Genotypic Characterization of the U.S. Peanut Core Collection

Area of Science:

• Agronomy
• Genetics
• Plant Science

Background:

• Cultivated peanut (Arachis hypogaea) is a globally significant crop for oil, food, and feed.
• The USDA peanut germplasm collection comprises 8,982 accessions, with an 812-accession core collection established in the 1990s.
• Genotyping the core collection provides insights into peanut's genetic diversity and origins.

Purpose of the Study:

• To genotype the entire peanut core collection using the Arachis_Axiom2 SNP array.
• To analyze the genotypic diversity, population structure, and biogeography of cultivated peanut.
• To investigate the origins and dispersal patterns of peanut genetic diversity.

Main Methods:

• Genotyping of 812 peanut accessions using the Arachis_Axiom2 SNP array, yielding 14,430 informative SNPs.
• Replication of 253 accessions to assess intra-accessional heterogeneity.
• Bioinformatic analysis of SNP data to determine genotypic clusters and population structure.

Main Results:

• Genotypic diversity is primarily structured into five clusters, correlating with botanical variety and market type, but not country of origin.
• A distinct cluster linked to *hypogaea/aequatoriana/peruviana* varieties, originating from Bolivia, Peru, and Ecuador, suggests early landrace origins.
• Analysis indicates an early genetic radiation from Southeast Bolivia, followed by South American distribution and global dissemination, retaining significant early diversity.

Conclusions:

• The genetic diversity of cultivated peanut is largely consistent with an origin in Southeast Bolivia, with subsequent radiation and dispersal.
• Subgenome exchanges between diploid progenitors have significantly contributed to the genetic diversity of tetraploid peanut.
• Understanding peanut's genetic structure aids in crop improvement and conservation efforts.