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<p>Cowpea (<i>Vigna unguiculata</i> L. Walp.) is an Africa-originated legume providing a vital source of protein for millions across resource constrained areas of Africa, Asia and Latin America. Understanding genetic diversity in cowpea is pivotal to its genetic improvement. Here, we assemble 20 high-quality genomes representing cowpea global diversity and construct a graph-based pan-genome to characterize genetic variation. The pan-genome comprises 29,557 orthogroups, with approximately 73% conserved across all accessions. Extensive structural variations (SVs) are uncovered, affecting thousands of coding sequences and gene expression. Thousands of SVs are found under selection between two cowpea subspecies, highlighting their roles in subspecies divergence. We pinpoint key SVs underlying variation in pod length and seed number per pod. Two SV clusters appear to modulate pod length through altering expression and function of <i>VuWAK</i> and <i>VuGA2ox2</i> genes. These findings provide insights into cowpea genetic diversity and establish a fundamental resource for cowpea genetic improvement.</p>

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Pan-genome analysis uncovers extensive structural variations in Africa’s indigenous legume crop cowpea

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年5月20日

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  • Shichao Sun,
  • Chuanzheng Wei,
  • Sofie Pearson,
  • Alan Cruickshank,
  • Yinzi Wang,
  • Yanbo Wang,
  • Tashi Dorjee,
  • Yi Zhou,
  • David Jordan,
  • Yan Yang,
  • Hongru Wang,
  • Xingtan Zhang,
  • Emma Mace,
  • Yongfu Tao

摘要

Cowpea (Vigna unguiculata L. Walp.) is an Africa-originated legume providing a vital source of protein for millions across resource constrained areas of Africa, Asia and Latin America. Understanding genetic diversity in cowpea is pivotal to its genetic improvement. Here, we assemble 20 high-quality genomes representing cowpea global diversity and construct a graph-based pan-genome to characterize genetic variation. The pan-genome comprises 29,557 orthogroups, with approximately 73% conserved across all accessions. Extensive structural variations (SVs) are uncovered, affecting thousands of coding sequences and gene expression. Thousands of SVs are found under selection between two cowpea subspecies, highlighting their roles in subspecies divergence. We pinpoint key SVs underlying variation in pod length and seed number per pod. Two SV clusters appear to modulate pod length through altering expression and function of VuWAK and VuGA2ox2 genes. These findings provide insights into cowpea genetic diversity and establish a fundamental resource for cowpea genetic improvement.