thus, identifying abiotic stress-responsive genes (SRGs) and proteins is important for plant breeding research. However, identifying such genes via established genetic approaches is laborious and resource intensive. Although transcriptome profiling has remained a reliable method of SRG identification, it is species specific. Additionally, identifying multistress responsive genes using gene expression studies is cumbersome. Thus, endorsing the need to develop a computational method for identifying the genes associated with different abiotic stresses. In this work, we aimed to develop a computational model for identifying genes responsive to six abiotic stresses: cold, drought, heat, light, oxidative, and salt. The predictions were performed using support vector machine (SVM), random forest, adaptive boosting (ADB), and extreme gradient boosting (XGB), where the autocross covariance (ACC) and K-mer compositional features were used as input. With ACC, K-mer, and ACC + K-mer compositional features, the overall accuracy of ∼60-77, ∼75-86, and ∼61-78% were respectively obtained using the SVM algorithm with fivefold cross-validation. The SVM also achieved higher accuracy than the other three algorithms. The proposed model was also assessed with an independent dataset and obtained an accuracy consistent with cross-validation. The proposed model is the first of its kind and is expected to serve the requirement of experimental biologists; however, the prediction accuracy was modest. Given its importance for the research community, the online prediction application, ASRpro, is made freely available (https://iasri-sg.icar.gov.in/asrpro/) for predicting abiotic SRGs and proteins.
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Affiliation(s)
| | | | - Ajit Gupta
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anuj Kumar
- Dep. of Microbiology and Immunology, Dalhousie Univ., Halifax, Nova Scotia, Canada
- Laboratory of Immunity, Shantou Univ. Medical College, Shantou, PRC
| | - Sachin Rustgi
- Dep. of Plant and Environmental Sciences, Pee Dee Research and Education Centre, Clemson Univ., Florence, SC, USA
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Peng Y, Cao H, Cui L, Wang Y, Wei L, Geng S, Yang L, Huang Y, Bie Z. CmoNAC1 in pumpkin rootstocks improves salt tolerance of grafted cucumbers by binding to the promoters of CmoRBOHD1, CmoNCED6, CmoAKT1;2 and CmoHKT1;1 to regulate H 2O 2, ABA signaling and K +/Na + homeostasis. HORTICULTURE RESEARCH 2023; 10:uhad157. [PMID: 37719275 PMCID: PMC10500151 DOI: 10.1093/hr/uhad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/04/2023] [Indexed: 09/19/2023]
Abstract
The NAC transcription factor is a type of plant-specific transcription factor that can regulate plant salt tolerance, but the underlying mechanism is unclear in grafted vegetables. H2O2 and ABA in pumpkin rootstocks can be transported to cucumber scion leaves, promoting stomatal closure to improve salt tolerance of grafted cucumbers. Despite these observations, the regulatory mechanism is unknown. Here, our research revealed that CmoNAC1 is a key transcription factor that regulates H2O2 and ABA signaling in pumpkin roots under salt stress. The function of CmoNAC1 was analyzed using root transformation and RNA-seq, and we found that pumpkin CmoNAC1 promoted the production of H2O2 and ABA via CmoRBOHD1 and CmoNCED6, respectively, and regulated K+/Na+ homeostasis via CmoAKT1;2, CmoHKT1;1, and CmoSOS1 to improve salt tolerance of grafted cucumbers. Root knockout of CmoNAC1 resulted in a significant decrease in H2O2 (52.9% and 32.1%) and ABA (21.8% and 42.7%) content and K+/Na+ ratio (81.5% and 56.3%) in leaf and roots of grafted cucumber, respectively, while overexpression showed the opposite effect. The root transformation experiment showed that CmoNCED6 could improve salt tolerance of grafted cucumbers by regulating ABA production and K+/Na+ homeostasis under salt stress. Finally, we found that CmoNAC1 bound to the promoters of CmoRBOHD1, CmoNCED6, CmoAKT1;2, and CmoHKT1;1 using yeast one-hybrid, luciferase, and electrophoretic mobility shift assays. In conclusion, pumpkin CmoNAC1 not only binds to the promoters of CmoRBOHD1 and CmoNCED6 to regulate the production of H2O2 and ABA signals in roots, but also binds to the promoters of CmoAKT1;2 and CmoHKT1;1 to increase the K+/Na+ ratio, thus improving salt tolerance of grafted cucumbers.
