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Kumar V, Majee A, Patwal P, Sairem B, Sane AP, Sane VA. A GARP transcription factor SlGCC positively regulates lateral root development in tomato via auxin-ethylene interplay. PLANTA 2024; 259:55. [PMID: 38300324 DOI: 10.1007/s00425-023-04325-7] [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: 05/02/2023] [Accepted: 12/27/2023] [Indexed: 02/02/2024]
Abstract
MAIN CONCLUSION SlGCC, a GARP transcription factor, functions as a root-related transcriptional repressor. SlGCC synchronizes auxin and ethylene signaling involving SlPIN3 and SlIAA3 as intermediate targets sketching a molecular map for lateral root development in tomato. The root system is crucial for growth and development of plants as it performs basic functions such as providing mechanical support, nutrients and water uptake, pathogen resistance and responds to various stresses. SlGCC, a GARP family transcription factor (TF), exhibited predominant expression in age-dependent (initial to mature stages) tomato root. SlGCC is a transcriptional repressor and is regulated at a transcriptional and translational level by auxin and ethylene. Auxin and ethylene mediated SlGCC protein stability is governed via proteasome degradation pathway during lateral root (LR) growth development. SlGCC over-expressor (OE) and under-expressed (UE) tomato transgenic lines demonstrate its role in LR development. This study is an attempt to unravel the vital role of SlGCC in regulating tomato LR architecture.
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Affiliation(s)
- Vinod Kumar
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | - Adity Majee
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pooja Patwal
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Babythoihoi Sairem
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aniruddha P Sane
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vidhu A Sane
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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2
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Silva LCC, Mayrink DB, Bueno RD, Piovesan ND, Ribeiro C, Dal-Bianco M. Reference Genes and Expression Analysis of Seed Desaturases Genes in Soybean Mutant Accessions. Biochem Genet 2022; 60:937-952. [PMID: 34554351 DOI: 10.1007/s10528-021-10135-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
Soybean oil is the second most-produced vegetable oil worldwide. To enhance the nutritional quality and oxidative stability of soybean oil, many soybean breeding programs are trying to increase oleic acid content and reduce linoleic and linolenic acid contents. The fatty acid profile of soybean oil is controlled by many genes, including those which code for omega-3 and omega-6 desaturases. Mutations in GmFAD2-1 and GmFAD3 genes are widely studied and their combinations can produce soybean oil with high oleic and low linoleic and linolenic content. However, few studies evaluate the effect of these mutations on gene expression. Therefore, the present study sought to identify reference genes, evaluate the expression of GmFAD2-1 and GmFAD3 seed desaturase genes in thirteen wild-type and mutated soybean accessions, and associate the expression patterns with fatty acid composition and with the GmFAD2-1 and GmFAD3 genotypes. GmCONS7 and GmUKN2 were identified as the best reference genes for combined use to normalize data. The GmFAD2-1A mutation of PI603452 accession was associated with a decrease in gene expression of GmFAD2-1A; however, downregulation may not be due to the truncated enzyme structure alone. These results suggested that there are factors other than GmFAD2-1A and GmFAD2-1B that have a considerable effect on oleic content, at least in soybeans with mutations in these two genes.
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Affiliation(s)
- Luiz Cláudio Costa Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, BA, 44036-900, Brazil.
| | | | - Rafael Delmond Bueno
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Newton Deniz Piovesan
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maximiller Dal-Bianco
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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3
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Chinese Cherry (Cerasus pseudocerasus Lindl.) ARF7 Participates in Root Development and Responds to Drought and Low Phosphorus. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020158] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this paper, an auxin-responsive transcription factor, CpARF7, was isolated from the roots of Chinese cherry (Cerasus pseudocerasus Lindl. Cv. “Manao Hong”). CpARF7 is highly homologous to AtARF7 or AtARF19 in Arabidopsis, and PavARF1 or PavARF14 in sweet cherry. However, in the phenotype of transgenic tomatoes, the root morphology changed, the main root elongated, and the lateral root increased. Both drought treatment and low-phosphorus conditions can elongate the roots of transgenic tomatoes. In addition, the drought resistance and low-phosphorus tolerance of the transgenic lines are improved, and the POD, SOD, and CAT activities under drought and low-phosphorus environments are increased. There is an effect on the tomato somatotropin suppressor gene, SlIAAs, in which SlIAA1/14/19/29 are up-regulated and SlIAA2/11/12/16 are down-regulated. These results indicate that CpARF7 plays an essential regulatory role in root formation and abiotic stress response, and deepens the understanding of auxin-responsive genes in root growth and abiotic stress.
