Cotton Genomics and Genetics 2025, Vol.16, No.4, 163-172 http://cropscipublisher.com/index.php/cgg 164 Research isn't about who lists the most genes; it's about whether these genes behave consistently across different cotton varieties. Some are normal in diploids, while others appear as extra copies in polyploid offspring, or even disappear altogether. Others change their "identity," taking on new roles, and even their regulatory mechanisms may be completely disrupted. These subtle changes at the genetic level may seem trivial, but they may be the underlying reason for the current improvement in fiber quality (You et al., 2022). The goal of this study, therefore, is not to discover entirely new genes from scratch, but rather to integrate existing research and understand the key changes that have occurred in these fiber-related gene families during their evolution. How did they expand? Is there a clear division of labor between the two subgenomes? How did the regulatory logic change? In particular, in the context of polyploidization coupled with artificial selection, how were some key traits progressively driven? We hope to provide more reliable references for subsequent cotton genetic improvement through the integration of genomic, transcriptomic and functional studies. 2 Genomic Background of Cotton 2.1 Diploid cotton genomes (e.g., G. arboreum, G. raimondii) G. arboreumand G. raimondii are considered the ancestors of modern cultivated cotton. With one A genome and one D genome, they diverged over millions of years, each pursuing its own path. Logically, given such a long time, their differences should be significant, but what happens? While their genome sizes differ, the positions of many genes still match remarkably. While there are a significant number of single-nucleotide polymorphisms (SNPs), 24 million, the overall structure remains relatively stable, with a relatively stable gene arrangement. Of course, there are some variations-some DNA is lost, and transposons have jumped around-but the overall framework remains. 2.2 Polyploid cotton genomes (e.g., G. hirsutum, G. barbadense) In fact, the upland cotton and sea island cotton we commonly cultivate were originally hybridized from two completely different wild cotton species. In the earliest times, there were no tetraploid cottons (those with doubled chromosome sets). Instead, there were two different wild cotton species, each with its own genome (called the A genome and the D genome). Somehow, these two species came together, and their chromosome counts unexpectedly doubled, resulting in the allotetraploid we know today (Figure 1) (Li et al., 2024). This situation is usually quite troublesome, as the combination of two genes creates a mess of duplicated genes, disrupting the chromosomes and even disrupting gene expression (the process by which genes function). But cotton species are accustomed to this chaotic environment. Furthermore, they sometimes incorporate gene fragments from their wild relatives, patching them together like a patchwork, creating a surprisingly effective genetic combination. Is this a coincidence? Ultimately, this combination has helped cotton grow better and become much more adaptable to various environments. 2.3 Comparative genome analysis Many details can't be discerned from a single genome. Comparing diploid and polyploid genomes side by side reveals which regions are "stabilized" and which are "turbulent." In some regions, the gene order is remarkably stable, much as it was millions of years ago; yet in others, the sequence is chaotic-inversions, translocations, and regulatory element shifts are common, especially in regions involved in fiber development. The same gene may perform completely different functions in the At and Dt subgenomes, one a primary operator and the other a minor one. Digging deeper, even more subtle differences emerge in the transcriptome and epigenetics, affecting not only expression levels but also chromatin folding (Wang et al., 2018; Han et al., 2022). These seemingly minor changes, however, are precisely what transformed cotton from a wild species into the high-yielding crop it is today, thanks to these "fine-tuning" changes. 3 Key Fiber-Related Gene Families 3.1 Cellulose synthase (CesA) gene family Cotton fibers contain a large amount of cellulose, a component that becomes particularly important in later stages, when the fibers thicken or stiffen. Cellulose doesn't just form out of thin air; its synthesis relies on a specialized set of genes. Three genes, GhCesA4, GhCesA7, and GhCesA8, have been identified as crucial in this process.
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