Cotton Genomics and Genetics 2025, Vol.16, No.1, 21-28 http://cropscipublisher.com/index.php/cgg 21 Research Report Open Access Metabolomics-Driven Optimization of Plant Architecture and Yield in Cotton Shanjun Zhu, Jinhua Cheng, Mengting Luo Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, China Corresponding email: mengting.luo@jicat.org Cotton Genomics and Genetics, 2025, Vol.16, No.1 doi: 10.5376/cgg.2025.16.0003 Received: 03 Jan., 2025 Accepted: 05 Feb., 2025 Published: 15 Feb., 2025 Copyright © 2025 Zhu et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhu S.J., Chen J.H., and Luo M.T., 2025, Metabolomics-driven optimization of plant architecture and yield in cotton, Cotton Genomics and Genetics, 16(1): 21-28 (doi: 10.5376/cgg.2025.16.0003) Abstract Cotton is an important economic crop in the world, and its yield is closely related to plant type structure. Traditional breeding methods have certain limitations in the coordinated optimization of plant type and yield. In recent years, the rise of metabolomics has provided a new perspective for analyzing the molecular mechanism of cotton growth and development. This study comprehensively analyzed the changes in key metabolites in the process of cotton plant type and yield formation, explored the mechanism of carbon and nitrogen metabolism, energy metabolism and signal transduction substances at different developmental stages, and identified several metabolic markers closely related to excellent plant type and high-yield traits through the integration of phenotypic and transcriptomic data. The research results not only deepened the understanding of metabolite regulation of plant type and yield, but also provided a theoretical basis for the construction of a precision breeding system based on metabolic information. This study hopes to promote the application of metabolomics in cotton genetic improvement and precision agriculture, and achieve the coordinated breeding goals of plant type optimization and yield improvement. Keywords Cotton; Metabolomics; Plant type optimization; Yield traits; Precision breeding 1 Introduction Cotton (Gossypiumspp.) is a crop that is very important to the world. It not only provides natural fiber, but also produces edible vegetable oil. Therefore, people have always attached great importance to cotton breeding and planting. Now everyone's goal is still the same - hope that cotton can have high and stable yields. However, some difficulties have been encountered in actual planting. For example, the labor force has become less, climate problems have become more serious, and people's requirements for environmental protection and sustainable planting have also become higher (Huang et al., 2022). Recent studies have found that if cotton is to be more drought-resistant and can produce yields in bad environments, its upper and lower structures, especially the underground root system, must be improved (Guo et al., 2024). Only when the roots grow well can they absorb more water and nutrients and survive drought. In addition to breeding technology, the advancement of management methods is also critical. For example, dense planting (multiple sites) and the use of some plant growth regulators have been proven to increase yields and make cotton more suitable for machine harvesting . When it comes to how cotton looks, plant shape is an important factor. Things like the height of cotton, the length of branches, the angle of branches, and the distribution of leaves will affect how it absorbs sunlight and uses nutrients, and ultimately affect yield (Zhang et al., 2020; An et al., 2022). We can use breeding techniques or planting management methods to adjust the plant type of cotton. This not only allows more cotton to be harvested, but also facilitates machine picking, especially in dense planting (Ji et al., 2020). In fact, when breeding in the past, people have already paid attention to these plant type characteristics. But now we have a new tool - metabolomics. Metabolomics can help us understand the relationship between plant type and yield more clearly. It can reveal which specific metabolites and regulatory pathways are at work behind the scenes. Through this method, we can find out the "key substances" and "regulatory networks" that are helpful to yield. This information can help us more accurately select and cultivate cotton varieties that grow reasonably and have high yields. This study systematically reviewed the current understanding of how plant architecture affects cotton yield, drawing on the latest advances in genetics, physiology and agronomy, exploring the emerging role of metabolomics in revealing the complex interactions between plant architecture and productivity, and proposing
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