Abstract
Epigenetic regulation of the activity of defense genes during onset of diseases or resistance against diseases in plants is an active area of research. In the present study, a pair of wheat NILs for leaf rust resistance gene Lr28 (R) in the background of an Indian cultivar HD2329 (S) was used for a study of DNA methylation mediated regulation of gene expression. Leaf samples were collected at 0 h before (S0 and R0) and 96 h after inoculation (S96 and R96). The DNA samples were subjected to BS-Seq and sequencing data were used for identification of differentially methylated/demethylated regions/genes (DMRs and DMGs). Following four pairs of comparisons were used for this purpose: S0 vs S96; S0 vs R0; R0 vs R96; S96 vs R96. Major role of CHH methylation relative to that of CG and CHG methylation was observed. Some important observations include the following: (i) abundance of CHH methylation among DMRs; (ii) predominance of DMRs in intergenic region, relative to other genomic regions (promoters, exons, introns, TSS and TTS); (iii) abundance of transposable elements (TEs) in DMRs with CHH context; (iv) demethylation mediated high expression of genes during susceptible reaction (S0 vs S96) and methylation mediated low expression of genes during resistant reaction (R0 vs R96 and S96 vs R96); (v) major genes under regulation encode proteins, which differ from those encoded by genes regulated during susceptible reaction and (vi) ~ 500 DMGs carried differential binding sites for H3K4/K27me3 marks suggesting joint involvement of DNA and H3 methylation. Thus, CHH methylation either alone or in combination with histone methylation plays a major role in regulating the expression of genes involved in wheat-leaf rust interaction.
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Data availability
The raw reads generated using BS-Seq analysis for all the eight samples which include two biological replicates of each of the resistant (R) and susceptible (S) NILs at 0 hbi and 96 hai are deposited in Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI), and can be accessed through bioproject accession number PRJNA745483. The raw reads for RNA-Seq and ChIP-Seq analysis are deposited under accession number PRJNA588134 of Bioproject Database.
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Acknowledgements
The work was carried out, when GS and TG held SRF positions under a research project funded under National Agricultural Science Fund (NASF) -ICAR program of Government of India. KS held the position of RA in a project funded by Department of Biotechnology, Govt. of India, New Delhi. HSB was awarded Senior Scientist and Hony. Scientist positions from Indian National Science Academy (INSA). NASF-ICAR (File No. NASF/ABP-6006/2016-17), New Delhi, India provided funds for carrying out this study. Bioinformatics Infrastructure Facility (BIF) laboratory was used for carrying out most of the bioinformatics analyses. Head, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, provided the necessary infrastructure. Thanks are also due to Ritu Batra for critical reading of the manuscript.
Funding
This work was supported by National Agricultural Science Fund-Indian Council of Agricultural Research (NASF-ICAR). Name of the project: “Epigenetic regulation of host–pathogen genetics of leaf rust resistance in wheat” NASF’s Project No.: NASF-ICAR File No. NASF/ABP-6006/2016-17.
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PKG and HSB conceived the experiment. KS conducted the bioinformatics analysis and wrote the first draft of the manuscript jointly with GS. GS was involved in data interpretation with other authors and also conducted qRT-PCR analysis jointly with TG. NJ raised and provided the seedlings for NILs. PP provided the inoculum for leaf rust pathotype 77-5. PKG and HSB finalized the manuscript with the help of KS and GS. All authors read the final version of the manuscript and approved it.
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Singh, K., Saripalli, G., Gautam, T. et al. BS-Seq reveals major role of differential CHH methylation during leaf rust resistance in wheat (Triticum aestivum L.). Mol Genet Genomics 297, 731–749 (2022). https://doi.org/10.1007/s00438-022-01879-1
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DOI: https://doi.org/10.1007/s00438-022-01879-1