Organ-Specific Gene Expression and Metabolite Accumulation in Fargesia rufa in Response to an Altitudinal Gradient

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.