miR169f regulation by lncRNA LASSO fine-tunes JA-dependent root immunity in rice

Root immunity is vital for defending plants against soilborne pathogens, yet the regulatory mechanisms underlying this process remain incompletely understood. Here, we characterize a novel regulatory module comprising the long non-coding RNA LASSO, microRNA miR169f, and the transcription factor NF-YA1 that regulates rice root immunity. miR169f overexpression lines were generated and investigated using pathogen susceptibility assays, transcriptome analysis (mRNA-seq), and hormone measurements. Target genes were validated using 5' RLM-RACE (RNA Ligase-Mediated Rapid Amplification of cDNA Ends), degradome sequencing, transient co-expression in Nicotiana benthamiana, and RT-qPCR was used to validate and extend the transcriptome dataset. miR169f-overexpression plants exhibit reduced susceptibility to nematodes and the oomycete Pythium arrhenomanes. On the contrary, lines with reduced miR169f expression (STTM169f) as well as LASSO- and NF-YA1-overexpression lines show enhanced susceptibility. LASSO is rapidly induced in roots in response to nematode secretions, and most likely acts as a target mimic that sequesters miR169f, thereby relieving repression of NF-YA1. The miR169f fine-tunes defence responses by influencing the jasmonic acid (JA) pathway under basal conditions while enabling strong JA-responsive gene activation during nematode infection. This dynamic regulation links post-transcriptional control with hormone signalling to shape root immunity. Together, our results reveal a previously uncharacterized non-coding RNA network that orchestrates root defence responses.