Cotton Genomics and Genetics 2025, Vol.16, No.4, 163-172 http://cropscipublisher.com/index.php/cgg 163 Feature Review Open Access Evolutionary Analysis of Fiber-Related Gene Families in Diploid and Polyploid Cotton Delong Wang, Jin Zhou, Jin Zhang Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding email: jin.zhang@hitar.org Cotton Genomics and Genetics, 2025, Vol.16, No.4 doi: 10.5376/cgg.2025.16.0016 Received: 01 May, 2025 Accepted: 10 Jun., 2025 Published: 01 Jul., 2025 Copyright © 2025 Wang 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: Wang D.L., Zhou J., and Zhang J., 2025, Evolutionary analysis of fiber-related gene families in diploid and polyploid cotton, Cotton Genomics and Genetics, 16(4): 163-172 (doi: 10.5376/cgg.2025.16.0016) Abstract Cotton is a globally important fiber crop. Both its diploid (varieties with normal chromosomes, such as Asiatic and Raymondia cotton) and polyploid (varieties with doubled chromosomes, such as Upland and Sea Island cotton) varieties provide valuable genetic resources for improving cotton fiber quality. This study, using comparative genomic approaches, conducted a detailed evolutionary analysis of gene families involved in fiber growth across different cotton varieties, primarily including cellulose synthase (CesA) genes responsible for cellulose synthesis, expansins, and the MYB transcription factor family. We also investigated how these gene families evolved through whole-genome duplications, small-scale duplications, and external selective pressures. Furthermore, we analyzed the expression of these genes at different stages of fiber development, their epigenetic regulation (influencing development by modulating gene activity), and their co-expression networks (how genes coordinate their function). Furthermore, we conducted an in-depth case study of the CesA gene in Upland cotton, including its classification, expression patterns during development, and functional validation. These studies can help us more clearly understand the evolution and functional differences of cotton fiber genes, and have practical significance for future molecular breeding, gene editing and protection of cotton genetic resources. Keywords Cotton genomics; Fiber-related genes; Gene duplication; Polyploidy; Molecular breeding 1 Introduction Everyone knows cotton is important, especially in agriculture. It serves as a fiber raw material and plays a fundamental role in the economies of many countries. However, its continued research stems from more than just its value. Its fiber structure is unique, making it a readily available model for those studying plant cell growth and cell walls (Yu, 2024). Furthermore, genetic improvements related to cotton yield, quality, and stress resistance ultimately revolve around these structures and mechanisms (Hu et al., 2019). In the past, no one wanted to study the cotton genome. Honestly, it's incredibly complex and daunting. Strangely enough, this complexity has actually benefited research, as it allows for much deeper investigation. In recent years, gene sequencing technology (the process of determining the specific information about a gene) has advanced rapidly, achieving dramatically higher accuracy. Now, we can even directly visualize what genes are doing (Chen et al., 2020; Pan et al., 2020), something we never dared to imagine before. This is especially true when studying fiber-related genes. Problems that were once the most daunting are now being considered as breakthroughs. Of course, this isn't entirely due to improved technology; research tools are now plentiful. For example, common techniques like assembling genomes, analyzing the evolutionary relationships of gene families, and comparing gene expression patterns are now available. Simply put, cotton researchers are truly living in a golden age. However, it would be wrong to say that these complexities are inherent to cotton. In fact, its genome has undergone a complex evolution. Initially a simple diploid, it subsequently doubled in size, becoming polyploid, and subgenomes were incorporated. This gradual accumulation of diversity has led to a natural diversification of fiber expression. Previously, polyploidy was daunting, often characterized by gene redundancy and structural overlap, making it difficult to understand (Zhang and Yang, 2024). This situation is no longer the case.
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