Genetic diversity, population structure, and selection of core germplasm sets from the USDA sweetpotatoe (lpomomea batatas) collection

Authors: Slonecki, Tyler; Rutter, William; OLUKOLU, BODE - University Of Tennessee; YENCHO, G. - North Carolina State University; Jackson, D; Wadl, Phillip

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2022
Publication Date: 2/2/2023
Citation: Slonecki, T.J., Rutter, W.B., Olukolu, B., Yencho, G.C., Jackson, D.M., Wadl, P.A. 2023. Genetic diversity, population structure, and selection of core germplasm sets from the USDA sweetpotatoe (lpomomea batatas) collection. Horticulture Research. https://doi.org/10.3389/fpls.2022.1022555.
DOI: https://doi.org/10.3389/fpls.2022.1022555

Interpretive Summary: Sweetpotato plays a crucial role in maintaining food security worldwide. Plant breeders are tasked with introducing, preserving, and combining desirable sweetpotato traits to meet stakeholder and consumer needs. Crop germplasm collections conserve genetic diversity and provide a critical source for plant breeders by providing diverse plant material for use in crop improvement programs. However, the complex genetic makeup of sweetpotato makes breeding very difficult without extensive genetic and computing resources. In this study, we characterized the genetic diversity and population structure of the USDA sweetpotato germplasm collection and identify a core set of accessions to allow for more efficient breeding program maintenance and selection in future studies. The results of our study will improve the efficiency and efficacy of the characterization of this sweetpotato collection and contribute significant genetic resources toward collective sweetpotato knowledge.

Technical Abstract: Sweetpotato (Ipomoea batatas) is the 6th most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the USDA, ARS, Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-by-sequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, core sets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and core germplasm sets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.