DNA polymorphisms and N6-methyladenosine RNA methylation influencing microRNA expression and regulatory activity in plants.

Plant subspecies that have colonized distinct natural habitats must evolve different phenotypic and physiological features to ensure survival. However, the underlying molecular mechanisms remain poorly understood. In this study, we selected seven Arabidopsis accessions and six rice varieties with significantly different natural habitat parameters to investigate the molecular mechanisms behind the differential expression and activity of microRNAs (miRNAs) at the subspecies level. Compared to Col-0, 24–35 differentially expressed miRNA precursors and 36–110 differentially expressed mature miRNAs were identified in the other six Arabidopsis accessions. Compared to Nipponbare, 19–40 differentially expressed precursors and 8–101 mature miRNAs were identified in the other five rice varieties. The expression patterns of the precursors correlate well with those of the mature miRNAs. Both m6A modification and single nucleotide polymorphisms (SNPs) associated with miRNA genes were closely linked to precursor transcription and miRNA maturation. Degradome sequencing data analysis revealed that the high miRNA level likely caused intense target cleavages in a specific subspecies. In some cases, the affinity of miRNA—target interactions was significantly influenced by SNPs. Notably, many target genes were functionally involved in organ development, reproduction or stress responses. The data presented here provide molecular hints into the different developmental processes and environmental responses among plant subspecies with distinct natural habitats.