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von Dahlen JK, Schulz K, Nicolai J, Rose LE. Global expression patterns of R-genes in tomato and potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1216795. [PMID: 37965025 PMCID: PMC10641715 DOI: 10.3389/fpls.2023.1216795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/28/2023] [Indexed: 11/16/2023]
Abstract
Introduction As key-players of plant immunity, the proteins encoded by resistance genes (R-genes) recognize pathogens and initiate pathogen-specific defense responses. The expression of some R-genes carry fitness costs and therefore inducible immune responses are likely advantageous. To what degree inducible resistance driven by R-genes is triggered by pathogen infection is currently an open question. Methods In this study we analyzed the expression of 940 R-genes of tomato and potato across 315 transcriptome libraries to investigate how interspecific interactions with microbes influence R-gene expression in plants. Results We found that most R-genes are expressed at a low level. A small subset of R-genes had moderate to high levels of expression and were expressed across many independent libraries, irrespective of infection status. These R-genes include members of the class of genes called NRCs (NLR required for cell death). Approximately 10% of all R-genes were differentially expressed during infection and this included both up- and down-regulation. One factor associated with the large differences in R-gene expression was host tissue, reflecting a considerable degree of tissue-specific transcriptional regulation of this class of genes. Discussion These results call into question the widespread view that R-gene expression is induced upon pathogen attack. Instead, a small core set of R-genes is constitutively expressed, imparting upon the plant a ready-to-detect and defend status.
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Affiliation(s)
- Janina K. von Dahlen
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Kerstin Schulz
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Jessica Nicolai
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Laura E. Rose
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
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Sun Y, Jia X, Chen D, Fu Q, Chen J, Yang W, Yang H, Xu X. Genome-Wide Identification and Expression Analysis of Cysteine-Rich Polycomb-like Protein (CPP) Gene Family in Tomato. Int J Mol Sci 2023; 24:ijms24065762. [PMID: 36982833 PMCID: PMC10058331 DOI: 10.3390/ijms24065762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The cysteine-rich polycomb-like protein (CPP) gene family is a class of transcription factors containing conserved cysteine-rich CRC structural domains that is involved in the regulation of plant growth and stress tolerance to adversity. Relative to other gene families, the CPP gene family has not received sufficient attention. In this study, six SlCPPs were identified for the first time using the most recent genome-wide identification data of tomato. Subsequently, a phylogenetic analysis classified SlCPPs into four subfamilies. The analysis of cis-acting elements in the promoter indicates that SlCPPs are involved in plant growth and development and also stress response. We present for the first time the prediction of the tertiary structure of these SlCPPs proteins using the AlphaFold2 artificial intelligence system developed by the DeepMind team. Transcriptome data analysis showed that SlCPPs were differentially expressed in different tissues. Gene expression profiling showed that all SlCPPs except SlCPP5 were up-regulated under drought stress; SlCPP2, SlCPP3 and SlCPP4 were up-regulated under cold stress; SlCPP2 and SlCPP5 were up-regulated under salt stress; all SlCPPs were up-regulated under inoculation with Cladosporium fulvum; and SlCPP1, SlCPP3, and SlCPP4 were up-regulated under inoculation with Stemphylium lycopersici. We performed a virus-induced gene silencing experiment on SlCPP3, and the results indicated that SlCPP3 was involved in the response to drought stress. Finally, we predicted the interaction network of the key gene SlCPP3, and there was an interaction relationship between SlCPP3 and 10 genes, such as RBR1 and MSI1. The positive outcome showed that SlCPPs responded to environmental stress. This study provides a theoretical and empirical basis for the response mechanisms of tomato in abiotic stresses.