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4
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Albuquerque GMR, Fonseca FCA, Boiteux LS, Borges RCF, Miller RNG, Lopes CA, Souza EB, Fonseca MEN. Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato 'Hawaii 7996' interactions. Sci Rep 2021; 11:18719. [PMID: 34548514 PMCID: PMC8455670 DOI: 10.1038/s41598-021-97854-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/31/2021] [Indexed: 11/26/2022] Open
Abstract
Reverse transcription-quantitative PCR (RT-qPCR) is an analytical tool for gene expression quantification. Reference genes are not yet available for gene expression analysis during interactions of Ralstonia solanacearum with ‘Hawaii 7996’ (the most stable source of resistance in tomato). Here, we carried out a multi-algorithm stability analysis of eight candidate reference genes during interactions of ‘Hawaii 7996’ with one incompatible/avirulent and two compatible/virulent (= resistance-breaking) bacterial isolates. Samples were taken at 24- and 96-h post-inoculation (HPI). Analyses were performed using the ∆∆Ct method and expression stability was estimated using BestKeeper, NormFinder, and geNorm algorithms. TIP41 and EF1α (with geNorm), TIP41 and ACT (with NormFinder), and UBI3 and TIP41 (with BestKeeper), were the best combinations for mRNA normalization in incompatible interactions at 24 HPI and 96 HPI. The most stable genes in global compatible and incompatible interactions at 24 HPI and 96 HPI were PDS and TIP41 (with geNorm), TIP41 and ACT (with NormFinder), and UBI3 and PDS/EXP (with BestKeeper). Global analyses on the basis of the three algorithms across 20 R. solanacearum-tomato experimental conditions identified UBI3, TIP41 and ACT as the best choices as reference tomato genes in this important pathosystem.
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Affiliation(s)
- Greecy M R Albuquerque
- Department of Agronomy, Universidade Federal Rural de Pernambuco (UFRPE), Recife, PE, Brazil.
| | - Fernando C A Fonseca
- Departament of Academic Areas, Instituto Federal de Goiás (IFG), Águas Lindas,, GO, Brazil
| | - Leonardo S Boiteux
- National Center for Vegetable Crops Research, Embrapa Vegetables (CNPH), Brasília, DF, Brazil
| | - Rafaela C F Borges
- Plant Pathology Department, ICB, Universidade de Brasília (UnB), Brasília, DF, Brazil
| | - Robert N G Miller
- Plant Pathology Department, ICB, Universidade de Brasília (UnB), Brasília, DF, Brazil.,Department of Cell Biology, ICB, Universidade de Brasília (UnB), Brasília, DF, Brazil
| | - Carlos A Lopes
- National Center for Vegetable Crops Research, Embrapa Vegetables (CNPH), Brasília, DF, Brazil
| | - Elineide B Souza
- Department of Biology, Universidade Federal Rural de Pernambuco (UFRPE), Recife, PE, Brazil
| | - Maria Esther N Fonseca
- National Center for Vegetable Crops Research, Embrapa Vegetables (CNPH), Brasília, DF, Brazil
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5
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Wrzesińska B, Zmienko A, Vu LD, De Smet I, Obrępalska-Stęplowska A. Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach. PLANT CELL REPORTS 2021; 40:1247-1267. [PMID: 34028582 PMCID: PMC8233301 DOI: 10.1007/s00299-021-02706-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE PSV infection changed the abundance of host plant's transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and cytosol, affecting photosynthesis, translation, transcription, and splicing. Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)-Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The 'omic' results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)-seq data were obtained to provide new insights into PSV-P-satRNA-plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.
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Affiliation(s)
- Barbara Wrzesińska
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection, National Research Institute, 20 Władysława Węgorka Street, 60-318, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704, Poznan, Poland
- Faculty of Computing Science, Institute of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965, Poznan, Poland
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Aleksandra Obrępalska-Stęplowska
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection, National Research Institute, 20 Władysława Węgorka Street, 60-318, Poznan, Poland.
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6
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Doddaraju P, Kumar P, Dashyal MS, Girigowda M. Identification of suitable reference genes for expression studies in pomegranate under different biotic and abiotic stress conditions. Mol Biol Rep 2021; 48:3935-3943. [PMID: 34028653 DOI: 10.1007/s11033-021-06389-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/29/2021] [Indexed: 10/21/2022]
Abstract
Pomegranate (Punica granatum L.) is an important economic fruit crop, facing many biotic and abiotic challenges during cultivation. Several research programs are in progress to understand both biotic and abiotic stress factors and mitigate these challenges using gene expression studies based on the qPCR approach. However, research publications are not available yet to select the standard reference gene for normalizing target gene expression values in pomegranate. The most suitable candidate reference gene is required to ensure precise and reliable results for qPCR analysis. Eight candidate reference genes' stability was evaluated under different stress conditions using different algorithms such as ∆Ct, geNorm, BestKeeper, NormFinder, and RefFinder. The various algorithms revealed that EFA1 and 18S rRNA were common and most stable reference genes (RGs) under abiotic and wilt stress. Whereas comprehensive ranking by RefFinder showed GAPDH and CYPF were the most stable RGs under combined biotic (pooled samples of all biotic stress) and bacterial blight samples. For normalizing target gene expression under wilt, nematode, bacterial blight, and abiotic stress conditions both GAPDH and CYPFreference genes are adequate for qPCR. The above data provide comprehensive details for the selection of a candidate reference gene in various stresses in pomegranate.
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Affiliation(s)
- Pushpa Doddaraju
- Bio-Control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Pavan Kumar
- Bio-Control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Mahesh S Dashyal
- Bio-Control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Manjunath Girigowda
- Bio-Control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India.
