CRISPR/Cas9: A new genome editing tool to accelerate cotton (Gossypium spp.) breeding

Abstract

Cotton has a tremendous economic value worldwide due to its high-quality fiber, edible oil and protein contents. However, the intensifying scenario of human population expansion and global environmental changes demand a proportionate increase in cotton production. In the past, several successful attempts have been made by introgression of many quality-and yield-related traits into elite cotton cultivars through conventional breeding. However, those measures are time consuming due to the reliance on introgression of naturally-existing genetic variation through extensive backcrossing. Nonetheless, plant breeding can be accelerated through modern genome editing (GE) tools. Various GE techniques including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced palindromic repeats and CRISPR-associated proteins systems (CRISPR/Cas)-based approaches have been successfully employed for various crop plants. Among them, CRISPR/Cas-based approaches hold great GE potential due to their simplicity, competency and versatility. In cotton, this system can regulate the gene expression associated with quality traits, to circumscribe phytopathogens and/or to stack molecular traits at a desired locus. In gene stacking through site-specific endonucleases, the desired genes can be introduced in close proximity to a specific locus in the cotton genome with a low risk of segregation. However, such executions are tedious to achieve through classical breeding techniques. Moreover, through the CRISPR/Cas-based approaches, transgene-free cotton plants can easily be produced by selfing or backcrossing to meet the current genetically modified organisms (GMO) guidelines. In this chapter, we address the potential application of CRISPR/Cas-based approaches in available whole cotton genomes to sustain cotton productivity, and achieve genetic improvement, pathogen resistance and agronomic traits. Future prospects of GE applications in cotton breeding are also addressed.