Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly

Abstract

Sweetpotato (Ipomoea batatas) plays a critical role in food security and is the most important root crop worldwide following potatoes and cassava. In the United States (US), it is valued at over $700 million USD. There are two sweetpotato germplasm collections (Plant Genetic Resources Conservation Unit and US Vegetable Laboratory) maintained by the USDA, ARS for sweetpotato crop improvement. To date, no genome-wide assessment of genetic diversity within these collections has been reported in the published literature. In our study, population structure and genetic diversity of 417 USDA sweetpotato accessions originating from 8 broad geographical regions (Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America) were determined using single nucleotide polymorphisms (SNPs) identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species. Population structure using Bayesian clustering analyses (STRUCTURE) with 32,784 segregating SNPs grouped the accessions into four genetic groups and indicated a high degree of mixed ancestry. A neighbor-joining cladogram and principal components analysis based on a pairwise genetic distance matrix of the accessions supported the population structure analysis. Pairwise F_ST values between broad geographical regions based on the origin of accessions ranged from 0.017 (Far East - Pacific Islands) to 0.110 (Australia - South America) and supported the clustering of accessions based on genetic distance. The markers developed for use with this collection of accessions provide an important genomic resource for the sweetpotato community, and contribute to our understanding of the genetic diversity present within the US sweetpotato collection and the species.

Keywords: Convolvulaceae; GBSpoly; SNPs; USDA germplasm; genotyping-by-sequencing; polyploid; sweetpotato.

FIGURE 1

Plot showing read depth thresholds and the associate SNP calling accuracy (or genotype stability with varying read depth).

FIGURE 2

Proportions of dose-dependent genotype calls at two different read depth thresholds of 6, 20, and 45 for 2x, 4x, and 6x genotypes, respectively, (top) and 6, 35, and 100 for 2x, 4x, and 6x genotypes, respectively (bottom).

FIGURE 3

Delta K values for different numbers of populations (K) assumed in STRUCTURE analysis.

FIGURE 4

(A) Bar plots of Bayesian assignment probabilities for each Ipomoea batatas accession analyzed with 32,784 SNPs using the program STRUCTURE for 2 (K = 2) or 4 clusters (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 clusters if ancestry is mixed. (B) Map of the sampled regions for 417 Ipomoea batatas accessions. Pie charts correspond to the population assignment for the four genetic groups defined by the Bayesian assignment of STRUCTURE. Accessions were assigned to a cluster based on probabilities calculated in STRUCTURE, where C1 is red, C2 is green, C3 is blue, and C4 is yellow. A q-value threshold of 0.65 was used to divide the accessions into one of the four clusters or as admixed (gray section of pie charts).

FIGURE 5

Neighbor-joining tree based on genetic distances for 417 Ipomoea batatas accessions from 8 geographical regions using 32,784 single nucleotide polymorphisms. The interior-branch test method (1,000 bootstrap replications) determined branch support and branches of less than 50% confidence were collapsed. Each accession is colored according to their geographical origin, with the RGB color value used in FigTree listed in parentheses. Africa = pink (F70A7B), Australia = yellow (F7DA10), Caribbean = purple (F77AF8), Central America = blue (030EF8), Far East = orange (F96509), North America = turquoise (00CCCC), Pacific Islands = red (BC0302), South America = green (0F890E).

FIGURE 6

Principle components analysis of 417 Ipomoea batatas accessions using 32,784 single nucleotide polymorphisms. The percent variation explained by each principle component is indicated in parentheses. Geographical regions are color-coded according to the legend.