Integrated GWAS Candidate Prioritization, Moso Bamboo Transcriptome Screening and Diverse Bamboo Shoot Multi-Omics Reveal a Multi-Layer Framework for Bamboo Property Formation

Bamboo shoot development influences subsequent culm architecture and material properties, but the biological relevance of GWAS-derived candidates remains unclear. A stepwise candidate-prioritization strategy integrated 99 previously reported property-associated candidates with large-scale moso bamboo transcriptome screening, multi-species bamboo shoot transcriptome–metabolome data, and qRT-PCR analysis. The candidates were classified into three functional layers: environmental adaptation/stress signaling, carbohydrate metabolism/carbon allocation, and cell wall biosynthesis/remodeling. A rule-based ranking that balanced candidate representation across the three functional categories retained 44 genes for transcriptomic evaluation, of which 30 showed strong or moderate expression support across 90 comparisons. Cell wall biosynthesis/remodeling genes exhibited the broadest transcriptional responses, whereas carbohydrate- and regulatory-related genes provided complementary metabolic and upstream evidence. Correlation analysis across 24 matched shoot variables and 5059 metabolites prioritized PH02Gene17228, PH02Gene00247, and PH02Gene51360, which were associated with amino acid/nitrogen metabolism, hormone/signaling-like metabolites, and organic acid/central carbon metabolism, respectively. qRT-PCR analysis independently supported their expression patterns in developing bamboo shoots. These results support a working model in which regulatory signaling, carbon allocation, and cell wall remodeling jointly contribute to bamboo property-related variation. The prioritized genes provide targets for functional validation and may inform future marker development and molecular breeding aimed at improving bamboo culm quality and material properties.