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7
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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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8
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Evaluation of the expression stability of reference genes in Apis mellifera under pyrethroid treatment. Sci Rep 2020; 10:16140. [PMID: 32999330 PMCID: PMC7527991 DOI: 10.1038/s41598-020-73125-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/04/2020] [Indexed: 11/08/2022] Open
Abstract
Honeybees (Apis mellifera L.), which unquestionably play an economically important role in pollination and agricultural production, are at risk of decline. To study changes in gene expression in insects upon exposure to pesticides or other external stimuli, appropriate reference genes are required for data normalization. Since there is no such gene that is absolutely invariable under all experimental conditions, the aim of this study was to identify the most stable targets suitable for subsequent normalization in quantitative experiments based on real-time polymerase chain reaction in honeybee research. Here, we evaluated the expression of fifteen candidate housekeeping genes from three breeding lines of honeybees treated with pyrethroids to identify the most stable genes. The tested insects were exposed to deltamethrin or lambda-cyhalothrin, and then, changes in the accumulation of selected transcripts were assessed, followed by statistical analyses. We concluded that AmRPL32, AmACT and AmRPL13a were the commonly recorded most stable genes in honeybees treated with the selected pyrethroids.
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9
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Vinutha T, Vanchinathan S, Bansal N, Kumar G, Permar V, Watts A, Ramesh SV, Praveen S. Tomato auxin biosynthesis/signaling is reprogrammed by the geminivirus to enhance its pathogenicity. PLANTA 2020; 252:51. [PMID: 32940767 DOI: 10.1007/s00425-020-03452-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/27/2020] [Indexed: 05/25/2023]
Abstract
Tomato leaf curl New Delhi virus-derived AC4 protein interacts with host proteins involved in auxin biosynthesis and reprograms auxin biosynthesis/signaling to help in viral replication and manifestation of the disease-associated symptoms. Perturbations of phytohormone-mediated gene regulatory network cause growth and developmental defects. Furthermore, plant viral infections cause characteristic disease symptoms similar to hormone-deficient mutants. Tomato leaf curl New Delhi Virus (ToLCNDV)-encoded AC4 is a small protein that attenuates the host transcriptional gene silencing, and aggravated disease severity in tomato is correlated with transcript abundance of AC4. Hence, investigating the role of AC4 in pathogenesis divulged that ToLCNDV-AC4 interacted with host TAR1 (tryptophan amino transferase 1)-like protein, CYP450 monooxygenase-the key enzyme of indole acetic acid (IAA) biosynthesis pathway-and with a protein encoded by senescence-associated gene involved in jasmonic acid pathway. Also, ToLCNDV infection resulted in the upregulation of host miRNAs, viz., miR164, miR167, miR393 and miR319 involved in auxin signaling and leaf morphogenesis concomitant with the decline in endogenous IAA levels. Ectopic overexpression of ToLCNDV-derived AC4 in tomato recapitulated the transcriptomic and disruption of auxin biosynthesis/signaling features of the infected leaves. Furthermore, exogenous foliar application of IAA caused remission of the characteristic disease-related symptoms in tomato. The roles of ToLCNDV-AC4 in reprogramming auxin biosynthesis, signaling and cross-talk with JA pathway to help viral replication and manifest the disease-associated symptoms during ToLCNDV infection are discussed.
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Affiliation(s)
- T Vinutha
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Vanchinathan
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Navita Bansal
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gaurav Kumar
- Division of Biochemistry, ICAR-National Rice Research Institute, Cuttack, Orissa, 753006, India
| | - Vipin Permar
- Division of Plant Pathology-Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Archana Watts
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S V Ramesh
- ICAR-Division of Physiology, Biochemistry and PHT, ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, 671124, India.
| | - Shelly Praveen
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Sarwar MB, Ahmad Z, Anicet BA, Sajid M, Rashid B, Hassan S, Ahmed M, Husnain T. Identification and validation of superior housekeeping gene(s) for qRT-PCR data normalization in Agave sisalana (a CAM-plant) under abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:567-584. [PMID: 32205931 PMCID: PMC7078421 DOI: 10.1007/s12298-020-00760-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 05/24/2023]
Abstract
The adaptive mechanisms in Agave species enable them to survive and exhibit remarkable tolerance to abiotic stresses. Quantitative real-time PCR is a highly reliable approach for validation of targeted differential gene expression. However, stable housekeeping gene(s) is prerequisite for accurate normalization of expression data by qRT-PCR. Till date, no systematic validation study for candidate housekeeping gene identification or evaluation has been carried-out in Agave species. A total of 17 candidate housekeeping genes were identified from the de novo assembled transcriptomic data of A. sisalana and rigorously analyzed for expression stability assessment under drought, heat, cold and NaCl stress. Different statistical algorithms like geNorm, BestKeeper, NormFinder, and RefFinder on expression data determined the superior housekeeping gene(s) for accurate normalization of the gene of interest (GOI). The comprehensive evaluation revealed the β-Tub 4, WIN-1 and CYC-A as the most stable, while EEF1α, GAPDH, and UBE2 were ranked as the least stable genes in pooled samples. Pairwise combination by geNorm showed that up to two housekeeping genes would be adequate to normalize the GOI expression data precisely. Validation of identified most and least stable housekeeping genes was carried-out by normalizing the expression data of AsHSP20 under abiotic stress conditions. Copy number of AsHSP20 gene supports the reliability of the genes used for normalization. This is the first report on the screening and validation of the housekeeping genes under abiotic stress condition in A. sisalana that would assist to understand the stress tolerance mechanisms by novel gene identification and accurate validation.
