Cotton Genomics and Genetics 2025, Vol.16, No.6, 300-309 http://cropscipublisher.com/index.php/cgg 303 promoter of cotton itself would be more effective. Despite significant progress, the "transformation bottleneck" still exists, which remains a hurdle that must be overcome before the large-scale promotion of gene editing. 3.3 Trait targets modified by genome editing On cotton, genome editing is no longer just a theoretical attempt; it has been applied to the improvement of various traits. For instance, in terms of fiber quality and yield, researchers have successfully improved textile performance by regulating genes related to fiber length, strength and development. In terms of stress resistance, editing certain genes can make cotton more capable of coping with pressures such as drought, salinity, high temperatures and even pests. Seed quality is also an important direction. The nutritional value of cotton seeds was enhanced by regulating lipid synthesis genes and inhibiting factors related to gossypol (Liang et al., 2020). In addition, modifications to plant structure and developmental genes, such as plant height, branching, and flowering time, are helping cotton better adapt to mechanization and environmental changes. Some studies have gone further by attempting to edit multiple target genes at one time and superimpose multiple superior traits in the same breed (Hui et al., 2024). Although it sounds like a "combination punch", this is precisely the charm of precision breeding. 4 Integration of Haplotypes and Genome Editing 4.1 Synergy between haplotypes and editing In the genetic improvement of cotton, haplotypes and genome editing are not two isolated methods. The former is like a precise map, showing the genetic differences behind complex traits. The latter is like a controllable scalpel, capable of precisely "cutting" at the target site. When the two are combined, things become interesting. Haplotype analysis can tell breeders which alleles are worthy of retention or superposition, and editing systems such as CRISPR/Cas can directly "implant" these beneficial combinations into superior germplasm (Peng et al., 2020). This not only avoids the lengthy process of repeated backcrossing in traditional breeding, but also bypasses the constraints of chain burdiness. Researchers can now even simultaneously improve multiple properties in one round of experiments. Fiber quality, yield, stress resistance, etc. can all be advanced simultaneously (Lyzenga et al., 2021; Kumar et al., 2024). This kind of synergy is not a simple superposition; rather, it is more like the combination of "positioning + precise repair", making complex genetic improvement more directional. 4.2 Functional validation of candidate haplotypes In the past, finding a "suspect gene" from GWAS or haplotype mapping was one thing, but proving that it was indeed related to traits was another. The emergence of genome editing has made the verification step more straightforward. Through the CRISPR/Cas system, researchers can create mutations, replace alleles, and even fine-tune specific sites to determine whether a certain haplotype truly affects the target trait. The experimental verification of genes related to cotton fiber quality is a typical example. The changes in the traits after editing clearly confirm the conclusion of haplotype analysis. In addition, the instantaneous expression system and the improved transformation scheme make the verification process more efficient (Ge et al., 2022). Gene functions that used to require several generations of screening to confirm can now often yield results in short-term experiments. In this way, the distance from genomic discovery to breeding application has been significantly shortened. 4.3 Accelerated breeding cycles For cotton breeding, time is often the greatest cost. Combining haplotype information with genome editing means that "pre-selection" can be carried out in advance at the genetic level, avoiding many detours. For instance, with the assistance of double haploid (DH) induction, researchers can obtain homozygous edited lines within one generation, eliminating the long wait of repeated backcrossing in traditional breeding. More importantly, with the advancement of multiple editing techniques and genotype-independent transformation systems, even those superior strains that were originally difficult to transform can be rapidly improved (Figure 2)
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