Articles
Apple ground color QTL discovery and characterization in a multi-family population
Article number
1412_27
Pages
175 – 182
Language
English
Abstract
Skin color plays a crucial role in the fruit’s appeal to consumers.
In apple, skin color consists of a ground color and an overcolor.
The ground color ranges from green to yellow, as exemplified by ‘Granny Smith’ and ‘Golden Delicious’, respectively, while overcolor, when present, adds a red color on top of the ground color.
While considerable attention has been given to understanding the genetics of overcolor, ground color and its genetic basis are less studied even though it is of importance.
For example, a green ground color may result in brownish overcolors which are less appealing to consumers.
To address the limited knowledge regarding the genetic factors controlling ground color, this study aimed to identify quantitative trait loci (QTLs) for this trait.
QTLs were discovered using an identity-by-descent/pedigree-based analysis approach with FlexQTL and using phenotypic and genotypic data from 902 seedlings across 20 families obtained through the European projects HiDRAS and FruitBreedomics, respectively.
Our results revealed three main QTLs, one on chromosome 3 and two on chromosome 10. In-depth analyses of the two chromosome 10 QTLs revealed that one of them was heterozygous in various ancestors, while the other was caused by a unique allele from a specific source.
Because the latter had a low level of representation, validation in new germplasm would be useful.
Functional alleles of all QTLs were determined and a QTL*QTL interaction effect was observed.
Furthermore, the ground color QTLs co-located with QTLs and genes known to be associated with harvest date and ethylene production.
However, we could not assess a functional correlation between them.
The identified QTL alleles represent an initial step toward DNA-informed breeding for ground color in apple.
In apple, skin color consists of a ground color and an overcolor.
The ground color ranges from green to yellow, as exemplified by ‘Granny Smith’ and ‘Golden Delicious’, respectively, while overcolor, when present, adds a red color on top of the ground color.
While considerable attention has been given to understanding the genetics of overcolor, ground color and its genetic basis are less studied even though it is of importance.
For example, a green ground color may result in brownish overcolors which are less appealing to consumers.
To address the limited knowledge regarding the genetic factors controlling ground color, this study aimed to identify quantitative trait loci (QTLs) for this trait.
QTLs were discovered using an identity-by-descent/pedigree-based analysis approach with FlexQTL and using phenotypic and genotypic data from 902 seedlings across 20 families obtained through the European projects HiDRAS and FruitBreedomics, respectively.
Our results revealed three main QTLs, one on chromosome 3 and two on chromosome 10. In-depth analyses of the two chromosome 10 QTLs revealed that one of them was heterozygous in various ancestors, while the other was caused by a unique allele from a specific source.
Because the latter had a low level of representation, validation in new germplasm would be useful.
Functional alleles of all QTLs were determined and a QTL*QTL interaction effect was observed.
Furthermore, the ground color QTLs co-located with QTLs and genes known to be associated with harvest date and ethylene production.
However, we could not assess a functional correlation between them.
The identified QTL alleles represent an initial step toward DNA-informed breeding for ground color in apple.
Authors
S. Vanderzande, E. van de Weg
Keywords
Malus domestica, skin color, pedigree-based analysis, identity-by-descent, FlexQTL
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