Cotton Genomics and Genetics 2025, Vol.16, No.6, 290-299 http://cropscipublisher.com/index.php/cgg 290 Feature Review Open Access Spatial Transcriptomics of Cotton Fibers During Elongation Stage Xiaojing Yang, Yuxin Zhu Modern Agriculture Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: yuxin.zhu@cuixi.org Cotton Genomics and Genetics, 2025, Vol.16, No.6 doi: 10.5376/cgg.2025.16.0029 Received: 17 Oct., 2025 Accepted: 27 Nov., 2025 Published: 16 Dec., 2025 Copyright © 2025 Yang and Zhu, 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: Yang X.J., and Zhu Y.X., 2025, Spatial transcriptomics of cotton fibers during elongation stage, Cotton Genomics and Genetics, 16(6): 290-299 (doi: 10.5376/cgg.2025.16.0029) Abstract Cotton fiber development plays a vital role in the global textile economy, and the elongation stage is crucial in determining fiber length and quality. In this study, we employed spatial transcriptomics to uncover the spatial organization of gene expression during the elongation phase of Gossypium hirsutum fibers. By integrating spatial barcoding and high-resolution transcriptomic mapping, we localized fiber-specific gene expression domains and identified elongation-zone-enriched transcripts. Our analysis revealed expression gradients of GhEXPA1, GhRDL1, and GhMYB25-like along fiber tips, highlighting region-specific transcriptional modules associated with cell wall remodeling, ROS scavenging, and energy metabolism. These findings provide functional insights into the spatial coordination of molecular pathways underlying fiber elongation. This study not only demonstrates the power of spatial transcriptomics in dissecting complex developmental processes but also lays a foundation for future applications in targeted breeding, genome editing, and molecular improvement of cotton fiber quality. Keywords Cotton fiber elongation; Spatial transcriptomics; Gene expression mapping; Gossypium hirsutum; Fiber development 1 Introduction Among the crops worldwide, cotton (Gossypiumspp.) holds an irreplaceable position. It is not only a natural fiber but also an integral part of the economic lifeline of many countries. Especially in developing countries, the cotton industry is related to the livelihoods of millions of people and the stability of regional economies (Wang and Zhang,, 2024). Today, the global annual cotton output has exceeded 25 million tons, among which India, China, the United States and Pakistan are the major producers (Khan et al., 2020). From farmlands to textile workshops, this crop has brought in hundreds of billions of dollars in economic benefits. The story of cotton fibers begins with the extension of those individual cells on the epidermis of the ovules. Its development is not achieved overnight but goes through stages such as initiation, elongation, formation of secondary cell walls and maturation. It is precisely these subtle processes that determine the final fiber quality and yield, and also determine whether cotton can become the raw material for high-quality textiles (Jan et al., 2022). In recent years, with the rapid progress of genomics, transcriptomics and molecular breeding techniques, people have begun to see more clearly the key genes and regulatory networks that control fibrous traits, which provides the possibility for the breeding of superior varieties. However, among all the stages, the extension stage seems to be the most crucial. Approximately 20 days after flowering, fibroblasts will rapidly expand and can grow to about 30 millimeters. This elongation capacity not only has a distinct hereditary nature but is also closely related to the mechanical properties of the fibers, such as tensile strength and fracture resistance (Mathangadeera et al., 2020). If fibers can be better stretched, the quality of yarns is often higher and there are fewer defects in textiles. Therefore, "increasing elongation" has become one of the core goals of improvement work. Researchers have found that transcription factors, plant hormones and REDOX balance all play key roles in this process (Tian et al., 2024). Meanwhile, an emerging technology, spatial transcriptomics, is quietly changing the perspective of plant molecular research. It is not merely about measuring gene expression, but rather being able to "see" the active locations of genes in the tissue space. This method enables people to track the differences in cell types and developmental trajectories in situ for the first time (Giacomello, 2021). Although the cell walls of plant tissues
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