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Liu Y, Xia W, Zhao W, Hao P, Wang Z, Yu X, Shentu X, Sun K. RT-RPA-PfAgo System: A Rapid, Sensitive, and Specific Multiplex Detection Method for Rice-Infecting Viruses. BIOSENSORS 2023; 13:941. [PMID: 37887134 PMCID: PMC10605773 DOI: 10.3390/bios13100941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023]
Abstract
The advancement in CRISPR-Cas biosensors has transmuted the detection of plant viruses owing to their rapid and higher sensitivity. However, false positives and restricted multiplexing capabilities are still the challenges faced by this technology, demanding the exploration of novel methodologies. In this study, a novel detection system was developed by integrating reverse transcriptome (RT) techniques with recombinase polymerase isothermal amplification (RPA) and Pyrococcus furiosus Argonaute (PfAgo). The RT-RPA-PfAgo system enabled the simultaneous detection of rice ragged stunt virus (RRSV), rice grassy stunt virus (RGSV), and rice black streaked dwarf virus (RBSDV). Identifying targets via guide DNA without being hindered by protospacer adjacent motif sequences is the inherent merit of PfAgo, with the additional advantage of it being simple, cost-effective, and exceptionally sensitive, with detection limits between 3.13 and 5.13 copies/µL, in addition to it effectively differentiating between the three distinct viruses. The field evaluations were also in accordance with RT-PCR methods. The RT-RPA-PfAgo system proved to be a robust, versatile, highly specific, and sensitive method with great potential for practicality in future plant virus diagnostics.
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Affiliation(s)
- Yan Liu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Y.L.); (W.Z.); (P.H.); (Z.W.); (X.Y.); (X.S.)
| | - Wenqiang Xia
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Wei Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Y.L.); (W.Z.); (P.H.); (Z.W.); (X.Y.); (X.S.)
| | - Peiying Hao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Y.L.); (W.Z.); (P.H.); (Z.W.); (X.Y.); (X.S.)
| | - Zhengliang Wang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Y.L.); (W.Z.); (P.H.); (Z.W.); (X.Y.); (X.S.)
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Y.L.); (W.Z.); (P.H.); (Z.W.); (X.Y.); (X.S.)
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Y.L.); (W.Z.); (P.H.); (Z.W.); (X.Y.); (X.S.)
| | - Kai Sun
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Y.L.); (W.Z.); (P.H.); (Z.W.); (X.Y.); (X.S.)
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Selection of suitable internal control gene for assaying gene expression in rice through qRT-PCR during sheath blight infection. J Biotechnol 2023; 362:1-11. [PMID: 36513313 DOI: 10.1016/j.jbiotec.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/11/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
qRT-PCR is a globally accepted technique for assaying gene expression in relative terms which compares the difference between critical threshold (CT) values of a gene calculated form two independently isolated RNA samples. Independent RNA isolations, however, include error due to batch effect which must be normalized for error-free calculation of relative gene expression. Hence, CT values of internal control (IC) genes are used for normalization during the calculation of expression fold-change in gene expression analysis. The expression of ICs genes expected to be stable in all the experimental conditions. However, it is almost impossible to find such a gene which do not depict expression fluctuation in response to the changes in experimental conditions. Hence, it is necessary to identify suitable IC gene(s) for any given experimental condition before conducting any particular gene expression study. Here, we examined the suitability of eight candidate IC genes, namely glyceraldehyde 3-phosphate dehydrogenase (GAPDH), eukaryotic elongation factor-1 (eEF-1α), 25 S rRNA (25 S), 18 S rRNA (18 S), ubiquitin C E2 ligase (UBC), Actin (Act), ubiquitin 5 (UBQ5) and ubiquitin 10 (UBQ10), for assaying gene expression in rice during sheath blight infection. Our analysis suggest that GAPDH might be the IC of choice when expression studies include contrasting genotypes differing in their tolerance to sheath blight pathogen as well as progressive infection time. While if expression analysis have to be performed only in one genotype but under progressive sheath blight infection, UBQ5 might be chosen as IC because of its high expression stability under the proposed experimental setup.
