Role of methylation-related genes and microRNA revealed from RNA-Seq study of FHB susceptible hexaploid wheat NIL in response to pathogen stress

Abstract

Wheat (Triticum aestivum L.), a most important crop among the cereals, accounts for over 20% of the total calories and protein available in human food. However, Fusarium graminearum, a devastating Fusarium head blight (FHB) pathogen of wheat, poses a greater threat to quality wheat grain production as it produces obnoxious mycotoxins. Presently, FHB is a minor disease in India but can cause significant yield and quality losses if rain occurs during mid-anthesis. In plants, epigenetics including DNA methylation and sRNA accumulation regulates gene expression and plays a definitive role in the adaptation to adverse environmental conditions. In a previous study response of wheat to F. graminearum was investigated through transcriptome analysis of lines differing for 2DL FHB resistance QTLs. However, a comprehensive analysis of methylation-related genes in response to pathogen was not performed in that study or any other studies. We re-analyzed the RNA-Seq data of said study to reveal the roles of methylation-related genes in response to F. graminearum. Sixteen methylation-related genes were down-regulated in a susceptible line, 2-2890 (pedigree of line). GO associated these genes with L-methionine salvage from methylthioadenosine and S-adenosylmethionine and steroid biosynthesis (p-value 0.001). Co-expression analysis of this NIL with methionine S-methyl-transferase gene (MSM; TraesCS1A02G013800) resulted in 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMGCR; TraesCS5A02G269300). HMGCR was negatively correlated (-1.00) with genes encoding pathogenesis-related and detoxification proteins and xylanase inhibitors. GO associated these genes with methionine S-methyl transferase (p-value 0.001). Expression of HMGCR was higher (Log2 levels from 3.25 to 4.00) in pathogen inoculated compared to MSM (Log2 levels from 1.25 to 3.25) in mock-inoculated samples. 43 genes were down-regulated by miR9678. These genes are associated with responses to biotic stimulus and glucan endo-1,4-beta-glucanase in GO.