Cotton Genomics and Genetics 2025, Vol.16, No.1, 39-47 http://cropscipublisher.com/index.php/cgg 41 3 Trait Improvements Facilitated by Comparative Genomics 3.1 Fiber quality traits It is actually quite difficult to improve the fiber quality of cotton by traditional methods, especially when facing traits such as fiber length, strength, uniformity, and elongation. What was the difficulty in the past? To a large extent, it was because we didn't know where the genes behind them were. But now it is different. Comparative genomics has broken this situation (Naoumkina and Kim, 2023). Relying on high-quality reference genomes and GWAS (genome-wide association analysis), researchers have found many QTLs and SNPs related to high-quality fibers (Wang et al., 2018a). These findings not only make marker-assisted selection more directional, but also make breeding more accurate. By the way, after adding transcriptome and gene network analysis, the accuracy of the prediction model has been significantly improved, especially in indicators such as elongation and strength, the improvement can reach 5% (Khalilisamani et al., 2024). Breeders can therefore understand more clearly how fibers develop and breed targeted varieties more quickly (Li et al., 2018; Ijaz et al., 2019). 3.2 Stress tolerance traits Not all varieties can survive adversities such as drought, pests and diseases, especially when extreme climates become more frequent. At this time, comparative genomics is particularly critical. It allows us to identify genes and regulatory pathways involved in stress resistance earlier, and these findings provide important clues for breeding "tough" cotton varieties (Yang et al., 2022a). Of course, identification alone is not enough. To really "use" these genes, we have to rely on tools like CRISPR/Cas9. Combining them with comparative genomics, we can make more precise modifications to stress resistance-related genes without having to select them slowly from generation to generation (Kumar et al., 2024). At present, the climate is unstable and the market pressure is high. Whoever can stabilize production will have the upper hand - so these technologies are not just "available", but truly "necessary". 3.3 Yield-related traits Comparative genomics is also helpful in improving cotton yield. Through this type of technology, researchers have found QTLs and candidate genes related to lint yield, kernel index, and oil content (Li et al., 2024). Some prediction models that integrate genomic information and pedigree data also have good prediction results for these yield traits, which makes selection in breeding more efficient (Li et al., 2022b). Through GWAS and QTL mapping, people have also discovered some new regions and candidate genes that are related to fiber yield and its related factors (Joshi et al., 2023). These methods can improve multiple yield-related traits at the same time, thereby increasing the overall value and total yield of cotton. 4 Evolutionary Insights into Cotton Genomes 4.1 Polyploidy and subgenome divergence Polyploidization has been a key process in cotton evolution, which has given cotton a complex genome containing multiple subgenomes. In the process of changing from diploid to tetraploid, the chromatin structure has undergone significant changes, such as the conversion of region A and region B, and the rearrangement of TAD (topologically associated domain). These changes affect the expression and regulation of genes (Wang et al., 2018b). Comparative analysis found that events such as deploidization or the formation of new tetraploids make the genome less stable, which may lead to the loss of some genes, inversion or translocation of DNA, and asymmetric evolution between the two subgenomes (Wang et al., 2016; Pan et al., 2020). These changes make the A subgenome and the D subgenome somewhat different in regulatory function, among which the A subgenome is more prone to structural changes and gene loss. Despite these changes, the number and arrangement order of most genes remain relatively stable. At the same time, transposon exchanges between different subgenomes and the expansion of gene families are also driving new evolutionary changes. 4.2 Domestication signatures in cotton genomes Domestication has had a significant impact on the cotton genome, especially in cultivated allotetraploid cotton. By comparing the entire genome, researchers have found many expression changes, structural variations, and gene family expansions that only occur in certain species, which are important reasons for the differences between
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