Symbiotic Cultivation of Gastrodia elata: Armillaria Strain Selection Reprograms Carbon Allocation to Balance Tuber Yield and Phenolic Glycosides

Gastrodia elata is a fully mycoheterotrophic orchid whose tuber development depends on carbon delivered by Armillaria fungi. Its formal inclusion in China’s “medicine and food homology” catalog has intensified demand for cultivated tubers combining high yield with consistent bioactive quality. Here, we tested whether Armillaria mellea strains steer host carbon allocation between biomass accumulation and phenolic glycoside biosynthesis. Using a standardized EPS symbiotic cultivation system (AM1, AM2, AM3; n = 3 biological replicates per strain), we integrated agronomic traits with widely targeted metabolomics and RNA-seq transcriptomics, including weighted gene co-expression network analysis (WGCNA). AM3 produced the highest tuber yield and higher primary carbon status (PCAI), but lower gastrodin/parishin-type phenolic glycosides and lower allocation efficiency (BER), whereas AM1 showed a quality-dominant profile with significantly higher BER. WGCNA highlighted an AM3-associated module enriched in starch-biosynthetic genes, and PCAI was strongly negatively correlated with the weighted Parishin-Gastrodin Index (wPGI) across samples (n = 9), consistent with a carbohydrate-storage versus phenolic-glycoside trade-off. These results indicate that fungal strain identity functions as an external regulator of source–sink dynamics in G. elata, supporting “precision symbiosis” for food-grade versus medicinal-grade production.