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Affiliation(s)
- Yaoguang Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xinyi Jia
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Dexia Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Qingjun Fu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Jinxiu Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Wenhui Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Huanhuan Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xiangyang Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
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Comparison of Tomato Transcriptomic Profiles Reveals Overlapping Patterns in Abiotic and Biotic Stress Responses. Int J Mol Sci 2023; 24:ijms24044061. [PMID: 36835470 PMCID: PMC9961515 DOI: 10.3390/ijms24044061] [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: 12/27/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Until a few years ago, many studies focused on the transcriptomic response to single stresses. However, tomato cultivations are often constrained by a wide range of biotic and abiotic stress that can occur singularly or in combination, and several genes can be involved in the defensive mechanism response. Therefore, we analyzed and compared the transcriptomic responses of resistant and susceptible genotypes to seven biotic stresses (Cladosporium fulvum, Phytophthora infestans, Pseudomonas syringae, Ralstonia solanacearum, Sclerotinia sclerotiorum, Tomato spotted wilt virus (TSWV) and Tuta absoluta) and five abiotic stresses (drought, salinity, low temperatures, and oxidative stress) to identify genes involved in response to multiple stressors. With this approach, we found genes encoding for TFs, phytohormones, or participating in signaling and cell wall metabolic processes, participating in defense against various biotic and abiotic stress. Moreover, a total of 1474 DEGs were commonly found between biotic and abiotic stress. Among these, 67 DEGs were involved in response to at least four different stresses. In particular, we found RLKs, MAPKs, Fasciclin-like arabinogalactans (FLAs), glycosyltransferases, genes involved in the auxin, ET, and JA pathways, MYBs, bZIPs, WRKYs and ERFs genes. Detected genes responsive to multiple stress might be further investigated with biotechnological approaches to effectively improve plant tolerance in the field.
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Wang S, Wang S, Li M, Su Y, Sun Z, Ma H. Combined transcriptome and metabolome analysis of Nerium indicum L. elaborates the key pathways that are activated in response to witches' broom disease. BMC PLANT BIOLOGY 2022; 22:291. [PMID: 35701735 PMCID: PMC9199210 DOI: 10.1186/s12870-022-03672-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 05/27/2022] [Indexed: 05/06/2023]
Abstract
BACKGROUND Nerium indicum Mill. is an ornamental plant that is found in parks, riversides, lakesides, and scenic areas in China and other parts of the world. Our recent survey indicated the prevalence of witches' broom disease (WBD) in Guangdong, China. To find out the possible defense strategies against WBD, we performed a MiSeq based ITS sequencing to identify the possible casual organism, then did a de novo transcriptome sequencing and metabolome profiling in the phloem and stem tip of N. indicum plants suffering from WBD compared to healthy ones. RESULTS The survey showed that Wengyuen county and Zengcheng district had the highest disease incidence rates. The most prevalent microbial species in the diseased tissues was Cophinforma mamane. The transcriptome sequencing resulted in the identification of 191,224 unigenes of which 142,396 could be annotated. There were 19,031 and 13,284 differentially expressed genes (DEGs) between diseased phloem (NOWP) and healthy phloem (NOHP), and diseased stem (NOWS) and healthy stem (NOHS), respectively. The DEGs were enriched in MAPK-signaling (plant), plant-pathogen interaction, plant-hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, linoleic acid and α-linoleic acid metabolism pathways. Particularly, we found that N. indicum plants activated the phytohormone signaling, MAPK-signaling cascade, defense related proteins, and the biosynthesis of phenylpropanoids and flavonoids as defense responses to the pathogenic infection. The metabolome profiling identified 586 metabolites of which 386 and 324 metabolites were differentially accumulated in NOHP vs NOWP and NOHS and NOWS, respectively. The differential accumulation of metabolites related to phytohormone signaling, linoleic acid metabolism, phenylpropanoid and flavonoid biosynthesis, nicotinate and nicotinamide metabolism, and citrate cycle was observed, indicating the role of these pathways in defense responses against the pathogenic infection. CONCLUSION Our results showed that Guangdong province has a high incidence of WBD in most of the surveyed areas. C. mamane is suspected to be the causing pathogen of WBD in N. indicum. N. indicum initiated the MAPK-signaling cascade and phytohormone signaling, leading to the activation of pathogen-associated molecular patterns and hypersensitive response. Furthermore, N. indicum accumulated high concentrations of phenolic acids, coumarins and lignans, and flavonoids under WBD. These results provide scientific tools for the formulation of control strategies of WBD in N. indicum.
