Fruit acidity and sweetness are important fruit quality traits in the apple and are therefore targets in apple breeding programs. Multiple quantitative trait loci (QTLs) associated with titratable acidity (TA) and soluble solids content (SSC) have been previously detected. In this study a pedigree-based QTL analysis approach was used to validate QTLs associated with TA and SSC in a ‘Honeycrisp’-derived germplasm set. TA and SSC data collected from 2014 to 2018 and curated genome-wide single nucleotide polymorphism (SNP) data were leveraged to validate three TA QTLs on linkage groups (LGs) 1, 8, and 16 and three SSC QTLs on LGs 1, 13, and 16. TA and SSC QTL haplotypes were characterized in six University of Minnesota apple breeding families representing eight breeding parents including ‘Honeycrisp’ and ‘Minneiska’. Six high-TA haplotypes, four low-TA haplotypes, 14 high-SSC haplotypes, and eight low-SSC haplotypes were characterized. The results of this study will enable more informed selection in apple breeding programs.

Multiple quantitative trait loci (QTLs) associated with fruit size have been reported in apple (Malus domestica Borkh.); however, few have been fully characterized and/or validated. A pedigree-based QTL analysis approach was used to examine the genetic basis of fruit weight in ‘Honeycrisp’-derived germplasm. Fourteen breeding parents were represented by 814 offspring from 13 full-sib families with breeding parents ‘Honeycrisp’ and ‘Minneiska’ being highly represented. Historical fruit weight data and curated genome-wide single nucleotide polymorphism (SNP) data were leveraged to map QTLs to chromosomes (Chrs) 8 and 16, which together accounted for 15% of the phenotypic variation. The Chr 16 QTL colocalized with other important Chr 16 trait loci. ‘Honeycrisp’ inherited two low fruit weight haplotypes at the Chr 8 QTL from progenitors ‘Northern Spy’ and ‘Grimes Golden’. At the Chr 16 QTL, ‘Honeycrisp’ inherited a low fruit weight haplotype from ‘Frostbite’ and a high fruit weight haplotype from ‘Duchess of Oldenburg’. The small-fruited ‘Honeycrisp’ progenitor ‘Frostbite’ had three low fruit weight haplotypes across the two QTLs. Non-additive interactions were observed at and across QTLs. Results will enable more informed parent selection and/or development of trait-predictive DNA tests for use in apple breeding programs.

Breeding apple cultivars with durable genetic resistance is a potential long-term solution to fire blight, a devastating bacterial disease caused by Erwinia amylovora. However, phenotyping resistance/susceptibility to fire blight is challenging due to E. amylovora strain virulence, differential host × strain interactions, quantitative host resistance, environmental influences on disease, and impacts of tree vigor on susceptibility. Inheritance of resistance/susceptibility to fire blight is complex and phenotypic information alone is insufficient to guide breeding decisions targeting resistance. Several quantitative trait loci (QTLs) associated with resistance/susceptibility to fire blight have been detected throughout the apple genome. Most resistance alleles at fire blight QTLs have been identified in wild Malus germplasm with poor fruit quality, which limits their breeding utility. Several QTLs have been identified in populations derived from cultivars and reduced-susceptibility alleles have been characterized in multiple important breeding parents. Although resistance to fire blight is an attractive target for DNA-informed breeding, relatively few trait-predictive DNA tests for breeding relevant fire blight QTLs are available. Here we discuss (1) considerations and challenges associated with phenotyping resistance/susceptibility to fire blight; (2) sources of resistance that have been identified for use as parents; and (3) our perspective on short and long-term strategies to breed apple cultivars with durable resistance to fire blight with emphasis on the potential contributions of reduced susceptibility alleles to achieve this goal.