N⁶-methyladenosine analysis unveils key mechanisms underlying long-term salt stress tolerance in switchgrass (Panicum...

N⁶-methyladenosine (m⁶A) RNA modification is critical for plant growth, development, and environmental stress response. While short-term stress impacts on m⁶A are well-documented, the consequences of prolonged stress remain underexplored. This study conducts a thorough transcriptome-wide analysis of m⁶A modifications following 28-day exposure to 200 mM NaCl. We detected 11,149 differentially expressed genes (DEGs) and 12,936 differentially methylated m⁶A peaks, along with a global decrease in m⁶A levels. Notably, about 62% of m⁶A-modified DEGs, including demethylase genes like PvALKBH6_N, PvALKBH9_K, and PvALKBH10_N, showed increased expression and reduced m⁶A peaks, suggesting that decreased m⁶A methylation may enhance gene expression under salt stress. Consistent expression and methylation patterns were observed in key genes related to ion homeostasis (e.g., H⁺-ATPase 1, High-affinity K⁺transporter 5), antioxidant defense (Catalase 1/2, Copper/zinc superoxide dismutase 2, Glutathione synthetase 1), and osmotic regulation (delta 1-pyrroline-5-carboxylate synthase 2, Pyrroline-5-carboxylate reductase). These findings provide insights into the adaptive mechanisms of switchgrass under long-term salt stress and highlight the potential of regulating m⁶A modifications as a novel approach for crop breeding strategies focused on stress resistance.