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Hou S, Zhao T, Yang D, Li Q, Liang L, Wang G, Ma Q. Selection and Validation of Reference Genes for Quantitative RT-PCR Analysis in Corylus heterophylla Fisch. × Corylus avellana L. PLANTS 2021; 10:plants10010159. [PMID: 33467497 PMCID: PMC7830083 DOI: 10.3390/plants10010159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 11/16/2022]
Abstract
(1) Background: the species of Corylus have sporophytic type of self-incompatibility. Several genes related to recognition reaction between pollen and stigma have been identified in hazelnuts. To better understand the self-incompatibility (SI) response, we screened the suitable reference genes by using quantitative real-time reverse transcription PCR (qRT-PCR) analysis in hazelnut for the first time. (2) Methods: the major cultivar "Dawei" was used as material. A total of 12 candidate genes were identified and their expression profiles were compared among different tissues and in response to various treatments (different times after self- and cross-pollination) by RT-qPCR. The expression stability of these 12 candidate reference genes was evaluated using geNorm, NormFinder, BestKeeper, Delta Ct, and RefFinder programs. (3) Results: the comprehensive ranking of RefFinder indicated that ChaActin, VvActin,
ChaUBQ14, and ChaEF1-α were the most suitable reference genes. According to the stability analysis of 12 candidate reference genes for each sample group based on four software packages, ChaActin and ChaEF1-α were most stable in different times after self-pollination and 4 h after self- and cross-pollination, respectively. To further validate the suitability of the reference genes identified in this study, CavPrx, which the expression profiles in Corylus have been reported, was quantified by using ChaActin and ChaEF1-α as reference genes. (4) Conclusions: our study of reference genes selection in hazelnut shows that the two reference genes, ChaActin and ChaEF1-α, are suitable for the evaluation of gene expression, and can be used for the analysis of pollen-pistil interaction in Corylus. The results supply a reliable foundation for accurate gene quantifications in Corylus species, which will facilitate the studies related to the reproductive biology in Corylus.
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Affiliation(s)
- Sihao Hou
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Tiantian Zhao
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Dan Yang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Qing Li
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Guixi Wang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
- Correspondence: ; Tel.: +86-1381-139-0689
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Yin Z, Xie F, Michalak K, Zhang B, Zimnoch-Guzowska E. Reference gene selection for miRNA and mRNA normalization in potato in response to potato virus Y. Mol Cell Probes 2020; 55:101691. [PMID: 33358935 DOI: 10.1016/j.mcp.2020.101691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/03/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]
Abstract
This was the first report on evaluating candidate reference genes for quantifying the expression profiles of both coding (e.g., mRNA) and non-coding (e.g., miRNA) genes in potato response to potato virus Y (PVY) inoculation. The reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) method was employed to quantify the expression profiles of eight selected candidate reference genes; their expression stability was analyzed by four statistical algorithms, i.e., geNorm, BestKeeper, NormFinder and RefFinder. The most stable reference genes were sEF1a, sTUBb and seIF5 with a high stability. The least stable ones were sPP2A, sSUI1 and sGAPDH. The same reference gene allows for normalization of both miRNA and mRNA levels from a single RNA sample using cDNAs synthesized in a single RT reaction, in which a stem-loop primer was used for miRNAs and the oligo (dT) for mRNAs.
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Affiliation(s)
- Zhimin Yin
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów Research Center, Platanowa 19, Młochów, PL-05-831, Poland.
| | - Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Krystyna Michalak
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów Research Center, Platanowa 19, Młochów, PL-05-831, Poland
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Ewa Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów Research Center, Platanowa 19, Młochów, PL-05-831, Poland
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Zhang T, Liang Q, Li C, Fu S, Kundu JK, Zhou X, Wu J. Transcriptome Analysis of Rice Reveals the lncRNA-mRNA Regulatory Network in Response to Rice Black-Streaked Dwarf Virus Infection. Viruses 2020; 12:v12090951. [PMID: 32867233 PMCID: PMC7552052 DOI: 10.3390/v12090951] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 01/05/2023] Open
Abstract
The plant genome can produce long non-coding RNAs (lncRNAs), some of which have been identified as important regulators of gene expression. To better understand the response mechanism of rice plants to Rice black-streaked dwarf virus (RBSDV) infection, we performed a comparative transcriptome analysis between the RBSDV-infected and non-infected rice plants. A total of 1342 mRNAs and 22 lncRNAs were identified to be differentially expressed after RBSDV infection. Most differentially expressed transcripts involved in the plant–pathogen interaction pathway were upregulated after RBSDV infection, indicating the activation of rice defense response by RBSDV. A network of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) was then constructed. In this network, there are 56 plant–pathogen interaction-related DEmRNAs co-expressing with 20 DElncRNAs, suggesting these DElncRNAs and DEmRNAs may play essential roles in rice innate immunity against RBSDV. Moreover, some of the lncRNA–mRNA regulatory relationships were experimentally verified in rice calli by a quick and effective method established in this study. Three DElncRNAs were selected to be tested, and the results indicated that five mRNAs were found to be regulated by them. Together, we give a whole landscape of rice mRNAs and lncRNAs in response to RBSDV infection, and a feasible method to rapidly verify the lncRNA–mRNA regulatory relationship in rice.
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Affiliation(s)
- Tianze Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | - Qian Liang
- Key Laboratory of microorganism technology and bioinformatics research of Zhejiang Province, NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang TianKe High-Technology Development Co. Ltd., Hangzhou 310023, China;
| | - Chenyang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | | | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
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Martins TF, Souza PFN, Alves MS, Silva FDA, Arantes MR, Vasconcelos IM, Oliveira JTA. Identification, characterization, and expression analysis of cowpea (Vigna unguiculata [L.] Walp.) miRNAs in response to cowpea severe mosaic virus (CPSMV) challenge. PLANT CELL REPORTS 2020; 39:1061-1078. [PMID: 32388590 DOI: 10.1007/s00299-020-02548-6] [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: 02/14/2020] [Revised: 04/04/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Cowpea miRNAs and Argonaute genes showed differential expression patterns in response to CPSMV challenge Several biotic stresses affect cowpea production and yield. CPSMV stands out for causing severe negative impacts on cowpea. Plants have two main induced immune systems. In the basal system (PTI, PAMP-triggered immunity), plants recognize and respond to conserved molecular patterns associated with pathogens (PAMPs). The second type (ETI, Effector-triggered immunity) is induced after plant recognition of specific factors from pathogens. RNA silencing is another important defense mechanism in plants. Our research group has been using biochemical and proteomic approaches to learn which proteins and pathways are involved and could explain why some cowpea genotypes are resistant whereas others are susceptible to CPSMV. This current study was conducted to determine the role of cowpea miRNA in the interaction between a resistant cowpea genotype (BRS-Marataoã) and CPSMV. Previously identified and deposited plant microRNA sequences were used to find out all possible microRNAs in the cowpea genome. This search detected 617 mature microRNAs, which were distributed in 89 microRNA families. Next, 4 out of these 617 miRNAs and their possible target genes that encode the proteins Kat-p80, DEAD-Box, GST, and SPB9, all involved in the defense response of cowpea to CPSMV, had their expression compared between cowpea leaves uninoculated and inoculated with CPSMV. Additionally, the differential expression of genes that encode the Argonaute (AGO) proteins 1, 2, 4, 6, and 10 is reported. In summary, the studied miRNAs and AGO 2 and AGO4 associated genes showed differential expression patterns in response to CPSMV challenge, which indicate their role in cowpea defense.
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Affiliation(s)
- Thiago F Martins
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Pedro F N Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Murilo S Alves
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Fredy Davi A Silva
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Mariana R Arantes
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Ilka M Vasconcelos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Jose T A Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil.
