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An efficient virus-induced gene silencing of PDS gene in Solanum lycopersicum (cv. Rio Grande) and its functional analysis

  • Genetics & Evolutionary Biology - Original Article
  • Published:
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Abstract

Solanum lycopersicum L. is the second most significant fruit crop after potato. It is a rich source of various vitamins, dietary components, and carotenoid content as well. Carotenoids are essential pigments in numerous physiological processes as well as accessory pigments in photosynthesis regulated by phytoene desaturase (PDS) gene. Although the role of PDS gene has been reported in various plants, its role in Pakistan’s local cultivar “Rio Grande” has not been investigated yet. Therefore, the current research aimed to evaluate PDS gene’s function via TRV-VIGS-based optimized transient silencing protocol. Briefly, PDS gene of tomato was studied computationally for its localization and potential functions. Afterward, the PDS gene was silenced in Rio Grande by agro-infiltration through TRV-VIGS. In order to ensure effective silencing, pigment analysis, PDS gene molecular analysis, and infiltration efficacy were all investigated. Computational studies revealed high conservation in the promoter of PDS gene among selected plant species with a prevalence of CAAT-box and TATA-box. The study highlighted chloroplast to be the principal cellular structure where the majority of PDS protein is found. A transcriptome study of the transiently silenced Rio Grande revealed a considerable reduction in PDS mRNA transcripts in leaves with reference to the respective control. Pigment analysis of the PDS-silenced albino plant leaves showed approximately 90% reduction in their chlorophyll a, chlorophyll b, and carotenoid content suggesting the successful silencing of PDS gene as its active expression plays a positive role in pigment synthesis. The obtained results highlight the role of PDS gene in Rio Grande as well as TRV-based VIGS to be a promising technique to improve crop attributes by efficiently silencing the target genes.

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Data availability

The data used to support the findings of this study are available from the corresponding author upon request.

References

  • Aamir M, Singh VK, Meena M, Upadhyay R, Gupta VK, Singh S (2017) Structural and functional insights into WRKY3 and WRKY4 transcription factors to unravel the WRKY–DNA (W-Box) complex interaction in tomato (Solanum lycopersicum L.). A computational approach. Front Plant Sci 8:1–24

    Article  Google Scholar 

  • Ali MY, Sina AA, Khandker SS, Neesa L, Tanvir EM, Kabir A, Khalil MI, Gan SH (2020) Nutritional composition and bioactive compounds in tomatoes and their impact on human health and disease: a review. Foods (basel, Switzerland) 10:45

    PubMed  Google Scholar 

  • Anu K, Joseph L, Bindu RC (2021) Tobacco rattle virus vector-based virus induced gene silencing-optimization of a functional genomics tool for hevea brasiliensis using reverse genetics approach. Plant Biol Crop Res 4:1035

    Google Scholar 

  • Eggersdorfer M, Wyss A (2018) Carotenoids in human nutrition and health. Arch Biochem Biophys 652:18–26

    Article  CAS  PubMed  Google Scholar 

  • Fang Y, Mei H, Zhou B, Xiao X, Yang M, Huang Y, Long X, Hu S, Tang C (2016) De novo transcriptome analysis reveals distinct defense mechanisms by young and mature leaves of Hevea brasiliensis (para rubber tree). Sci Rep 6:1–10

    Article  Google Scholar 

  • Garg R, Jain M (2013) RNA-Seq for transcriptome analysis in non-model plants. Legume Genomics 1069:43–58

    Article  CAS  Google Scholar 

  • Gerszberg A, Hnatuszko-Konka K (2017) Tomato tolerance to abiotic stress: a review of most often engineered target sequences. Plant Growth Regul 83:175–198

    Article  CAS  Google Scholar 

  • Huang Y, Li MY, Wu P, Xu ZS, Que F, Wang F, Xiong AS (2016) Members of WRKY group III transcription factors are important in TYLCV defense signaling pathway in tomato (Solanum lycopersicum). BMC Genom 17:1–18

    Article  Google Scholar 

  • Karkute SG, Gujjar RS, Rai A, Akhtar M, Singh M, Singh B (2018) Genome wide expression analysis of WRKY genes in tomato (Solanum lycopersicum) under drought stress. Plant Gene 13:8–17

    Article  CAS  Google Scholar 

  • Krishnan A, Mahadevan C, Mani T, Sakuntala M (2015) Virus-induced gene silencing (VIGS) for elucidation of pathogen defense role of serine/threonine protein kinase in the non-model plant piper colubrinum link. Plant Cell Tissue Organ Cult 122:269–283

    Article  CAS  Google Scholar 

  • Kumagi MH, Donson J, Della-Cioppa G, Harvey D, Hanley K, Grill LK (1995) Cytoplamic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc Natl Acad Sci 92:1679–1683

    Article  Google Scholar 

  • McQuinn RP, Wong B, Giovannoni JJ (2018) AtPDS overexpression in tomato: exposing unique patterns of carotenoid self-regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnol J 16:482–494

    Article  CAS  PubMed  Google Scholar 

  • Nadeem M, Khan AA, Khan AA, Nadeem J, Fatima U (2023) Cloning and characterization of Trichoderma glucanase gene for plant transformation. Int J Agri Biosci 12:31–46

    Google Scholar 

  • Naing AH, Kyu SY, Pe PPW, Park KIL, Lee JM, Lim KB, Kim CK (2019) Silencing of the phytoene desaturase (PDS) gene affects the expression of fruit-ripening genes in tomatoes. Plant Met 15:1–10

    CAS  Google Scholar 

  • Noman MU, Azhar S (2023) Metabolomics, a potential way to improve abiotic stresses tolerance in cereal crops. Int J Agri Biosci 12:47–55

