{
  "abstract": "Watermelon (Citrullus lanatus) has undergone severe loss of genetic diversity due to domestication, necessitating the exploitation of wild relatives for trait improvement. While structural variations (SVs) represent a major source of genetic diversity, high-throughput SV genotyping remains technically challenging, and existing single-nucleotide polymorphism (SNP) arrays fail to capture presence/absence variations (PAVs) that differentiate wild from cultivated germplasm. Here, we developed the ‘Watermelon 40K SNP-SV Chip,’ the first liquid-phase genotyping chip enriched with SV markers, leveraging a telomere-to-telomere super-pangenome of seven Citrullus species. The chip comprises 7087 SV markers (enriched for PAVs) and 11 383 SNP/InDel markers. Technical validation in 12 accessions and large-scale genotyping of 228 diverse accessions demonstrated high reproducibility (≥98.5% concordance) and robust call rates (>97%), though performance declined in deeply divergent wild species. Genome-wide association studies revealed SV-specific signals for flesh color and rind pattern that co-localized with known quantitative trait loci (QTL), including a strong candidate regulatory PAV upstream of LCYB. The predominance of rare variants (74.3% SVs with minor allele frequency < 0.05) limits statistical power for detecting QTL underlying polygenic domestication traits such as yield but confers exceptional utility for tracking wild introgressions in early-generation breeding populations. The 40K SNP-SV chip bridges the gap between fundamental SV research and practical breeding, enabling SV-assisted genomic selection for watermelon improvement.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 11,
  "authors": [
    {
      "name": "Mingxia Zhao"
    },
    {
      "name": "Rui Cheng"
    },
    {
      "name": "Yongchun Wang"
    },
    {
      "name": "Jisheng Liu"
    },
    {
      "name": "Xiaoni Li"
    },
    {
      "name": "Lifang Xue"
    },
    {
      "name": "Taohong Fang"
    },
    {
      "name": "Yudong Sun"
    },
    {
      "name": "Yun Deng"
    },
    {
      "name": "Yunbi Xu"
    },
    {
      "name": "Xingping Zhang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/f0pnxx127j2wh.bib",
  "cited_by": 0,
  "doi": "10.1093/hr/uhag221",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13722873/?tool=EBI",
  "id": "f0pnxx127j2wh",
  "issns": [
    "2662-6810",
    "2052-7276"
  ],
  "landing_url": "https://europepmc.org/article/PMC/PMC13722873",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI01140"
    ],
    [
      "heading",
      "AcademicSubjects/SCI01210"
    ],
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "1311|Advances in Cucurbitaceae Research"
    ]
  ],
  "openalex": "W7163405784",
  "pdf_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13722873/pdf/?tool=EBI",
  "pmcid": "PMC13722873",
  "pmid": "42967047",
  "published": "2026-06-03",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/f0pnxx127j2wh.ris",
  "sources": [
    {
      "first_seen": "2026-11-02T03:21:51Z",
      "native_id": "PMC:PMC13722873",
      "source": "europepmc",
      "url": "https://europepmc.org/article/PMC/PMC13722873"
    },
    {
      "first_seen": "2026-11-04T12:21:36Z",
      "native_id": "PMC13722873",
      "source": "pmc",
      "url": "https://doi.org/10.1093/hr/uhag221"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Advances in Cucurbitaceae Research",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Development and application of a 40K liquid chip enriched with structural variation markers for watermelon breeding",
  "title_text": "Development and application of a 40K liquid chip enriched with structural variation markers for watermelon breeding",
  "type": "peer-reviewed",
  "updated_at": "2026-11-04T12:21:36Z",
  "url": "https://research.draconitic.com/paper/f0pnxx127j2wh",
  "venue": "Horticulture research",
  "versions": []
}