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<p>Pumpkin (<i>Cucurbita moschata</i>) is an important crop used both for consumption and as a cucurbit rootstock. We evaluated the genetic diversity and performed a GWAS on 167 accessions, mostly from East Asia, using 10,528 high-quality SNPs obtained by genotyping-by-sequencing. Four traits were investigated: fruit shape, fruit rind color, leaf lobes, and leaf silver patches. Phylogenetic, PCA, and population structure analyses divided the accessions into three subpopulations which were consistent with the classification based on geographical origin and usage. Pairwise genetic differentiation values indicated the greatest divergence between subpopulations 1 and 3 (0.161), while AMOVA showed that most genetic variation (86.5%) occurred within populations, suggesting frequent gene flow. GWAS of four traits detected 25 significant loci explaining 4.4–23.0% of phenotypic variation, of which 23 were novel and two overlapped with known regions. The strongest association was near <i>CmoCh03G011750</i>, an ortholog of <i>CpDll</i> in <i>C. pepo</i>, a key regulator of leaf lobes. Based on lead SNPs, HRM and KASP markers were developed and validated in 35 additional accessions, showing complete genotype–phenotype concordance and confirming their utility for marker-assisted breeding.</p>

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Genetic diversity and genome-wide association study of horticultural traits in pumpkins (Cucurbita moschata) originating from East Asia

  • 期刊论文

  • 发表日期：

    2026年3月10日

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  • Eun Su Lee,
  • Yoon Jeong Jang,
  • Ye-Rin Lee,
  • Oakjin Lee,
  • Hee-Bum Yang,
  • Hye-Eun Lee,
  • Koeun Han,
  • Do-Sun Kim

摘要

Pumpkin (Cucurbita moschata) is an important crop used both for consumption and as a cucurbit rootstock. We evaluated the genetic diversity and performed a GWAS on 167 accessions, mostly from East Asia, using 10,528 high-quality SNPs obtained by genotyping-by-sequencing. Four traits were investigated: fruit shape, fruit rind color, leaf lobes, and leaf silver patches. Phylogenetic, PCA, and population structure analyses divided the accessions into three subpopulations which were consistent with the classification based on geographical origin and usage. Pairwise genetic differentiation values indicated the greatest divergence between subpopulations 1 and 3 (0.161), while AMOVA showed that most genetic variation (86.5%) occurred within populations, suggesting frequent gene flow. GWAS of four traits detected 25 significant loci explaining 4.4–23.0% of phenotypic variation, of which 23 were novel and two overlapped with known regions. The strongest association was near CmoCh03G011750, an ortholog of CpDll in C. pepo, a key regulator of leaf lobes. Based on lead SNPs, HRM and KASP markers were developed and validated in 35 additional accessions, showing complete genotype–phenotype concordance and confirming their utility for marker-assisted breeding.