Climate change and the diversity of consumer needs require innovative methods to continuously and rapidly modify existing crops for the development of new varieties.In the past decade genome editing by CRISPR/Cas and derivatives has emerged as a novel and effective technology for functional studies and gene discovery as well as for breeding new traits and genotypes.The development of novel CRISPR/Cas platforms, methods for the delivery of editing reagents, and methods for controlling gene regulation and detection of mutants have all expanded the scope of genome editing and other CRISPR/Cas-based approaches. The discovery of the CRISPR/Cas genome-editing system has revolutionized our understanding of the plant genome. CRISPR/Cas has been used for over a decade to modify plant genomes for the study of specific genes and biosynthetic pathways as well as to speed up breeding in many plant species, including both model and non-model crops. Although the CRISPR/Cas system is very efficient for genome editing, many bottlenecks and challenges slow down further improvement and applications. In this review we discuss the challenges that can occur during tissue culture, transformation, regeneration, and mutant detection. We also review the opportunities provided by new CRISPR platforms and specific applications related to gene regulation, abiotic and biotic stress response improvement, and de novo domestication of plants.