Unique Features of the m(6)A Methylome and Its Response to Salt Stress in the Roots of Sugar Beet (Beta vulgaris)

Salt is one of the most important environmental factors in crop growth and development. N(6)-methyladenosine (m(6)A) is an epigenetic modification that regulates plant–environment interaction at transcriptional and translational levels. Sugar beet is a salt-tolerant sugar-yielding crop, but how m(6)A modification affects its response to salt stress remains unknown. In this study, m(6)A-seq was used to explore the role of m(6)A modification in response to salt stress in sugar beet (Beta vulgaris). Transcriptome-wide m(6)A methylation profiles and physiological responses to high salinity were investigated in beet roots. After treatment with 300 mM NaCl, the activities of peroxidase and catalase, the root activity, and the contents of Na(+), K(+), and Ca(2+) in the roots were significantly affected by salt stress. Compared with the control plants, 6904 differentially expressed genes (DEGs) and 566 differentially methylated peaks (DMPs) were identified. Association analysis revealed that 243 DEGs contained DMP, and 80% of these DEGs had expression patterns that were negatively correlated with the extent of m(6)A modification. Further analysis verified that m(6)A methylation may regulate the expression of some genes by controlling their mRNA stability. Functional analysis revealed that m(6)A modifications primarily affect the expression of genes involved in energy metabolism, transport, signal transduction, transcription factors, and cell wall organization. This study provides evidence that a post-transcriptional regulatory mechanism mediates gene expression during salt stress by affecting the stability of mRNA in the root.