Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

Nicholas P. Howard; Eric van de Weg; John Tillman; Cindy B.S. Tong; Kevin A.T. Silverstein; James J. Luby

doi:10.1007/s11295-017-1216-y

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

Nicholas P. Howard, Eric van de Weg, John Tillman, Cindy B.S. Tong, Kevin A.T. Silverstein, James J. Luby

Research output: Contribution to journal › Article › peer-review

26 Scopus citations

Abstract

Soft scald and soggy breakdown are important postharvest physiological disorders of apple (Malus × domestica). ‘Honeycrisp’ and some of its offspring are particularly susceptible to developing these disorders. The purpose of this study was to identify molecular markers associated with high incidences of soft scald and soggy breakdown for use in marker-assisted breeding. Towards this aim, we employed a pedigree-based approach using mostly germplasm related to ‘Honeycrisp.’ Two quantitative trait loci (QTL) were consistently identified on linkage groups (LGs) 2 and 16 across the 2014 and 2015 harvest years. The same QTL were identified for both storage disorders, indicating that they may be physiologically related. ‘Honeycrisp’ is homozygous for an identical by state haplotype at the LG2 QTL that was consistently associated with a deleterious effect on soft scald and soggy breakdown incidence. This haplotype was traced through SNP-confirmed pedigrees to the following cultivars: ‘Grimes Golden,’ ‘Northern Spy,’ ‘Rome Beauty,’ and ‘Fireside’ and is common in derived apple germplasm. Haplotypes at the LG16 QTL could not be adequately characterized due to variation between years combined with effects of this QTL being of relatively smaller size and being most evident in individuals that carry two copies of the deleterious haplotype at the LG2 QTL. These results suggest that limiting homozygosity of the deleterious haplotype at the LG2 QTL through marker-assisted breeding would be a valid strategy to limit soft scald and soggy breakdown incidences in apple seedling populations.

Original language	English (US)
Article number	2
Journal	Tree Genetics and Genomes
Volume	14
Issue number	1
DOIs	https://doi.org/10.1007/s11295-017-1216-y
State	Published - Feb 1 2018

Bibliographical note

Funding Information:
This work was partially supported by the USDA National Institute of Food and Agriculture—Specialty Crop Research Initiative projects, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808) and “RosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars” (2014-51181-22378). Some genetic data and technical expertise was provided by the FruitBreedomics project: Integrated approach for increasing breeding efficiency in fruit tree crops (www.FruitBreedomics.com), which was co-funded by the EU seventh Framework Programme, project N° 265582. We thank David Bedford, Matthew Clark, Emmi Klarer, Sarah Kostick, Ken Mullin, Hannah Hauan, Elizabeth Blissett, and Ashley Powell for assistance in harvesting and phenotyping. SNP calls and phenotype data for seedling individuals evaluated in this study can be found in Table S2.

Funding Information:
Acknowledgements This work was partially supported by the USDA National Institute of Food and Agriculture—Specialty Crop Research Initiative projects, BRosBREED: Enabling marker-assisted breeding in Rosaceae^ (2009-51181-05808) and BRosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars^ (2014-51181-22378).

Publisher Copyright:
© 2017, The Author(s).

