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Hortic Res. 2017 Feb 22;4:17003. doi: 10.1038/hortres.2017.3. eCollection 2017.

Elucidation of the 'Honeycrisp' pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus×domestica) pedigree-connected SNP data set.

Author information

Department of Horticultural Science, University of Minnesota , St Paul, MN 55104, USA.
Department of Plant Breeding, Wageningen University and Research , Wageningen 6700AJ, The Netherlands.
Department of Horticulture and Landscape Architecture, Washington State University , Pullman, WA 99164, USA.
Department of Horticulture, Michigan State University , East Lansing, MI 48824, USA.


The apple (Malus×domestica) cultivar Honeycrisp has become important economically and as a breeding parent. An earlier study with SSR markers indicated the original recorded pedigree of 'Honeycrisp' was incorrect and 'Keepsake' was identified as one putative parent, the other being unknown. The objective of this study was to verify 'Keepsake' as a parent and identify and genetically describe the unknown parent and its grandparents. A multi-family based dense and high-quality integrated SNP map was created using the apple 8 K Illumina Infinium SNP array. This map was used alongside a large pedigree-connected data set from the RosBREED project to build extended SNP haplotypes and to identify pedigree relationships. 'Keepsake' was verified as one parent of 'Honeycrisp' and 'Duchess of Oldenburg' and 'Golden Delicious' were identified as grandparents through the unknown parent. Following this finding, siblings of 'Honeycrisp' were identified using the SNP data. Breeding records from several of these siblings suggested that the previously unreported parent is a University of Minnesota selection, MN1627. This selection is no longer available, but now is genetically described through imputed SNP haplotypes. We also present the mosaic grandparental composition of 'Honeycrisp' for each of its 17 chromosome pairs. This new pedigree and genetic information will be useful in future pedigree-based genetic studies to connect 'Honeycrisp' with other cultivars used widely in apple breeding programs. The created SNP linkage map will benefit future research using the data from the Illumina apple 8 and 20 K and Affymetrix 480 K SNP arrays.

Conflict of interest statement

The University of Minnesota receives royalty payments related to the ‘Honeycrisp’ apple cultivar. JJL and DSB, and the University of Minnesota have a royalty interest in this cultivar. These relationships have been reviewed and managed by the University of Minnesota in accordance with its Conflict of Interest policies. The remaining authors declare no conflict of interest.

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