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Tan L, Qu M, Zhu Y, Peng C, Wang J, Gao D, Chen C. ZINC TRANSPORTER5 and ZINC TRANSPORTER9 Function Synergistically in Zinc/Cadmium Uptake. PLANT PHYSIOLOGY 2020; 183:1235-1249. [PMID: 32341004 PMCID: PMC7333683 DOI: 10.1104/pp.19.01569] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/15/2020] [Indexed: 05/24/2023]
Abstract
The elements Zinc (Zn) and cadmium (Cd) have similar chemical and physical properties, but contrasting physiological effects in higher organisms. In plants, Zn/Cd transport is mediated by various transporter proteins belonging to different families. In this study, we functionally characterized two Zn transporter genes in rice (Oryza sativa), ZINC TRANSPORTER5 (OsZIP5) and ZINC TRANSPORTER9 (OsZIP9), which are tandem duplicates and act synergistically in Zn/Cd uptake. Both genes encode plasma membrane-localized proteins with influx transporter activity. The expression profiles of OsZIP5 and OsZIP9 overlap in the root epidermis and respond to the local Zn status in the root. However, OsZIP9 is also regulated by systemic signals of Zn status from the shoot. OsZIP5 functions redundantly to OsZIP9, but has a relatively weaker effect. Plants with the knockout mutations oszip5, oszip9, or oszip5oszip9 show impaired Zn/Cd uptake. The decreased Zn/Cd levels and growth retardation in the oszip5 mutant are less severe than in the oszip9 mutant. However, the double mutant oszip5oszip9 showed an enhanced Zn deficiency phenotype compared with the single mutants, and few double-knockout plants were able to survive the entire growth cycle without excessive Zn supply. Transgenic plants overexpressing OsZIP9 had markedly enhanced Zn/Cd levels in the aboveground tissues and brown rice. The results of our study fill a gap in current knowledge of Zn uptake and improve our understanding of Zn/Cd accumulation in rice.
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Affiliation(s)
- Longtao Tan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410205, China
| | - Mengmeng Qu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410205, China
| | - Yuxing Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410205, China
| | - Can Peng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410205, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410205, China
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410205, China
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Lu R, Liu Z, Shao Y, Su J, Li X, Sun F, Zhang Y, Li S, Zhang Y, Cui J, Zhou Y, Shen W, Zhou T. Nitric Oxide Enhances Rice Resistance to Rice Black-Streaked Dwarf Virus Infection. RICE (NEW YORK, N.Y.) 2020; 13:24. [PMID: 32291541 PMCID: PMC7156532 DOI: 10.1186/s12284-020-00382-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/12/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Rice black-streaked dwarf virus (RBSDV) causes one of the most important rice virus diseases of plants in East Asia. However, molecular mechanism(s)controlling rice resistance to infection is largely unknown. RESULTS In this paper, we showed that RBSDV infection in rice significantly induced nitric oxide (NO) production. This finding was further validated through a genetic approach using a RBSDV susceptible (Nipponbare) and a RBSDV resistant (15HPO187) cultivar. The production of endogenous NO was muchhigher in the 15HPO187 plants, leading to a much lower RBSDV disease incidence. Pharmacological studies showed that the applications of NO-releasingcompounds (i.e., sodium nitroprusside [SNP] and nitrosoglutathione [GSNO]) to rice plants reduced RBSDV disease incidence. After RBSDV infection, the levels of OsICS1, OsPR1b and OsWRKY 45 transcripts were significantly up-regulated by NO in Nipponbare. The increased salicylic acid contents were also observed. After the SNP treatment, protein S-nitrosylation in rice plants was also increased, suggesting that the NO-triggered resistance to RBSDV infection was partially mediated at the post-translational level. Although Osnia2 mutant rice produced less endogenous NO after RBSDV inoculation and showed a higher RBSDV disease incidence, its RBSDV susceptibility could be reduced by SNP treatment. CONCLUSIONS Collectively, our genetic and molecular evidence revealed that endogenous NO was a vital signal responsible for rice resistance to RBSDV infection.
