Transcriptome Analysis Reveals a Potential Response Mechanism of Morchella to Soybean Meal Addition

Morchella is an edible and medicinal fungus valued for its distinctive flavor and nutritional properties. However, unstable yield and quality remain major constraints on its commercial cultivation. Although soybean meal is used as an organic nutrient supplement in edible mushroom production, its effects on protein accumulation and transcriptional regulation in Morchella remain unclear. This study combined fruiting-body protein measurements with transcriptome analysis to compare soybean meal supplied through soil application or exogenous nutrient bags and to characterize tissue-specific responses in the cap and stipe. Soybean meal increased protein content in an application method-, concentration-, and tissue-dependent manner. Soil application was more effective than nutrient-bag supplementation, while stipes exhibited a stronger transcriptional response than caps. RNA sequencing detected 11,982 expressed genes and revealed both shared and tissue-specific responses to the two supplementation methods. Gene Ontology analysis showed broadly similar functional categories among comparison groups, whereas KEGG enrichment analysis revealed distinct metabolic responses. In caps, soil application was associated with glutathione metabolism and amino sugar and nucleotide sugar metabolism, while nutrient-bag supplementation was associated with the pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, and pentose and glucuronate interconversions. In stipes, the genes involved in ribosome and aminoacyl-tRNA biosynthesis were downregulated under soil application and nutrient-bag supplementation, respectively. Weighted gene co-expression network analysis identified three modules associated with protein content and highlighted ribosome, aminoacyl-tRNA biosynthesis, glycerophospholipid metabolism, and arginine biosynthesis as candidate pathways. The most highly connected genes in each key module were identified as hub genes, and selected expression patterns were supported by qRT-PCR. These findings provide a transcriptomic framework for understanding how soybean meal supplementation is associated with protein accumulation and tissue-specific physiological responses in Morchella.