Revealing the genetic diversity in the global ex situ sweetpotato collection with next generation sequencing technologies

Abstract

The in trust sweetpotato accessions housed at the International Potato Center, Lima, Peru (CIP) represent a large genetic resource collection of this important staple crop, with almost 6, 000 cultivated accessions and 904 crop wild relatives (CWRs). The entire cultivated collection (5,930 accessions of which 22 were tetraploids), was genotyped using high-density Diversity Arrays Technologies sequencing (High Density DArTseq) producing 110,428 SilicoDArT markers (presence-absence variation, PAV) and 94, 096 single nucleotide polymorphic (SNPs) markers. After filtering the data, 57,715 SilicoDArTs and 20,101 SNPs were used for analysis. Genetic identity, diversity, and population structure within the sweetpotato germplasm collection were assessed. Phylogenetic analyses revealed the intraspecific relationships within the entire ex situ sweetpotato collection maintained at CIP. High redundancy was observed in materials from Peru and Latin America, matching and confirming morphological assessments and previous data from SSR markers. Based on the SilicoDArT marker data and a cutoff threshold of ≤97.5% genetic similarity, approximately 3,431 accessions (58.07% of the cultivated collection) are genetically distinguishable (non-redundant) accessions. This suggests that much of the collection is highly duplicated or genetically similar and could potentially be archived to save resources, as clonal collections are expensive to maintain. Population structure analyses indicated support for four ancestral populations and revealed low levels of genetic admixture among the inferred populations. This was especially true for germplasm derived from Peru and Africa. A core collection of 342 accessions was constructed from the 3,431 non-redundant subset (representing 9.97% of this subset). Additionally, material from the sweetpotato collection at the Centre for Pacific Crops and Trees (CePaCT) in Fiji was genotyped to rationalize the material between the CePaCT and CIP germplasm collections. Some genetic redundancy was also revealed in the CePaCT collection, with accessions bearing the same name but originating from different sources, having identical fingerprints via DArTseq markers. To the authors’ knowledge, this is the first report of high-density genotyping of an entire cultivated sweetpotato germplasm collection.