Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection

Tyler J Slonecki; William B Rutter; Bode A Olukolu; G Craig Yencho; D Michael Jackson; Phillip A Wadl

doi:10.3389/fpls.2022.1022555

Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection

Front Plant Sci. 2023 Feb 2:13:1022555. doi: 10.3389/fpls.2022.1022555. eCollection 2022.

Authors

Tyler J Slonecki¹, William B Rutter¹, Bode A Olukolu², G Craig Yencho³, D Michael Jackson¹, Phillip A Wadl¹

Affiliations

¹ United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States.
² Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States.
³ Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States.

Abstract

Sweetpotato (Ipomoea batatas) is the sixth 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 United States Department of Agriculture (USDA), Agricultural Research Service (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, breeder germplasm subsets 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 breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.

Keywords: DAPC; SNPs; USDA germplasm; breeder subsets; convolvulaceae; genotyping-by-sequencing (GBS); polyploid; sweetpotato.