Omics-based approaches for decoding root dynamics in legumes

Legume roots serve as dynamic interfaces for nutrient uptake, symbiotic nitrogen (N) fixation, and adaptation to environmental stresses such as drought, salinity, extreme temperatures, and flooding. Despite their key role in legume productivity and sustainability, the complex and hidden nature of root systems has hindered their integration into breeding programs. This review synthesizes omics-based advances including genomics (GWAS/QTL mapping), transcriptomics, proteomics, metabolomics, epigenomics, and phenomics that have revolutionized our understanding of root system architecture (RSA) and its regulation in major legumes including soybean, chickpea, lentil, pea, pigeonpea, cowpea, and groundnut. We discuss how high-resolution genomic mapping, single-cell and spatial transcriptomics, and epigenetic profiling have identified key regulators of nodulation, root development, and stress responses. Proteomic and metabolomic studies further uncover molecular networks regulating aquaporin activity, ROS (Reactive Oxygen Species) detoxification, carbon-N metabolism, and cell-wall remodeling, linking these pathways to enhanced resource-use efficiency and resilience. Integration with high-throughput root phenotyping platforms such as RhizoTubes, DIRT/3D, and tomographic imaging (X-ray CT/MRI) enables precise visualization of root traits and facilitates multi-omics data integration. Collectively, these approaches provide a systems-level understanding of RSA plasticity and its genetic control. The review also highlights how translating omics discoveries into breeder-ready biomarkers and genomic selection models can accelerate the development of climate-resilient legume ideotypes with deeper, more efficient of RSA. This article serves as a valuable reference for researchers aiming to bridge molecular insights and field applications toward sustainable legume improvement.