Construction of an SNP Fingerprinting Database and Population Genetic Analysis of <i>Auricularia heimuer</i>

<i>Auricularia heimuer</i> is the second most widely cultivated edible fungus in China, with significant food and medicinal value, and is highly popular throughout Asia and globally. However, the differentiation of <i>A. heimuer</i> is simple, as its morphology is characterized by a small “black disc”, making it difficult to distinguish among germplasms with highly similar agronomic traits, thus posing challenges for germplasm identification. To address this issue, this study conducted whole-genome resequencing analysis on 150 <i>A. heimuer</i> germplasms. Through filtering 9,589,911 SNPs obtained from 280 G resequencing data, a total of 1,202,947 high-quality SNP sites were identified. Based on these high-quality SNPs, population structure analysis, principal component analysis (PCA), and phylogenetic tree analysis revealed that the 150 <i>A. heimuer</i> germplasms could be divided into five groups, with wild strains from the same geographical origin exhibiting significant geographical clustering patterns. This finding underscores the relationship between the genetic diversity of wild <i>A. heimuer</i> and its geographical distribution in China. A further selection of 71 SNP sites was made, and 61 KASP markers were successfully developed using kompetitive allele-specific PCR (KASP) technology, with 54 of them demonstrating good polymorphism. The average values for the polymorphism information content (PIC), minor allele frequency (MAF), gene diversity, and heterozygosity of these core KASP markers were 0.34, 0.35, 0.34, and 0.43, respectively. Based on the 54 core KASP markers, a DNA fingerprinting map of the 150 <i>A. heimuer</i> germplasms was constructed in this study. The findings provide important molecular marker resources and theoretical support for the identification of <i>A. heimuer</i> germplasm, molecular marker-assisted breeding, and the selection of superior varieties.