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Affiliation(s)
- Rongfei Lu
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiyang Liu
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yudong Shao
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiuchang Su
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuejuan Li
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Feng Sun
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yihua Zhang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuo Li
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yali Zhang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu Province, China
| | - Jin Cui
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yijun Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Tong Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China.
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Lu R, Liu Z, Shao Y, Sun F, Zhang Y, Cui J, Zhou Y, Shen W, Zhou T. Melatonin is responsible for rice resistance to rice stripe virus infection through a nitric oxide-dependent pathway. Virol J 2019; 16:141. [PMID: 31752902 PMCID: PMC6869260 DOI: 10.1186/s12985-019-1228-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022] Open
Abstract
Rice stripe virus (RSV) causes one of the most important rice virus diseases of plants in East Asia. However, the molecular mechanisms controlling rice resistance to RSV infection are largely unknown. Recently, several studies presented a novel model that melatonin (MT) and nitric oxide (NO) participate in the plant-pathogen interaction in a synergetic manner. In this study, there was a difference in MT content between two rice varieties that correlated with one being susceptible and one being resistant to RSV, which suggested that MT is related to RSV resistance. In addition, a test with two NO biosynthesis inhibitors revealed that NO inhibitor were able to increase the disease incidence of RSV. A pharmacological experiment with exogenous MT and NO showed that increased MT and NO in the MT-pretreated plants led to lower disease incidences; however, only NO increased in a NO-releasing reagent [sodium nitroprusside (SNP)] pretreated plants. The expressions level of OsPR1b and OsWRKY 45 were significantly induced by MT and NO. These results suggest that rice resistance to RSV can be improved by increased MT through a NO-dependent pathway.
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Affiliation(s)
- Rongfei Lu
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.,Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Zhiyang Liu
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yudong Shao
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.,Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Feng Sun
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yali Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jin Cui
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yijun Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Tong Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu Province, China. .,School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu Province, China. .,International Rice Research Institute and Jiangsu Academy of Agricultural Sciences Joint Laboratory, Nanjing, 210095, China.
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10
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Okuda M, Shiba T, Hirae M, Masunaka A, Takeshita M. Analysis of Symptom Development in Relation to Quantity of Rice stripe virus in Rice (Oryza sativa) to Simplify Evaluation of Resistance. PHYTOPATHOLOGY 2019; 109:701-707. [PMID: 30328779 DOI: 10.1094/phyto-07-18-0277-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rice stripe virus (RSV) is one of the most devastating pathogens of rice (Oryza sativa) in rice-growing regions of East Asia. We analyzed the increase in RSV accumulation in infected rice plants over time and evaluated the association between disease severity and RSV accumulation with the aim of establishing an experimental system for accurate and efficient evaluation of RSV resistance in rice. As an index of RSV accumulation in plants, relative concentration of RNA corresponding to the coat protein gene region was measured using reverse-transcription quantitative polymerase chain reaction. Actin and elongation factor 1a were used as the host reference genes. RSV concentrations tended to increase with time from 7 to 28 days after inoculation, and a strong positive correlation was observed between the log RSV concentrations in the midsections of the uppermost leaves and in the stems at the first leaf sheath position. We analyzed RSV concentrations at these two locations 21 days after inoculation with RSV and assessed severity of disease symptoms based on a commonly used scale (Washio's six-grade scale) rated as A (most severe), B, Bt, C, Cr, or D (mild symptoms). RSV concentrations at both locations were high in plants graded A, B, or Bt, with no significant difference in concentration of RSV among the three grades, but concentrations were significantly higher in the three grades compared with that in the plants in grade D. RSV concentrations were highly variable among plants in grades C and Cr. On the basis of these data, we propose a new formula to estimate the range of disease severities with greater ease and practical value. The values calculated by the new formula corresponded well to those based on Washio's six-grade scale.
