{
  "abstract": "Pearl millet (Cenchrus americanus; syn. Pennisetum glaucum (L.) R. Br.) is an important cereal crop mainly grown in semi-arid areas. However, in pearl millet, genes underlying many agronomic traits remain unknown. Our previous genome-wide association study (GWAS) was based primarily on genotype data derived from restriction site-associated DNA sequencing (RAD-seq), which contained a high proportion of missing genotypes and may have limited mapping resolution. To address this limitation, we used whole-genome sequencing (WGS)-derived genotype data from 21 elite lines as a reference panel to impute missing genotypes in the RAD-seq-derived dataset. Genotype imputation reduced the proportion of missing genotypes from 82.42% to 0% and increased the mean density of non-missing genotypes from 569.61 to 1,158.09 genotypes/Mb. Leave-one-out validation yielded a mean genotype concordance of 89.9% (SD = 4.6%). GWAS using the imputed dataset showed more localized association signals for several traits. Homologs of rice SHORT INTERNODES1, Arabidopsis FLOWERING LOCUS Y, and rice EPIDERMAL PATTERNING FACTOR 2 were identified as candidates for genes regulating culm height, days to panicle emergence, and awn growth, respectively. These results demonstrate that reference-panel-based genotype imputation can increase the utility of reduced-representation genotype datasets and facilitate candidate gene identification in pearl millet.",
  "abstract_shown": true,
  "affiliations": [
    "The University of Tokyo"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "name": "K. Kambara"
    },
    {
      "name": "S. K. Gupta"
    },
    {
      "affs": [
        0
      ],
      "name": "D. Tsugama"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/acm1xrh0xrtrz.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.16.759592",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.16.759592v1.full",
  "id": "acm1xrh0xrtrz",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.16.759592v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ],
    [
      "openalex",
      "1311|Genetic Mapping and Diversity in Plants and Animals"
    ]
  ],
  "openalex": "W7223204794",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.16.759592v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-16",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/acm1xrh0xrtrz.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:12Z",
      "native_id": "10.64898/2026.10.16.759592",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.16.759592v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Genotype imputation improves GWAS resolution and facilitates candidate gene identification in pearl millet",
  "title_text": "Genotype imputation improves GWAS resolution and facilitates candidate gene identification in pearl millet",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:12Z",
  "url": "https://research.draconitic.com/paper/acm1xrh0xrtrz",
  "venue": "bioRxiv",
  "versions": []
}