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Article|03 May 2023|OPEN
Genomewide selection for fruit quality traits in apple: breeding insights gained from prediction and postdiction 
Sarah A. Kostick1 , Rex Bernardo2 and James J. Luby,1 ,
1Department of Horticultural Science, University of Minnesota, Saint Paul, MN 55108, USA
2Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
*Corresponding author. E-mail:

Horticulture Research 10,
Article number: uhad088 (2023)
Views: 133

Received: 28 Feb 2023
Accepted: 26 Apr 2023
Published online: 03 May 2023


Many fruit quality traits in apple (Malus domestica Borkh.) are controlled by multiple small-effect quantitative trait loci (QTLs). Genomewide selection (genomic selection) might be an effective breeding approach for highly quantitative traits in woody perennial crops with long generation times like apple. The goal of this study was to determine if genomewide prediction is an effective breeding approach for fruit quality traits in an apple scion breeding program. Representative apple scion breeding germplasm (nindividuals = 955), high-quality single nucleotide polymorphism (SNP) data (nSNPs = 977), and breeding program fruit quality trait data at harvest were analyzed. Breeding parents `Honeycrisp' and `Minneiska' were highly represented. Moderate to high predictive abilities were observed for most fruit quality traits at harvest. For example, when 25% random subsets of the germplasm set were used as training sets, mean predictive abilities ranged from 0.35 to 0.54 across traits. Trait, training and test sets, family size for within family prediction, and number of SNPs per chromosome affected model predictive ability. Inclusion of large-effect QTLs as fixed effects resulted in higher predictive abilities for some traits (e.g. percent red overcolor). Postdiction (i.e. retrospective) analyses demonstrated the impact of culling threshold on selection decisions. The results of this study demonstrate that genomewide selection is a useful breeding approach for certain fruit quality traits in apple.