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

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Abstract

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.

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Acknowledgements

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.

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Author notes

  1. Gautam Saripalli and Chanchal Sharma have contributed equally.

Authors and Affiliations

  1. Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, Uttar Pradesh, 250004, India

    Gautam Saripalli, Chanchal Sharma, Tinku Gautam, P. K. Sharma, H. S. Balyan & P. K. Gupta

  2. Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan City, 38453, Gyeongbook, South Korea

    Chanchal Sharma

  3. Bioinformatics Infrastructure Facility (BIF) Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, Uttar Pradesh, 250004, India

    Kalpana Singh & H. S. Balyan

  4. Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110022, India

    Neelu Jain, J. B. Sharma & K. V. Prabhu

  5. Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India

    Pramod Prasad

  6. National Agri-Food Biotechnology Institute, Mohali, Punjab, 140306, India

    J. K. Roy

  7. Protection of Plant Varieties and Farmers’ Rights Authority, Government of India, New Delhi, India

    K. V. Prabhu

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  1. Gautam Saripalli
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  2. Chanchal Sharma
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  8. J. B. Sharma
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  9. P. K. Sharma
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  11. H. S. Balyan
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  12. P. K. Gupta
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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.

Corresponding author

Correspondence to P. K. Gupta.

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Saripalli, G., Sharma, C., Gautam, T. et al. Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem. Mol Biol Rep 47, 1339–1360 (2020). https://doi.org/10.1007/s11033-019-05236-1

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  • DOI: https://doi.org/10.1007/s11033-019-05236-1

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