Cotton Genomics and Genetics 2025, Vol.16, No.4, 163-172 http://cropscipublisher.com/index.php/cgg 166 4 Evolutionary Mechanisms Driving Gene Family Diversification 4.1 Whole-genome duplication and gene retention The emergence of upland cotton (Gossypium hirsutum) is actually the result of several major genome duplications (Wei et al., 2022). While this seemingly spectacular duplication of an entire gene set may seem, not every gene survives. Many replicated genes disappear after a while, leaving key genes involved in fiber development more likely to survive. These surviving genes are often grouped in pairs, located in similar locations within the At and Dt subgenomes. However, these repeated genome duplications have left some residual effects (Tao et al., 2021). Occasionally, genes that are usually quiet will suddenly "wake up" and stir in seemingly erratic patterns, but perhaps cotton's new characteristics emerge from this unstable state. 4.2 Tandem and segmental duplications The expansion of the cotton genome doesn't necessarily require the large-scale duplication of entire chromosomes; it's more often the result of the gradual addition of small fragments. Gene families like the WAK and RING genes (which play important roles in plant growth regulation and stress tolerance (Shuya et al., 2023)) have gradually expanded through this type of localized duplication. While these small duplications may seem inactive during normal times, they can be highly effective in challenging environments like drought or salinity (Qiao et al., 2019), helping cotton cope with these challenges. Another type of "jumping genes" called transposable elements, such as Copia and Gypsy, are usually quite quiet, but once activated, they can roam the genome, sometimes carrying other genes along with them, like moving a whole load of luggage. While this seemingly chaotic movement may seem chaotic, this "order within chaos" may be precisely how the cotton genome evolves. What may seem unstable may actually be an opportunity for growth. 4.3 Selection pressure and functional divergence Whether a gene persists after duplication depends on environmental support. Sometimes genes that maintain their original functions are more likely to survive (Malik et al., 2020), but others may branch out and develop new functions (Wu et al., 2024). In polyploid cotton (those with chromosomes duplicated in pairs), the situation is even more complex. Many genes have "backups," allowing mutations to be easily masked if one fails. However, this "masking" can surprisingly allow some harmful mutations to slip through. The At and Dt subgenomes have different abilities to handle these mutations, and over time, the differences between them have widened (Conover and Wendel, 2021). Recent studies have also revealed that some unique genes are not found in all cotton varieties, but are present only in certain varieties (Li et al., 2021). Although these genes are few in number and generally inconspicuous, they can be crucial, such as in the breeding of high-quality cotton. 5 Gene Expression and Regulatory Networks in Fiber Development 5.1 Stage-specific expression of fiber genes Not all genes in cotton fiber production begin to function simultaneously. While many genes do indeed begin to activate immediately after pollination, many don't show significant changes until 16~17 days after flowering (Grover et al., 2024). Surprisingly, researchers have found that despite numerous experiments, only a few genes are consistently expressed across different cotton varieties (You et al., 2023). One gene, GhRALF1, which regulates cotton growth rhythms, is quite unusual (Wang et al., 2023), being particularly active during the day and inactive at night. This diurnal shift may affect fiber growth rates, or it may simply reflect the cotton plant's natural rhythm; the answer remains elusive. 5.2 Epigenetic regulation and non-coding RNAs In addition to the genes themselves, several small molecules also secretly participate in cotton fiber development. For example, siRNAs, microRNAs that don't produce protein (but can control the activation of other genes), despite their small size, play a significant role in regulating key genes like MYB-MIXTA. Another type of long noncoding RNA, called lncRNAs, such as the recently mentioned MST23 (Wang et al., 2024), is usually less noticeable, but by activating the GhKCR2 gene, which controls fatty acid synthesis, it can indirectly influence the rate of fiber growth. Furthermore, epigenetic mechanisms such as DNA methylation and histone modifications (which regulate gene activity without altering the DNA sequence) also play a subtle role behind the scenes.
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