Genetic diversity and population structure of the USDA sweetpotato (Ipomoea batatas) germplasm collection using GBSpoly

Authors: Wadl, Phillip; OLUKOLU, BODE - University Of Tennessee; Branham, Sandra; Jarret, Robert - Bob; YENCHO, G. CRAIG - North Carolina State University; JACKSON, D. MICHAEL - Collaborator

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/23/2018
Publication Date: 8/21/2018
Citation: Wadl, P.A., Olukolu, B.A., Branham, S., Jarret, R.L., Yencho, G., Jackson, D. 2018. Genetic diversity and population structure of the USDA sweetpotato (Ipomoea batatas) germplasm collection using GBSpoly. Frontiers in Plant Science. 9:1166. https://doi.org/10.3389/fpls.2018.01166.
DOI: https://doi.org/10.3389/fpls.2018.01166

Interpretive Summary: Sweetpotato plays a critical role in food security and is the third most important root crop worldwide following potatoes and cassava. The crop in the United States (US) is valued at over $700 million dollars annually. Improvement of sweetpotato through plant breeding is difficult because of the complex genetics and high variability within the crop. However, marker-assisted breeding allows assessment of young plants for multiple traits of interest, greatly reducing costs associated with growing the plants to maturity. This approach is especially valuable for sweetpotato, where the expense of long-term field evaluation is a major limiting factor in breeding efforts. Furthermore, genomic data can be used to determine genetic relationships among parental lines and potentially identify new sources of genetic variation associated with resistance/tolerance to pests, disease, environmental stress, and other high value traits. The US sweetpotato germplasm collection is maintained by the USDA, ARS, Plant Genetic Resources Conservation Unit (PGCRU) and provides the genetic foundation that supports ongoing research in breeding and genetics programs for the improvement of sweetpotato. The USDA sweetpotato breeding program at the US Vegetable Laboratory in Charleston, SC (USVL) was initiated more than 45 years ago with the goal of developing new sweetpotato material that is resistant to soil insect pests while maintaining good horticultural characteristics. There is a lack of knowledge with regard to the level of genetic diversity within both the PGCRU and USVL sweetpotato collections. USDA scientists in collaboration with researchers at North Carolina State University and the University of Tennessee evaluated genetic diversity of the PGCRU and USVL sweetpotato collections using over 30,000 DNA markers. Our results indicate that there is high genetic diversity within these US sweetpotato collections. The DNA markers developed in this study provide an important genomic resource for the sweetpotato community and contribute to our understanding of the genetic diversity present in the US sweetpotato germplasm.

Technical Abstract: Sweetpotato, Ipomoea batatas, plays a critical role in food security and is the third most important root crop worldwide following potatoes and cassava. Sweetpotato is an important crop in the United States (US) and is valued at over $700 million dollars annually. The sweetpotato germplasm collection of the US is maintained by the USDA, ARS, Plant Genetic Resources Conservation Unit and provides the genetic basis for sweetpotato crop improvement. To date, no genome-wide assessment of genetic diversity within this collection has been reported. In our study, population structure and genetic diversity of 417 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 over 30,000 single nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) protocol optimized for highly heterozygous and polyploid species. Bayesian clustering analyses (STRUCTURE) grouped the accessions into four genetic groups (Central American, North American, South American, other regions) and indicated a high degree of mixed ancestry. A neighbor-joining cladogram, principal components analysis, and a genetic distance matrix of the accessions supported the population structure analysis. Pairwise FST 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.