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Affiliation(s)
- Muhammad Bilal Sarwar
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Zarnab Ahmad
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Batcho Agossa Anicet
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Moon Sajid
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Bushra Rashid
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Sameera Hassan
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Mukhtar Ahmed
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
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Frąckowiak P, Pospieszny H, Smiglak M, Obrępalska-Stęplowska A. Assessment of the Efficacy and Mode of Action of Benzo(1,2,3)-Thiadiazole-7-Carbothioic Acid S-Methyl Ester (BTH) and Its Derivatives in Plant Protection Against Viral Disease. Int J Mol Sci 2019; 20:E1598. [PMID: 30935036 PMCID: PMC6480033 DOI: 10.3390/ijms20071598] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/17/2022] Open
Abstract
Systemic acquired resistance (SAR) induction is one of the primary defence mechanisms of plants against a broad range of pathogens. It can be induced by infectious agents or by synthetic molecules, such as benzo(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH). SAR induction is associated with increases in salicylic acid (SA) accumulation and expression of defence marker genes (e.g., phenylalanine ammonia-lyase (PAL), the pathogenesis-related (PR) protein family, and non-expressor of PR genes (NPR1)). Various types of pathogens and pests induce plant responses by activating signalling pathways associated with SA, jasmonic acid (JA) and ethylene (ET). This work presents an analysis of the influence of BTH and its derivatives as resistance inducers in healthy and virus-infected plants by determining the expression levels of selected resistance markers associated with the SA, JA, and ET pathways. The phytotoxic effects of these compounds and their influence on the course of viral infection were also studied. Based on the results obtained, the best-performing BTH derivatives and their optimal concentration for plant performance were selected, and their mode of action was suggested. It was shown that application of BTH and its derivatives induces increased expression of marker genes of both the SA- and JA-mediated pathways.
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Affiliation(s)
- Patryk Frąckowiak
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection, National Research Institute, ul. Władysława Węgorka 20, 60-318 Poznań, Poland.
| | - Henryk Pospieszny
- Department of Virology and Bacteriology, Institute of Plant Protection, National Research Institute, ul. Władysława Węgorka 20, 60-318 Poznań, Poland.
| | - Marcin Smiglak
- Poznań Science and Technology Park, Adam Mickiewicz University Foundation, ul. Rubież 46, 61-612 Poznań, Poland.
| | - Aleksandra Obrępalska-Stęplowska
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection, National Research Institute, ul. Władysława Węgorka 20, 60-318 Poznań, Poland.
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Wieczorek P, Wrzesińska B, Frąckowiak P, Przybylska A, Obrępalska-Stęplowska A. Contribution of Tomato torrado virus Vp26 coat protein subunit to systemic necrosis induction and virus infectivity in Solanum lycopersicum. Virol J 2019; 16:9. [PMID: 30642343 PMCID: PMC6332883 DOI: 10.1186/s12985-019-1117-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 01/06/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Tomato torrado virus (ToTV) infection manifests with burn-like symptoms on leaves, leaflets and upper stem parts of susceptible infected plants. The symptoms caused by ToTV may be considered as one of the most severe virus-induced forms of systemic necrosis, which spreads within the whole plant and leads to a lethal phenotype. However, to date there are no data revealing which viral genes encode for a specific pathogenicity determinant that triggers the plant necrotic response for any torradovirus. In this study we evaluated the influence of three coat protein subunits of ToTV: Vp23, Vp26 and Vp35, transiently expressed from a PVX-based vector, and checked their association with the induction of systemic necrosis in infected Solanum lycopersicum L. (cv. Beta Lux), a natural host of ToTV. METHODS To estimate how ToTV coat protein subunits might contribute in plant response to virus infection we over-expressed the proteins from PVX-based vector in tomato and analyzed enzymatic activities related with plant defense response. By doing protein qualitative analysis performed by mass spectrometry we indicated the PR10 in protein fraction with induced ribonuclease activity. RESULTS We observed that only the Vp26 enhanced PVX pathogenicity causing severe necrosis of the infected plant. Moreover, we indicated increased RNase and oxidative activities in plants infected with PVX-Vp26 chimeras only. Importantly, we suspected that this increased RNase activity is associated with increased accumulation of PR10 mRNA and products of its translation. CONCLUSIONS On the basis of the obtained results, we indicated that Vp26 acts as the elicitor of hypersensitive response-like reactions of PVX-Vp26 manifesting with enhanced pathogenicity of the recombined PVX. This might be the first described suspected necrosis determinant of torradoviruses infecting tomatoes.
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Affiliation(s)
- Przemysław Wieczorek
- Department of Entomology, Animal Pests & Biotechnology, Institute of Plant Protection-National Research Institute, Władysława Węgorka 20 St, 60-318, Poznań, Poland
| | - Barbara Wrzesińska
- Department of Entomology, Animal Pests & Biotechnology, Institute of Plant Protection-National Research Institute, Władysława Węgorka 20 St, 60-318, Poznań, Poland
| | - Patryk Frąckowiak
- Department of Entomology, Animal Pests & Biotechnology, Institute of Plant Protection-National Research Institute, Władysława Węgorka 20 St, 60-318, Poznań, Poland
| | - Arnika Przybylska
- Department of Entomology, Animal Pests & Biotechnology, Institute of Plant Protection-National Research Institute, Władysława Węgorka 20 St, 60-318, Poznań, Poland
| | - Aleksandra Obrępalska-Stęplowska
- Department of Entomology, Animal Pests & Biotechnology, Institute of Plant Protection-National Research Institute, Władysława Węgorka 20 St, 60-318, Poznań, Poland.
