Transcriptome-Wide N(6)-Methyladenosine (m(6)A) Profiling of Susceptible and Resistant Wheat Varieties Reveals the Involvement of Variety-Specific m(6)A Modification Involved in Virus-Host Interaction Pathways

N(6)-methyladenosine (m(6)A) methylation is the most prevalent internal modification of post-transcriptional modifications in mRNA, tRNA, miRNA, and long non-coding RNA in eukaryotes. m(6)A methylation has been proven to be involved in plant resistance to pathogens. However, there are no reports on wheat (Triticum aestivum) m(6)A transcriptome-wide map and its potential biological function in wheat resistance to wheat yellow mosaic virus (WYMV). To the best of our knowledge, this study is the first to determine the transcriptome-wide m(6)A profile of two wheat varieties with different resistances to WYMV. By analyzing m(6)A-sequencing (m(6)A-seq) data, we identified 25,752 common m(6)A peaks and 30,582 common m(6)A genes in two groups [WYMV-infected resistant wheat variety (WRV) and WYMV-infected sensitive wheat variety (WSV)], and all these peaks were mainly enriched in 3′ untranslated regions and stop codons of coding sequences. Gene Ontology analysis of m(6)A-seq and RNA-sequencing data revealed that genes that showed significant changes in both m(6)A and mRNA levels were associated with plant defense responses. Kyoto Encyclopedia of Genes and Genomes analysis revealed that these selected genes were enriched in the plant–pathogen interaction pathway. We further verified these changes in m(6)A and mRNA levels through gene-specific m(6)A real-time quantitative PCR (RT-qPCR) and normal RT-qPCR. This study highlights the role of m(6)A methylation in wheat resistance to WYMV, providing a solid basis for the potential functional role of m(6)A RNA methylation in wheat resistance to infection by RNA viruses.