Cotton Genomics and Genetics 2025, Vol.16, No.6, 300-309 http://cropscipublisher.com/index.php/cgg 300 Feature Review Open Access Precision Breeding of Cotton Using Haplotypes and Genome Editing Tools ZhenLi Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: zhen.li@hibio.org Cotton Genomics and Genetics, 2025, Vol.16, No.6 doi: 10.5376/cgg.2025.16.0030 Received: 20 Nov., 2025 Accepted: 12 Dec., 2025 Published: 25 Dec., 2025 Copyright © 2025 Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li Z., 2025, Precision breeding of cotton using haplotypes and genome editing tools, Cotton Genomics and Genetics, 16(6): 300-309 (doi: 10.5376/cgg.2025.16.0030) Abstract Cotton, as one of the world's most important fiber crops, requires precision breeding strategies to meet the growing demands for yield, quality, and sustainability. This study focuses on the integration of haplotype-based methods and genome editing tools as innovative approaches to accelerate cotton genetic improvement. First, we discuss the definition, identification, and application of haplotypes in resolving complex traits; second, we outline genome editing systems, particularly CRISPR-Cas technology for modifying specific gene targets in cotton. This study emphasizes the synergistic effect of haplotype information and genome editing as a means to validate candidate gene function and shorten breeding cycles. A case study demonstrating the application potential of these precision tools in improving fiber quality is presented. While exploring challenges such as technological limitations, regulatory hurdles, and data integration, this study predicts that emerging advances in pan-genome analysis, graph-based haplotype analysis, and next-generation editing platforms will establish robust processes for sustainable cotton breeding and genetic innovation. Keywords Cotton breeding; Haplotypes; Genome editing; CRISPR-Cas; Precision agriculture 1 Introduction Cotton (Gossypiumspp.) is almost present in everyone's life, from clothing to industries. It is not only the core of the global textile industry but also feeds countless families. However, this seemingly stable crop is facing multiple predicaments: the climate is becoming unpredictable, the threat of pests and diseases is intensifying, and the market is constantly urging higher yields and better fiber quality (Thangaraj et al., 2024). In the past, people believed that traditional breeding could solve these problems. Indeed, it has brought about many successful cases, but as time went by, this approach became increasingly cumbersome. The long breeding cycle, the complex polyploid genome, and the narrow genetic basis of superior varieties have made the "ideal trait" a difficult goal to achieve quickly. The polyploid characteristics make the genes of cotton like a book that has been rewritten repeatedly, redundant and complex. It often takes researchers several years to identify the key genes that determine yield or stress resistance. Slow phenotypic selection and low genetic diversity make the pace of improvement seem heavy (Sreedasyam et al., 2024). Under the dual pressures of climate and market, it is clearly unsustainable to continue relying on traditional means. The pace of breeding has long been out of step with the rhythm of environmental changes. Fortunately, the development of genomics has brought new breakthroughs to this field. By identifying haplotypes, that is, specific combinations of superior genes at adjacent gene loci, scientists can more clearly see the "genetic puzzle" that determines agronomic traits (Khalilisamani et al., 2024). This not only makes molecular marker-assisted breeding more targeted, but also makes precision breeding a reality. Meanwhile, the emergence of genome editing technology, especially the CRISPR/Cas system, has provided researchers with a tool that can directly "rewrite" genes (Khan et al., 2023). Genetic improvement that used to take many years now has the opportunity to be accomplished in a shorter period of time. When haplotype analysis is combined with genome editing, breeders are no longer just passively screening but can actively design. They can directly superimpose beneficial genes on superior germplasm to create new varieties that are both high-yielding, high-quality and stress-resistant.
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