Harnessing microRNA regulatory networks for engineering climate resilience and nutritional enhancement in millets

Abstract

Millets are increasingly promoted as climate-resilient nutri-cereals that can stabilize production and support nutritious diets under drought, heat, salinity, and low-input farming. MicroRNAs (miRNAs) provide a powerful post-transcriptional regulatory layer that regulates stress signaling, crop development, nutrient homeostasis, and grain filling by targeting key transcription factors and transporter networks. Millet miRNA research remains at an early developmental stage. To date, most studies have focused predominantly on miRNA identification and expression profiling, while rigorous functional characterization and mechanistic dissection of regulatory networks are still limited. Moreover, integration of miRNA dynamics with genotype (G) × environment (E) interactions, particularly under field-relevant stress conditions, remains insufficiently explored. In this review, we synthesize stress- and nutrition-associated miRNAs reported across major cereals, highlighting conserved regulatory modules, and summarize emerging millet-specific candidates linked to drought, salinity, grain quality, and micronutrient accumulation. We critically evaluate methodological gaps, such as incomplete degradome support, inconsistent phenotyping, and limited grain ionomics, that constrain translational application to breeding. Finally, we propose a practical roadmap that combines tissue- and stage-resolved miRNA atlases, target validation using degradome sequencing, RNA Ligase-Mediated Rapid Amplification of cDNA Ends (RLM-RACE), and reporter assays, together with functional intervention platforms such as Short Tandem Target Mimic (STTM), artificial miRNAs (amiRNAs), and CRISPR-mediated editing of miRNA loci or target sites, all integrated with marker-enabled selection and genomic prediction. Advancing from descriptive miRNA catalogues toward experimentally validated regulatory networks will enable miRNA-based breeding and genome editing for climate-smart, micronutrient-dense millet cultivars.