Pedigree reconstruction for triploid apple cultivars using single nucleotide polymorphism array data

Societal Impact Statement Many economically, culturally, and historically important apple cultivars are triploids, which have three copies of each chromosome instead the more typical two in diploids. Despite their prevalence importance, there been conflicting reports regarding origin ability to beget New genetic analysis methodologies outlined this study clarified triploid suggest that triploidy has a dead end historic pedigrees. The specific results resolved pedigrees many cultivars, including famous English cultivar Cox's Orange Pippin oldest known US Roxbury Russet. Summary In (Malus × domestica), most diploid, though sizeable number tend be stronger growing, robust, bear larger fruit. However, is also associated with strongly reduced fertility. Some recorded for historical include triploids as parents diploids, despite reputation poor This information, coupled some initiatives using breeding efforts, result confusion about how possible or common it diploid offspring. To date, no studies systematically evaluated identified resolve these contradictions. Here, we describe method make genotype calls Illumina Infinium single nucleotide polymorphism (SNP) array data through novel Python script: ploidyClassifier. SNP 219 unique was compared alongside 2498 accessions conduct pedigree reconstruction. Unreduced gamete-donating were over half accessions. From those, nearly half. Full partial classic uncovered, American cultivar, ‘Roxbury Russet’. All tested from literature listed diploids deemed false, well-known ‘Cox's Pippin’, whose previously unreported second parent here ‘Rosemary These together mostly solely product parentage