Cotton Genomics and Genetics 2025, Vol.16, No.5, 210-221 http://cropscipublisher.com/index.php/cgg 214 4 Genetic Diversity Unveiled by the Cotton Pan-Genome 4.1 Contribution of wild species and landraces to gene pool expansion Nowadays, there are indeed many varieties of cotton being cultivated, and it seems that the genetic resources are sufficient. But if we really want to explore genetic diversity, many "treasures" are actually hidden in those marginalized materials-such as wild species and local old breeds. These materials may no longer be seen in the fields, but the set of "old genes" within them is precisely what modern varieties lack. Many studies, after analysis using molecular markers such as SSR and SNP, all point to a similar conclusion: Genetic differences between species far exceed those within cultivated varieties (Gurmessa et al., 2024; Arslan et al., 2025). The meaning is quite simple-if wild resources are excluded, it will instead limit the breadth of the entire gene pool. When it comes to improving properties, these "obscure materials" often play an unexpected role. Through means such as population mapping and backcrossing, those "rare alleles" that originally existed only in wild species were gradually introduced into cultivated species, not only broadening the genetic background, but also opening up new ideas in directions such as fiber quality improvement, disease and stress resistance (Van Deynze et al., 2009). They haven't disappeared; they just haven't been used in the right places all along. 4.2 SNPs, InDels, and CNVs as markers of intraspecific variation There are more than one marker used to identify the differences among cotton varieties, but SNP, InDel and CNV are the three structural variations that are currently the most widely used and effective. Take the CottonSNP63K chip as an example. It can simultaneously detect tens of thousands of SNPS, significantly enhancing the discrimination between varieties and also assisting in identifying key regions related to agronomic traits (Hinze et al., 2017; Yang et al., 2019). However, the "battlefield" of mutations does not always occur in the coding area. Some Indels and SNPS are actually located in regulatory or non-coding regions and have a significant impact on gene expression (Shen et al., 2017). There are also types such as CNV and PAV involving large fragment structural changes, which not only expand the diversity of genomic structures but also intensify the trait differences among different materials (Song et al., 2018). These seemingly "trivial" variations are actually the key markers that distinguish the diversity of cotton germplasm. 4.3 Implications of gene presence/absence variation for trait diversity and evolution Gene deletion is not necessarily a bad thing-in cotton, this "presence/absence variation" (PAV) has instead become one of the main causes of the diversity and adaptive evolution of many traits. Such variations are usually enriched in genes related to environmental adaptation, reproduction and fiber development, and their associations with multiple key traits have been clarified through GWAS and QTL mapping (Sun et al., 2017). Interestingly, PAV is not only an important driver in natural evolution but is also regarded as a "hidden tool" in the process of human domestication. The drought and disease resistance traits of some high-quality fibers are actually manifested precisely because of the "absence" of certain genes (Ma et al., 2018). This also explains why pan-genome research is becoming increasingly important in cotton improvement-it makes us realize that to find key variations, we cannot just focus on "whether there are or not", but also need to look at "whether there are deficiencies". 5 Subgenome Dominance and Expression Bias in Cotton 5.1 Evidence for subgenome expression asymmetry in allopolyploid cotton In allopolyploid cotton, the performance of the two subgenomes -At and Dt- is not always evenly matched. Early studies have found that the At subgenome often steals the show in terms of expression levels, especially during the early stage of fiber development, when this advantage is more pronounced (Naoumkina et al., 2014). However, this bias is not static. For instance, some AT-derived genes are particularly crucial in the process of fiber elongation; Meanwhile, Dt is not completely silent. Some of its activating genes also play a significant role in yield traits and stress responses (Peng et al., 2020). That is to say, the phenomenon of expression asymmetry is more like a "dynamic balance"-in different tissues, at different developmental stages, and even in different environments, the expression contributions of AT and Dt may be reversed. 5.2 Regulatory mechanisms underlying biased expression and gene retention It is no coincidence that some genes in the At subgenome are always more active than those on the Dt side. If you really want to trace back to the root cause, most of the time you have to start from the aspect of "regulation". Take
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