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ARS Home » Plains Area » Stillwater, Oklahoma » Wheat, Peanut, and Other Field Crops Research » Research » Publications at this Location » Publication #373417

Research Project: Genetic Improvement of Peanut for Production in the Southwest United States Region

Location: Wheat, Peanut, and Other Field Crops Research

Title: Genotypic characterization of the U.S. peanut core collection

Author
item OTYAMA, PAUL - Iowa State University
item KULKARNI, ROSHAN - US Department Of Agriculture (USDA)
item Chamberlin, Kelly
item OZIAS-AKINS, PEGGY - University Of Georgia
item CHU, YE - University Of Georgia
item Lincoln, Lori
item MACDONALD, GEORGORY - University Of Florida
item ANGLIN, NOLLE - International Potato Center
item DASH, SUDHANSU - National Center For Genome Resources
item BERTIOLI, DAVID - University Of Georgia
item FERNANDEZ-BACA, DAVID - Iowa State University
item Graham, Michelle
item Cannon, Steven
item Cannon, Ethalinda

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2020
Publication Date: 11/5/2020
Citation: Otyama, P.I., Kulkarni, R., Chamberlin, K.D., Ozias-Akins, P., Chu, Y., Lincoln, L.M., Macdonald, G.E., Anglin, N., Dash, S., Bertioli, D., Fernandez-Baca, D., Graham, M.A., Cannon, S.B., Cannon, E.K. 2020. Genotypic characterization of the U.S. peanut core collection. G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.120.401306.
DOI: https://doi.org/10.1534/g3.120.401306

Interpretive Summary: Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The U.S. peanut collection contains 8,982 accessions. From these accessions, 812 were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the core collection. We found that the genotypic diversity of the core is mostly captured in 5 genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut's rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. Comparisons with the diploid progenitors suggest that subgenome exchange contributes to ongoing accumulation of diversity in peanut.

Technical Abstract: Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The U.S. peanut collection contains 8,982 accessions. From these accessions, 812 were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the core collection. The specific objectives of this study were to 1) provide genotype data for each accession, 2) assess genetic diversity of the collection, 3) analyze population structure, 4) estimate the incidence of heterogenous or mixed accessions, and 5) assess relationships between genotypic groups and common traits and phenotypic classes. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of the collection was genotyped in replicate, using between two and five seeds per accession. We find that the genotypic diversity of the core is mostly captured in 5 genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut's rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. Comparisons with the diploid progenitors suggest that subgenome exchange contributes to ongoing accumulation of diversity in peanut.