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

Ethan Thompson; Walid Korani; Dongliang Wu; Vanika Garg; Brandon Tonnis; Mingli Wang; C Corley Holbrook; Peggy Ozias-Akins; Albert K Culbreath; Rajeev K Varshney; Baozhu Guo; Josh P Clevenger

doi:10.1038/s41467-025-67371-7

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

Journal article

Open access

Peer reviewed

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

Ethan Thompson, Walid Korani, Dongliang Wu, Vanika Garg, Brandon Tonnis, Mingli Wang, C Corley Holbrook, Peggy Ozias-Akins, Albert K Culbreath, Rajeev K Varshney, …

Nature communications, Vol.17(1), 654

2025

DOI: https://doi.org/10.1038/s41467-025-67371-7

PMID: 41429781

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Abstract

Arachis - genetics

Arachis - metabolism

Fatty Acid Desaturases - genetics

Fatty Acid Desaturases - metabolism

Genome, Plant

Genotype

Haplotypes

Oleic Acid - genetics

Oleic Acid - metabolism

Phenotype

Plant Proteins - genetics

Plant Proteins - metabolism

Polymorphism, Single Nucleotide

Whole Genome Sequencing

Accumulating evidences have shown that the mid-oleic fatty acid phenotype in peanuts cannot be explained by the traditional two-gene model involving AhFAD2A and AhFAD2B, which are genes encoding fatty-acid desaturase 2. But the underlying genetic mechanism remains unclear. Here, we present a population-specific pangenome using the eight founder genomes of the PeanutMAGIC population. This graph-based pangenome serves as a comprehensive reference, capturing all segregating haplotypes within the population. We conduct whole genome sequencing for the MAGIC Core, a subset of 310 RILs, for genotyping. Using pangenome-based genotypes, we trace recombination for detailed genomic analysis and phenotypic association. This investigation identifies a unique third gene, named AhFAD2C, near AhFAD2B. When recombination occurs, AhFAD2C segregates from AhFAD2B. We reveal the genotype determining mid-oleic fatty acid phenotype. Our findings underscore the limitations of a single-reference genome, which leads to false association and marker discovery. In contrast, a population-specific pangenome provides a more reliable framework for genomic studies. This study reveals insights into the genetic mechanism of peanut oil quality and demonstrates the advantages of population-specific pangenomes.

Details

Title: Population-specific pangenome unveils a third FAD2 gene and solves the peanut mid-oleic fatty acid mystery
Authors/Creators: Ethan Thompson - Agricultural Research Service
Walid Korani - HudsonAlpha Institute for Biotechnology
Dongliang Wu - Agricultural Research Service
Vanika Garg - Murdoch University, Centre for Crop and Food Innovation
Brandon Tonnis - Agricultural Research Service
Mingli Wang - Agricultural Research Service
C Corley Holbrook - USDA-ARS Crop Genetics and Breeding Research Unit, Tifton, GA, USA
Peggy Ozias-Akins - Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, USA
Albert K Culbreath - University of Georgia
Rajeev K Varshney - Murdoch University, Food Futures Institute
Baozhu Guo - Southeast Watershed Research Laboratory
Josh P Clevenger - HudsonAlpha Institute for Biotechnology
Publication Details: Nature communications, Vol.17(1), 654
Publisher: Springer Nature
Number of pages: 13
Identifiers: 991005852587207891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre; Food Futures Institute
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: No Topic Assigned; No Topic Assigned; No Topic Assigned
Web Of Science research areas: Genetics & Heredity
ESI research areas: Molecular Biology & Genetics