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Aviña-Padilla K, Rivera-Bustamante R, Kovalskaya NY, Hammond RW. Pospiviroid Infection of Tomato Regulates the Expression of Genes Involved in Flower and Fruit Development. Viruses 2018; 10:v10100516. [PMID: 30241423 PMCID: PMC6213050 DOI: 10.3390/v10100516] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 12/22/2022] Open
Abstract
Viroids are unencapsidated, single-stranded, covalently-closed circular, highly structured, noncoding RNAs of 239–401 nucleotides that cause disease in several economically important crop plants. In tomato (Solanum lycopersicum cv. Rutgers), symptoms of pospiviroid infection include stunting, reduced vigor, flower abortion, and reduced size and number of fruits, resulting in significant crop losses. Dramatic alterations in plant development triggered by viroid infection are the result of differential gene expression; in our study, we focused on the effect of tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) infection on gene networks associated with the regulation of flower and fruit development. The expression of several of the genes were previously reported to be affected by viroid infection, but two genes not previously studied were included. Changes in gene expression of SlBIGPETAL1 (bHLH transcription factor) and SlOVA6 (proline-like tRNA synthetase) are involved in petal morphology and fertility, respectively. Expression of SlOVA6 was down-regulated in flowers of TPMVd- and MPVd-infected plants, while expression of SlBIGPETAL1 was up-regulated in flowers. Up-regulation of SlBIGPETAL1 and down-regulation of SlOVA6 were positively correlated with symptoms such as reduced petal size and flower abortion. Expression analysis of additional tomato genes and a prediction of a global network association of genes involved in flower and fruit development and impacted by viroid infection may further elucidate the pathways underlying viroid pathogenicity.
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Affiliation(s)
- Katia Aviña-Padilla
- Campus Juriquilla, Universidad Nacional Autónoma de Mexico, Querátaro Qro 76300, Mexico.
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato 36821, Mexico.
| | - Rafael Rivera-Bustamante
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato 36821, Mexico.
| | - Natalia Y Kovalskaya
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
| | - Rosemarie W Hammond
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
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14
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Wan Q, Chen S, Shan Z, Yang Z, Chen L, Zhang C, Yuan S, Hao Q, Zhang X, Qiu D, Chen H, Zhou X. Stability evaluation of reference genes for gene expression analysis by RT-qPCR in soybean under different conditions. PLoS One 2017; 12:e0189405. [PMID: 29236756 PMCID: PMC5728501 DOI: 10.1371/journal.pone.0189405] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 11/26/2017] [Indexed: 12/23/2022] Open
Abstract
Real-time quantitative reverse transcription PCR is a sensitive and widely used technique to quantify gene expression. To achieve a reliable result, appropriate reference genes are highly required for normalization of transcripts in different samples. In this study, 9 previously published reference genes (60S, Fbox, ELF1A, ELF1B, ACT11, TUA5, UBC4, G6PD, CYP2) of soybean [Glycine max (L.) Merr.] were selected. The expression stability of the 9 genes was evaluated under conditions of biotic stress caused by infection with soybean mosaic virus, nitrogen stress, across different cultivars and developmental stages. ΔCt and geNorm algorithms were used to evaluate and rank the expression stability of the 9 reference genes. Results obtained from two algorithms showed high consistency. Moreover, results of pairwise variation showed that two reference genes were sufficient to normalize the expression levels of target genes under each experimental setting. For virus infection, ELF1A and ELF1B were the most stable reference genes for accurate normalization. For different developmental stages, Fbox and G6PD had the highest expression stability between two soybean cultivars (Tanlong No. 1 and Tanlong No. 2). ELF1B and ACT11 were identified as the most stably expressed reference genes both under nitrogen stress and among different cultivars. The results showed that none of the candidate reference genes were uniformly expressed at different conditions, and selecting appropriate reference genes was pivotal for gene expression studies with particular condition and tissue. The most stable combination of genes identified in this study will help to achieve more accurate and reliable results in a wide variety of samples in soybean.
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Affiliation(s)
- Qiao Wan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Shuilian Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Zhihui Shan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Zhonglu Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Limiao Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Chanjuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Songli Yuan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Qinnan Hao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Xiaojuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Dezhen Qiu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Haifeng Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Xinan Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
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15
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Barbierato V, Sala T, Rinaldi P, Bassolino L, Barchi L, Rotino GL, Toppino L. A spiking strategy facilitates housekeeping selection for RT-qPCR analysis under different biotic stresses in eggplant. PROTOPLASMA 2017; 254:2215-2223. [PMID: 28429149 DOI: 10.1007/s00709-017-1111-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/04/2017] [Indexed: 05/27/2023]
Abstract
Endogenous housekeeping genes are traditionally employed to normalize the expression of target genes in RT-qPCR studies. Assuming that a perfect housekeeping suitable for every condition does not exist, expression stability of the chosen reference gene should be evaluated at every new experiment. The housekeeping selection process reveals furthermore complicated and time-consuming when different conditions have to be compared in the same experimental dataset. As an alternative strategy, we spiked an external reference transcript (ERT) into all RNA samples of our dataset (eggplant roots subjected to different biotic stresses), and used it to normalize the expression levels of native candidate housekeeping. ERT expression resulted highly stable across all samples and enabled to indicate glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as the most stable endogenous housekeeping. This result was confirmed by the use of GeNorm, Normfinder, and BestKeeper algorithms. This method might be generally applied to expedite the selection process of the best reference gene.
