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CC BY-NC-ND V4.0, Open Access
Journal article
Population-specific pangenome unveils a third FAD2 gene and solves the peanut mid-oleic fatty acid mystery
Nature communications, Vol.17(1), 654
2025
PMID: 41429781
Abstract
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 ServiceWalid Korani - HudsonAlpha Institute for BiotechnologyDongliang Wu - Agricultural Research ServiceVanika Garg - Murdoch University, Centre for Crop and Food InnovationBrandon Tonnis - Agricultural Research ServiceMingli Wang - Agricultural Research ServiceC Corley Holbrook - USDA-ARS Crop Genetics and Breeding Research Unit, Tifton, GA, USAPeggy Ozias-Akins - Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, USAAlbert K Culbreath - University of GeorgiaRajeev K Varshney - Murdoch University, Food Futures InstituteBaozhu Guo - Southeast Watershed Research LaboratoryJosh P Clevenger - HudsonAlpha Institute for Biotechnology
- Publication Details
- Nature communications, Vol.17(1), 654
- Publisher
- Springer Nature
- Number of pages
- 13
- Identifiers
- 991005852587207891
- Copyright
- © The Author(s) 2025
- 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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