The genetic and developmental enigma of rhizomes: crucial traits with limited understanding

Rhizomes play fundamental roles in plant evolution, persistence, and environmental adaptation by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across diverse plant lineages, the genetic and developmental regulation of rhizomes remains poorly characterized. Here, we synthesize findings from in vitro induction studies, in vivo physiological and developmental analyses, quantitative trait loci (QTL) mapping, comparative transcriptomics, and limited functional studies to evaluate current knowledge and highlight outstanding questions in rhizome biology. Results show that phytohormones are central regulators of rhizome initiation and growth, with effects mediated in a context-dependent manner through interactions with environmental and developmental cues. Across rhizomatous species, traits such as rhizome initiation, branching, and elongation are typically under polygenic control, although comparatively simpler genetic architectures have been documented in emerging model systems like Mimulus. Transcriptomic analyses further highlight hormone signaling, stress-response, and carbohydrate metabolism pathways as key regulatory components. However, few genes have been functionally validated, underscoring the need for experimentally tractable systems for genetic dissection. Perennial Mimulus species are proposed as promising models for rhizome research due to their experimental accessibility, ecological relevance, and established genomic resources. Integrated approaches leveraging fine-mapping, near-isogenic lines, multi-omics network reconstruction, and genome editing are poised to accelerate the discovery of causal loci and regulatory networks underlying rhizome development, thereby illuminating key processes involved in plant adaptation and perenniality, with direct implications for evolutionary biology and crop improvement.