Development of KASP markers, SNP fingerprinting and population genetic analysis of Auricularia cornea

Auricularia cornea is an important edible and medicinal mushroom; however, its genetic improvement has been constrained by the limited understanding of its genetic diversity and the absence of robust molecular markers. In this study, we resequenced 140 accessions and identified 2,512,778 high-confidence SNPs after stringent quality filtering. Population structure, principal component, and phylogenetic analyses consistently resolved the accessions into four distinct genetic groups. Wild accessions from similar geographic regions exhibited pronounced regional clustering, indicating a strong correspondence between genetic differentiation and geographic distribution. Based on the genome-wide SNP dataset, we developed a core panel of 50 highly informative Kompetitive Allele-Specific PCR (KASP) markers. These markers exhibited high levels of polymorphism, with mean polymorphism information content (PIC), minor allele frequency (MAF), gene diversity, and heterozygosity values of 0.36, 0.35, 0.25, and 0.43, respectively. Using this marker panel, we established a standardized DNA fingerprinting scheme for all accessions, facilitating precise and high-resolution germplasm discrimination. This core KASP marker set and reference fingerprinting system provide robust molecular tools for germplasm authentication, variety validation, and marker-assisted breeding, thereby laying a solid foundation for advancing the genetic improvement and efficient utilization of A. cornea resources.