Population-specific pangenome unveils a third FAD2 gene and solves the peanut mid-oleic fatty acid mystery

Authors: THOMPSON, ETHAN - University Of Georgia; KORANI, WALID - Hudsonalpha Institute For Biotechnology; WU, DONGLIANG - University Of Georgia; GARG, VANIKA - Murdoch University; Tonnis, Brandon; Wang, Ming; Holbrook Jr, C; OZIAS-AKINS, PEGGY - University Of Georgia; CULBREATH, ALBERT - University Of Georgia; VARSHNEY, RAJEEV - Murdoch University; Guo, Baozhu; CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/18/2025
Publication Date: 12/23/2025
Citation: Thompson, E., Korani, W., Wu, D., Garg, V., Tonnis, B.D., Wang, M.L., Holbrook Jr, C.C., Ozias-Akins, P., Culbreath, A.K., Varshney, R.K., Guo, B., Clevenger, J.P. 2026. Population-specific pangenome unveils a third FAD2 gene and solves the peanut mid-oleic fatty acid mystery. Nature Communications. 17:654. https://doi.org/10.1038/s41467-025-67371-7.
DOI: https://doi.org/10.1038/s41467-025-67371-7

Interpretive Summary: Peanut oleic and linoleic fatty acids are two heart-healthy and the major components of the total oil content in peanut seeds. Therefore, peanut seed oil composition is an important quality trait for confectionery and wholesale markets, leading to a focus on oil composition in breeding programs and functional studies. The term of “mid-oleic” has been used and could not be explained by two recessive-gene model and the hypothesis was that a third recessive gene along with AhFAD2A and AhFAD2B is needed to maintain the high oleic fatty acid trait in peanut. The mystery of “mid-oleic” or “not-high-oleic” has been puzzled in the peanut community, particularly for confectionery industry in consistency of quality products. In this study, we present high quality genome sequences of eight parents of Peanut MAGIC and constructed a population-specific pangenome. Using the genotyping information from the population-specific pangenome we visualized the genomic detailed recombination within Peanut MAGIC for detailed marker trait association of oleic fatty acid. We identified a new third fatty-acid desaturase 2 (AhFAD2) gene, named AhFAD2C, located on the same chromosome as AhFAD2B. AhFAD2C which contributed to high oleic acid trait, solved the sought-after mystery of three-gene model theory in high oleic peanut.

Technical Abstract: Cultivated peanut (Arachis hypogaea L.) is an important oil and protein crop. However, the “mid-oleic” fatty acid is still puzzling the peanut community. We constructed a population-specific pangenome from the eight founder genomes of the PeanutMAGIC population. This graph-based pangenome serves as a reference for all segregating founder variations within PeanutMAGIC of 3,187 RILs. Whole genome sequencing was conducted for the MAGIC Core of 310 RILs, a subset of PeanutMAGIC. Using the genotyping information from the population-specific pangenome we visualized the genomic recombination within MAGIC Core for detailed marker trait association of oleic acid. We identified a novel third fatty-acid desaturase 2 (AhFAD2) gene, named AhFAD2C, located on the same chromosome as AhFAD2B. AhFAD2C can independently segregate in breeding populations and solved the sought-after mystery of three-gene model theory in high oleic peanut. The limitation of a single reference in comparison to population specific pangenome for marker calling is the resulted false calling for association study and downstream application.