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Affiliation(s)
- Valeria Barbierato
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Tea Sala
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Paola Rinaldi
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Laura Bassolino
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Lorenzo Barchi
- DISAFA Plant Genetics and Breeding, University of Torino, Grugliasco, 10095, Torino, Italy
| | - Giuseppe Leonardo Rotino
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Laura Toppino
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy.
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16
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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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17
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Cheng Y, Bian W, Pang X, Yu J, Ahammed GJ, Zhou G, Wang R, Ruan M, Li Z, Ye Q, Yao Z, Yang Y, Wan H. Genome-Wide Identification and Evaluation of Reference Genes for Quantitative RT-PCR Analysis during Tomato Fruit Development. FRONTIERS IN PLANT SCIENCE 2017; 8:1440. [PMID: 28900431 PMCID: PMC5581943 DOI: 10.3389/fpls.2017.01440] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/03/2017] [Indexed: 05/19/2023]
Abstract
Gene expression analysis in tomato fruit has drawn increasing attention nowadays. Quantitative real-time PCR (qPCR) is a routine technique for gene expression analysis. In qPCR operation, reliability of results largely depends on the choice of appropriate reference genes (RGs). Although tomato is a model for fruit biology study, few RGs for qPCR analysis in tomato fruit had yet been developed. In this study, we initially identified 38 most stably expressed genes based on tomato transcriptome data set, and their expression stabilities were further determined in a set of tomato fruit samples of four different fruit developmental stages (Immature, mature green, breaker, mature red) using qPCR analysis. Two statistical algorithms, geNorm and Normfinder, concordantly determined the superiority of these identified putative RGs. Notably, SlFRG05 (Solyc01g104170), SlFRG12 (Solyc04g009770), SlFRG16 (Solyc10g081190), SlFRG27 (Solyc06g007510), and SlFRG37 (Solyc11g005330) were proved to be suitable RGs for tomato fruit development study. Further analysis using geNorm indicate that the combined use of SlFRG03 (Solyc02g063070) and SlFRG27 would provide more reliable normalization results in qPCR experiments. The identified RGs in this study will be beneficial for future qPCR analysis of tomato fruit developmental study, as well as for the potential identification of optimal normalization controls in other plant species.
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Affiliation(s)
- Yuan Cheng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Wuying Bian
- Zhejiang Agricultural Technology Extension CenterHangzhou, China
| | - Xin Pang
- Suzhou Polytechnic Institute of AgricultureSuzhou, China
| | - Jiahong Yu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | | | - Guozhi Zhou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Rongqing Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Meiying Ruan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Zhimiao Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Qingjing Ye
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Zhuping Yao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Yuejian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Hongjian Wan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
- *Correspondence: Hongjian Wan
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18
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Wrzesińska B, Wieczorek P, Obrępalska-Stęplowska A. Recombination-based generation of the agroinfectious clones of Peanut stunt virus. J Virol Methods 2016; 237:179-186. [PMID: 27659243 DOI: 10.1016/j.jviromet.2016.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/05/2016] [Accepted: 09/15/2016] [Indexed: 12/13/2022]
Abstract
Full-length cDNA clones of Peanut stunt virus strain P (PSV-P) were constructed and introduced into Nicotiana benthamiana plants via Agrobacterium tumefaciens. The cDNA fragments corresponding to three PSV genomic RNAs and satellite RNA were cloned into pGreen binary vector between Cauliflower mosaic virus (CaMV) 35S promoter and nopaline synthase (NOS) terminator employing seamless recombinational cloning system. The plasmids were delivered into A. tumefaciens, followed by infiltration of hosts plants. The typical symptoms on systemic leaves of infected plants similar to those of wild-type PSV-P were observed. The presence of the virus was confirmed by means of RT-PCR and Western blotting. Re-inoculation to N. benthamiana, Phaseolus vulgaris, and Pisum sativum resulted in analogous results. Generation of infectious clones of PSV-P enables studies on virus-host interaction as well as revealing viral genes functions.
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Affiliation(s)
- Barbara Wrzesińska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection - National Research Institute, Władysława Węgorka 20 St, 60-318, Poznań, Poland
| | - Przemysław Wieczorek
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection - National Research Institute, Władysława Węgorka 20 St, 60-318, Poznań, Poland
| | - Aleksandra Obrępalska-Stęplowska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection - National Research Institute, Władysława Węgorka 20 St, 60-318, Poznań, Poland.
