• Whole-genome resequencing of 140 A. cornea accessions identified 2.51 million SNPs and four genetic groups. • Population structure analysis revealed geographic differentiation of wild germplasm and intergroup overlap with gene flow. • Fifty high-quality SNPs were selected and successfully converted into KASP markers. • A DNA fingerprinting system based on 50 KASP markers was developed for A. cornea germplasm identification. 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 2512,778 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.
Sun et al. (Sun,) studied this question.