Summary The application of the CRISPR/Cas system as a biotechnological tool for genome editing has revolutionized plant biology. Recently, the repertoire was expanded by CRISPR‐Kill, enabling CRISPR/Cas‐mediated tissue engineering through genome elimination by tissue‐specific expression. Using the Cas9 nuclease from Staphylococcus aureus (SaCas9), CRISPR‐Kill relies on the induction of multiple double‐strand breaks (DSBs) in conserved repetitive genome regions, such as the rDNA, causing cell death of the targeted cells. Here, we show that in addition to spatial control by tissue‐specific expression, temporal control of CRISPR‐mediated cell death is feasible in Arabidopsis thaliana. We established a chemically inducible tissue‐specific CRISPR‐Kill system that allows the simultaneous detection of targeted cells by fluorescence markers. As proof of concept, we were able to eliminate lateral roots and ablate root stem cells. Moreover, using a multi-tissue promoter, we induced targeted cell death at defined time points in different organs at select developmental stages. Thus, using this system makes it possible to gain new insights into the developmental plasticity of certain cell types. In addition to enabling tissue engineering in plants, our system provides an invaluable tool to study the response of developing plant tissue to cell elimination through positional signaling and cell‐to‐cell communication.

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