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19
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Wieczorek P, Obrępalska-Stęplowska A. The N-terminal fragment of the tomato torrado virus RNA1-encoded polyprotein induces a hypersensitive response (HR)-like reaction in Nicotiana benthamiana. Arch Virol 2016; 161:1849-58. [PMID: 27072852 PMCID: PMC4908173 DOI: 10.1007/s00705-016-2841-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/19/2016] [Indexed: 11/30/2022]
Abstract
The hypersensitive response (HR) is a defence reaction observed during incompatible plant-pathogen interactions in plants infected with a wide range of fungi, bacteria and viruses. Here, we show that an N-terminal polyprotein fragment encoded by tomato torrado virus RNA1, located between the first ATG codon and the protease cofactor (ProCo) motif, induces an HR-like reaction in Nicotiana benthamiana. Agrobacterium tumefaciens-mediated transient expression of the first 105 amino acids (the calculated molecular weight of the fragment was ca. 11.33 kDa, hereafter refered to as the 11K domain) from ToTV RNA1 induced an HR-like phenotype in infiltrated leaves. To investigate whether the 11K domain could influence the virulence and pathogenicity of a recombinant virus, we created a potato virus X (PVX) with the 11K coding sequence inserted under a duplicated coat protein promoter. We found that 11K substantially increased the virulence of the recombinant virus. Disease phenotype induced in N. benthamiana by PVX-11K was characterized by strong local and systemic necrosis. This was not observed when the 11K domain was expressed from PVX in an antisense orientation. Further analyses revealed that the 11K domain could not suppress posttranscriptional gene silencing (PTGS) of green fluorescent protein (GFP) in the N. benthamiana 16c line. In silico analysis of the predicted secondary structure of the 11K domain indicated the presence of two putative helices that are highly conserved in tomato-infecting representatives of the genus Torradovirus.
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Affiliation(s)
- Przemysław Wieczorek
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka St, 60-318, Poznan, Poland
| | - Aleksandra Obrępalska-Stęplowska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka St, 60-318, Poznan, Poland.
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20
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Landeo-Ríos Y, Navas-Castillo J, Moriones E, Cañizares MC. The p22 RNA Silencing Suppressor of the Crinivirus Tomato chlorosis virus is Dispensable for Local Viral Replication but Important for Counteracting an Antiviral RDR6-Mediated Response during Systemic Infection. Viruses 2016; 8:E182. [PMID: 27367718 PMCID: PMC4974517 DOI: 10.3390/v8070182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/15/2016] [Accepted: 06/23/2016] [Indexed: 01/01/2023] Open
Abstract
Among the components of the RNA silencing pathway in plants, RNA-dependent RNA polymerases (RDRs) play fundamental roles in antiviral defence. Here, we demonstrate that the Nicotiana benthamiana RDR6 is involved in defence against the bipartite crinivirus (genus Crinivirus, family Closteroviridae) Tomato chlorosis virus (ToCV). Additionally, by producing a p22-deficient ToCV infectious mutant clone (ToCVΔp22), we studied the role of this viral suppressor of RNA silencing in viral infection in both wild-type and RDR6-silenced N. benthamiana (NbRDR6i) plants. We demonstrate that p22 is dispensable for the replication of ToCV, where RDR6 appears not to have any effect. Furthermore, the finding that ToCV∆p22 systemic accumulation was impaired in wild-type N. benthamiana but not in NbRDR6i plants suggests a role for p22 in counteracting an RDR6-mediated antiviral response of the plant during systemic infection.
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Affiliation(s)
- Yazmín Landeo-Ríos
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", 29750 Algarrobo-Costa, Málaga, Spain.
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", 29750 Algarrobo-Costa, Málaga, Spain.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", 29750 Algarrobo-Costa, Málaga, Spain.
| | - M Carmen Cañizares
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", 29750 Algarrobo-Costa, Málaga, Spain.
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21
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Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. actinidiae. Sci Rep 2015; 5:16961. [PMID: 26581656 PMCID: PMC4652207 DOI: 10.1038/srep16961] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/22/2015] [Indexed: 12/17/2022] Open
Abstract
Normalization of data, by choosing the appropriate reference genes (RGs), is fundamental for obtaining reliable results in reverse transcription-quantitative PCR (RT-qPCR). In this study, we assessed Actinidia deliciosa leaves inoculated with two doses of Pseudomonas syringae pv. actinidiae during a period of 13 days for the expression profile of nine candidate RGs. Their expression stability was calculated using four algorithms: geNorm, NormFinder, BestKeeper and the deltaCt method. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and protein phosphatase 2A (PP2A) were the most stable genes, while β-tubulin and 7s-globulin were the less stable. Expression analysis of three target genes, chosen for RGs validation, encoding the reactive oxygen species scavenging enzymes ascorbate peroxidase (APX), superoxide dismutase (SOD) and catalase (CAT) indicated that a combination of stable RGs, such as GAPDH and PP2A, can lead to an accurate quantification of the expression levels of such target genes. The APX level varied during the experiment time course and according to the inoculum doses, whereas both SOD and CAT resulted down-regulated during the first four days, and up-regulated afterwards, irrespective of inoculum dose. These results can be useful for better elucidating the molecular interaction in the A. deliciosa/P. s. pv. actinidiae pathosystem and for RGs selection in bacteria-plant pathosystems.
