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

doi:10.1007/s11295-014-0709-1

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 journal › Article › peer-review

25 Scopus citations

Abstract

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 language	English (US)
Pages (from-to)	627-639
Number of pages	13
Journal	Tree Genetics and Genomes
Volume	10
Issue number	3
DOIs	https://doi.org/10.1007/s11295-014-0709-1
State	Published - 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.

Keywords

Genetic map
JoinMap
Linkage map
Malus × domestica

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1007/s11295-014-0709-1

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@article{0e2e40c3968046be8075d4c96b90a04e,

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

abstract = "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.",

keywords = "Genetic map, JoinMap, Linkage map, Malus × domestica",

author = "Clark, {Matthew D.} and Schmitz, {Cari A.} and Rosyara, {Umesh R.} and Luby, {James J.} and Bradeen, {James M.}",

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.",

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doi = "10.1007/s11295-014-0709-1",

language = "English (US)",

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N1 - 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.

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N2 - 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.

AB - 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.

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

Abstract

Bibliographical note

Keywords

UN SDGs

Publisher link

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Open Access Publishing Fund

Cite this

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

Abstract

Bibliographical note

Keywords

UN SDGs

Publisher link

Find It

Other files and links

Fingerprint

Projects

Open Access Publishing Fund

Cite this