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Affiliation(s)
- Mitsuru Okuda
- 1 Central Region Agricultural Research Center, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Takuya Shiba
- 1 Central Region Agricultural Research Center, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Masahiro Hirae
- 1 Central Region Agricultural Research Center, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Akira Masunaka
- 2 Western Region Agricultural Research Center, NARO, 6-12-1 Nishifukatsu-cho, Fukuyama-shi, Hiroshima 721-8514, Japan; and
| | - Minoru Takeshita
- 3 Faculty of Agriculture, University of Miyazaki, Gakuen-kibanadai-nishi-1-1, Miyazaki, 889-2192, Japan
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11
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Pombo MA, Ramos RN, Zheng Y, Fei Z, Martin GB, Rosli HG. Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana. Sci Rep 2019; 9:1632. [PMID: 30733563 PMCID: PMC6367355 DOI: 10.1038/s41598-018-38247-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
RT-qPCR is a widely used technique for the analysis of gene expression. Accurate estimation of transcript abundance relies strongly on a normalization that requires the use of reference genes that are stably expressed in the conditions analyzed. Initially, they were adopted from those used in Northern blot experiments, but an increasing number of publications highlight the need to find and validate alternative reference genes for the particular system under study. The development of high-throughput sequencing techniques has facilitated the identification of such stably expressed genes. Nicotiana benthamiana has been extensively used as a model in the plant research field. In spite of this, there is scarce information regarding suitable RT-qPCR reference genes for this species. Employing RNA-seq data previously generated from tomato plants, combined with newly generated data from N. benthamiana leaves infiltrated with Pseudomonas fluorescens, we identified and tested a set of 9 candidate reference genes. Using three different algorithms, we found that NbUbe35, NbNQO and NbErpA exhibit less variable gene expression in our pathosystem than previously used genes. Furthermore, the combined use of the first two is sufficient for robust gene expression analysis. We encourage employing these novel reference genes in future RT-qPCR experiments involving N. benthamiana and Pseudomonas spp.
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Affiliation(s)
- Marina A Pombo
- Instituto de Fisiología Vegetal, INFIVE, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina
| | - Romina N Ramos
- Instituto de Fisiología Vegetal, INFIVE, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, 14853, USA
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Hernan G Rosli
- Instituto de Fisiología Vegetal, INFIVE, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina.
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12
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Zhao C, Sun F, Li X, Lan Y, Du L, Zhou T, Zhou Y. Reverse transcription-recombinase polymerase amplification combined with lateral flow strip for detection of rice black-streaked dwarf virus in plants. J Virol Methods 2018; 263:96-100. [PMID: 30395887 DOI: 10.1016/j.jviromet.2018.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 10/27/2022]
Abstract
Rice black-streaked dwarf virus (RBSDV) infects rice plants, a major crop, and is transmitted via the small brown planthopper (SBPH: Laodelphax striatellus Fallén), causing significant economic loss in China. To rapidly diagnose RBSDV, a reverse transcription-recombinase polymerase amplification (RT-RPA) method was developed using P10 virus-specific primers and probes. Detection of terminally labeled amplification products was achieved with the lateral flow strip method. Our results demonstrate that RT-RPA and RT-PCR assays offer similar sensitivity and specificity in RBSDV detection using cDNA as template. The optimum RT-RPA reaction temperature and time was 37 °C and 20 min, respectively. By screening twenty-one field suspected rice plants, the RT-RPA assay was confirmed to be simple, rapid and reliable. Thus, the RBSDV RT-RPA assay developed here will be a successful tool for quick diagnosis of RBSDV-infected rice plants.
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Affiliation(s)
- Chong Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Food Safety Evaluation, MOA, Nanjing, 210014, China
| | - Feng Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Food Safety Evaluation, MOA, Nanjing, 210014, China
| | - Xuejuan Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Food Safety Evaluation, MOA, Nanjing, 210014, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Food Safety Evaluation, MOA, Nanjing, 210014, China
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Food Safety Evaluation, MOA, Nanjing, 210014, China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Food Safety Evaluation, MOA, Nanjing, 210014, China
| | - Yijun Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Food Safety Evaluation, MOA, Nanjing, 210014, China.