    Google Scholar 

  • Norkunas K, Harding R, Dale J, Dugdale B (2018) Improving agroinfiltration-based transient gene expression in Nicotiana benthamiana. Plant Methods 14:71

    Article  PubMed  PubMed Central  Google Scholar 

  • Quinet M, Angosto T, Yuste-Lisbona FJ, Blanchard-Gros R, Bigot S, Martinez JP, Lutts S (2019) Tomato fruit development and metabolism. Front Plant Sci 10:1554

    Article  PubMed  PubMed Central  Google Scholar 

  • Rehman I, Shaukat F, Abbas M, Ijaz A, Anwar Z (2022) Applications of crispr/cas system in plants. Int J Agri Biosci 11:231–237

    Google Scholar 

  • Senthil-Kumar M, Mysore KS (2014) Tobacco rattle virus–based virus-induced gene silencing in Nicotiana benthamiana. Nat Protoc 9:1549–1562

    Article  CAS  PubMed  Google Scholar 

  • Senthil-Kumar M, Hema R, Anand A, Kang L, Udayakumar M, Mysore KS (2007) A systematic study to determine the extent of gene silencing in Nicotiana benthamiana and other Solanaceae species when heterologous gene sequences are used for virus-induced gene silencing. New Phytol 176:782–791

    Article  CAS  PubMed  Google Scholar 

  • Shi G, Hao M, Tian B, Cao G, Wei F, Xie Z (2021) A methodological advance of tobacco rattle virus-induced gene silencing for functional genomics in plants. Front Plant Sci 12:671091

    Article  PubMed  PubMed Central  Google Scholar 

  • Sun T, Tadmor Y, Li L (2020) Pathways for carotenoid biosynthesis, degradation, and storage. In Plant and Food Carotenoids 2083:3–23

    Article  CAS  Google Scholar 

  • Sun B, Jiang M, Xue S, Zheng A, Zhang F, Tang H (2018) Bioinformatics analysis of the phytoene dehydrogenase gene in cabbage (Brassica Oleracea Var. Capitata). In: 2nd International conference on material science, energy and environmental engineering (MSEEE 2018), pp 300–305

  • Tandon G, Singh S, Kaur S, Iquebal MA, Rai A, Kumar D (2017) Computational deciphering of biotic stress associated genes in tomato (Solanum lycopersicum). Genom Data 14:82–90

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Velásquez AC, Chakravarthy S, Martin GB (2009) Virus-induced gene silencing (VIGS) in Nicotiana benthamiana and tomato. J vis Exp 28:20–23

    Google Scholar 

  • Wang M, Wang G, Ji J, Wang J (2009) The effect of PDS gene silencing on chloroplast pigment composition, thylakoid membrane structure and photosynthesis efficiency in tobacco plants. Plant Sci 177:222–226

    Article  CAS  Google Scholar 

  • Wang TT, Yu TF, Fu JD, Su HG, Chen J, Zhou YB, Chen M, Guo J, Ma YZ, Wei WL (2020) Genome-wide analysis of the GRAS gene family and functional identification of GmGRAS37 in drought and salt tolerance. Front Plant Sci 11:2024

    Article  Google Scholar 

  • Zheng X, Yi D, Shao L, Cong LI (2017) In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula. J Integr Agric 16:1576–1591

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors extend their appreciation to the Researchers Supporting Project number (RSP-2024R369), King Saud University, Riyadh, Saudi Arabia. The authors would like to thank the National Institute of genomics and advanced biotechnology (NIGAB), NARC, Islamabad, for providing the necessary facilities for this study and TAIR (The Arabidopsis Information Resource) database for providing TRV-VIGS vectors.

Funding

Researchers Supporting Project number (RSP-2024R369), King Saud University.

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Authors and Affiliations

  1. Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Islamabad, Pakistan

    Iqra Mehboob, Muhammad Mughees, Ayesha Baig, Yasar Sajjad & Mohammad Maroof Shah

  2. Plant Biotechnology, NIGAB, NARC Islamabad, Islamabad, Pakistan

    Shaukat Ali

  3. Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha, Pakistan

    Shahid Iqbal

  4. Department of Horticulture, Faculty of Agriculture, Ghazi University, Dera Ghazi Khan, Pakistan

    Zahoor Hussain

  5. Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan

    Sajid Fiaz

  6. The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China

    Farhat Abbas

  7. Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia

    Kotb A. Attia

  8. Biotechnology School, Nile University, 26Th of July Corridor, Sheikh Zayed City, Giza, 12588, Egypt

    Asmaa M. Abushady

Authors
  1. Iqra Mehboob
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  2. Muhammad Mughees
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  11. Asmaa M. Abushady
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Contributions

IM performed all the experiments, formal analysis of all data, and writing—review and editing of the manuscript. MM involved in formal analysis and writing—review and editing of the manuscript. AB designed the study, supervised, and finalized the drafting. YS, KAA, and AMA reviewed original draft. SI and ZH reviewed the manuscript. SA, SF, and FA involved in supervision and review of the manuscript. MMS supervised and finalized original draft.

Corresponding authors

Correspondence to Ayesha Baig or Sajid Fiaz.

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This is an observational study, and this article does not contain any studies with human participants or animals performed by any of the authors.

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Mehboob, I., Mughees, M., Baig, A. et al. An efficient virus-induced gene silencing of PDS gene in Solanum lycopersicum (cv. Rio Grande) and its functional analysis. Braz. J. Bot 46, 881–892 (2023). https://doi.org/10.1007/s40415-023-00941-5

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