The present study aimed to dissect tree architectural plasticity into genetic, ontogenetic and environmental effects over the first 4 years of growth of an apple F1 progeny by means of quantitative traits loci (QTL) mapping. Both growth and branching processes were phenotyped on the consecutive annual shoots of different axes within a tree. For each studied trait, predicted values (best linear unbiased predictors, BLUPs) of the genotypic (G) effect or its interaction with tree age (G×A) and climatic year (G×Y) were extracted from mixed linear models of repeated data. These BLUPs, which are independent from autocorrelations between repeated measurements, were used for QTL mapping. QTL detection power was improved by this two-step approach. For each architectural process, numerous QTLs were detected and some particularly interesting co-localised in common genomic regions, for internode lengthening, top diameter, and number and percentage of axillary shoots. When several QTLs were detected for a given trait, global models were estimated, which explained a maximum of 40% of the total variance for both internode length and top diameter and 28% for branching. QTLs detected for BLUPs of G×Y effects were interpreted as resulting from the interaction between genetic maximal potential of growth and climatic factors, while those for G×A effects were interpreted in relation to tree ontogeny. Most of the latter ones were found to be concomitant with key development stages during which the trait average started to decrease, but with different magnitudes depending on genotype