(A–C) Genetic tracing induced at E12.5 in Col2a1-CreERT2/R26Confetti shows recombination in chondrocytes (B) only and not in a lineage of membranous bone osteoblasts and their progenitors (C), 25 µm cryo-sections (A–D, G–H) were imaged with a confocal microscope (A–C) or phase contrast microscope (D, G–H). (D) Traced sections have been stained using Alcian Blue (cartilage, blue) and von Kossa (brown, mineralized tissue). (E–F) Wild type (E) and Col2a1-CreERT2/R26DTA (F) embryos with cartilage being partially ablated as a result of tamoxifen injection (2.5 mg) at E12.5, both analyzed at E17.5. (G–H) Sagittal sections of the anterior head from wild type (G) and Col2a1-CreERT2/R26DTA (H) embryos stained with Alcian Blue (blue, stains for cartilage) and von Kossa staining (black, stains for mineralized bone tissue). Olfactory system is outlined by green dashed line for better orientation. Note that physiological growth of the cartilage sets the proper size of the facial compartment. (I–O) 3D-reconstructions of frontal chondrocranium together with bone and teeth primordia in control (I, L, M) and cartilage-ablated (J, N, O) embryos. (K) Best fit comparison of control (red) and cartilage-ablated (light green) 3D chondrocranium models. (P) 3D-reconstruction of frontal chondrocranium and formed cartilage including GOM Inspect software analysis of the mutant bone (Q) overview of analyzed mutants (injected with low dose of tamoxifen (2.5 mg) at both E13.5 and E14.5 and analyzed at E15.5) and formed bone in one representative control and three mutants (R) Bar-graphs showing the manual 3D segmentation of the surface area of cartilage. Data are obtained from three control samples and three mutant mice for (E15.5) and three control samples and one mutant sample with the most pronounced phenotype for (E17.5). The error bars show mean and standard deviation (SD). For the comparison, we used unpaired Student t-test (95% confidence interval −9974138 to −6056665). Raw data are available in Figure 1—source data 1.