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Affiliation(s)
- Yuquan Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Haishun Cao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China
| | - Lvjun Cui
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ying Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Lanxing Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Shouyu Geng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Li Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yuan Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhilong Bie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
- Hubei Hongshan Laboratory, 430070 Wuhan, China
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Zhang Y, Xu J, Li R, Ge Y, Li Y, Li R. Plants' Response to Abiotic Stress: Mechanisms and Strategies. Int J Mol Sci 2023; 24:10915. [PMID: 37446089 DOI: 10.3390/ijms241310915] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Abiotic stress is the adverse effect of any abiotic factor on a plant in a given environment, impacting plants' growth and development. These stress factors, such as drought, salinity, and extreme temperatures, are often interrelated or in conjunction with each other. Plants have evolved mechanisms to sense these environmental challenges and make adjustments to their growth in order to survive and reproduce. In this review, we summarized recent studies on plant stress sensing and its regulatory mechanism, emphasizing signal transduction and regulation at multiple levels. Then we presented several strategies to improve plant growth under stress based on current progress. Finally, we discussed the implications of research on plant response to abiotic stresses for high-yielding crops and agricultural sustainability. Studying stress signaling and regulation is critical to understand abiotic stress responses in plants to generate stress-resistant crops and improve agricultural sustainability.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Jing Xu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Ruofan Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Yanrui Ge
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Yufei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Ruili Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
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Li M, Wu Z, Gu H, Cheng D, Guo X, Li L, Shi C, Xu G, Gu S, Abid M, Zhong Y, Qi X, Chen J. AvNAC030, a NAC Domain Transcription Factor, Enhances Salt Stress Tolerance in Kiwifruit. Int J Mol Sci 2021; 22:ijms222111897. [PMID: 34769325 PMCID: PMC8585034 DOI: 10.3390/ijms222111897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/21/2023] Open
Abstract
Kiwifruit (Actinidia chinensis Planch) is suitable for neutral acid soil. However, soil salinization is increasing in kiwifruit production areas, which has adverse effects on the growth and development of plants, leading to declining yields and quality. Therefore, analyzing the salt tolerance regulation mechanism can provide a theoretical basis for the industrial application and germplasm improvement of kiwifruit. We identified 120 NAC members and divided them into 13 subfamilies according to phylogenetic analysis. Subsequently, we conducted a comprehensive and systematic analysis based on the conserved motifs, key amino acid residues in the NAC domain, expression patterns, and protein interaction network predictions and screened the candidate gene AvNAC030. In order to study its function, we adopted the method of heterologous expression in Arabidopsis. Compared with the control, the overexpression plants had higher osmotic adjustment ability and improved antioxidant defense mechanism. These results suggest that AvNAC030 plays a positive role in the salt tolerance regulation mechanism in kiwifruit.
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Affiliation(s)
- Ming Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
- Correspondence: (M.L.); (M.A.)
| | - Zhiyong Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Hong Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Dawei Cheng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Xizhi Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Lan Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Caiyun Shi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Guoyi Xu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Shichao Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Muhammad Abid
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
- Correspondence: (M.L.); (M.A.)
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
| | - Jinyong Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (Z.W.); (H.G.); (D.C.); (X.G.); (L.L.); (C.S.); (G.X.); (S.G.); (Y.Z.); (X.Q.); (J.C.)
