Cotton Genomics and Genetics 2025, Vol.16, No.1, 21-28 http://cropscipublisher.com/index.php/cgg 24 4.2 Early prediction of plant architecture using metabolic markers The metabolome can also be used for prediction. It can identify metabolic markers related to plant structure, which can predict future performance before the cotton grows (Villate et al., 2020). These metabolic markers are like "early warning tools" that can pick out genotypes with great potential before the traits are expressed. This is particularly useful for breeding. Moreover, if metabolomics is used together with other "omics" platforms, the prediction results will be more accurate (Kumar et al., 2017; Shen et al., 2022). This will make the improvement work more targeted and more efficient. 4.3 Directed improvement of architecture through metabolic pathway regulation To purposefully change how cotton grows, we must first understand the metabolic pathways that control its plant type (Hong et al., 2016; Shen et al., 2022). With this information, we can start through metabolomics breeding or metabolic engineering. For example, adjust the pathways that control plant hormone synthesis or stress resistance to make cotton grow the way we want (Kumar et al., 2017). This method does not rely on luck, but directly regulates the biochemical reactions that occur in plants. This can more accurately improve the structure of cotton, increase its yield, resistance and ability to adapt to the environment (Raza, 2020). 5 Identification of Yield-Related Metabolites 5.1 Carbon and nitrogen metabolites associated with reproductive growth Some key carbon and nitrogen metabolites, such as sucrose, alanine, aspartic acid, citric acid and malic acid, are closely related to cotton reproductive growth and yield (Levi et al., 2011; Jiang et al., 2012). If the activity of sucrose synthase (GhSusA1) is enhanced, the fiber yield and biomass of cotton can be increased. At the same time, if the nitrogen content in the leaves increases, it can also increase the activity of the enzyme, enhance photosynthesis, and make more sucrose. This series of changes will eventually make the cotton bolls heavier and the seeds more (Iqbal et al., 2022). During drought, the levels of some amino acids and organic acids in the plant will increase. This change can help cotton regulate its body water, alleviate the effects of drought, and also help restore reproductive growth. 5.2 Secondary metabolites involved in biomass accumulation and distribution Cotton also produces some secondary metabolites, such as phenolic acids, flavonoids, and compounds involved in the metabolism of phenylpropanoids, tyrosine, and phenylalanine. These substances are particularly important when cotton copes with adversities (such as pests and diseases, drought, strong light, etc.). They can help plants enhance their defense capabilities and make cotton yield more stable under difficult environments (Prakash et al., 2023). These metabolic pathways are also related to the early maturity and fiber quality of cotton. By regulating these metabolic processes, the overall performance of cotton may also be improved. 5.3 Comparative metabolomic profiles of high-yield cotton lines The metabolome comparison of some high-yield cotton lines found that their metabolites had some obvious characteristics. For example, these varieties have higher levels of certain solutes and metabolites. High-yield cotton may use different physiological strategies to increase yield. For example, they may use light more efficiently, have a higher harvest index, or accumulate more biomass (Virk et al., 2023). In near-isogenic lines with yield-related QTLs introduced, it was found that these cottons accumulated more glycerol, inositol, and some organic acids under stressful conditions. The increase in these metabolites may be related to their high yield and enhanced stress resistance (Levi et al., 2011). These research results show that metabolomics can help us find out which metabolites are related to yield. This is very valuable for screening and breeding high-yield cotton varieties. 6 Integration of Metabolomics with Genetic Breeding 6.1 Combined analysis of metabolomics and QTLs Nowadays, many studies will combine metabolomics data with QTL positioning. This can find some genetic regions called mQTL, which are gene locations related to certain metabolites (Litvinov et al., 2021; Sakurai, 2022). In this way, we can link the changes in a certain metabolite with the genes behind it. In this way, it is easier to find the key pathways that affect cotton structure and yield, or important "candidate genes" (Fernie and Schauer, 2009). In addition, analyzing metabolites and QTLs together can also improve the accuracy of molecular markers used in breeding, and can also more quickly introduce useful genes into excellent cotton varieties.
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