Cotton Genomics and Genetics 2025, Vol.16, No.6, 300-309 http://cropscipublisher.com/index.php/cgg 305 In the past, traditional breeding has tried countless methods: hybridization, backcrossing, and screening. However, when both yield and quality had to be taken into account simultaneously, the results were always unsatisfactory. It was not until the concept of precision breeding emerged that people had new ideas. Through means such as molecular markers, haplotype analysis and genome editing, breeders have begun to "find breakthroughs" at the genetic level, attempting to break free from the limitations of traditional methods. 5.2 Precision approach implemented In recent years, some research teams have attempted to re-analyze and improve the fibrous traits of cotton by using multi-parent hybrid populations in combination with molecular techniques. For instance, by using KASP (competitive allele-specific PCR) labeling, favorable haplotypes can be polymerized at key sites, thereby picking out strains with longer and stronger fibers. Some people have also used GWAS (Genome-wide Association Analysis) and high-density SNP chips to mine candidate genes and verify their relationship with fiber quality, providing a basis for marker-assisted selection and genomic selection. Some studies have gone even further, no longer stopping at "screening", but directly "taking action". By modifying genes related to fiber development through gene editing or transgenic methods, such as key genes affecting auxin synthesis and transport, researchers have successfully increased both fiber yield and quality simultaneously in some varieties (Chu et al., 2024). Although such attempts are complex, they also provide a practical and feasible path for precision breeding. 5.3 Outcomes and lessons learned The combination of haplotype analysis and molecular tools has achieved quite remarkable results. The fiber length of many improved series has increased by more than 10%, and the strength has risen by over 17%. What is even more remarkable is that some special allele combinations have broken the long-standing dilemma of "high yield must be low quality", and have cultivated new strains that have both high cotton fiber content and excellent fiber quality. Of course, such achievements were not obtained easily. Genomic selection and marker-assisted breeding do indeed enhance efficiency, but this is only possible if there are reliable molecular markers, solid phenotypic data, and validation of the functions of candidate genes. None can be missing. Judging from these experiences, relying solely on advanced technology is not enough. Researchers generally recognize that to continuously improve the quality of cotton fibers, it is necessary to integrate multi-omics information, expand genetic diversity, and at the same time, enable traditional breeding experience to work in synergy with modern technology. Precision tools are just the starting point; the key lies in how to make good use of them. 6 Challenges and Limitations 6.1 Technical and biological barriers The genome of cotton itself is like a maze, huge in size and complex in polyploid structure. It is not easy to operate precisely in such a system. Whether it is haplotype analysis or genome editing, they all have to first confront this naturally complex background. Genetic redundancy is an old problem. A function is often shared by several copies of homologous genes, which makes the design of sgRNA tricky. It is almost a dilemma to be both specific and efficient. The risk of missing the target thus rises, and truly achieving "precise editing" is much more difficult than it sounds. Besides, not all cotton varieties are "obedient". Many superior strains are difficult to transform. Traditional Agrobacteria-mediated or gene gun methods are inefficient and rely on specific genotypes (Li et al., 2022). In addition, the tissue culture and regeneration steps are time-consuming and labor-intensive, and the entire process often drags on extremely long. Although multiple editing and gene superposition are theoretically feasible, achieving stable inheritance in polyploid cotton still requires further exploration. What can be achieved in the laboratory is still far from being applied in the field.
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