Temporal Dynamics of Small RNAs and Their Targets Under Salt Stress in Soybean Roots

we systematically integrated small RNA, degradome, and transcriptome sequencing data to comprehensively profile miRNA expression patterns and target interactions in salt-tolerant (QH34) and salt-sensitive (DN50) soybean cultivars under salt stress conditions. Our analysis identified 168 miRNA loci, including 16 novel miRNAs, that exhibited specific responsiveness to salt treatment. Degradome analysis further revealed 133 high-confidence miRNA-target pairs, elucidating both conserved and genotype-specific regulatory modules. Expression profiling demonstrated that most known miRNAs were downregulated under salt stress, whereas novel miRNAs displayed dynamic, genotype-dependent expression patterns. Network analysis subsequently identified key regulatory hubs, notably gma-miR396 and gma-miR160 and a novel miRNA coordinate stress response