Identification and Characterization of Differentially Expressed microRNAs and Target Gene Related to Flax Stem Development

Flax fiber was one of the earliest natural fibers utilized by humans. Current research on flax fiber development is mainly focused on functions of key genes, with few reports investigating regulation of microRNA expression. Here, miRNA-seq was employed to explore miRNA expression profiles of middle stem tissues of high-fiber flax variety Agatha-MB and low-fiber flax variety White Flower during the rapid growth period (RGP) and mature green stage (MGS) to reveal miRNAs related to flax stem fiber development. The results revealed that 24 and 26 known miRNAs were identified that exhibited significant expression differences during MGSAgatha-MB-vs-RGPAgatha-MB and MGSWF-vs-RGPWF, respectively. Forty-one miRNA-target pairs exhibited inverse expression pattern changes as compared to our previously reported transcriptome profiling results. Pathway enrichment analysis of miRNA target genes showed that the plant hormone signal transduction pathway yielded the highest number of miRNA target genes in both varieties between the two developmental stages. To confirm the accuracy and reliability of these miRNA-seq results, qRT-PCR analysis of expression changes of six selected Lus-miRNA demonstrated similar trends as observed using miRNA-seq. These findings will enhance our understanding of miRNA regulatory mechanisms in flax stem development and will provide a foundation for future functional studies of these key miRNAs.