Identification and Characterization of Copper-Responsive miRNAs and Their Target Genes in Jerusalem Artichoke

microRNAs (miRNAs) are key regulators of gene expression in plants, significantly contributing to various biological processes and stress responses. While their roles have been extensively studied in Arabidopsis thaliana and other model plants, the response of miRNAs to copper (Cu) stress in Jerusalem artichoke remains unknown. This study addresses this gap by investigating Cu-responsive miRNAs and their regulatory roles in Jerusalem artichoke under Cu stress. Through small RNA library analysis, six miRNA families-miR168, miR394, miR397, miR398, miR408, and miR858-were identified in Cu-stressed and control plants of the Jerusalem artichoke cv. NY1. These miRNAs possess characteristic stem-loop precursor structures and detectable miRNA* sequences, with miR858 having unusually long precursors (1524-6448 nt). This study outlines a framework for miRNA-mediated Cu stress responses in Jerusalem artichoke, highlighting the roles of both well-established Cu-responsive miRNAs (miR397, miR398, and miR408) and other conserved miRNAs (miR168, miR394, and miR858). These miRNAs are suggested to influence Cu stress adaptation by modulating target genes involved in essential metabolic, physiological, and morphological processes, offering new insights into miRNA-mediated stress regulation in plants.