Rice specific novel miRNA, Osa-miR39 targets 9-cis-epoxycarotenoid dioxygenases (NCEDs) to regulate fluoride stress...

Fluoride contamination in rice poses a serious risk to human health. MicroRNAs (miRNAs) regulate gene expression under stress conditions, yet their role in fluoride stress remains unclear. Comparative profiling of fluoride-sensitive (IR-64) and tolerant (Gobindobhog, GB) cultivars identified 436 fluoride-responsive miRNAs, of which 39 (30 conserved and 9 novel) were differentially expressed. Target prediction and expression analyses revealed regulation of stress-associated transcription factors, with inverse correlations between several miRNAs and their targets. A novel miRNA, Osa-miR39, was strongly induced in GB but suppressed in IR-64 under fluoride stress. The expression levels of its three abscisic acid (ABA)-responsive target genes encoding 9-cis-epoxycarotenoid dioxygenases (NCED3 & NCED5) and aldehyde oxidase (AO) were suppressed in GB, suggesting a potential role in fluoride tolerance. The regulatory interaction between Osa-miR39 and its targets was further validated through transient co-expression assays in Nicotiana benthamiana. Moreover, the overexpression of Osa-miR39 in the sensitive rice cultivar IR-64 conferred enhanced fluoride tolerance concomitant with repression of OsNCED genes. Collectively, these findings identify Osa-miR39 as a key regulator of fluoride stress tolerance in rice.