Conventional tools induce mutations randomly throughout the cotton genome—making breeding difficult and challenging. During the last decade, progress has been made to edit the gene of interest in a very precise manner. Targeted genome engineering with engineered nucleases (ENs) specifically zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases (e.g., Cas9) has been described as a “game-changing technology” for diverse fields as human genetics and plant biotechnology. In eukaryotic systems, ENs create double-strand breaks (DSBs) at the targeted DNA sequence which are repaired by nonhomologous end joining (NHEJ) or homology-directed recombination (HDR) mechanisms. ENs have been used successfully for targeted mutagenesis, gene knockout, and multisite genome editing (GenEd) in model plants and crop plants such as cotton, rice, and wheat. Recently, cotton genome has also been edited for targeted mutagenesis through CRISPR/Cas for improved lateral root formation. In addition, an efficient and fast method has been developed to evaluate guide RNAs transiently in cotton. The targeted disruption of undesirable genes or metabolic pathway can be achieved to increase quality of cotton. Undesirable metabolites like gossypol in cottonseed can be targeted efficiently using ENs for seed-specific low-gossypol cotton. Moreover, ENs are also helpful in gene stacking for herbicide resistance, insect resistance, and abiotic stress tolerance.
Part of the book: Past, Present and Future Trends in Cotton Breeding