Tagged_Fruit: contains measurements of three orthogonal diameters for nine fruits from each of five FRU and five THI trees in 16 dates.

Sampled_fruits: contains measurements of three orthogonal diameters, dry weight and canopy level for 413 fruits, sampled in 6 dates (of which 238 FRU and 175 THI; 358 from ancillary trees and 55 tagged fruits after harvest). It contains also estimates of fruit volume and density.

Fruit_yield: contains yields for five FRU and five THI trees.

Tagged_Shoot: contains measurements of length for about 20% shoots of five FRU and five DEF trees (468 shoots) in 9 dates. It also includes: a monitoring of the basal diameters for about 10 shoots per tree in four dates, shoot orientation (North/South); the number of fruits present on individual shoots and on their carrying branch as for one date in early June; the height of the carrying branch at its insertion point into the trunk, its diameter and a measure of pruning intensity evaluated after the end of the growing season.

Sampled_shoots: contains length, basal and apical diameter, number of leaves, leaf and shoot dry weight and canopy level of 182 shoots sampled from ancillary FRU trees on 6 dates.

Sampled_shoots_End_Growing_season: contains shoot fresh mass, volume and the calculated density of 40 shoots (20 FRU and 20 DEF) sampled after the end of the growing season.

Tagged_Trunk: contains measurements of trunk circumferences of five FRU and five DEF trees in 7 dates.

DegreeDays: contains the growing degree days and accumulated growing degree days from the date of full bloom, after cut off of temperatures below 5°C and below 35°C, for year 2014 in the study site.

Field monitoring and sampling was performed in an intensive orchard located in the apple production area of the Adige river floodplain, Caldaro municipality, Trentino Alto Adige region, Italy (46° 21’ N, 11° 16’ E; 240 m a.s.l.). Trees were planted in year 2000, trained as spindelbush and spaced 1 m along the tree rows and 3 m between the rows. Orchard management followed organic guidelines, including winter pruning and tree topping at 3.6 m. A superficial water table and a drip irrigation system assured no water stress, while the availability of soil phosphorous, nitrogen and exchangeable potassium was at optimal levels [1]. Fifteen trees were selected along a tree row and randomly split in three classes: unmanipulated trees (FRU), thinned trees (THI) and defruited trees (DEF). FRU trees followed common practices for commercial orchard and hold an average of 0.47 fruits per shoot or spur. Both THI and DEF trees underwent fruit thinning on 23^rd April 2014 (150 GDD – Growing Degree Days after bloom). THI trees were heavily thinned, so that about 10-15 fruits were left per tree, with no more than one fruit per bourse shoot or spur. Conversely, fruits were completely removed in DEF trees. Mean FRU tree yield (26.2 kg/tree) was above the average yield at orchard level in previous years (Max = 22.3 kg/tree in years 2009-2012). A meteorological station was installed in the field, measuring mean daily air temperature at 2 m height.

Nine fruits were tagged along a vertical transect comprising the whole tree height, on each FRU and THI tree. Three orthogonal largest diameters were measured on each tagged fruit using a digital caliper: the largest transversal diameter, a second transversal diameter obtained by turning the fruit by about 90 degrees along its longitudinal axis, and a diameter passing from the petiole to the fruit bottom, so that the fruit dimensions could be acquired similarly across different fruits and dates. Measurements were repeated about weekly. Fruits volume was estimated using the formula for a rotational spheroids (Volume = 4/3 π r1 r2 r3).

About 15 or more additional fruits were sampled from the different canopy levels on each date, alternately from additional FRU or THI ancillary trees. Finally, tagged fruits were also collected at harvest time. Sampled fruit diameters, volumes and dry weights (after petiole removal) were determined using a precision scale, after drying at 70 °C until constant weight was reached.

For each tree, the trunk was marked at 1.20 and 2.40 m height, dividing it horizontally in three levels (Low, Medium, High). From the lower part to the top of each level, one first order branch every five was tagged and numbered sequentially.

On each tagged branch, from the insertion point in the main axis to the branch apex, every shoot and spur were tagged and lettered sequentially. The length of each tagged shoot/spur, from its insertion point in the carrying branch to its apex, was measured with a tape measure, every about two weeks from April to July and once a month in August and September in year 2014.

Secondary shoot growth was monitored on about 10 tagged shoots for each DEF and FRU trees, by measuring the basal diameters, respectively above the shoot bases on four dates (mid-July, mid-August, early-September and after the end of the growing season).

About 30 vegetative shoots were also sampled from additional FRU trees according to a stratified sampling, taking into account level, orientation and shoot length. Sampling occurred in six dates (DOY 148, 162, 188, 205, 234, 251) from years 2014 and 2015. Leaves were separated from their shoots by means of a lancet and counted. The shoot basal diameters were measured 1 cm above their bases, by means of a digital caliper. Leaves and shoots fresh weight were determined. They were then dried in a stove at 70 °C until constant weight was reached, brought to room temperature in a desiccator and weighted again. Shoots and leaves dry weights were obtained using a precision scale. 20 additional shoots per treatment were also sampled after fruit harvest. Their volume was obtained by submersion in water in a graduated cylinder, and their dry weight obtained after oven drying at 70 °C. Shoot density was calculated as the ratio between shoot dry weight and volume.

The number of fruits present on each tagged branch and on the monitored shoot/spur contained in them was also counted on 18^th June 2014.

The height and diameter of each tagged branch were respectively measured with a tape measure and a digital caliper by the end of the vegetative season. On the same date, the branches/shoots cross sections left exposed after the winter pruning from previous years were visually compared to the cross section of the carrying branch. Branches were then classed according to four pruning intensities: 1, 2 and 3 for cross section areas respectively smaller, equal and larger than the area of the cross section of the carrying branch; 0 for no evidences of pruning. Diameters were measured next to the insertion point into the main axis (< 1 cm far), except when pruning had occurred next to the basis of the branch. In this latter case, measurements were made just following the pruning.

The dataset presents a few missing measurements: lengths and diameters (< 1 %) when shoots/spurs were difficult to find because of occlusion due to the high leaf density; branch diameters, when they originated directly from the tree main axis, or were difficult to reach because too high in the canopy.

Each DEF and FRU tree was equipped with a trunk collar, mounted at 10 cm above the grafting point (about 40 cm above the ground). Measurements of trunk circumference were also taken every two weeks.