Molecular Biology Reports

, Volume 47, Issue 2, pp 1339–1360 | Cite as

Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem

  • Gautam Saripalli
  • Chanchal Sharma
  • Tinku Gautam
  • Kalpana Singh
  • Neelu Jain
  • Pramod Prasad
  • J. K. Roy
  • J. B. Sharma
  • P. K. Sharma
  • K. V. Prabhu
  • H. S. Balyan
  • P. K. GuptaEmail author
Original Article


Differential DNA methylation due to Lr28 was examined in susceptible (S) wheat cv. HD2329 and its resistant (R) near isogenic line (NIL) (HD2329+Lr28) using two approaches: methylation sensitive amplified polymorphism (MSAP) and methylated DNA immunoprecipitation (MeDIP). S/R lines each had a large number of hypomethylated genes and relatively fewer hypermethylated genes at 96 hai (hours after inoculation) relative to 0 hbi (hours before inoculation), suggesting activation of many genes during the passage of time (96 hai), although identity of genes may differ in S and R lines. When R NIL was compared with S cultivar, there were many hypermethylated and fewer hypomethylated genes in R NIL relative to S cultivar, suggesting that many genes that are active in S cultivar are silenced in R NIL, both at 0 hbi and at 96 hai. Level of methylation was generally abundant in intergenic regions followed by that in promoters, transcription termination sites (TTSs) and exons/introns. Hypermethylation in promoter and gene body regions was not always associated with inhibition of gene expression and vice-versa, indicating that more than one regulatory mechanisms may control the expression of genes due to pathogen attack in presence and absence of Lr28. MSAP analysis also showed abundance of mCG methylation in S cultivar and that of mCCG methylation in R NIL (at 96 hai), suggesting differences in methylation context in NILs with and without Lr28. The results of the present study improved our understanding of the epigenetic control of leaf rust resistance in wheat.


Wheat Leaf rust Lr28 DNA methylation Gene expression 



Financial assistance from the Department of Biotechnology (Grant Number BT/PR3337/AGR/2/819/2011), Government of India for carrying out this study is gratefully acknowledged. GS, CK, TG and KS were each awarded JRF/SRF/RA by the Department of Biotechnology, Government of India. PKG and HSB were each awarded the position of Senior Scientist by Indian National Science Academy, New Delhi. PKG was also awarded a National Academy of Sciences India (NASI) Senior Scientist Platinum Jubilee Fellowship during the tenure of this research work. Facilities available in DBT-sponsored Bioinformatics Infrastructure Facility (BIF) were also utilized for this work.

Author contributions

PKG and HSB conceived the experiment. GS with the help of CS, KS and TG conducted data analysis. GS and CS also prepared the first draft of the manuscript which was edited and finalised by PKG, HSB and PKS. PP provided inoculum for leaf rust pathotype 77-5 and NJ, KVP and JBS raised and provided the seedlings tissues. JKR assisted GS and CS in conducting MSAP analysis.

Compliance with ethical standards

Conflict of interest

All the authors declare that there is no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Supplementary material 1 (DOC 67.0 kb)
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Supplementary material 2 (DOC 86 kb)
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Supplementary material 3 (XLS 2436.5 kb)
11033_2019_5236_MOESM4_ESM.xls (73 kb)
Supplementary material 4 (XLS 73.0 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Gautam Saripalli
    • 1
  • Chanchal Sharma
    • 1
    • 2
  • Tinku Gautam
    • 1
  • Kalpana Singh
    • 3
  • Neelu Jain
    • 4
  • Pramod Prasad
    • 5
  • J. K. Roy
    • 6
  • J. B. Sharma
    • 4
  • P. K. Sharma
    • 1
  • K. V. Prabhu
    • 4
    • 7
  • H. S. Balyan
    • 1
    • 3
  • P. K. Gupta
    • 1
    Email author
  1. 1.Department of Genetics and Plant BreedingCh.Charan Singh UniversityMeerutIndia
  2. 2.Department of Biotechnology, College of EngineeringDaegu UniversityGyeongsan CitySouth Korea
  3. 3.Bioinformatics Infrastructure Facility (BIF) Laboratory, Department of Genetics and Plant BreedingCh. Charan Singh UniversityMeerutIndia
  4. 4.Division of GeneticsICAR-Indian Agricultural Research Institute (IARI)New DelhiIndia
  5. 5.Regional Station, ICAR-Indian Institute of Wheat and Barley ResearchShimlaIndia
  6. 6.National Agri-Food Biotechnology InstituteMohaliIndia
  7. 7.Protection of Plant Varieties and Farmers’ Rights AuthorityGovernment of IndiaNew DelhiIndia

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