Genetic diversity analysis and multi-fingerprint map construction of Naematelia aurantialba germplasm resources

Abstract Due to its asexual reproduction characteristics, Naematelia aurantialba faces limitations in genetic diversity, germplasm identification, and intellectual property protection, necessitating molecular-level approaches to address these challenges. This study utilized resequencing data from 36 germplasm resources of N. aurantialba to conduct a population structure analysis and construct fingerprint maps based on core multinucleotide polymorphisms (MNPs), core single nucleotide polymorphisms (SNPs), and core insertions/deletions (INDELs), while also calculating genetic similarity among strains based on different variant sites. The results indicated that when K = 2, the genetic structure of individual strains was more distinctly divided, a finding corroborated by both the phylogenetic tree and the principal component analysis. A total of 108 core MNPs (comprising 333 SNPs), 54 core SNPs, and 40 core INDELs were identified. Fingerprint maps for the 36 germplasm resources of N. aurantialba were constructed using combinations of different core variant sites. In strains with high similarity, the genetic similarity identified by the three types of core variant sites was all above 97%, and could reach up to 100%, achieving mutual complementary validation. Therefore, it is preliminarily determined that strains with genetic similarity above 97% can be considered as the same strain. These achievements provide valuable resources for the identification of N. aurantialba germplasm and for intellectual property protection. Additionally, the multi-fingerprint map construction method offers new insights for research on other edible fungi.