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Wang B, Zhang M, Zhang J, Huang L, Chen X, Jiang M, Tan M. Profiling of rice Cd-tolerant genes through yeast-based cDNA library survival screening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:429-436. [PMID: 32814279 DOI: 10.1016/j.plaphy.2020.07.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
The bioaccumulation of cadmium (Cd) in crop and the subsequent food chain has aroused extensive concerns. However, the underlying molecular mechanisms of plant Cd tolerance remain to be clarified from the viewpoint of novel candidate genes. Here we described a highly efficient approach for preliminary identifying rice Cd-tolerant genes through the yeast-based cDNA library survival screening combined with high-throughput sequencing strategy. About 690 gene isoforms were identified as being Cd-tolerant candidates using this shotgun approach. Among the Cd-tolerant genes identified, several categories of genes such as BAX inhibitor (BI), NAC transcription factors and Rapid ALkalinization Factors (RALFs) were of particular interest, and their function of Cd tolerance was further validated via heterologous expression, which suggested that SNAC1, RALF12, OsBI-1 can confer Cd tolerance in yeast and tobacco leaves. Regarding the genes involved in ion transport, the validated Cd-tolerant heavy metal-associated domain (HMAD) isoprenylated protein HIPP42 was particularly noteworthy. Further elucidation of these genes associated with Cd tolerance in rice will benefit agricultural activities.
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Affiliation(s)
- Baoxiang Wang
- Lianyungang Institute of Agricultural Sciences in Jiangsu Xuhuai Region, Jiangsu Academy of Agricultural Sciences, Lianyungang, China.
| | - Manman Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Jie Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Liping Huang
- School of Food Science and Engineering, Foshan University, Foshan, China.
| | - Xi Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Mingyi Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Mingpu Tan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
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Identification of Quantitative Trait Loci Controlling High-Temperature Tolerance in Cucumber ( Cucumis sativus L.) Seedlings. PLANTS 2020; 9:plants9091155. [PMID: 32906664 PMCID: PMC7570005 DOI: 10.3390/plants9091155] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 12/23/2022]
Abstract
High temperature is one of the major abiotic stresses that affect cucumber growth and development. Heat stress often leads to metabolic malfunction, dehydration, wilting and death, which has a great impact on the yield and fruit quality. In this study, genetic analysis and quantitative trait loci (QTL) mapping for thermotolerance in cucumber seedlings was investigated using a recombinant inbred line (RILs; HR) population and a doubled haploid (DH; HP) population derived from two parental lines ‘65G’ (heat-sensitive) and ‘02245′ (heat-tolerant). Inheritance analysis suggested that both short-term extreme and long-term mild thermotolerance in cucumber seedlings were determined by multiple genes. Six QTLs for heat tolerance including qHT3.1, qHT3.2, qHT3.3, qHT4.1, qHT4.2, and qHT6.1 were detected. Among them, the major QTL, qHT3.2, was repeatedly detected for three times in HR and HP at different environments, explained 28.3% of the phenotypic variability. The 481.2 kb region harbored 79 genes, nine of which might involve in heat stress response. This study provides a basis for further identifying thermotolerant genes and helps understanding the molecular mechanism underlying thermotolerance in cucumber seedlings.
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Lai W, Zhou Y, Pan R, Liao L, He J, Liu H, Yang Y, Liu S. Identification and Expression Analysis of Stress-Associated Proteins (SAPs) Containing A20/AN1 Zinc Finger in Cucumber. PLANTS (BASEL, SWITZERLAND) 2020; 9:E400. [PMID: 32213813 PMCID: PMC7154871 DOI: 10.3390/plants9030400] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/01/2020] [Accepted: 03/02/2020] [Indexed: 12/21/2022]
Abstract
Stress-associated proteins (SAPs) are a class of zinc finger proteins that confer tolerance to a variety of abiotic and biotic stresses in diverse plant species. However, in cucumber (Cucumis sativus L.), very little is known about the roles of SAP gene family members in regulating plant growth, development, and stress responses. In this study, a total of 12 SAP genes (named as CsSAP1-CsSAP12) were identified in the cucumber genome, which were unevenly distributed on six chromosomes. Gene duplication analysis detected one tandem duplication and two segmental duplication events. Phylogenetic analysis of SAP proteins from cucumber and other plants suggested that they could be divided into seven groups (sub-families), and proteins in the same group generally had the same arrangement of AN1 (ZnF-AN1) and A20 (ZnF-A20) domains. Most of the CsSAP genes were intronless and harbored a number of stress- and hormone-responsive cis-elements in their promoter regions. Tissue expression analysis showed that the CsSAP genes had a broad spectrum of expression in different tissues, and some of them displayed remarkable alteration in expression during fruit development. RT-qPCR results indicated that all the selected CsSAP genes displayed transcriptional responses to cold, drought, and salt stresses. These results enable the first comprehensive description of the SAP gene family in cucumber and lay a solid foundation for future research on the biological functions of CsSAP genes.