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13
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Huang R, Li Y, Tang G, Hui S, Yang Z, Zhao J, Liu H, Cao J, Yuan M. Dynamic phytohormone profiling of rice upon rice black-streaked dwarf virus invasion. JOURNAL OF PLANT PHYSIOLOGY 2018; 228:92-100. [PMID: 29886196 DOI: 10.1016/j.jplph.2018.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
Rice black-streaked dwarf virus (RBSDV) is the causal agent of rice black-streaked dwarf disease, a serious constraint to rice production. A great deal of effort has been made to elucidate the transcriptome and proteome changes of rice upon virus inoculation. However, the relationship between RBSDV invasion and rice endogenous phytohormone profiling is largely unclear. Here, we surveyed the dynamic content profiling of endogenous phytohormones, which were severely disturbed by RBSDV invasion. The levels of abscisic acid (ABA) and cytokinins (CTKs) increased, while indole-3-acetic acid (IAA), gibberellins (GAs), jasmonic acid (JA), and salicylic acid (SA) decreased, accompanied by changes in the transcripts of genes participating in phytohormone metabolism and signalling pathways. Moreover, exogenously supplied GA3 could rescue the typical dwarfing symptom, and pre-application of SA largely decreased the occurrence of RBSDV disease in rice. The results partially suggest that RBSDV successfully invaded host rice by modulating the expression patterns of phytohormone metabolism to upset the balance of plant endogenous phytohormones.
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Affiliation(s)
- Renyan Huang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yueyue Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Guilin Tang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shugang Hui
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zeyu Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Junwei Zhao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbo Cao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Nguyen DQ, Eamens AL, Grof CPL. Reference gene identification for reliable normalisation of quantitative RT-PCR data in Setaria viridis. PLANT METHODS 2018; 14:24. [PMID: 29581727 PMCID: PMC5861610 DOI: 10.1186/s13007-018-0293-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/15/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Quantitative real-time polymerase chain reaction (RT-qPCR) is the key platform for the quantitative analysis of gene expression in a wide range of experimental systems and conditions. However, the accuracy and reproducibility of gene expression quantification via RT-qPCR is entirely dependent on the identification of reliable reference genes for data normalisation. Green foxtail (Setaria viridis) has recently been proposed as a potential experimental model for the study of C4 photosynthesis and is closely related to many economically important crop species of the Panicoideae subfamily of grasses, including Zea mays (maize), Sorghum bicolor (sorghum) and Sacchurum officinarum (sugarcane). Setaria viridis (Accession 10) possesses a number of key traits as an experimental model, namely; (i) a small sized, sequenced and well annotated genome; (ii) short stature and generation time; (iii) prolific seed production, and; (iv) is amendable to Agrobacterium tumefaciens-mediated transformation. There is currently however, a lack of reference gene expression information for Setaria viridis (S. viridis). We therefore aimed to identify a cohort of suitable S. viridis reference genes for accurate and reliable normalisation of S. viridis RT-qPCR expression data. RESULTS Eleven putative candidate reference genes were identified and examined across thirteen different S. viridis tissues. Of these, the geNorm and NormFinder analysis software identified SERINE/THERONINE-PROTEIN PHOSPHATASE 2A (PP2A), 5'-ADENYLYLSULFATE REDUCTASE 6 (ASPR6) and DUAL SPECIFICITY PHOSPHATASE (DUSP) as the most suitable combination of reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. To demonstrate the suitability of the three selected reference genes, PP2A, ASPR6 and DUSP, were used to normalise the expression of CINNAMYL ALCOHOL DEHYDROGENASE (CAD) genes across the same tissues. CONCLUSIONS This approach readily demonstrated the suitably of the three selected reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. Further, the work reported here forms a highly useful platform for future gene expression quantification in S. viridis and can also be potentially directly translatable to other closely related and agronomically important C4 crop species.
