Unveiling Differential Epigenetic Regulation of ABC Transporter Genes in Wild and Domestic Rice in Response to Heavy Metal Stress

Plants are continually subjected to heavy metal (HM) stress, which impairs critical physiological and metabolic processes. ATP-binding cassette (ABC) transporters play an important role in heavy metal detoxification, their epigenetic regulation under heavy metal stress remains poorly understood. Epigenetic changes, such as DNA methylation (5mC) and N6-methyladenine (6mA), are emerging as important regulators of stress-responsive genes. We studied the epigenetic regulation of ABC transporter genes in three Oryza species Oryza sativa indica , Oryza rufipogon , and Oryza glaberrima by analysing promoter methylation patterns. Our data show that 5mC is abundant in CHG motifs, whereas 6mA is mostly found at AHCA motifs, indicating sequence-specific methylation preferences across different rice species. Notably, indica rice exhibited higher promoter methylation levels compared to O. rufipogon and O. glaberrima , suggesting a potential link between increased DNA methylation and reduced ABC transporter expression, which may contribute to heightened HM sensitivity in cultivated rice. Phylogenetic analysis further highlighted species-specific variations in methylation patterns, supporting the role of epigenetics in shaping HM stress adaptation. These results provide new insights into the regulatory mechanisms governing heavy metal tolerance in rice and open avenues for epigenetic-based crop improvement strategies.