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Affiliation(s)
- Wei Lai
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yong Zhou
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Rao Pan
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liting Liao
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Juncheng He
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Haoju Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yingui Yang
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shiqiang Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
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Cao S, Zhang Z, Wang C, Li X, Guo C, Yang L, Guo Y. Identification of a Novel Melon Transcription Factor CmNAC60 as a Potential Regulator of Leaf Senescence. Genes (Basel) 2019; 10:genes10080584. [PMID: 31370358 PMCID: PMC6723929 DOI: 10.3390/genes10080584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/25/2019] [Accepted: 07/30/2019] [Indexed: 12/02/2022] Open
Abstract
NAC transcription factors (TFs) play important roles in plants’ responses to abiotic stresses and developmental processes, including leaf senescence. Oriental melon (Cucumis melo var. makuwa Makino) is an important vegetable crop in China and eastern Asia countries. However, little is known about the functions of the melon NAC family members. In this study, a phylogenetic tree was constructed to show that CmNAC60 and the senescence regulator AtNAP were in the same cluster, which implied that CmNAC60 might be a NAC related to leaf senescence. The expression analysis of CmNAC60 in different melon organs showed that the expression of CmNAC60 was highest in the male flowers and lowest in the hypocotyl. In addition, the expression level of CmNAC60 in the senescing leaves was significantly higher than in the non-senescing leaves. Similarly, the expression level of CmNAC60 in the dark-treated leaves was significantly higher than in the untreated leaves. Furthermore, the subcellular localization and transcriptional activation assays indicated that CmNAC60 was a nucleus localized NAC transcription factor with a C-terminal transactivation domain. An analysis of the tissue specific expression showed that the promoter of CmNAC60 may contain cis-acting regulatory elements responsive to leaf senescence. CmNAC60 overexpressing lines of Arabidopsis showed a precocious senescence compared with the wild type (WT). Collectively, our results showed that CmNAC60 was associated with leaf senescence, and could be potentially utilized in molecular breeding to improve melon yield or to extend the postharvest shelf life by delaying leaf senescence.
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Affiliation(s)
- Songxiao Cao
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zhenbiao Zhang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Chenghui Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoxu Li
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Cun Guo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Liyu Yang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yongfeng Guo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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Wang X, Yu G, Zhao J, Cui N, Yu Y, Fan H. Functional Identification of Corynespora cassiicola-Responsive miRNAs and Their Targets in Cucumber. FRONTIERS IN PLANT SCIENCE 2019; 10:668. [PMID: 31214213 PMCID: PMC6554439 DOI: 10.3389/fpls.2019.00668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Target leaf spot (TLS), which is caused by Corynespora cassiicola (C. cassiicola), is one of the most important diseases in cucumber (Cucumis sativus L.). Our previous research identified several C. cassiicola-responsive miRNAs in cucumber by high-throughput sequencing, including two known miRNAs and two novel miRNAs. The target genes of these miRNAs were related to secondary metabolism. In this study, we verified the interaction between these miRNAs and target genes by histochemical staining and fluorescence quantitative assays of GUS. We transiently expressed the candidate miRNAs and target genes in cucumber cotyledons to investigate the resistance to C. cassiicola. Transient expression of miR164d, miR396b, Novel-miR1, and Novel-miR7 in cucumber resulted in decreased resistance to C. cassiicola, while transient expression of NAC (inhibited by miR164d), APE (inhibited by miR396b), 4CL (inhibited by Novel-miR1), and PAL (inhibited by Novel-miR7) led to enhanced resistance to C. cassiicola. In addition, overexpression of 4CL and PAL downregulated lignin synthesis, and overexpression of Novel-miR1 and Novel-miR7 also downregulated lignin synthesis, indicating that the regulation of 4CL and PAL by Novel-miR1 and Novel-miR7 could affect lignin content. The tobacco rattle virus (TRV) induced short tandem target mimic (STTM)-miRNA silencing vector was successfully constructed, and target miRNAs were successfully silenced. The identification of disease resistance and lignin content showed that silencing candidate miRNAs could improve cucumber resistance to C. cassiicola.
