FIGURE S1 | QC Boxplot showing distribution of quality scores of raw reads in a multiplexed library containing 96 Ipomoea batatas accessions. Buffer sequence lie within the first 8 base calls, while variable barcodes (6–9 bp) lie at position 14–17 bp.

FIGURE S2 | Proportion raw reads matching both reference subgenomes (6x genotypes) and those specific to each of the subgenomes (4x and 2x genotypes derived Ipomoea trifida and I. triloba, respectively).

FIGURE S3 | Boxplot shows relatively uniform read depth across individual samples and genomic loci after de-multiplexing pool samples. Only genotypes with 6 alleles/dose are shown here.

FIGURE S4 | Bar plots of Bayesian assignment probabilities for each Ipomoea batatas accession analyzed with segregating 32,784 SNPs using the program STRUCTURE for K = 4. The x-axis indicates accession and the y-axis indicates the assignment probability of that accession to each of the four clusters. Each vertical line represents an individual’s probability of belonging to one of K clusters (represented by different colors) or a combination of if ancestry is mixed. The asterisk (∗) indicates the cultivar Porto Rico, which is a foundational line of the sweetpotato industry in the US. The plus sign (+) indicates that this accession was used as parental material in the mass selection populations developed by Jones et al. (1991). The USDA, ARS, US Vegetable Laboratory (USVL) W-lines and USVL-lines originate from the mass selection populations. Information for all accessions is found in Supplementary Table S1.

FIGURE S5 | Linkage disequilibrium estimates (r2) of all genome-wide marker pairs plotted against corresponding interval between marker pairs. Curve (blue line) based on game smoothing method function shows distribution of all data points. Top and middle plot based on genotype data with allelic dosage information, while bottom plot is based on diploidized genotypes.

TABLE S1 | Information of Ipomoea batatas accessions analyzed by GBSpoly.

TABLE S2 | Pairwise genetic distance matrix between Ipomoea batatas accessions.

TABLE S3 | Information for individual SNPs used for data analyses.

DATASET S1 | Structure data file for Ipomoea batatas accessions.