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<p>Accumulating evidences have shown that the mid-oleic fatty acid phenotype in peanuts cannot be explained by the traditional two-gene model involving <i>AhFAD2A</i> and <i>AhFAD2B</i>, 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 <i>AhFAD2C</i>, near <i>AhFAD2B</i>. When recombination occurs, <i>AhFAD2C</i> segregates from <i>AhFAD2B</i>. 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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月23日

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  • 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

摘要

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.