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Affiliation(s)
- Xiangyu Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Guangchao Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Junyue Zhao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Na Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yang Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang, China
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10
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Jan S, Abbas N, Ashraf M, Ahmad P. Roles of potential plant hormones and transcription factors in controlling leaf senescence and drought tolerance. PROTOPLASMA 2019; 256:313-329. [PMID: 30311054 DOI: 10.1007/s00709-018-1310-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Plant leaves offer an exclusive windowpane to uncover the changes in organs, tissues, and cells as they advance towards the process of senescence and death. Drought-induced leaf senescence is an intricate process with remarkably coordinated phases of onset, progression, and completion implicated in an extensive reprogramming of gene expression. Advancing leaf senescence remobilizes nutrients to younger leaves thereby contributing to plant fitness. However, numerous mysteries remain unraveled concerning leaf senescence. We are not still able to correlate leaf senescence and drought stress to endogenous and exogenous environments. Furthermore, we need to decipher how molecular mechanisms of the leaf senescence and levels of drought tolerance are advanced and how is the involvement of SAGs in drought tolerance and plant fitness. This review provides the perspicacity indispensable for facilitating our coordinated point of view pertaining to leaf senescence together with inferences on progression of whole plant aging. The main segments discussed in the review include coordination between hormonal signaling, leaf senescence, drought tolerance, and crosstalk between hormones in leaf senescence regulation.
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Affiliation(s)
- Sumira Jan
- ICAR- Central Institute of Temperate Horticulture, Rangreth, Air Field, Srinagar, Jammu and Kashmir, India
| | - Nazia Abbas
- Indian Institute of Integrative Medicine, Sanatnagar, Srinagar, Jammu and Kashmir, India
| | | | - Parvaiz Ahmad
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
- Department of Botany, S.P. College, Srinagar, Jammu and Kashmir, 190001, India.
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11
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Li J, Zhang X, Lu Y, Feng D, Gu A, Wang S, Wu F, Su X, Chen X, Li X, Liu M, Fan S, Feng D, Luo S, Xuan S, Wang Y, Shen S, Zhao J. Characterization of Non-heading Mutation in Heading Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). FRONTIERS IN PLANT SCIENCE 2019; 10:112. [PMID: 30809236 PMCID: PMC6379458 DOI: 10.3389/fpls.2019.00112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/23/2019] [Indexed: 05/26/2023]
Abstract
Heading is a key agronomic trait of Chinese cabbage. A non-heading mutant with flat growth of heading leaves (fg-1) was isolated from an EMS-induced mutant population of the heading Chinese cabbage inbred line A03. In fg-1 mutant plants, the heading leaves are flat similar to rosette leaves. The epidermal cells on the adaxial surface of these leaves are significantly smaller, while those on the abaxial surface are much larger than in A03 plants. The segregation of the heading phenotype in the F2 and BC1 population suggests that the mutant trait is controlled by a pair of recessive alleles. Phytohormone analysis at the early heading stage showed significant decreases in IAA, ABA, JA and SA, with increases in methyl IAA and trans-Zeatin levels, suggesting they may coordinate leaf adaxial-abaxial polarity, development and morphology in fg-1. RNA-sequencing analysis at the early heading stage showed a decrease in expression levels of several auxin transport (BrAUX1, BrLAXs, and BrPINs) and responsive genes. Transcript levels of important ABA responsive genes, including BrABF3, were up-regulated in mid-leaf sections suggesting that both auxin and ABA signaling pathways play important roles in regulating leaf heading. In addition, a significant reduction in BrIAMT1 transcripts in fg-1 might contribute to leaf epinastic growth. The expression profiles of 19 genes with known roles in leaf polarity were significantly different in fg-1 leaves compared to wild type, suggesting that these genes might also regulate leaf heading in Chinese cabbage. In conclusion, leaf heading in Chinese cabbage is controlled through a complex network of hormone signaling and abaxial-adaxial patterning pathways. These findings increase our understanding of the molecular basis of head formation in Chinese cabbage.
