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

Nicholas P Howard, Diego Micheletti, James J. Luby, Charles Eric Durel, Caroline Denancé, Hélène Muranty, Matthew Ordidge, Dirk C. Albach

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


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

Original languageEnglish (US)
Pages (from-to)98-111
Number of pages14
JournalPlants People Planet
Issue number1
StatePublished - Jan 2023

Bibliographical note

Funding Information:
The authors thank the following groups for providing accessions used in this study: Joanie Cooper, who provided samples from the Temperate Orchard Conservancy in Molalla, Oregon, USA; Dan Bussey, who provided samples from Seed Savers Exchange in Decorah, Iowa, USA; Dankwart Seipp, who provided samples from Esteburg Obstbauzentrum Jork, Germany; Detlef Strang, who provided samples from Ökowerk in Emden, Germany; Hans‐Joachim Bannier, who provided samples from his private orchard; Peter Heyne, who provided samples from his private orchard; and members of the following French amateur associations and conservatories who maintain the plant material and provided samples: Les Croqueurs de pommes®, Les Mordus de la pomme, Centre Végétal Régional d'Aquitaine (CVRA), Centre Régional de Ressources Génétiques des Hauts‐de‐France (CRRG), Société Pomologique du Berry, I z'on creuqué eun′ pomm′, Fédération Départementale Variétés Locales 12, Jardin du Luxembourg, the INRAE Biological Resource Center “Pome Fruits and Roses” (RosePom: ), and the INRAE Horticulture Experimental Facility (UE HORTI: ). Funding for this research was in part provided by the Niedersächsisches Ministerium für Wissenschaft und Kultur through the EGON project: “Research for a sustainable agricultural production: Development of organically bred fruit cultivars in creative commons initiatives,” the USDA NIFA Specialty Crop Research Initiative projects, “RosBREED: Enabling marker‐assisted breeding in Rosaceae” (2009‐51181‐05808) and “RosBREED 2: Combining disease resistance with horticultural quality in new rosaceous cultivars” (2014‐51181‐22378), USDA NIFA Hatch project 1014919, and State Agricultural Experiment Station ‐ University of Minnesota Project MIN‐21‐040. Part of the 20K Infinium SNP data and all the 480K Axiom SNP data came from the FruitBreedomics project no 265582: “Integrated approach for increasing breeding efficiency in fruit tree crops,” which was co‐funded by the EU seventh Framework Programme. Additional 20K SNP genotyping was performed by the INRAE EPGV Unit, Evry, France, with the help of the CNRGH Illumina Platform and DNA bank Teams for technical assistance.

Publisher Copyright:
© 2022 The Authors. Plants, People, Planet published by John Wiley & Sons Ltd on behalf of New Phytologist Foundation.


  • Malus
  • apple
  • genetics
  • pedigree reconstruction
  • polyploidy
  • single nucleotide polymorphism array
  • triploid


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