Fig 1.
Elevation map with the geographic location of A. duranensis accessions.
Colored circles correspond to the five populations identified by the sparse non-negative matrix factorization sNMF method (Fig 2). Color scale bar indicates meters above sea level. The map was generated with the raster R package [32] using the ETOPO2 data with a 15 arc-second resolution [33].
Table 1.
Accessions of A. duranensis used in this study listed in group order.
Fig 2.
Genetic diversity of A. duranensis represented in the USDA peanut germplasm collection.
(A) Plot of ancestry coefficients obtained from the sparse non-negative matrix factorization analysis (sNMF) for 58 individuals. Each individual genotype is represented by a vertical bar. Numbers 1–5 represent the groups. References for genotype IDs are listed in Table 1. (B) Neighbor-Joining dendrogram based on 2810 SNPs. (C) Population structure based on the first three components of the PCA. Colored circles in (A) and (B) correspond to the five ancestral populations identified by sNMF.
Fig 3.
Correlation between the first three principal components (Bio-PC1–3), elevation, and environmental variables (BIO1–BIO19).
Positive correlations are represented in blue and negative correlations in red. Color intensity and size of squares are proportional to the correlation coefficients (p < 0.01). Bioclimatic variables (BIO1-BIO19) are described in S1 Table.
Fig 4.
Manhattan plot for SNP p-values from the LFMM2 analysis.
(A) First principal component (Bio-PC1). (B) Second principal component (Bio-PC2). Single Nucleotide Polymorphisms that were significant after adjusting for multiple testing are above the grey dotted line.
Fig 5.
Evaluation of Leaf spot resistance of final defoliation (FD).
(A) Manhattan plot for SNP p-values from the LFMM2 analysis. SNPs that remained significant after adjusting for multiple testing (q < 0.05) are above the gray dot line. (B) Accession PI 468197. (C) Accession PI 497268.