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Affiliation(s)
- Jingrui Li
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaomeng Zhang
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yin Lu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Dongxiao Feng
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Aixia Gu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shan Wang
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Fang Wu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiangjie Su
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xueping Chen
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xing Li
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Mengyang Liu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuangxi Fan
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Daling Feng
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuangxia Luo
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxin Xuan
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yanhua Wang
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxing Shen
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
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12
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Li Y, Shi H, Zhang H, Chen S. Amelioration of drought effects in wheat and cucumber by the combined application of super absorbent polymer and potential biofertilizer. PeerJ 2019; 7:e6073. [PMID: 30643688 PMCID: PMC6330032 DOI: 10.7717/peerj.6073] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/06/2018] [Indexed: 11/20/2022] Open
Abstract
Biofertilizer is a good substitute for chemical fertilizer in sustainable agriculture, but its effects are often hindered by drought stress. Super absorbent polymer (SAP), showing good capacity of water absorption and retention, can increase soil moisture. However, limited information is available about the efficiency of biofertilizer amended with SAP. This study was conducted to investigate the effects of synergistic application of SAP and biofertilizers (Paenibacillus beijingensis BJ-18 and Bacillus sp. L-56) on plant growth, including wheat and cucumber. Potted soil was treated with different fertilizer combinations (SAP, BJ-18 biofertilizer, L-56 biofertilizer, BJ-18 + SAP, L-56 + SAP), and pot experiment was carried out to explore its effects on viability of inoculants, seed germination rate, plant physiological and biochemical parameters, and expression pattern of stress-related genes under drought condition. At day 29 after sowing, the highest viability of strain P. beijingensis BJ-18 (264 copies ng-1 gDNA) was observed in BJ-18 + SAP treatment group of wheat rhizosphere soil, while that of strain Bacillus sp. L-56 (331 copies ng-1 gDNA) was observed in the L-56 + SAP treatment group of cucumber rhizosphere soil. In addition, both biofertilizers amended with SAP could promote germination rate of seeds (wheat and cucumber), plant growth, soil fertility (urease, sucrose, and dehydrogenase activities). Quantitative real-time PCR analysis showed that biofertilizer + SAP significantly down-regulated the expression levels of genes involved in ROS scavenging (TaCAT, CsCAT, TaAPX, and CsAPX2), ethylene biosynthesis (TaACO2, CsACO1, and CsACS1), stress response (TaDHN3, TaLEA, and CsLEA11), salicylic acid (TaPR1-1a and CsPR1-1a), and transcription activation (TaNAC2D and CsNAC35) in plants under drought stress. These results suggest that SAP addition in biofertilizer is a good tactic for enhancing the efficiency of biofertilizer, which is beneficial for plants in response to drought stress. To the best of our knowledge, this is the first report about the effect of synergistic use of biofertilizer and SAP on plant growth under drought stress.
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Affiliation(s)
- Yongbin Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haowen Shi
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haowei Zhang
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Sanfeng Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
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13
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Zhang X, Lai Y, Zhang W, Ahmad J, Qiu Y, Zhang X, Duan M, Liu T, Song J, Wang H, Li X. MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod. BMC Genomics 2018; 19:819. [PMID: 30442111 PMCID: PMC6238408 DOI: 10.1186/s12864-018-5204-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and long vs. short photoperiod. RESULTS A total of 164 known miRNAs derived from 68 families and 203 novel miRNAs from 182 families were identified. Their 4611 targets were predicted using psRobot and TargetFinder, amongst which 349 were validated by degradome sequencing. Fourteen targets of six miRNAs were differentially expressed between the treatments. A total of eight known and 16 novel miRNAs were affected by temperature and photoperiod. Functional annotations revealed that "Plant hormone signal transduction" pathway was significantly over-represented in the miRNA targets. The miR156/157/SBP-Boxes and novel-mir153/ethylene-responsive transcription factor/senescence-related protein/aminotransferase/acyl-CoA thioesterase are the two most credible miRNA/targets combinations modulating the plant's responsive processes to the temperature-photoperiod changes. Moreover, the newly evolved, cucumber-specific novel miRNA (novel-mir153) was found to target 2087 mRNAs by prediction and has 232 targets proven by degradome analysis, accounting for 45.26-58.88% of the total miRNA targets in this plant. This is the largest sum of genes targeted by a single miRNA to the best of our knowledge. CONCLUSIONS These results contribute to a better understanding of the miRNAs mediating plant adaptation to combinations of temperature and photoperiod and sheds light on the recent evolution of new miRNAs in cucumber.
