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

Rhizomes, horizontal underground stems, play fundamental roles in plant persistence and perennial growth by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across plant lineages, the genetic and developmental regulation of rhizomes remains poorly characterized. Here, we synthesize findings from in vitro induction studies, in vivo 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 from both in vitro and whole-plant studies show that phytohormones, particularly auxin, cytokinin, and gibberellin, 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 often polygenic, although comparatively simpler genetic architectures associated with repeated rhizome evolution 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 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, and gene editing are poised to accelerate discovery of causal loci and regulatory networks underlying rhizome development, thereby clarifying the genetic and developmental bases of rhizome traits underlying their repeated evolution, with broader implications for perenniality, environmental responses, and crop improvement.