Multilocus genetic and functional profiling of Indian-origin Lentinula edodes strains: Implications for cultivation and nutraceutical breeding.

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Citation abstract

Lentinula edodes (shiitake mushroom) is a widely cultivated edible and medicinal fungus, valued for its bioactive compounds. While East Asian strains have been well studied, Indian populations remain under-characterized. This study explores the genetic and functional diversity of five Indian-origin L. edodes strains (DMRO-34, DMRO-35, DMRO-356, DMRO-388s, and DMRO-623) using multilocus sequence analysis targeting ITS, LSU, TEF1-α, and β-tubulin regions (660-1200 bp). Phylogenetic analyses (neighbor-joining, maximum likelihood, and Bayesian inference) revealed three well-supported clusters (bootstrap > 90 %; posterior probability > 0.95). AMOVA (p < 0.01) and diversity indices confirmed significant genetic differentiation. DMRO-356 and DMRO-388s showed close genetic relatedness and phenotypic consistency, while DMRO-623 was genetically distinct. Nonsynonymous mutations were identified in genes linked to stress response, metabolism, and β-glucan biosynthesis. Transcriptomic profiling showed higher expression of β-glucan synthesis genes (FKS1, GLS2) in DMRO-356 and DMRO-388s, indicating potential for nutraceutical use. DMRO-623 exhibited upregulation of stress-responsive genes (SOD, HSP70), suggesting adaptation to environmental stress and suitability for resilient cultivation. Compared to traditional markers (RAPD, SSR), the multilocus approach offered improved resolution for distinguishing closely related strains. Strong correlations (r = 0.80-0.88) between genetic variation and key traits (β-glucan content, antioxidant activity, yield) emphasize the functional significance of the observed diversity. This first multilocus-based study of Indian-origin L. edodes strains provides a genomic framework for marker-assisted breeding, trait optimization, and conservation, supporting their commercial and ecological value in diverse environments.