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Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunsong Lai
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jalil Ahmad
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoxue Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mengmeng Duan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tongjin Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiangping Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiping Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xixiang Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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14
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Zhou Y, Ahammed GJ, Wang Q, Wu C, Wan C, Yang Y. Transcriptomic insights into the blue light-induced female floral sex expression in cucumber (Cucumis sativus L.). Sci Rep 2018; 8:14261. [PMID: 30250053 PMCID: PMC6155147 DOI: 10.1038/s41598-018-32632-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/12/2018] [Indexed: 02/07/2023] Open
Abstract
In cucurbitaceous crops, sex differentiation of flower buds is a crucial developmental process that directly affects fruit yield. Here we showed that the induction of female flower was the highest in the blue light-treated monoecious cucumber plants compared with that in other light qualities (white, green and red). High-throughput RNA-Seq analysis of the shoot apexes identified a total of 74 differently-expressed genes (DEGs), in which 52 up-regulated and 22 down-regulated under the blue light compared with that in white light. The DEGs were mainly involved in metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction, starch and sucrose metabolism and phenylpropanoid biosynthesis. While the ethylene and gibberellins synthesis and signaling related genes were down-regulated, the abscisic acid and auxin signal transduction pathways were up-regulated by the blue light treatment. Furthermore, the blue light treatment up-regulated the transcription of genes relating to photosynthesis, starch and sucrose metabolism. Meanwhile, the blue light suppressed the GA3 concentration but promoted the concentrations of auxin and photosynthetic pigments. Taken together, the results suggest that the blue light-induced female floral sex expression is closely associated with the blue light-induced changes in abscisic acid, auxin, gibberellins, photosynthesis, starch and sucrose metabolism pathways, which is potentially different from the traditional ethylene-dependent pathway.
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Affiliation(s)
- Yong Zhou
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, College of Agronomy/College of Science, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Golam Jalal Ahammed
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, China
| | - Qiang Wang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, College of Agronomy/College of Science, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chaoqun Wu
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, College of Agronomy/College of Science, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chunpeng Wan
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, College of Agronomy/College of Science, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Youxin Yang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, College of Agronomy/College of Science, Jiangxi Agricultural University, Nanchang, 330045, China.
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15
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Wang J, Zhang L, Cao Y, Qi C, Li S, Liu L, Wang G, Mao A, Ren S, Guo YD. CsATAF1 Positively Regulates Drought Stress Tolerance by an ABA-Dependent Pathway and by Promoting ROS Scavenging in Cucumber. PLANT & CELL PHYSIOLOGY 2018; 59:930-945. [PMID: 29415202 DOI: 10.1093/pcp/pcy030] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/31/2018] [Indexed: 05/21/2023]
Abstract
The NAC transcription factors play vital roles in responding to drought stress in plants; however, the molecular mechanisms remain largely unknown in cucumber. Suppression of CsATAF1 via RNA interference (RNAi) weakened drought stress tolerance in cucumber due to a higher water loss rate in leaves, a higher level of hydrogen peroxide (H2O2) and superoxide radicals (O2·-), increased malondialdehyde (MDA) content, lower Fv/Fm ratios and lower antioxidant enzyme activity. The analysis of root length and stomatal apertures showed that CsATAF1-RNAi cucumber plants were less responsive to ABA. In contrast, CsATAF1-overexpression (OE) plants showed increased drought stress tolerance and sensitivity to ABA. Quantitative PCR (qPCR) analysis showed that expression of several stress-responsive genes was significantly up-regulated in CsATAF1-OE transformants and down-regulated in CsATAF1-RNAi transformants. CsABI5, CsCu-ZnSOD and CsDREB2C were verified as direct target genes of CsATAF1. Yeast one-hybrid analysis and electrophoretic mobility shift assay (EMSA) further substantiated that CsATAF1 bound to the promoters of CsABI5, CsCu-ZnSOD and CsDREB2C. Transient expression in tobacco leaves and cucumber protoplasts showed that CsATAF1 directly up-regulated the expression of CsABI5, CsCu-ZnSOD and CsDREB2C. Our results demonstrated that CsATAF1 functioned as a positive regulator in response to drought stress by an ABA-dependent pathway and decreasing reactive oxygen species (ROS) accumulation in cucumber.
