pubmed.ncbi.nlm.nih.gov

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 - PubMed

  • ️Sun Jan 01 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

Nicholas P Howard et al. Hortic Res. 2017.

Abstract

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.

PubMed Disclaimer

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.

Figures

Figure 1
Figure 1

Haplotype composition and areas of recombination for parental and grandparental gametes for all 17 pairs of linkage groups of 'Honeycrisp' color coded for grandparental contribution from 'Frostbite' and 'Northern Spy' through parent ‘Keepsake’, and from 'Duchess of Oldenburg' and 'Golden Delicious' through the previously unidentified parent MN1627. Marker organization between linkage groups for grandparents that have no known parents is arbitrary as no parental data was available to organize them. Regions of uncertainty between haplotypes due to haplotypes that are identical by state (IBS) are shown via regions with two colors. Regions of homozygosity in 'Honeycrisp' that are due to haplotypes that are likely identical by descent from the grandparental pair 'Frostbite' and 'Duchess of Oldenburg' or the grandparental pair 'Northern Spy' and 'Golden Delicious' (see Supplementary Table 2) are highlighted by a dashed box around the region. These regions share at least 25 SNPs and 8 cM between each pair of grandparents. SNP, single-nucleotide polymorphism.

Figure 2
Figure 2

Reconstructed pedigree for 'Honeycrisp' supported by this study. Maternal DNA was not evaluated in this study, meaning the order of parents and grandparents from left to right within crosses is arbitrary.

Similar articles

Cited by

References

    1. Gallardo RK , Hanrahan I , Hong YA , Luby JJ . Crop load management and the market profitability of ‘Honeycrisp’ apples. Hort Technol 2015; 25: 575–584.
    1. Luby J , Bedford DS . Apple tree: Honeycrisp. Regents of the University of Minnesota, assignee, US patent, US PP7197, 1990.
    1. Mann H , Bedford D , Luby J , Vickers Z , Tong C . Relationship of instrumental and sensory texture measurements of fresh and stored apples to cell number and size. Hortscience 2005; 40: 1815–1820.
    1. Tong C , Krueger D , Vickers Z , Bedford D , Luby J , El-Shiekh A et al. Comparison of softening-related changes during storage of ‘Honeycrisp' apple, its parents, and ‘Delicious'. J Am Soc Hort Sci 1999; 124: 407–415.
    1. Rosenberger D , Schupp J , Watkins C , Iungerman K , Hoying S , Straub D et al. Honeycrisp: promising profit maker or just another problem child. NY Fruit Quarterly 2001; 9: 9–13.