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

Metadata Updated: February 21, 2020

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.

Access & Use Information

Public: This dataset is intended for public access and use. License: Creative Commons CCZero

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Dates

Metadata Created Date February 21, 2020
Metadata Updated Date February 21, 2020

Metadata Source

Harvested from USDA JSON

Additional Metadata

Resource Type Dataset
Metadata Created Date February 21, 2020
Metadata Updated Date February 21, 2020
Publisher Agricultural Research Service
Unique Identifier 85548a97-476e-41cc-af08-27b68318dbe7
Maintainer
Wadl, Phillip A.
Maintainer Email
Public Access Level public
Bureau Code 005:18
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id 59dacddc-a84d-4869-8e42-8a06ad01eafe
Harvest Source Id 50ca39af-9ddb-466d-8cf3-84d67a204346
Harvest Source Title USDA JSON
License https://creativecommons.org/publicdomain/zero/1.0/
Data Last Modified 2019-08-05
Program Code 005:040
Source Datajson Identifier True
Source Hash da7827d82ad02d9ef5ff475b5199deeafdcec6b1
Source Schema Version 1.1

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