Identification of Shade Avoidance Response MicroRNAs and Their Targets in Solanum tuberosum L. via High-Throughput Sequencing

MicroRNAs (miRNAs) are non-coding, single-stranded RNA molecules that regulate gene expression post-transcriptionally. Potato, an essential crop for food and fodder, experiences reduced quality and yield under shading. Although miRNAs have known roles in various plants, their regulatory mechanisms in potato shade avoidance remain unexplored. To investigate this, we constructed nine small RNA libraries from potato samples at 0, 5, and 10 days post-shade treatment. High-throughput sequencing identified 525 miRNAs (307 known and 218 novel) from 99 families, and 166 differentially expressed miRNAs (DEMs) were detected. qRT-PCR verified 10 DEMs, confirming sequencing reliability. Using TargetFinder, we predicted 4320 target genes of DEMs, which were enriched in plant–pathogen interaction and hormone signal transduction pathways, among others. These findings indicate that miRNAs may play key regulatory roles in potato shade avoidance by targeting specific genes, providing valuable insights for future functional studies and potential yield enhancement.