Keywords

FlexQTL™
Marker-assisted breeding
PBA
Storage disorders

Access

10.1007/s11295-017-1216-y

OpenUrl availability

Full text

Cite this

@article{c46e9bc4b8f244b1b035ac4a671e76ff,

title = "Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families",

abstract = "Soft scald and soggy breakdown are important postharvest physiological disorders of apple (Malus × domestica). {\textquoteleft}Honeycrisp{\textquoteright} and some of its offspring are particularly susceptible to developing these disorders. The purpose of this study was to identify molecular markers associated with high incidences of soft scald and soggy breakdown for use in marker-assisted breeding. Towards this aim, we employed a pedigree-based approach using mostly germplasm related to {\textquoteleft}Honeycrisp.{\textquoteright} Two quantitative trait loci (QTL) were consistently identified on linkage groups (LGs) 2 and 16 across the 2014 and 2015 harvest years. The same QTL were identified for both storage disorders, indicating that they may be physiologically related. {\textquoteleft}Honeycrisp{\textquoteright} is homozygous for an identical by state haplotype at the LG2 QTL that was consistently associated with a deleterious effect on soft scald and soggy breakdown incidence. This haplotype was traced through SNP-confirmed pedigrees to the following cultivars: {\textquoteleft}Grimes Golden,{\textquoteright} {\textquoteleft}Northern Spy,{\textquoteright} {\textquoteleft}Rome Beauty,{\textquoteright} and {\textquoteleft}Fireside{\textquoteright} and is common in derived apple germplasm. Haplotypes at the LG16 QTL could not be adequately characterized due to variation between years combined with effects of this QTL being of relatively smaller size and being most evident in individuals that carry two copies of the deleterious haplotype at the LG2 QTL. These results suggest that limiting homozygosity of the deleterious haplotype at the LG2 QTL through marker-assisted breeding would be a valid strategy to limit soft scald and soggy breakdown incidences in apple seedling populations.",

keywords = "FlexQTL{\texttrademark}, Marker-assisted breeding, PBA, Storage disorders",

author = "Howard, {Nicholas P.} and {van de Weg}, Eric and John Tillman and Tong, {Cindy B.S.} and Silverstein, {Kevin A.T.} and Luby, {James J.}",

note = "Funding Information: This work was partially supported by the USDA National Institute of Food and Agriculture—Specialty Crop Research Initiative projects, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808) and “RosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars” (2014-51181-22378). Some genetic data and technical expertise was provided by the FruitBreedomics project: Integrated approach for increasing breeding efficiency in fruit tree crops (www.FruitBreedomics.com), which was co-funded by the EU seventh Framework Programme, project N° 265582. We thank David Bedford, Matthew Clark, Emmi Klarer, Sarah Kostick, Ken Mullin, Hannah Hauan, Elizabeth Blissett, and Ashley Powell for assistance in harvesting and phenotyping. SNP calls and phenotype data for seedling individuals evaluated in this study can be found in Table S2. Funding Information: Acknowledgements This work was partially supported by the USDA National Institute of Food and Agriculture—Specialty Crop Research Initiative projects, BRosBREED: Enabling marker-assisted breeding in Rosaceae^ (2009-51181-05808) and BRosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars^ (2014-51181-22378). Publisher Copyright: {\textcopyright} 2017, The Author(s).",

year = "2018",

month = feb,

day = "1",

doi = "10.1007/s11295-017-1216-y",

language = "English (US)",

volume = "14",

journal = "Tree Genetics and Genomes",

issn = "1614-2942",

publisher = "Springer Verlag",

number = "1",

}

TY - JOUR

T1 - Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

AU - Howard, Nicholas P.

AU - van de Weg, Eric

AU - Tillman, John

AU - Tong, Cindy B.S.

AU - Silverstein, Kevin A.T.

AU - Luby, James J.

N1 - Funding Information: This work was partially supported by the USDA National Institute of Food and Agriculture—Specialty Crop Research Initiative projects, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808) and “RosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars” (2014-51181-22378). Some genetic data and technical expertise was provided by the FruitBreedomics project: Integrated approach for increasing breeding efficiency in fruit tree crops (www.FruitBreedomics.com), which was co-funded by the EU seventh Framework Programme, project N° 265582. We thank David Bedford, Matthew Clark, Emmi Klarer, Sarah Kostick, Ken Mullin, Hannah Hauan, Elizabeth Blissett, and Ashley Powell for assistance in harvesting and phenotyping. SNP calls and phenotype data for seedling individuals evaluated in this study can be found in Table S2. Funding Information: Acknowledgements This work was partially supported by the USDA National Institute of Food and Agriculture—Specialty Crop Research Initiative projects, BRosBREED: Enabling marker-assisted breeding in Rosaceae^ (2009-51181-05808) and BRosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars^ (2014-51181-22378). Publisher Copyright: © 2017, The Author(s).

