{
  "abstract": "Linkage disequilibrium (LD) analysis is central to candidate-gene refinement, haplotype characterization, marker selection, and the interpretation of genome-wide association studies. However, commonly used LD programs often require format conversion, platform-specific binaries, or separate tools for LD calculation, block detection, regional annotation, subgroup comparison, and publication-quality visualization. We developed LDblockR, a pure-R, cross-platform toolkit that unifies regional LD analysis from VCF/VCF.GZ, HapMap, PLINK BED/BIM/FAM or PED/MAP files, and numeric 0/1/2 genotype matrices. LDblockR calculates dosage- or phased-haplotype-based r² and Lewontin’s D′, estimates haplotype frequencies for unphased diploid genotypes using an expectation-maximization procedure, and supports multiple block definitions, tag-SNP selection, LD-neighbor searches, LD decay, haplotype frequencies, population-group comparisons, and batch regional analysis. Its principal contribution is workflow integration and interoperability rather than a new LD estimator: a single R-native object model links heterogeneous genotype inputs, established LD statistics, regional annotation, and publication-ready visualization. In the bundled phased benchmark of 60 diploid samples and 42 variants (861 unique pairs), LDblockR agreed with LDBlockShow 1.41 to the three-decimal precision reported by LDBlockShow, with all r² and D′ values within 0.00051. We additionally analyze the official TASSEL/rTASSEL maize HapMap tutorial dataset, comprising 281 maize inbred lines and 3,093 genome-wide markers. After allele-consistency, missingness, and MAF filtering, 2,526 markers remain, including 428 SNPs on chromosome 1. Chromosome-wide dosage r² analysis covers 91,378 pairs; a highlighted 1-Mb interval contains 16 SNPs and 120 pairs. Independent pairwise calculations match the archived regional reference table to a maximum absolute difference of 5.01 × 10 ⁻¹³ . This real-data example demonstrates regional LD analysis on crop genotypes with observed missing calls and allele-metadata conflicts. LDblockR therefore provides a transparent bridge between genotype input, regional LD analysis, and post-GWAS interpretation for plant association genetics and breeding.",
  "abstract_shown": true,
  "affiliations": [
    "North Henan Medical University",
    "Key Laboratory of Tropical Fruit Biology of Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Xiaofeng Song"
    },
    {
      "affs": [
        0
      ],
      "name": "Pengyu Chen"
    },
    {
      "affs": [
        1
      ],
      "name": "Fei Liang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/954bdpc4zq7s7.bib",
  "cited_by": 0,
  "doi": "10.3389/fpls.2026.1991155",
  "fulltext_url": null,
  "id": "954bdpc4zq7s7",
  "issns": [
    "1664-462X"
  ],
  "landing_url": "https://www.frontiersin.org/articles/10.3389/fpls.2026.1991155/full",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1311|Genetic Associations and Epidemiology"
    ]
  ],
  "openalex": "W7223682967",
  "pdf_url": "https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2026.1991155/pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-26",
  "publisher": "Frontiers Media SA",
  "ris": "https://research.draconitic.com/paper/954bdpc4zq7s7.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:25Z",
      "native_id": "10.3389/fpls.2026.1991155",
      "source": "crossref",
      "url": "https://www.frontiersin.org/articles/10.3389/fpls.2026.1991155/full"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Genetic Associations and Epidemiology",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "LDblockR: a cross-platform R toolkit for multi-format linkage disequilibrium analysis and integrated regional genomics visualization",
  "title_text": "LDblockR: a cross-platform R toolkit for multi-format linkage disequilibrium analysis and integrated regional genomics visualization",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:25Z",
  "url": "https://research.draconitic.com/paper/954bdpc4zq7s7",
  "venue": "Frontiers in Plant Science",
  "versions": []
}