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22
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Fang P, Lu R, Sun F, Lan Y, Shen W, Du L, Zhou Y, Zhou T. Assessment of reference gene stability in Rice stripe virus and Rice black streaked dwarf virus infection rice by quantitative Real-time PCR. Virol J 2015; 12:175. [PMID: 26497487 PMCID: PMC4619528 DOI: 10.1186/s12985-015-0405-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stably expressed reference gene(s) normalization is important for the understanding of gene expression patterns by quantitative Real-time PCR (RT-qPCR), particularly for Rice stripe virus (RSV) and Rice black streaked dwarf virus (RBSDV) that caused seriously damage on rice plants in China and Southeast Asia. METHODS The expression of fourteen common used reference genes of Oryza sativa L. were evaluated by RT-qPCR in RSV and RBSDV infected rice plants. Suitable normalization reference gene(s) were identified by geNorm and NormFinder algorithms. RESULTS UBQ 10 + GAPDH and UBC + Actin1 were identified as suitable reference genes for RT-qPCR normalization under RSV and RBSDV infection, respectively. When using multiple reference genes, the expression patterns of OsPRIb and OsWRKY, two virus resistance genes, were approximately similar with that reported previously. Comparatively, by using single reference gene (TIP41-Like), a weaker inducible response was observed. CONCLUSIONS We proposed that the combination of two reference genes could obtain more accurate and reliable normalization of RT-qPCR results in RSV- and RBSDV-infected plants. This work therefore sheds light on establishing a standardized RT-qPCR procedure in RSV- and RBSDV-infected rice plants, and might serve as an important point for discovering complex regulatory networks and identifying genes relevant to biological processes or implicated in virus.
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Affiliation(s)
- Peng Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. .,Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014, China. .,College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Rongfei Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Feng Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. .,Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014, China.
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. .,Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014, China.
| | - Wenbiao Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. .,Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014, China.
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. .,Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014, China.
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. .,Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014, China.
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Müller OA, Grau J, Thieme S, Prochaska H, Adlung N, Sorgatz A, Bonas U. Genome-Wide Identification and Validation of Reference Genes in Infected Tomato Leaves for Quantitative RT-PCR Analyses. PLoS One 2015; 10:e0136499. [PMID: 26313760 PMCID: PMC4552032 DOI: 10.1371/journal.pone.0136499] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/04/2015] [Indexed: 11/18/2022] Open
Abstract
The Gram-negative bacterium Xanthomonas campestris pv. vesicatoria (Xcv) causes bacterial spot disease of pepper and tomato by direct translocation of type III effector proteins into the plant cell cytosol. Once in the plant cell the effectors interfere with host cell processes and manipulate the plant transcriptome. Quantitative RT-PCR (qRT-PCR) is usually the method of choice to analyze transcriptional changes of selected plant genes. Reliable results depend, however, on measuring stably expressed reference genes that serve as internal normalization controls. We identified the most stably expressed tomato genes based on microarray analyses of Xcv-infected tomato leaves and evaluated the reliability of 11 genes for qRT-PCR studies in comparison to four traditionally employed reference genes. Three different statistical algorithms, geNorm, NormFinder and BestKeeper, concordantly determined the superiority of the newly identified reference genes. The most suitable reference genes encode proteins with homology to PHD finger family proteins and the U6 snRNA-associated protein LSm7. In addition, we identified pepper orthologs and validated several genes as reliable normalization controls for qRT-PCR analysis of Xcv-infected pepper plants. The newly identified reference genes will be beneficial for future qRT-PCR studies of the Xcv-tomato and Xcv-pepper pathosystems, as well as for the identification of suitable normalization controls for qRT-PCR studies of other plant-pathogen interactions, especially, if related plant species are used in combination with bacterial pathogens.
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Affiliation(s)
- Oliver A. Müller
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Grau
- Institute for Informatics, Department of Bioinformatics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sabine Thieme
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Heike Prochaska
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Norman Adlung
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Anika Sorgatz
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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Heat shock factors in carrot: genome-wide identification, classification, and expression profiles response to abiotic stress. Mol Biol Rep 2014; 42:893-905. [PMID: 25403331 DOI: 10.1007/s11033-014-3826-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/10/2014] [Indexed: 12/16/2022]
Abstract
Heat shock factors (HSFs) play key roles in the response to abiotic stress in eukaryotes. In this study, 35 DcHSFs were identified from carrot (Daucus carota L.) based on the carrot genome database. All 35 DcHSFs were divided into three classes (A, B, and C) according to the structure and phylogenetic relationships of four different plants, namely, Arabidopsis thaliana, Vitis vinifera, Brassica rapa, and Oryza sativa. Comparative analysis of algae, gymnosperms, and angiosperms indicated that the numbers of HSF transcription factors were related to the plant's evolution. The expression profiles of five DcHsf genes (DcHsf 01, DcHsf 02, DcHsf 09, DcHsf 10, and DcHsf 16), which selected from each subfamily (A, B, and C), were detected by quantitative real-time PCR under abiotic stresses (cold, heat, high salinity, and drought) in two carrot cultivars, D. carota L. cvs. Kurodagosun and Junchuanhong. The expression levels of DcHsfs were markedly increased by heat stress, except that of DcHsf 10, which was down regulated. The expression profiles of different DcHsfs in the same class also differed under various stress treatments. The expression profiles of these DcHsfs were also different in tissues of two carrot cultivars. This study is the first to identify and characterize the DcHSF family transcription factors in plants of Apiaceae using whole-genome analysis. The results of this study provide an in-depth understanding of the DcHSF family transcription factors' structure, function, and evolution in carrot.
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