Cotton Genomics and Genetics 2025, Vol.16, No.1, 39-47 http://cropscipublisher.com/index.php/cgg 39 Research Insight Open Access Research Progress on Traits Improvement of Cotton Plants Based on Comparative Genomics ZhenLi Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: xiaoyan.chen@cuixi.org Cotton Genomics and Genetics, 2025, Vol.16, No.1 doi: 10.5376/cgg.2025.16.0005 Received: 17 Jan., 2025 Accepted: 20 Feb., 2025 Published: 28 Feb., 2025 Copyright © 2025 Li, 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: Li Z., 2025, Research progress on traits improvement of cotton plants based on comparative genomics, Cotton Genomics and Genetics, 16(1): 39-47 (doi: 10.5376/cgg.2025.16.0005) Abstract Cotton is a globally significant crop, valued for its fiber and oil, and improving its traits remains a priority for sustainable agriculture. This study examines recent advancements in cotton trait improvement through comparative genomics, emphasizing the utility of genome sequencing, synteny and orthology analyses, and gene expression profiling across cotton species. We discuss how comparative genomics has facilitated the identification of key genes and regulatory elements linked to fiber quality, stress tolerance, and yield-related traits. This study also explores evolutionary insights such as polyploidy, subgenome divergence, and domestication signatures, and presents a case study comparing Gossypium hirsutumand Gossypium barbadense, revealing critical genomic features that guide breeding programs. Despite notable progress, challenges such as incomplete genomic resources and integration with other omics persist. We conclude that comparative genomics offers powerful tools for trait dissection and cultivar development, and future efforts should focus on multi-omics integration and advanced bioinformatic platforms to fully harness its potential for sustainable cotton improvement. Keywords Comparative Genomics; Cotton improvement; Trait dissection; Fiber quality; Polyploidy 1 Introduction Cotton (Gossypiumspp.) is a very important crop planted worldwide. It is the main source of natural fiber for the textile industry and contributes greatly to the economies of many countries (Fang et al., 2017; Zhang et al., 2019). Due to its large planting area, cotton fiber quality, yield and stress resistance have always been the focus of attention. Improving these traits is critical to meet market demand and achieve sustainable agricultural development (Ma et al., 2021; Joshi et al., 2023). However, the cotton genome is complex, with both polyploidy and various structural changes, which poses considerable challenges to genetic improvement, but also provides some opportunities (Wang et al., 2022; Manivannan and Amal, 2023). Comparative genomics is a useful method to study the genetic basis of fiber quality, yield and stress resistance in cotton (Li et al., 2022b). Now, with great progress in high-throughput sequencing and genome assembly technologies, it is easier to find quantitative trait loci (QTLs), structural variations, and candidate genes associated with traits (He et al., 2021). The breeding and evolution of cotton, on the surface, seems to be a step-by-step process driven by humans, but in fact, there are many hidden genetic changes involved. When researchers compare the genomes of different cotton species and varieties, they cannot draw clear conclusions at the beginning. They noticed that in some gene regions, there were traces of selection, gene introgression and even recombination. These changes did not occur in isolation, but connected some key nodes in the long-term evolution of cotton (Shen et al., 2019). Although these differences at the genetic level are not always directly reflected in the traits, they do provide us with a more accurate breeding "roadmap" - not only can we improve a certain trait in a targeted manner, but also optimize multiple aspects at the same time (Li et al., 2024). This study summarizes the research results of using comparative genomics to improve cotton traits in recent years, focusing on the progress of genome sequencing, the discovery of genes and structural variations related to
RkJQdWJsaXNoZXIy MjQ4ODYzNA==