Acidity and sweetness are important qualities for apple breeders and understanding their genetic regulation can improve the breeding process. In previous QTL studies, fruit quality assessments were performed using instrumental measurements, leading to the identification of two major QTL Ma and Ma3. Here, we use sensorial data to investigate the role of known and unknown genetic factors in the perception of acidity and sweetness in three pedigreed full-sib families. For 2 years, these families were phenotyped by a trained panel, at harvest and after 2 months of cold storage, and genotyped with a new 50 K SNP array. FlexQTLTM analyses using both an additive and an additive + dominance model resulted in the identification of Ma and Ma3 for acidity as well as sweetness, whereas the use of the additive model yielded decisive evidence for the discovery of two additional QTL on LG1 and LG6 for acidity. QTL genotypes were qualified as the inverse of each other, which indicates that individuals with the less-acidity alleles of Ma and Ma3 are perceived sweeter. Due to the genetic configuration in the families studied, resulting from a link with the Pale Green Disorder locus, no incomplete dominance effect could be detected for the Ma locus, although previously reported in the literature. For the Ma3 locus, however, an incomplete dominance effect (58%) is reported here for the first time. The Ma3 locus was also further confined to a 2–4-cM region and a predictive marker for this locus was identified.

Main shoot and sylleptic shoot growth characteristics were measured during and after the first year of growth of 255 Telamon x Braeburn apple seedlings. Although mean main shoot growth characteristics between branched and non-branched trees were significantly different, many non-branched trees expressed similar main shoot growth to branched trees. The variables describing length, number and position of the sylleptic shoots were used to classify branched trees into architecturally different groups. A continuum from trees with few and short shoots to trees with many long shoots is observed. The release of axillary buds from apical dominance is not under complete control by the apical meristem. Genetic seedling difference at the level of roots presumably plays an important role in sylleptic branching. Genetic variation in terms of number, position, and subsequent elongation of sylleptic shoots is clearly observed.