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, Eric Van De Weg, David S Bedford, Cameron P. Peace, Stijn Vanderzande, Matthew D Clark, Soon Li Teh, Lichun Cai, James J Luby

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14 Citations (Scopus)

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.

Original languageEnglish (US)
Article number17003
JournalHorticulture Research
Volume4
DOIs
StatePublished - Feb 22 2017

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Malus
Pedigree
pedigree
Haplotypes
chromosome mapping
Single Nucleotide Polymorphism
haplotypes
apples
grandparents
Breeding
Chromosomes
breeding
Siblings
cultivars
Chromosomes, Human, Pair 17
Chemical analysis
Datasets
chromosomes

Cite this

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title = "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",
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.",
author = "Howard, {Nicholas P.} and {Van De Weg}, Eric and Bedford, {David S} and Peace, {Cameron P.} and Stijn Vanderzande and Clark, {Matthew D} and Teh, {Soon Li} and Lichun Cai and Luby, {James J}",
year = "2017",
month = "2",
day = "22",
doi = "10.1038/hortres.2017.3",
language = "English (US)",
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journal = "Horticulture Research",
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T1 - 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

AU - Howard, Nicholas P.

AU - Van De Weg, Eric

AU - Bedford, David S

AU - Peace, Cameron P.

AU - Vanderzande, Stijn

AU - Clark, Matthew D

AU - Teh, Soon Li

AU - Cai, Lichun

AU - Luby, James J

PY - 2017/2/22

Y1 - 2017/2/22

N2 - 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.

AB - 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.

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