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Affiliation(s)
- Shengjie Wang
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Shengkun Wang
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Ming Li
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Yuhang Su
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Zhan Sun
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Haibin Ma
- The Key Laboratory of National Forestry and Grassland Administration for Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
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Momo J, Kumar A, Islam K, Ahmad I, Rawoof A, Ramchiary N. A comprehensive update on Capsicum proteomics: Advances and future prospects. J Proteomics 2022; 261:104578. [DOI: 10.1016/j.jprot.2022.104578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 10/18/2022]
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Cheng C, Liu F, Tian N, Mensah RA, Sun X, Liu J, Wu J, Wang B, Li D, Lai Z. Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing. Sci Rep 2021; 11:16363. [PMID: 34381122 PMCID: PMC8358008 DOI: 10.1038/s41598-021-95832-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/29/2021] [Indexed: 12/03/2022] Open
Abstract
Fusarium wilt disease, caused by Fusarium oxysporum f.sp. cubense (Foc), has been recognized as the most devastating disease to banana. The regulatory role of long non-coding RNAs (lncRNAs) in plant defense has been verified in many plant species. However, the understanding of their role during early FocTR4 (Foc tropical race 4) infection stage is very limited. In this study, lncRNA sequencing was used to reveal banana root transcriptome profile changes during early FocTR4 infection stages. Quantitative real time PCR (qRT-PCR) was performed to confirm the expression of eight differentially expressed (DE) lncRNAs (DELs) and their predicted target genes (DETs), and three DE genes (DEGs). Totally, 12,109 lncRNAs, 36,519 mRNAs and 2642 novel genes were obtained, of which 1398 (including 78 DELs, 1220 DE known genes and 100 DE novel genes) were identified as FocTR4 responsive DE transcripts. Gene function analysis revealed that most DEGs were involved in biosynthesis of secondary metabolites, plant–pathogen interaction, plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism and so on. Coincidently, many DETs have been identified as DEGs in previous transcriptome studies. Moreover, many DETs were found to be involved in ribosome, oxidative phosphorylation, lipoic acid metabolism, ubiquitin mediated proteolysis, N-glycan biosynthesis, protein processing in endoplasmic reticulum and DNA damage response pathways. QRT-PCR result showed the expression patterns of the selected transcripts were mostly consistent with our lncRNA sequencing data. Our present study showed the regulatory role of lncRNAs on known biotic and abiotic stress responsive genes and some new-found FocTR4 responsive genes, which can provide new insights into FocTR4-induced changes in the banana root transcriptome during the early pathogen infection stage.
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Affiliation(s)
- Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Fan Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Na Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Raphael Anue Mensah
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueli Sun
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiapeng Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Junwei Wu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bin Wang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Campos MD, Félix MDR, Patanita M, Materatski P, Varanda C. High throughput sequencing unravels tomato-pathogen interactions towards a sustainable plant breeding. HORTICULTURE RESEARCH 2021; 8:171. [PMID: 34333540 PMCID: PMC8325677 DOI: 10.1038/s41438-021-00607-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 05/24/2023]
Abstract
Tomato (Solanum lycopersicum) is one of the most economically important vegetables throughout the world. It is one of the best studied cultivated dicotyledonous plants, often used as a model system for plant research into classical genetics, cytogenetics, molecular genetics, and molecular biology. Tomato plants are affected by different pathogens such as viruses, viroids, fungi, oomycetes, bacteria, and nematodes, that reduce yield and affect product quality. The study of tomato as a plant-pathogen system helps to accelerate the discovery and understanding of the molecular mechanisms underlying disease resistance and offers the opportunity of improving the yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques, that allow the identification of plant key functional genes in susceptible and resistant responses, and the understanding of the molecular basis of compatible interactions during pathogen attack. Next-generation sequencing technologies (NGS), which produce massive quantities of sequencing data, have greatly accelerated research in biological sciences and offer great opportunities to better understand the molecular networks of plant-pathogen interactions. In this review, we summarize important research that used high-throughput RNA-seq technology to obtain transcriptome changes in tomato plants in response to a wide range of pathogens such as viruses, fungi, bacteria, oomycetes, and nematodes. These findings will facilitate genetic engineering efforts to incorporate new sources of resistance in tomato for protection against pathogens and are of major importance for sustainable plant-disease management, namely the ones relying on the plant's innate immune mechanisms in view of plant breeding.