PY - 2018/2/1

Y1 - 2018/2/1

N2 - Soft scald and soggy breakdown are important postharvest physiological disorders of apple (Malus × domestica). ‘Honeycrisp’ and some of its offspring are particularly susceptible to developing these disorders. The purpose of this study was to identify molecular markers associated with high incidences of soft scald and soggy breakdown for use in marker-assisted breeding. Towards this aim, we employed a pedigree-based approach using mostly germplasm related to ‘Honeycrisp.’ Two quantitative trait loci (QTL) were consistently identified on linkage groups (LGs) 2 and 16 across the 2014 and 2015 harvest years. The same QTL were identified for both storage disorders, indicating that they may be physiologically related. ‘Honeycrisp’ is homozygous for an identical by state haplotype at the LG2 QTL that was consistently associated with a deleterious effect on soft scald and soggy breakdown incidence. This haplotype was traced through SNP-confirmed pedigrees to the following cultivars: ‘Grimes Golden,’ ‘Northern Spy,’ ‘Rome Beauty,’ and ‘Fireside’ and is common in derived apple germplasm. Haplotypes at the LG16 QTL could not be adequately characterized due to variation between years combined with effects of this QTL being of relatively smaller size and being most evident in individuals that carry two copies of the deleterious haplotype at the LG2 QTL. These results suggest that limiting homozygosity of the deleterious haplotype at the LG2 QTL through marker-assisted breeding would be a valid strategy to limit soft scald and soggy breakdown incidences in apple seedling populations.

AB - Soft scald and soggy breakdown are important postharvest physiological disorders of apple (Malus × domestica). ‘Honeycrisp’ and some of its offspring are particularly susceptible to developing these disorders. The purpose of this study was to identify molecular markers associated with high incidences of soft scald and soggy breakdown for use in marker-assisted breeding. Towards this aim, we employed a pedigree-based approach using mostly germplasm related to ‘Honeycrisp.’ Two quantitative trait loci (QTL) were consistently identified on linkage groups (LGs) 2 and 16 across the 2014 and 2015 harvest years. The same QTL were identified for both storage disorders, indicating that they may be physiologically related. ‘Honeycrisp’ is homozygous for an identical by state haplotype at the LG2 QTL that was consistently associated with a deleterious effect on soft scald and soggy breakdown incidence. This haplotype was traced through SNP-confirmed pedigrees to the following cultivars: ‘Grimes Golden,’ ‘Northern Spy,’ ‘Rome Beauty,’ and ‘Fireside’ and is common in derived apple germplasm. Haplotypes at the LG16 QTL could not be adequately characterized due to variation between years combined with effects of this QTL being of relatively smaller size and being most evident in individuals that carry two copies of the deleterious haplotype at the LG2 QTL. These results suggest that limiting homozygosity of the deleterious haplotype at the LG2 QTL through marker-assisted breeding would be a valid strategy to limit soft scald and soggy breakdown incidences in apple seedling populations.

KW - FlexQTL™

KW - Marker-assisted breeding

KW - PBA

KW - Storage disorders

UR - http://www.scopus.com/inward/record.url?scp=85037349697&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85037349697&partnerID=8YFLogxK

U2 - 10.1007/s11295-017-1216-y

DO - 10.1007/s11295-017-1216-y

M3 - Article

AN - SCOPUS:85037349697

SN - 1614-2942

VL - 14

JO - Tree Genetics and Genomes

JF - Tree Genetics and Genomes

IS - 1

M1 - 2

ER -

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

Abstract

Bibliographical note

Keywords

Access

OpenUrl availability

Other files and links

Fingerprint

Cite this