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Affiliation(s)
- Jinfang Wang
- College of Horticulture, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Lei Zhang
- College of Horticulture, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Yunyun Cao
- College of Horticulture, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Chuandong Qi
- College of Horticulture, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Shuangtao Li
- College of Horticulture, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Lun Liu
- College of Horticulture, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Gongle Wang
- College of Horticulture, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Aijun Mao
- Beijing Key Lab of Vegetable Germplasm Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shuxin Ren
- School of Agriculture, Virginia State University, PO Box 9061, Petersburg, VA 23806, USA
| | - Yang-Dong Guo
- College of Horticulture, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
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16
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Karanja BK, Xu L, Wang Y, Muleke EM, Jabir BM, Xie Y, Zhu X, Cheng W, Liu L. Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish ( Raphanus sativus L.). PeerJ 2017; 5:e4172. [PMID: 29259849 PMCID: PMC5733918 DOI: 10.7717/peerj.4172] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/28/2017] [Indexed: 01/23/2023] Open
Abstract
NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.
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Affiliation(s)
- Bernard Kinuthia Karanja
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Everlyne M'mbone Muleke
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Bashir Mohammed Jabir
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Wanwan Cheng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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17
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Hu D, Xu X, Cai T, Wang WY, Wu CJ, Ye LM. Simultaneous Determination of Isopyrazam and Azoxystrobin in Cucumbers by Liquid Chromatography-Tandem Mass Spectrometry. J Food Prot 2017; 80:2112-2118. [PMID: 29166175 DOI: 10.4315/0362-028x.jfp-17-228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A rapid and sensitive analytical method based on high-performance liquid chromatography-tandem mass spectrometry was developed and validated for the determination of isopyrazam (IZM) and azoxystrobin (AZT) in cucumbers. A modified QuEChERS (quick, easy, cheap, effective, rugged, and safe) method was used as the pretreatment procedure. The samples were extracted with acetonitrile and cleaned up with octadecylsilyl silica (C18) and graphite carbon black. The proposed method resulted in satisfactory recovery of IZM and AZT (91.48 to 114.62%), and relative standard deviations were less than 13.1% at fortification concentrations of 1, 20, and 500 μg kg-1 (n = 3). The limits of quantification for IZM and AZT were 0.498 and 0.499 μg kg-1, respectively, which are far below the maximum residue level (0.5 mg kg-1) established for this type of sample. Matrix effects were also evaluated. This study established a sensitive and fast method for the detection of IZM and AZT in cucumber samples.
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Affiliation(s)
- Dan Hu
- 1 West China School of Pharmacy, Sichuan University, Chengdu 610041, People's Republic of China
| | - Xu Xu
- 2 Chengdu Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chengdu 610041, People's Republic of China; and
| | - Tian Cai
- 2 Chengdu Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chengdu 610041, People's Republic of China; and
| | - Wei-Ying Wang
- 1 West China School of Pharmacy, Sichuan University, Chengdu 610041, People's Republic of China
| | - Chun-Jie Wu
- 3 College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Li-Ming Ye
- 1 West China School of Pharmacy, Sichuan University, Chengdu 610041, People's Republic of China
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