Frequent strain degeneration during subcultivation, characterized by impaired sporulation and fruiting body formation, represents a major constraint in fungal agricultural production. Our study systematically investigated two naturally degenerated Lentinula edodes strains classified as abortive (Abt: L808-13, L808-14) and malformed (Abn: L808-18) fruiting-body phenotypes, through comprehensive phenotypic characterization, enzymatic profiling, thermotolerance assessment, and transcriptomic analysis. While vegetative growth remained unaffected, degenerated strains exhibited premature hyphal knotting, significantly reduced thermotolerance, and Abn-specific suppression of carboxymethyl cellulase (CMCase) activity. Comparative transcriptomics revealed 1239 and 582 differentially expressed genes (DEGs) in Abt and Abn groups, respectively, accompanied by a global dysregulation in carbohydrate catabolism, phospholipid metabolism, and redox homeostasis. Furthermore, protein–protein interaction (PPI) networks and RT-qPCR data highlighted 12 core hub genes enriched in glycoside hydrolysis, cytochrome P450 signaling, and membrane lipid dynamics. These findings provide mechanistic insights into the molecular basis of fruiting body degeneration and establish a foundation for developing diagnostic indicators to screen for early-stage degeneration in industrial mushroom production.

The cultivation of Hericium erinaceus in China accounts for about 85% of the global supply. Its decentralized production systems have developed across diverse climate zones, leading to distinct, location-specific practices recorded in local technical standards. This scoping review synthesizes these empirical protocols from five agro-climatic regions. It illustrates how adaptive strategies such as cold-tolerant strains in the northeast and market-driven precision in the subtropics are associated with yield stability. These practices reflect two interconnected forms of diversity. One is the diversity of cultivation systems themselves, from forest-based methods to industrial-scale production systems. The other is the diversity of locally adapted strains developed for specific environments. We use the Intelligent Germplasm–Cultivation–Processing–Market (GCPM) Integration framework to connect local practices with broader questions of systemic resilience. The evidence draws on field-validated standards, not controlled experiments, reflecting the current state of research. This work presents China’s practical knowledge as a reference for designing context-sensitive, climate-resilient cultivation systems elsewhere, suggesting that resilience may depend more on intelligent adaptation to local conditions than on one-size-fits-all solutions.