Research on Bamboo Shoot Bud Development: A Leap from Tissue Heterogeneity to Single-Cell Spatial Atlas

China has rich bamboo resources, with Moso bamboo (Phyllostachys edulis) being the most economically important species. Bamboo shoot bud development directly determines the eating quality of the shoots and the properties of bamboo materials; however, the intrinsic biological characteristics of this process have hindered foundational research. Traditional methods using whole shoot buds or mixed tissues obscure cellular and tissue heterogeneity, limiting our mechanistic understanding. This review synthesizes cytological features, molecular networks, and technical limitations pertaining to Moso bamboo shoot bud development, identifying four key bottlenecks: tissue homogenization masking cellular heterogeneity, loss of spatial positional information impeding analysis of position effects, challenges in single-cell technology application due to sample preparation and data interpretation issues, and unresolved coupling between chromatin accessibility and transcriptional regulation. To address these, we propose a core strategy centered on constructing a single-cell resolution, spatially resolved, multi-omics integrated, and functionally validated framework. Key approaches include developing bamboo-specific single-cell sequencing and spatial transcriptomics, integrating positional information with multi-omics data to identify spatially distinct regulatory targets, standardizing technical pipelines and functional validation platforms, and elucidating epigenetic–transcriptional coupling. Overcoming these bottlenecks will reveal the molecular basis of bamboo’s unique developmental patterns and provide key targets for the genetic improvement of the shoot quality and mechanical properties of bamboo.