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

Publication Overview
TitleThe use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry.
AuthorsHoward NP, Peace C, Silverstein KATS, Poets A, Luby JJ, Vanderzande S, Durel CE, Muranty H, Denancé C, and van de Weg E.
TypeJournal Article
Journal NameHorticulture Research
Volume8
Year2021
Page(s)202
CitationHoward, N.P., Peace, C., Silverstein, K.A.T. et al. The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry. Hortic Res 8, 202 (2021). https://doi.org/10.1038/s41438-021-00637-5

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.
Projects
This publication contains information about 1 projects:
Project NameDescription
Apple_SNP_genotype_Howard_2021Apple_SNP_genotype_Howard_2021
Stocks
This publication contains information about 507 stocks:
Stock NameUniquenameType
146_11_09146_11_09breeding_research_material
146_12_09146_12_09breeding_research_material
ACW 11567ACW 11567breeding_research_material
ACW 18522ACW 18522breeding_research_material
ACW 6104ACW 6104breeding_research_material
Adamss PearmainAdamss Pearmaincultivar
Adersleber KalvillAdersleber Kalvillcultivar
AkaneAkanecultivar
Aldwick BeautyAldwick Beautycultivar
AlkmeneAlkmenecultivar
Allington PeppingAllington Peppingcultivar
AlroAlrocultivar
Altlander JakobsapfelAltlander Jakobsapfelcultivar
Ananas ReinetteAnanas Reinettecultivar
Annie ElizabethAnnie Elizabethcultivar
AnnurcaAnnurcacultivar
Antonovka 16.19Antonovka 16.19breeding_research_material
Antonovka 34.15Antonovka 34.15breeding_research_material
Antonovka 34.16Antonovka 34.16breeding_research_material
Antonovka 34.26Antonovka 34.26breeding_research_material
Antonovka KrasnobochkaAntonovka Krasnobochkacultivar
Antonovka NovaaAntonovka Novaacultivar
Antonovka OBAntonovka OBcultivar
Antonovka OB NTTT2Antonovka OB NTTT2cultivar
Antonowka SafranAntonowka Safrancultivar

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