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Affiliation(s)
- Maria Doroteia Campos
- MED - Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal.
| | - Maria do Rosário Félix
- MED - Mediterranean Institute for Agriculture, Environment and Development & Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal
| | - Mariana Patanita
- MED - Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal
| | - Patrick Materatski
- MED - Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal
| | - Carla Varanda
- MED - Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal
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Yu J, Gonzalez JM, Dong Z, Shan Q, Tan B, Koh J, Zhang T, Zhu N, Dufresne C, Martin GB, Chen S. Integrative Proteomic and Phosphoproteomic Analyses of Pattern- and Effector-Triggered Immunity in Tomato. FRONTIERS IN PLANT SCIENCE 2021; 12:768693. [PMID: 34925416 PMCID: PMC8677958 DOI: 10.3389/fpls.2021.768693] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/12/2021] [Indexed: 05/04/2023]
Abstract
Plants have evolved a two-layered immune system consisting of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI and ETI are functionally linked, but also have distinct characteristics. Unraveling how these immune systems coordinate plant responses against pathogens is crucial for understanding the regulatory mechanisms underlying plant defense. Here we report integrative proteomic and phosphoproteomic analyses of the tomato-Pseudomonas syringae (Pst) pathosystem with different Pst mutants that allow the dissection of PTI and ETI. A total of 225 proteins and 79 phosphopeptides differentially accumulated in tomato leaves during Pst infection. The abundances of many proteins and phosphoproteins changed during PTI or ETI, and some responses were triggered by both PTI and ETI. For most proteins, the ETI response was more robust than the PTI response. The patterns of protein abundance and phosphorylation changes revealed key regulators involved in Ca2+ signaling, mitogen-activated protein kinase cascades, reversible protein phosphorylation, reactive oxygen species (ROS) and redox homeostasis, transcription and protein turnover, transport and trafficking, cell wall remodeling, hormone biosynthesis and signaling, suggesting their common or specific roles in PTI and/or ETI. A NAC (NAM, ATAF, and CUC family) domain protein and lipid particle serine esterase, two PTI-specific genes identified from previous transcriptomic work, were not detected as differentially regulated at the protein level and were not induced by PTI. Based on integrative transcriptomics and proteomics data, as well as qRT-PCR analysis, several potential PTI and ETI-specific markers are proposed. These results provide insights into the regulatory mechanisms underlying PTI and ETI in the tomato-Pst pathosystem, and will promote future validation and application of the disease biomarkers in plant defense.
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Affiliation(s)
- Juanjuan Yu
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, College of Life Sciences, Henan Normal University, Xinxiang, China
- *Correspondence: Juanjuan Yu,
| | - Juan M. Gonzalez
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
| | - Zhiping Dong
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Qianru Shan
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Bowen Tan
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Jin Koh
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Tong Zhang
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Ning Zhu
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Craig Dufresne
- Thermo Fisher Scientific Inc., West Palm Beach, FL, United States
| | - Gregory B. Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Sixue Chen,
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Yang H, Shen F, Wang H, Zhao T, Zhang H, Jiang J, Xu X, Li J. Functional analysis of the SlERF01 gene in disease resistance to S. lycopersici. BMC PLANT BIOLOGY 2020; 20:376. [PMID: 32799800 PMCID: PMC7429758 DOI: 10.1186/s12870-020-02588-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 08/09/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Tomato gray leaf spot caused by Stemphylium lycopersici (S. lycopersici) is a serious disease that can severely hinder tomato production. To date, only Sm has been reported to provide resistance against this disease, and the molecular mechanism underlying resistance to this disease in tomato remains unclear. To better understand the mechanism of tomato resistance to S. lycopersici, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR)-based analysis, physiological indexes, microscopy observations and transgenic technology were used in this study. RESULTS Our results showed that the expression of SlERF01 was strongly induced by S. lycopersici and by exogenous applications of the hormones salicylic acid (SA) and jasmonic acid (JA). Furthermore, overexpression of SlERF01 enhanced the hypersensitive response (HR) to S. lycopersici and elevated the expression of defense genes in tomato. Furthermore, the accumulation of lignin, callose and hydrogen peroxide (H2O2) increased in the transgenic lines after inoculation with S. lycopersici. Taken together, our results showed that SlERF01 played an indispensable role in multiple SA, JA and reactive oxygen species (ROS) signaling pathways to provide resistance to S. lycopersici invasion. Our findings also indicated that SlERF01 could activate the expression of the PR1 gene and enhance resistance to S. lycopersici. CONCLUSIONS We identified the SlERF01 gene, which encodes a novel tomato AP2/ERF transcription factor (TF). Functional analysis revealed that SlERF01 positively regulates tomato resistance to S. lycopersici. Our findings indicate that SlERF01 plays a key role in multiple SA, JA and ROS signaling pathways to provide resistance to invasion by S. lycopersici. The findings of this study not only help to better understand the mechanisms of response to pathogens but also enable targeted breeding strategies for tomato resistance to S. lycopersici.
