MMMAS: open-source tool flags pedigree errors and duplicate accessions in large germplasm collections

Researchers have posted a preprint to bioRxiv describing MMMAS (Mendelian Mismatch Matrix Analysis System) v1.0.0, an open-source software tool designed to improve the quality of pedigree and kinship information held in large germplasm collections, which are repositories of plant genetic material used in crop breeding and conservation research.

The tool converts pairwise Mendelian mismatch numbers — counts of loci at which the genotypes of two individuals are inconsistent with the expected inheritance pattern given their recorded relationship — into an N × N matrix across an entire collection. From this matrix, MMMAS derives five population-scale diagnostics intended to detect erroneous pedigree records, duplicate accessions, and previously undocumented kinship relationships.

Germplasm collections underpin much of modern plant breeding and genetic research, but their pedigree records are frequently incomplete or contain errors accumulated through decades of seed sharing and inadequate documentation. Tools that can flag these issues computationally before they propagate into downstream analyses are of practical value to plant breeders, conservation geneticists, and researchers using these collections as mapping populations. MMMAS is positioned as a pre-screening step rather than a replacement for more detailed relatedness analyses. As a preprint, the tool and its validation have not yet been peer-reviewed.