{
  "abstract": "Pedigree errors, duplicate accessions, and undocumented kinship limit the effective use of large genebank collections. Existing tools such as CERVUS and COLONY require allele-frequency estimates and return relationship-level assignments, providing no collection-wide view of Mendelian consistency. We developed the Mendelian Mismatch Matrix (MMM) framework and its open-source implementation, MMMAS (Mendelian Mismatch Matrix Analysis System). We applied MMM to apple (Malus x domestica; 1,085 accessions, 15 SSRs) and sweet cherry (Prunus avium; 383 accessions, 13 SSRs) datasets from the German Fruit Genebank. MMM converts pairwise Mendelian mismatch numbers (Mmn) into an N x N symmetric matrix, from which we derive four collection-scale indices (Mmin, the Mendelian minimum mismatch number; Mavg, the Mendelian average mismatch number; Mzmp, the Mendelian zero-mismatch partner number; Mmmd, the Mendelian mismatch-mode duplication index) and the Mendelian Exhaustive Stratification (MES) grading system. Apple showed a gradient-type structure (Mendelian Grade-gap Index, MGI = 0.125), sweet cherry a broken-type structure (MGI = 0.545). The Mmin-Mavg strategy identified 20 and 10 distinct accessions in apple and sweet cherry, including the scab-resistance donor Malus x floribunda 821 (Rvi6) and the fire-blight donor M. x robusta 5. The Mmmd index flagged one literature-confirmed pair of duplicate genotypes in sweet cherry. Of CERVUS-confirmed parent-offspring pairs, 97.31% in apple and 100% of high-confidence pairs in sweet cherry fell within Mmn <= 1. Mzmp rankings matched documented breeding history, with 'Cox Orange' (Mzmp = 57) and 'Luebecker Bunte' (Mzmp = 49) ranking first in each species. The complete end-to-end analysis of all 588,070 apple pairwise comparisons took 7.24 s on an ordinary workstation. This deterministic pre-screening framework, with a parameter-free core, supports routine quality assessment in germplasm collections.",
  "abstract_shown": true,
  "affiliations": [
    "Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences; Hubei Key Laboratory of Fruit Tree Germplasm Innovation and Utilization"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "name": "Q. Chen"
    },
    {
      "name": "L. chen"
    },
    {
      "name": "J. Fan"
    },
    {
      "name": "X. Yang"
    },
    {
      "name": "J. Zhang"
    },
    {
      "name": "W. Du"
    },
    {
      "name": "W. Liu"
    },
    {
      "name": "Z. Liu"
    },
    {
      "affs": [
        0
      ],
      "name": "H. Hu"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1xd0zcrnhm9pe.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.02.742285",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.02.742285v4.full",
  "id": "1xd0zcrnhm9pe",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.02.742285v4",
  "language": null,
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genetics"
    ],
    [
      "openalex",
      "1311|Genetic diversity and population structure"
    ]
  ],
  "openalex": "W7201880421",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.02.742285v4.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-02",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/1xd0zcrnhm9pe.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:33Z",
      "native_id": "10.64898/2026.08.02.742285",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.02.742285v4"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genetics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "MMM: A deterministic Mendelian mismatch matrix framework for germplasm collection quality assessment, demonstrated in apple and sweet cherry",
  "title_text": "MMM: A deterministic Mendelian mismatch matrix framework for germplasm collection quality assessment, demonstrated in apple and sweet cherry",
  "type": "preprint",
  "updated_at": "2026-10-30T12:24:33Z",
  "url": "https://research.draconitic.com/paper/1xd0zcrnhm9pe",
  "venue": "bioRxiv",
  "versions": []
}