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High-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap Mushroom Stropharia rugosoannulata

Summary

Scientists developed a new genetic tool called cgMNP markers to accurately identify different strains of wine cap mushrooms (Stropharia rugosoannulata). By analyzing the DNA of 105 mushroom strains collected from across China, they discovered that a single gene containing 865 genetic variations was sufficient to distinguish between all cultivated varieties. This breakthrough provides a practical way for mushroom farmers and researchers to identify specific strains quickly, which is important for breeding better mushrooms and maintaining quality in commercial production.

Background

Stropharia rugosoannulata is an economically important edible mushroom with substantial annual production exceeding 490,000 tons in China. Despite its ecological and industrial significance, accurate strain-level identification remains challenging due to limited genomic resources and lack of high-resolution molecular markers.

Objective

To develop core gene-associated multiple nucleotide polymorphism (cgMNP) markers for efficient strain discrimination in S. rugosoannulata and establish a framework for high-resolution strain identification applicable to fungal species.

Results

Analysis identified over 2.7 million SNPs across the genome, with 2,205 SNPs associated with 83 core genes. The most variable gene, Phosphatidate cytidylyltransferase mitochondrial, contained 865 SNPs enabling 100% discrimination of all 85 cultivars. Phylogenetic analysis revealed two distinct cultivar pedigrees with pronounced genetic differentiation and nucleotide diversity (π) ranging from 0.0000 to 0.0160 across core genes.

Conclusion

cgMNP markers provide a robust and transferable framework for high-resolution strain identification in S. rugosoannulata and demonstrate promise for broader fungal phylogenomics applications. These findings establish a genomic foundation for advancing breeding programs, conservation strategies, and functional genomics while offering a universal tool for strain identification across diverse fungal taxa.
  • Published in:Microorganisms,
  • Study Type:Genomic Analysis Study,
  • Source: PMID: 40732194, DOI: 10.3390/microorganisms13071685
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