Cotton Genomics and Genetics 2025, Vol.16, No.1, 29-38 http://cropscipublisher.com/index.php/cgg 34 Figure 2 Screenshots of the iCottonQTL R/Shiny App. The application is available at https://gbru-ars.shinyapps.io/iCottonQTL/ (Adopted from Schoonmaker et al., 2023) 7.2 Managing genetic trade-offs and complexity Things are often not that simple. If we focus all our attention on a single resistance trait during breeding, we may unknowingly sacrifice other traits. Some disease-resistant genes are expressed more strongly, but the result is that the plants become more vulnerable to other diseases. Cotton itself is polyploid, which makes the relationship between genes more complicated. In many cases, a gene may affect more than one trait (Arora et al., 2017; Huang et al., 2021; Zhao et al., 2022). Of course, we hope to take into account resistance, yield, and fiber quality, but in reality it is not easy to do several things at the same time. Although tools such as CRISPR/Cas and genomic selection do bring new hope, we still have to be cautious in the operation process, so as not to solve a problem and bring new troubles (Yang et al., 2022). 7.3 Policy, regulation, and technology adoption Technology is not the biggest problem, promotion is. There are more and more research results on gene editing and genetic modification, but not many are widely used. Behind this, in addition to the strict regulatory process,
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