Fargesia rufa, one of the main food bamboo species for giant pandas, exhibits significant changes in nutritional composition with altitudinal gradient. However, the molecular mechanisms underlying this adaptation and its impact on the foraging behavior of giant pandas remain unclear. In this study, metabolomic and transcriptomic analyses were integrated to compare gene expression and metabolite profiles in leaves and rhizomes of F. rufa collected from 1000 m and 2000 m altitudes. With increasing altitude, 710 metabolites were up-regulated and 1032 were down-regulated in the leaves of F. rufa, whereas 684 metabolites were up-regulated and 1342 were down-regulated in the rhizomes; only 629 differential metabolites were shared between the two organs. Further analyses revealed that F. rufa responds to altitudinal changes through organ-specific metabolic reprogramming: leaves adopt a “metabolic conservation” strategy, downregulating the majority of flavonoid and phenylpropanoid metabolites, while rhizomes take an “active storage” strategy, significantly enhancing secondary metabolite synthesis and starch accumulation. This functional differentiation is consistent with the biological roles of the organs: the metabolic simplification of leaves may enhance the palatability of high-altitude leaves, while the nutritional reserves in rhizomes support bamboo shoot emergence. This study reveals the molecular mechanisms of bamboo’s altitudinal adaptation at the organ level, clarifies the intrinsic link between plant metabolism and animal diet, and provides a theoretical basis for giant panda habitat conservation.

Bamboo shoots, as the most nutritionally valuable food source for giant pandas during key reproductive seasons, are critical for conservation because their availability and timing directly influence panda foraging and habitat use. However, the molecular mechanisms through which altitudinal temperature variation governs rhizome shooting in staple food bamboos remain largely unknown. Here, we performed integrated metabolomic and transcriptomic analyses of Fargesia rufa rhizomes collected along an elevational gradient (1000 m, 1500 m, and 2000 m), with a critical paired comparison at 2000 m between a non-shooting cold gully-edge site (16.4 °C) and a shooting warm gully-center site (21.1 °C), where soil temperature is elevated by approximately 4 °C due to prolonged solar exposure. Our results demonstrate that soil temperature, rather than elevation per se, acts as the primary driver of rhizome shooting, with an apparent threshold near 20 °C. A core shooting metabolome (CSM) comprising 843 metabolites was consistently accumulated across all shooting conditions, which featured gibberellin/auxin precursors, TCA cycle intermediates, and phenylpropanoid compounds. Correspondingly, a core shooting transcriptome (Rh_shooting) of 10,970 genes was identified, which resolved into three functionally distinct temporal clusters: “shooting-on” (activated upon threshold crossing, enriched in hormone signaling and cell wall metabolism), “temperature-dose” (progressively upregulated with rising temperature, enriched in energy metabolism and defense), and “microenvironment-enhanced” (specifically upregulated in the high-elevation warm gully, enriched in photosynthesis and antioxidant pathways). Integrative network analysis further revealed zeatin riboside and multiple hub genes as central coordinators linking hormone signaling, energy metabolism, and cell wall remodeling. Collectively, these findings establish a molecular framework linking altitudinal temperature variation to bamboo rhizome regeneration—a process that directly determines the spatiotemporal availability of bamboo shoots for giant pandas. This work provides mechanistic insights into giant panda foraging ecology and has direct implications for predicting habitat quality under climate change and informing evidence-based conservation strategies for this flagship species and its critical food resource.