Cotton Genomics and Genetics 2025, Vol.16, No.3, 126-136 http://cropscipublisher.com/index.php/cgg 131 control (Xiao et al., 2020). The response of cotton is not visible all at once, so the sampling time points are also set more dispersed, with both early responses and long-term adaptation observations. Salt stress is handled slightly differently. Instead of treating the entire plant, it focuses on the roots of the seedlings. The researchers directly treated the roots with a solution containing NaCl and then quickly collected samples because protein changes caused by this type of stress usually occur quickly. To figure out which proteins in the roots and leaves change, they also used technologies such as TMT and iTRAQ. These methods can help them perform quantitative analysis on a high-throughput basis with high efficiency and high precision. Compared with traditional methods, this combination of methods is obviously more suitable for processing complex samples under field conditions. 7.2 Major findings Proteomic analysis under drought stress conditions revealed that many proteins related to metabolism, stress defense, ion transport and hormone signaling were changed in expression (Wang et al., 2024). The study found that at the beginning of drought, proteins related to cutin, suberin and wax synthesis were upregulated in cotton fine roots. If the drought lasted for a long time, there would be extensive changes in carbohydrate, energy, fatty acid and amino acid metabolism (Figure 2). Under salt stress conditions, some important differentially expressed proteins (DEPs) were found, which were involved in carbohydrate and energy metabolism, cell wall structure, cytoskeleton formation, membrane transport (such as TIPs and PIPs) and signal transduction (such as LRR-RLKs) (Li et al., 2015). In addition, the levels of antioxidant enzymes such as superoxide dismutase and peroxidase increased, indicating that they are related to improving stress tolerance. Some key genes confirmed by joint proteomic and transcriptomic analysis were also shown to play an important role in salt tolerance. If these genes are turned off, plants will become more susceptible to salt stress and more reactive oxygen will accumulate. Figure 2 Model showing the responses of the fine roots of cotton plants (Adopted from Xiao et al., 2020) 7.3 Implications for breeding and biotechnology Not all proteins can become the "new favorites" of breeding, but those related to drought and salt stress have indeed given researchers a lot of inspiration. Some proteins are involved in defense responses, some involve
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