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Affiliation(s)
- Huanhuan Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China
| | - Fengyi Shen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China
| | - Hexuan Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China
| | - Tingting Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China
| | - He Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China.
| | - Jingfu Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China.
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Gao H, Yang W, Li C, Zhou X, Gao D, Khashi u Rahman M, Li N, Wu F. Gene Expression and K + Uptake of Two Tomato Cultivars in Response to Sub-Optimal Temperature. PLANTS 2020; 9:plants9010065. [PMID: 31947736 PMCID: PMC7020494 DOI: 10.3390/plants9010065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/24/2019] [Accepted: 12/26/2019] [Indexed: 11/16/2022]
Abstract
Sub-optimal temperatures can adversely affect tomato (Solanum lycopersicum) growth, and K+ plays an important role in the cold tolerance of plants. However, gene expression and K+ uptake in tomato in response to sub-optimal temperatures are still not very clear. To address these questions, one cold-tolerant tomato cultivar, Dongnong 722 (T722), and one cold-sensitive cultivar, Dongnong 708 (S708), were exposed to sub-optimal (15/10 °C) and normal temperatures (25/18 °C), and the differences in growth, K+ uptake characteristics and global gene expressions were investigated. The results showed that compared to S708, T722 exhibited lower reduction in plant growth rate, the whole plant K+ amount and K+ net uptake rate, and T722 also had higher peroxidase activity and lower K+ efflux rate under sub-optimal temperature conditions. RNA-seq analysis showed that a total of 1476 and 2188 differentially expressed genes (DEGs) responding to sub-optimal temperature were identified in S708 and T722 roots, respectively. Functional classification revealed that most DEGs were involved in “plant hormone signal transduction”, “phenylpropanoid biosynthesis”, “sulfur metabolism” and “cytochrome P450”. The genes that were significantly up-regulated only in T722 were involved in the “phenylpropanoid biosynthesis” and “plant hormone signal transduction” pathways. Moreover, we also found that sub-optimal temperature inhibited the expression of gene coding for K+ transporter SIHAK5 in both cultivars, but decreased the expression of gene coding for K+ channel AKT1 only in S708. Overall, our results revealed the cold response genes in tomato roots, and provided a foundation for further investigation of mechanism involved in K+ uptake in tomato under sub-optimal temperatures.
