N6-methyladenosine mRNA methylation is important for the light response in soybean

N6-methyladenosine (m(6)A) modification of messenger RNA (mRNA) is the most prevalent and abundant modification in eukaryotic mRNA and posttranscriptionally modulates the transcriptome at almost all stages of mRNA metabolism. In plants, m(6)A is crucial for embryonic-phase growth, flowering time control, microspore generation and fruit maturation. However, the role of m(6)A in plant responses to light, the most important environmental stimulus, remains unexplored. Here, we profile the m(6)A transcriptome of Williams 82, a soybean cultivar, and reveal that m(6)A is highly conserved and plays an important role in the response to light stimuli in soybean. Similar to the case in Arabidopsis, m(6)A in soybean is enriched not only around the stop codon and within the 3’UTR but also around the start codon. Moreover, genes with methylation occurring in the 3’UTR have higher expression levels and are more prone to alternative splicing. The core genes in the light signaling pathway, GmSPA1a, GmPRR5e and GmBIC2b, undergo changes in methylation modification and transcription levels in response to light. KEGG pathway analysis revealed that differentially expressed genes with differential m(6)A peaks were involved in the “photosynthesis” and “circadian rhythm” pathways. Our results highlight the important role played by epitranscriptomic mRNA methylation in the light response in soybean and provide a solid basis for determining the functional role of light on RNA m(6)A modification in this plant.