Targeted genome editing for cotton improvement: prospects and challenges

Cotton is a highly profitable agricultural crop globally, valued for its valuable natural cellulosic fibres, renewable biofuel potential, and rich edible oil content. Global cotton production is impeded by multiple biotic and abiotic stresses, compounded with the ever-increasing human population and demands, necessitating enhanced and sustainable yields<bold>.</bold> Although traditional breeding and transgenic technologies have demonstrated efficiency in enhancing economic agronomic traits, their effectiveness is hindered by reliance on limited genetic variability and a time-consuming process involving multiple backcrosses and stringent trait selections. The relatively large and complex genome (similar to 2.5 Gb) with high functional gene redundancy poses significant challenges to genomic manipulations in cotton. The rapid advancement of sequence-specific engineered nucleases, particularly RNA-guided CRISPR-based Cas nucleases, have revolutionised gene manipulation techniques, proving effective in precise targeted mutagenesis and multiplexed genome editing across diverse organisms, including plants. The CRISPR/Cas9 genome editing technology, known for its simplicity, flexibility, consistency, and remarkable efficiency, has the potential to facilitate extensive genetic modifications in cotton traits, heralding a new era of precision cotton breeding. Recent cotton genome sequencing initiatives provide valuable data for identifying new gene targets, paving the way for advancements in crop sustainability. Integrated genome sequencing and gene editing signify a precision era in cotton breeding, facilitating progress in functional genomics and trait improvement. In this review, we summarised the genome editing tools available for targeted genome modification in plants and the current status of targeted genome editing applications in cotton for trait improvement. Additionally, we highlighted the existing cotton genes, which have been functionally validated as both negative and positive regulators of important agronomic traits for their utilization in future cotton genome editing programs. Finally, we discussed the current challenges and future prospects of these genome engineering tools for their comprehensive applications in cotton functional genomics and breeding to enhance productivity and resilience to climate change. [GRAPHICS] .