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Affiliation(s)
- Huan Gao
- Department of Horticulture, Northeast Agricultural University, Harbin 150030, China; (H.G.); (C.L.); (X.Z.); (D.G.); (M.K.uR.); (N.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Wanji Yang
- Department of Computer and Information Engineering, Heilongjiang University of Science and Technology, Harbin150030, China;
| | - Chunxia Li
- Department of Horticulture, Northeast Agricultural University, Harbin 150030, China; (H.G.); (C.L.); (X.Z.); (D.G.); (M.K.uR.); (N.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xingang Zhou
- Department of Horticulture, Northeast Agricultural University, Harbin 150030, China; (H.G.); (C.L.); (X.Z.); (D.G.); (M.K.uR.); (N.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Danmei Gao
- Department of Horticulture, Northeast Agricultural University, Harbin 150030, China; (H.G.); (C.L.); (X.Z.); (D.G.); (M.K.uR.); (N.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Muhammad Khashi u Rahman
- Department of Horticulture, Northeast Agricultural University, Harbin 150030, China; (H.G.); (C.L.); (X.Z.); (D.G.); (M.K.uR.); (N.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Naihui Li
- Department of Horticulture, Northeast Agricultural University, Harbin 150030, China; (H.G.); (C.L.); (X.Z.); (D.G.); (M.K.uR.); (N.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Fengzhi Wu
- Department of Horticulture, Northeast Agricultural University, Harbin 150030, China; (H.G.); (C.L.); (X.Z.); (D.G.); (M.K.uR.); (N.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: or ; Tel.: +86-0451-5519-0215
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Zhao T, Liu W, Zhao Z, Yang H, Bao Y, Zhang D, Wang Z, Jiang J, Xu Y, Zhang H, Li J, Chen Q, Xu X. Transcriptome profiling reveals the response process of tomato carrying Cf-19 and Cladosporium fulvum interaction. BMC PLANT BIOLOGY 2019; 19:572. [PMID: 31856725 PMCID: PMC6923989 DOI: 10.1186/s12870-019-2150-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 11/19/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND During tomato cultivation, tomato leaf mould is a common disease caused by Cladosporium fulvum (C. fulvum). By encoding Cf proteins, which can recognize corresponding AVR proteins produced by C. fulvum, Cf genes provide resistance to C. fulvum, and the resistance response patterns mediated by different Cf genes are not identical. Plants carrying the Cf-19 gene show effective resistance to C. fulvum in the field and can be used as new resistant materials in breeding. In this study, to identify key regulatory genes related to resistance and to understand the resistance response process in tomato plants carrying Cf-19, RNA sequencing (RNA-seq) was used to analyse the differences between the response of resistant plants (CGN18423, carrying the Cf-19 gene) and susceptible plants (Moneymaker (MM), carrying the Cf-0 gene) at 0, 7 and 20 days after inoculation (dai). RESULTS A total of 418 differentially expressed genes (DEGs) were identified specifically in the CGN18423 response process. Gene Ontology (GO) analysis revealed that GO terms including "plasma membrane (GO_Component)", "histidine decarboxylase activity (GO_Function)", and "carboxylic acid metabolic process (GO_Process)", as well as other 10 GO terms, were significantly enriched. The "plant hormone signal transduction" pathway, which was unique to CGN18423 in the 0-7 dai comparison, was identified. Moreover, ten key regulatory points were screened from the "plant hormone signal transduction" pathway and the "plant pathogen interaction" pathway. Hormone content measurements revealed that the salicylic acid (SA) contents increased and peaked at 7 dai, after which the contents deceased and reached minimum values in both CGN18423 and MM plants at 20 dai. The jasmonic acid (JA) content increased to a very high level at 7 dai but then decreased to nearly the initial level at 20 dai in CGN18423, while it continued to increase slightly during the whole process from 0 to 20 dai in MM. CONCLUSIONS The initial responses are very different between the resistant and susceptible plants. The "plant hormone signal transduction" pathway is important for the formation of Cf-19-mediated immunity. In addition, both JA and SA play roles in regulating the Cf-19-dependent resistance response.
