Cotton Genomics and Genetics 2025, Vol.16, No.5, 210-221 http://cropscipublisher.com/index.php/cgg 217 6.3 Expression bias between a-and d-subgenomes during fiber elongation and maturation How are cotton fibers grown? Although it may seem like a unified process on the surface, it is actually not that simple behind the scenes. During this developmental process, the A subgenome (At) and the D subgenome (Dt) are not "evenly matched"; their performance is somewhat "biased". The genes on the At side are particularly active during the initial elongation stage of the fibers, with a very high level of participation. The role of Dt is more likely to occur in the later stage of development or to "push up" when cotton encounters environmental pressure. But this state of "who is busy and who is idle" is not static. This division of labor in expression varies depending on the type of tissue, the time point of development, and even whether it has been artificially cultivated and domesticated (Nobles et al., 2025). Sometimes, the two sets of genomes seem to cooperate with each other and perform their own duties. Sometimes, however, they seem to be filling in for each other-when one becomes stronger, the other takes a slight step back. At and Dt have chosen different expression paths, which is equivalent to "operating separately", but their ultimate goal is the same: to enable cotton to exhibit appropriate developmental and trait characteristics at different stages. 7 Applications in Cotton Breeding and Biotechnology 7.1 Utilizing pan-genome resources for GWAS and QTL mapping In the past, when conducting GWAS or QTL mapping, the thinking basically revolved around a reference genome. This is of course simple, but it's also very easy to miss something-many genes related to important traits are not included in that "standard version" at all. It was not until the introduction of the pan-genome that research began to broaden. Researchers integrated tens of thousands of germplasm resources, including many local varieties and wild materials, and as a result, they identified over 160 gene loci related to agronomic traits at once. What is more worth mentioning is that 84 of these loci have not been discovered before, and another 47 are directly associated with 16 core agronomic traits (Kushanov et al., 2021; Tan et al., 2024). Behind these advancements, it is actually closely related to the inclusion of variant types such as PAV and SV in the analysis. Previously overlooked "invisible markers" can now come into view, providing more detailed and practical references for subsequent marker-assisted breeding. In other words, when it comes to breeding, one doesn't necessarily have to revolve around a "single version". 7.2 Identification of novel gene targets for CRISPR and transgenic approaches Gene editing tools like CRISPR are not in short supply, but what is really hard to find is the "right target". At the beginning, everyone was picking targets from the reference genome, but the problem was that the set of data itself was limited. The emergence of the pan-genome has broken this limitation-it no longer only looks at that one "standard version", but integrates data from tens of thousands of samples. Now, researchers suddenly have many new genes that they couldn't find before. Although they are not in the mainstream reference genome, they are often linked to cotton yield, stress resistance performance, and even fiber growth. These newly added candidate genes and regulatory fragments have become a very useful "target resource library" for editing technologies such as CRISPR/Cas9. Now, in terms of fiber quality improvement and stress resistance enhancement, many initial editing achievements have begun to show results (Peng et al., 2021; Kumar et al., 2024; Thangaraj et al., 2024; Sheri et al., 2025). Ultimately, the role of the pan-genome is not merely to discover new genes. Instead, it provides us with more alternative paths when doing gene editing. With more starting points, the space for improvement naturally expands. 7.3 Incorporation of dispensable genes into elite cultivars for yield and stress tolerance When many people hear the term "non-essential genes", their first reaction is: Are these genes of no use? In the past, when we were doing breeding, indeed, no one paid much attention to them. However, upon analysis of the pan-genome data, the results were somewhat unexpected-these "private genes" that only appear in some materials have instead played a significant role in enhancing the disease resistance of cotton, increasing its yield, and even in addressing climate change. In particular, some genes from local or wild varieties, which were previously overlooked because they were not included in mainstream breeding materials, are now being "rediscovered" through the pan-genome. These genes are like "sleeping resources". Once they are excavated and reasonably introduced into superior materials, not only can the genetic diversity of cotton be expanded, but also a new
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