Naematelia aurantialba, a rare yellow edible fungus with both nutritional and medicinal properties, is of significant importance in industrial cultivation due to its color-changing characteristics. This study was designed to develop novel color-changing germplasm resources and to explore associated functional genes. We applied aeronautical mutagenesis to the strains and utilized whole-genome resequencing to analyze the mutational profiles, thereby identifying candidate genes associated with color change. In the color-changed strains, we detected 201 SNPs and 307 InDels, predominantly located in the upstream (46.83%) and downstream (43.77%) regions of genes. By integrating SNP and InDels data, we identified seven mutational sites that were co-mutated in at least three strains. Gene annotation of these sites revealed 29 candidate genes, including three with unknown functions, which may significantly influence the color change trait in N. aurantialba. qRT-PCR results indicated significant differences in the expression of NAU27003649 between white and yellow strains, suggesting its potential role in the color variation. This research pioneers the application of aviation mutagenesis to generate new germplasm for N. aurantialba, offering new insights into the genetic basis of its color change traits.
