A consensus 'Honeycrisp' apple (Malus × domestica) genetic linkage map from three full-sib progeny populations

Matthew D. Clark, Cari A. Schmitz, Umesh R. Rosyara, James J. Luby, James M. Bradeen

Research output: Contribution to journalArticlepeer-review

24 Scopus citations


The apple cultivar Honeycrisp is emerging in North American markets due to its outstanding eating quality. A set of three 'Honeycrisp' progeny populations from the University of Minnesota apple breeding program were utilized to construct parental and consensus 'Honeycrisp' linkage maps to enable marker-assisted breeding. Two populations were segregated for fruit texture traits and a third was of interest in examining disease resistance. All available individuals were genotyped with the International RosBREED SNP Consortium (IRSC) apple 8K SNP array v1, for a total of 318 progeny individuals. Three unique 'Honeycrisp' parental maps ('Honeycrisp' × 'Monark,' 'Honeycrisp' × 'Gala,' and 'Honeycrisp' × MN1764) were developed, consisting of 1,018, 1,042, and 1,041 single-nucleotide polymorphism (SNP) markers, respectively. Among all three 'Honeycrisp' parental maps, 951 SNP markers were in common. Combining these maps with the MergeMap tool, a consensus 'Honeycrisp' linkage map with 1,091 SNP markers was developed with an average distance of 1.36 cM between consecutive markers. The 'Honeycrisp' consensus map was largely in agreement with the physical position of markers in the 'Golden Delicious' reference genome sequence (v1.0, as of February 2013). The consensus linkage map is informative for an elite cultivar that is being utilized in breeding programs worldwide for its superb fruit quality traits.

Original languageEnglish (US)
Pages (from-to)627-639
Number of pages13
JournalTree Genetics and Genomes
Issue number3
StatePublished - Jun 2014

Bibliographical note

Funding Information:
Acknowledgments This work was partially funded by USDA's National Institute of Food and Agriculture—Specialty Crop Research Initiative project, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808). The authors gratefully acknowledge Elisabeth Alperin, April Nyberg, and Nahla Bassil (National Clonal Germplasm Repository, Corvallis, OR); Amy Iezzoni (Department of Horticulture, Michigan State University), the Michigan State University Infinium SNP Genotyping Lab, and the Minnesota Supercomputing Institute for providing advice, resources, and services integral to this project.


  • Genetic map
  • JoinMap
  • Linkage map
  • Malus × domestica


Dive into the research topics of 'A consensus 'Honeycrisp' apple (Malus × domestica) genetic linkage map from three full-sib progeny populations'. Together they form a unique fingerprint.

Cite this