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Article|01 Sep 2021|OPEN
The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry
Nicholas P. Howard1,6, Kevin A. T. Silverstein2, Ana Poets2, James J. Luby1, Stijn Vanderzande3, Charles-Eric Durel4, Hélène Muranty4, Caroline Denancé4, Eric van de Weg5 & Cameron Peace3,
1Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
2Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
3Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, WA, USA
4Université d’Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
5Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands
6Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky University, Oldenburg, Germany

Horticulture Research 8,
Article number: 202 (2021)
doi: 10.1038/hortres.2021.202
Views: 46

Received: 08 Feb 2021
Revised: 05 Jul 2021
Accepted: 17 Jul 2021
Published online: 01 Sep 2021

Abstract

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.