Gene targeting (GT), or homology-directed repair (HDR), is used routinely in plant genome engineering to insert specific sequences,  with the first published example of GT in plants in the 1980s. However, gene targeting is particularly challenging in higher plants due to the low rates of Homologous Recombination, or Homology Directed Repair, in higher plants and the low rate of transformation (DNA uptake) by many plant species. However, there has been much effort to increase the frequencies of gene targeting in plants in the past decades, as it is very useful to be able to introduce specific sequences in the plant genome for plant genome engineering. The most significant improvement to gene targeting frequencies in plants was the induction of double-strand-breaks through site specific nucleases such as CRISPR, as described above. Other strategies include in planta gene targeting, whereby the homology repair template is embedded within the plant genome and then liberated using CRISPR cutting; upregulation of genes involved in the homologous recombination pathway; downregulation of the competing Non-Homologous-End-Joining pathway; increasing copy numbers of the homologous repair template; and engineering Cas variants to be optimised for plant tissue culture. Some of these approaches have also been used to improve gene targeting efficiencies in mammalian cells.
Plants that have been gene-targeted include Arabidopsis thaliana (the most commonly used model plant), rice, tomato, maize, tobacco and wheat.