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

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 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.

Dataset Info

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FieldValue
Authors
Wadl, Phillip A.
(ORCID)
Olukolu, Bode A.
(ORCID)
Branham, Sandra E.
(ORCID)
Jarret, Robert L.
(ORCID)
Yencho, G. Craig
(ORCID)
Jackson, D. Michael
(ORCID)
Product Type
Genome/Genetics Data
Spatial / Geographical Coverage Location
Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America
Intended Use
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.
Publisher
Frontiers in Plant Science
Contact Name
Wadl, Phillip A.
Contact Email
Public Access Level
Public
Primary Article

Wadl, P. A., Olukolu, B. A., Branham, S. E., Jarret, R. L., Yencho, G. C., & Jackson, D. M. (2018). Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly. Frontiers in Plant Science, 9:1166

License
Funding Source(s)
Agricultural Research Service
6080-22000-027-00D
Agricultural Research Service
SCINet 0500-00093-001-00-D
Dataset DOI (digital object identifier)
10.3389/fpls.2018.01166
Program Code
005:037 - Department of Agriculture - Research and Education
Bureau Code
005:18 - Agricultural Research Service
Modified Date
2018-11-08
Release Date
2018-11-07
Ag Data Commons Keywords: 
  • Plants & Crops
  • Traits
  • Plants & Crops
  • Genomics & Genetics
  • Metagenomics
  • Genomics & Genetics
ISO Topic(s):