The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

Nicholas P. Howard, Cameron Peace, Kevin Silverstein, Ana Poets, James J. Luby, Stijn Vanderzande, Charles Eric Durel, Hélène Muranty, Caroline Denancé, Eric van de Weg

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


Pedigree information is of fundamental importance in breeding programs and related genetics efforts. However, many individuals have unknown pedigrees. While methods to identify and confirm direct parent–offspring relationships are routine, those for other types of close relationships have yet to be effectively and widely implemented with plants, due to complications such as asexual propagation and extensive inbreeding. The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes (referred to in this study as “summed potential lengths of shared haplotypes”, SPLoSH). A custom Python script, HapShared, was developed to generate SPLoSH data in apple and sweet cherry. HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops. These distributions were then used to estimate previously unknown relationships. Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data. For cherry, a full-sib relationship was deduced for ‘Emperor Francis, and ‘Schmidt’, a half-sib relationship for ‘Van’ and ‘Windsor’, and the paternal grandparents of ‘Stella’ were confirmed. For apple, 29 cultivars were found to share an unknown parent, the pedigree of the unknown parent of ‘Cox’s Pomona’ was reconstructed, and ‘Fameuse’ was deduced to be a likely grandparent of ‘McIntosh’. Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets, integrated genetic maps, and previously identified pedigree relationships. Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

Original languageEnglish (US)
Article number202
JournalHorticulture Research
Issue number1
StatePublished - Dec 2021

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; and Hans-Joachim Bannier, who provided samples from his private orchard in Bielefeld, Germany. 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 20 K Infinium SNP data came from the FruitBreedomics project no 265582: “Integrated approach for increasing breeding efficiency in fruit tree crops”50, which was co-funded by the EU seventh Framework Programme.

Publisher Copyright:
© 2021, The Author(s).


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