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Affiliation(s)
- Tingting Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Wenhong Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Zhentong Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Huanhuan Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Yufang Bao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Dongye Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Ziyu Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Ying Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - He Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Jingfu Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
| | - Qingshan Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
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Cao Z, Li L, Kapoor K, Banniza S. Using a transcriptome sequencing approach to explore candidate resistance genes against stemphylium blight in the wild lentil species Lens ervoides. BMC PLANT BIOLOGY 2019; 19:399. [PMID: 31510924 PMCID: PMC6740027 DOI: 10.1186/s12870-019-2013-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/30/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Stemphylium blight (SB), caused by Stemphylium botryosum, is a devastating disease in lentil production. Although it is known that accessions of Lens ervoides possess superior SB resistance at much higher frequency than the cultivated lentil species, very little is known about the molecular basis regulating SB resistance in L. ervoides. Therefore, a comprehensive molecular study of SB resistance in L. ervoides was needed to exploit this wild resource available at genebanks for use by plant breeders in resistance breeding. RESULTS Microscopic and qPCR quantification of fungal growth revealed that 48, 96, and 144 h post-inoculation (hpi) were interesting time points for disease development in L. ervoides recombinant inbred lines (RILs) LR-66-637 (resistant to SB) and LR-66-577 (susceptible to SB). Results of transcriptome sequencing at 0, 48, 96 and 144 hpi showed that 8810 genes were disease-responsive genes after challenge by S. botryosum. Among them, 7526 genes displayed a similar expression trend in both RILs, and some of them were likely involved in non-host resistance. The remaining 1284 genes were differentially expressed genes (DEGs) between RILs. Of those, 712 DEGs upregulated in LR-66-637 were mostly enriched in 'carbohydrate metabolic process', 'cell wall organization or biogenesis', and 'polysaccharide metabolic process'. In contrast, there were another 572 DEGs that were upregulated in LR-66-577, and some of them were enriched in 'oxidation-reduction process', 'asparagine metabolic process' and 'asparagine biosynthetic process'. After comparing DEGs to genes identified in previously described quantitative trait loci (QTLs) for resistance to SB, nine genes were common and three of them showed differential gene expression between a resistant and a susceptible bulk consisting of five RILs each. Results showed that two genes encoding calcium-transporting ATPase and glutamate receptor3.2 were candidate resistance genes, whereas one gene with unknown function was a candidate susceptibility gene. CONCLUSION This study provides new insights into the mechanisms of resistance and susceptibility in L. ervoides RILs responding to S. botryosum infection. Furthermore, we identified candidate resistance or susceptibility genes which warrant further gene function analyses, and which could be valuable for resistance breeding, if their role in resistance or susceptibility can be confirmed.
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Affiliation(s)
- Zhe Cao
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Li Li
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Karan Kapoor
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Sabine Banniza
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
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Tang J, Bassham DC. Autophagy in crop plants: what's new beyond Arabidopsis? Open Biol 2018; 8:180162. [PMID: 30518637 PMCID: PMC6303781 DOI: 10.1098/rsob.180162] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/08/2018] [Indexed: 12/19/2022] Open
Abstract
Autophagy is a major degradation and recycling pathway in plants. It functions to maintain cellular homeostasis and is induced by environmental cues and developmental stimuli. Over the past decade, the study of autophagy has expanded from model plants to crop species. Many features of the core machinery and physiological functions of autophagy are conserved among diverse organisms. However, several novel functions and regulators of autophagy have been characterized in individual plant species. In light of its critical role in development and stress responses, a better understanding of autophagy in crop plants may eventually lead to beneficial agricultural applications. Here, we review recent progress on understanding autophagy in crops and discuss potential future research directions.
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Affiliation(s)
- Jie Tang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
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Cui Y, Jiang J, Yang H, Zhao T, Xu X, Li J. Virus-induced gene silencing (VIGS) of the NBS-LRR gene SLNLC1 compromises Sm-mediated disease resistance to Stemphylium lycopersici in tomato. Biochem Biophys Res Commun 2018; 503:1524-1529. [PMID: 30037434 DOI: 10.1016/j.bbrc.2018.07.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 07/16/2018] [Indexed: 01/16/2023]
Abstract
In a previous study, when resistant tomato plants (cv. Motelle) carrying the Sm gene were challenged with S. lycopersici, the SLNLC1 gene was significantly upregulated. In this study, to verify the function of the SLNLC1 gene response to disease resistance against S. lycopersici, virus-induced gene silencing (VIGS) was used to downregulate the expression level of the SLNLC1 gene in resistant tomato plants inoculated with S. lycopersici. After inoculation with S. lycopersici, a susceptible phenotype was observed in the silenced SLNLC1-resistant plants. Through microscopy, impaired hypersensitive response (HR) and decreased ROS accumulation were also observed in the silenced SLNLC1 plants. In addition, the production of lignin and callose were decreased in the silenced SLNLC1 plants. Taken together, these results indicated that silencing the SLNLC1 gene attenuated the resistance of tomato plants resistant to S. lycopersici.
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Affiliation(s)
- Yanan Cui
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Jingbin Jiang
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Huanhuan Yang
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Tingting Zhao
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Xiangyang Xu
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Jingfu Li
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
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