a, View inside the foil tunnel in Germany. b, Spatial distribution of blocks and replicates in a split block design. Two independent blocks per watering condition were set up, with four spatially separated blocks within these two blocks. The 517 genotypes were then randomized within spatial blocks. The surface area of these blocks were the size of 18 or 26 quickpot trays for replicates with a high density of plants (a small population was grown per pot) or low density of plants (individual plants were grown per pot), respectively. In total, we placed 346 quickpot trays in Spain and 346 in Germany. Each quickpot tray had 40 cells of which 36 were used to sow plants (the corners were excluded). In total, 23,154 pots were successfully planted, which included about 14,500 pots with single plants (after thinning), and about 9,500 pots in which 30 seeds were planted and left to grow into small population without intervention. c, d, Soil water content (c) and soil surface temperature (d) retrieved from the 34 sensors monitoring each experimental block and the conditions outside the tunnel. Violin plots represent the distribution of recorded temperature and moisture values that were recorded every 10 min during the day and the night from three days after the day of sowing (16 November 2015 in Spain and 22 October 2015 in Germany) until the day at which all plants had completed their cycle and were dry (25 April 2016 in Spain and 15 April 2016 in Germany; n = 10,000 subsampled values of the time series). e, Set-up and examples of image-based high-throughput in situ phenotyping. (1) Customized dark box (Fotomatón) for image acquisition and (2) example tray with the corresponding green (3) and red (4) segmentation image products. Image-based monitoring was done for 23,154 pots, of which 375 pots were identified as failed replicates using the red flags placed in the field by experimenters (2 and 4). (5) Example image of a cut inflorescence of an adult plant and (6) segmentation of the inflorescence from background, (7) inflorescence path or skeletonization and (8) branch and end-point detection. In total, inflorescence images of 13,849 pots were taken and analysed. The variables extracted from inflorescence image processing (6–8) were used as predictors in a linear model that accurately estimated the number of fruits on an inflorescence, a relationship that was calibrated by manually counting fruits of small, medium and large representative plants (R2 = 0.97, n = 11, P = 10−4). a, e, All photographs were taken by M.E.-A.