Aeronautical Mutagenesis and Whole-genome Resequencing Reveal the Genetic Basis of Color Change in Naematelia aurantialba

Abstract

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.

Keywords: Naematelia aurantialba; aeronautical mutagenesis; candidate gene; color-changing; whole-genome resequencing.

Figure 1.

Strain control chart. The yellow color is the space mutagenized strain, and the white color is the control strain.

Figure 2.

Distribution of SNPs and InDels on 12 chromosomes. (A) SNP distribution density map; (B) InDels distribution density map. (A, B) The distribution of SNPs and InDels across the 12 chromosomes, based on the comprehensive analysis of all strains included in the study (both the original 25 strains stored at 4 °C and the 29 strains in the experimental group). The plots highlight the overall genetic variation without distinction between the different strain groupings.

Figure 3.

Genetic diversity analysis. (A) Phylogenetic tree analysis illustrating the genetic relationships among different strains. The tree is color-coded to represent three distinct genetic groups: green for group 1, red for group 2, and blue for group 3; (B) principal component analysis (PCA) plot showing the genetic variation among strains. The plot displays the first two principal components (PC1 and PC2) that explain the maximum variance in the data. Different colors represent different sub-populations: green for Sub-pop1, red for Sub-pop2, and blue for Sub-pop3; (C) Kinship analysis represented as a heatmap showing the pairwise relatedness coefficients among the strains. The color gradient from blue to red indicates the degree of kinship, with red representing higher positive correlations and blue representing higher negative correlations; (D) selection signal analysis with fixation index (Fst) values between different subgroups. The size of the circles represents the strength of the selection signal, with larger circles indicating higher Fst values, suggesting stronger selection pressures.

Figure 4.

Proportion of mutation sites in each genomic region. This bar plot shows the distribution of mutation sites across different genomic regions: downstream (DOWNSTREAM), exon (EXON), intergenic (INTERGENIC), intron (INTRON), and upstream (UPSTREAM). The y-axis represents the ratio (%) of mutation sites in each region, and the x-axis lists the different genomic regions. The color-coded bars correspond to the legend, indicating the type of genomic region each bar represents.

Figure 5.

Venn diagram of various types of mutation sites. (A) SNP mutation Venn diagram showing the overlap of unique and shared SNP sites among five different strains (D3A, D25A, D40A, D13A, D60A, and D2A). The numbers within each section represent the count of SNPs; (B) InDels mutation Venn diagram illustrating the overlap of unique and shared InDel sites among the same strains. The numbers within each section represent the count of InDels; (C) SNP–InDels mutation Venn diagram showing the combined overlap of SNP and InDel sites among the strains. The numbers within each section represent the count of combined SNP and InDel sites.

Figure 6.

Relative expression levels of the candidate gene NAU27003649. Control represents the white strain; test represents the yellow strain. **p<0.01.