Cotton Genomics and Genetics 2025, Vol.16, No.6, 259-268 http://cropscipublisher.com/index.php/cgg 263 photosynthetic efficiency was improved, and ultimately the yield increased. What is more concerning is that when favorable SV haplotypes are aggregated, the originally unbalanced relationship between high yield and superior fibers may also be disrupted (Zhao et al., 2024). This means that by rationally utilizing structural variations, it is expected to achieve a variety improvement direction that takes into account both yield and quality. 5 Mechanistic Insights: How SVs Drive Divergence 5.1 Role of transposable elements in SV formation In the cotton genome, there are always some components that are "restless". The turntable component (TE) is one of the most active types. They are like vagrants in the genome, from time to time jumping out of their original positions and inserting into new sites, disrupting the originally orderly sequence. Such "turmoil" may seem unregulated, but it often leads to far-reaching consequences-genomic expansion, changes in the number of genes, and even the reorganization of regulatory networks. Studies have shown that in diploid and polyploid cotton, the activation of long-end repeat (LTR) retrotransposons-particularly in the Gypsy and Copia families-is closely related to differences in genome size and has also given rise to some species-specific genes (He et al., 2024). Sometimes, a single TE insertion is sufficient to rewrite the fate of a gene: it may disrupt the original structure, causing an existence-deletion variation (PAV). It is also possible that due to carrying new regulatory fragments, the expression mode of genes is completely renewed (Tian et al., 2025). In addition, the activities of TE will also promote gene replication, fusion, and even facilitate new regulatory pathways. These changes have invisibly widened the gap in traits between upland cotton and Pima cotton. However, the TE activities of each lineage are not the same. Some are almost silent, while others will suddenly "explode" under multiple amplification or environmental stress. A single amplification is enough to accelerate the process of differentiation. 5.2 Homologous recombination and genome plasticity The source of structural variation is not entirely due to the "disruption" of the turntable components. In cotton, reorganization is also a force that cannot be ignored. After polyploidy, mismatches or fragment exchanges often occur between homologous chromosomes. This recombination does not always occur at allelic sites; sometimes it even "accidentally collides" between non-allelic homologous sequences, thereby triggering complex structural changes such as inversions, deletions or duplications. The seemingly chaotic movement of genes has instead endowed the cotton genome with greater flexibility. As this plasticity increases, gene families begin to expand or contract, with some functions gradually lost while new ones are born. It is worth noting that non-homologous end joining and DNA repair mechanisms tend to be more active in stressful environments, which invisibly increase the frequency of structural variations (Krasileva, 2019). However, these genome-level adjustments are not isolated events. They are intertwined with the domestication process-selective pressure, on the one hand, eliminates unfavorable rearrangements, while on the other hand, retains variations that can enhance adaptability. Over time, the morphological and physiological differences between upland cotton and Pima cotton gradually took shape in such a dynamic balance. 5.3 Epigenetic consequences of SVs When studying the cotton genome, people often focus first on sequence changes, while the epigenetic effects hidden behind them are frequently overlooked. But once you look deeper, you will find that their influence is not light. Especially when it comes to structural variations involving transposition elements (tes), such changes are often not merely about rewriting DNA sequences; they can also disrupt the state of local chromatin, causing alterations in methylation levels or the pattern of histone modifications. Take transposon-related variations (TRV) as an example. Differences in methylation often affect the transcriptional activity of adjacent genes, thereby influencing the development of cotton fibers (Liu et al., 2025). However, the problem is not limited to this. Structural variations sometimes also disrupt the boundaries of topologically associated domains (TAds), causing the three-dimensional structure of chromatin to refold and the connections between regulatory elements and target genes to be recombined. Such disturbances sometimes bring about stable expression patterns, while at other times they make regulation more flexible, enabling different lineages of cotton to respond more quickly to environmental changes and gradually form their own unique phenotypes.
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