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Affiliation(s)
- Duc Quan Nguyen
- Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
| | - Andrew L. Eamens
- Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
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15
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Baek E, Yoon JY, Palukaitis P. Validation of reference genes for quantifying changes in gene expression in virus-infected tobacco. Virology 2017; 510:29-39. [PMID: 28689086 DOI: 10.1016/j.virol.2017.06.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/23/2017] [Accepted: 06/24/2017] [Indexed: 11/25/2022]
Abstract
To facilitate quantification of gene expression changes in virus-infected tobacco plants, eight housekeeping genes were evaluated for their stability of expression during infection by one of three systemically-infecting viruses (cucumber mosaic virus, potato virus X, potato virus Y) or a hypersensitive-response-inducing virus (tobacco mosaic virus; TMV) limited to the inoculated leaf. Five reference-gene validation programs were used to establish the order of the most stable genes for the systemically-infecting viruses as ribosomal protein L25 > β-Tubulin > Actin, and the least stable genes Ubiquitin-conjugating enzyme (UCE) < PP2A < GAPDH. For local infection by TMV, the most stable genes were EF1α > Cysteine protease > Actin, and the least stable genes were GAPDH < PP2A < UCE. Using two of the most stable and the two least stable validated reference genes, three defense responsive genes were examined to compare their relative changes in gene expression caused by each virus.
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Affiliation(s)
- Eseul Baek
- Dept. of Horticultural Sciences, Seoul Women's University, Seoul 01797, Republic of Korea
| | - Ju-Yeon Yoon
- Dept. of Horticultural Sciences, Seoul Women's University, Seoul 01797, Republic of Korea; National Institute of Horticultural & Herbal Science, RDA, Wanju 55365, Republic of Korea
| | - Peter Palukaitis
- Dept. of Horticultural Sciences, Seoul Women's University, Seoul 01797, Republic of Korea.
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Ren H, Wu X, Lyu Y, Zhou H, Xie X, Zhang X, Yang H. Selection of reliable reference genes for gene expression studies in Botrytis cinerea. J Microbiol Methods 2017; 142:71-75. [PMID: 28917607 DOI: 10.1016/j.mimet.2017.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/30/2017] [Accepted: 09/10/2017] [Indexed: 01/06/2023]
Abstract
Botrytis cinerea is an important plant pathogen causing grey mold disease in a wide range of plant species. The aim of this study was to identify reliable reference genes that can be used for the analysis of relative gene expression in B. cinerea with quantitative real-time reverse transcription PCR (qRT-PCR). Six commonly used housekeeping genes including actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ubiquitin (UBQ), ubiquitin-conjugating enzyme (UCE), α-tubulin (α-TUB) and β-tubulin (β-TUB) were selected to test their expression stabilities in B. cinerea treated with different concentration of oxalic acid (1, 5 and 10mM) and confronted with antagonistic Trichoderma afroharzianum. Four in silico algorithms (geNorm, BestKeeper, NormFinder and Comparative ΔCt) were applied to evaluate the expression stabilities of these genes, and the UBQ gene was identified as the most stably expressed. It was used to normalize the expression levels of three genes related to oxalic acid production (NADPH, VEL1 and OAH) when B. cinerea was challenged by T. afroharzianum. The results of this study are useful for gene expression analysis in B. cinerea.
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Affiliation(s)
- He Ren
- College of Life Science, Shandong University of Technology, Zibo 255000, Shandong Province, People's Republic of China; Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Xiaoqing Wu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Yuping Lyu
- College of Life Science, Shandong University of Technology, Zibo 255000, Shandong Province, People's Republic of China; Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Hongzi Zhou
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Xueying Xie
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Xinjian Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China.
| | - Hetong Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
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Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-Pseudomonas pathosystem. Sci Rep 2017; 7:44905. [PMID: 28317896 PMCID: PMC5357963 DOI: 10.1038/srep44905] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/14/2017] [Indexed: 12/26/2022] Open
Abstract
The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in different systems suggest that many of these genes are not stably expressed. The development of high throughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identification of transcriptionally stable genes that can be adopted as novel and robust reference genes. Here we take advantage of a large set of RNA-seq data originating from tomato leaves infiltrated with different immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Specifically, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT-qPCR experiments involving this pathosystem.
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