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<p>Pangenomes are increasingly important for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here we present a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated genomes representing all seven species. This super-pangenome captures approximately 1 million structural variants (SVs), enabling accurate variant genotyping across 914 accessions. Broader sampling within the pangenome provides insights into watermelon genome evolution and the origin of cultivated watermelon. Incorporating SVs into genome-wide association studies improves mapping resolution and reveals a copy number variant upstream of <i>ClFCI1</i> that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, these findings and genomic resources establish a foundation for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crops.</p>

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Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

  • 期刊论文

  • 发表日期：

    2026年5月5日

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  • Honghe Sun,
  • Jie Zhang,
  • Shengjin Liao,
  • Shaogui Guo,
  • Zhe Zhou,
  • Xuebo Zhao,
  • Shan Wu,
  • Jiantao Zhao,
  • Guoyi Gong,
  • Jinfang Wang,
  • Maoying Li,
  • Yongtao Yu,
  • Yi Ren,
  • Shouwei Tian,
  • Shaofang Li,
  • Haiying Zhang,
  • Sue A. Hammar,
  • Cecilia McGregor,
  • Robert Jarret,
  • Patrick Wechter,
  • Sandra E. Branham,
  • Chandrasekar Kousik,
  • Amnon Levi,
  • Rebecca Grumet,
  • Zhangjun Fei,
  • Yong Xu

摘要

Pangenomes are increasingly important for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here we present a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated genomes representing all seven species. This super-pangenome captures approximately 1 million structural variants (SVs), enabling accurate variant genotyping across 914 accessions. Broader sampling within the pangenome provides insights into watermelon genome evolution and the origin of cultivated watermelon. Incorporating SVs into genome-wide association studies improves mapping resolution and reveals a copy number variant upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, these findings and genomic resources establish a foundation for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crops.