Cotton Genomics and Genetics 2024, Vol.15, No.2, 112-126 http://cropscipublisher.com/index.php/cgg 112 Review and Progress Open Access Next-Generation Sequencing Technologies: A Game Changer in Cotton Genomics Jiayi Wu, Tianze Zhang Modern Agriculture Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding author: tianze.zhang@cuixi.org Cotton Genomics and Genetics, 2024, Vol.15, No.2 doi: 10.5376/cgg.2024.15.0011 Received: 03 Mar., 2024 Accepted: 15 Apr., 2024 Published: 27Apr., 2024 Copyright © 2024 Wu and Zhang, 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: Wu J.Y., and Zhang T.Z., 2024, Next-Generation sequencing technologies: a game changer in cotton genomics, Cotton Genomics and Genetics, 15(2): 112-126 (doi: 10.5376/cgg.2024.15.0011) Abstract Next-generation sequencing (NGS) technology has revolutionized the field of cotton genomics, providing unprecedented insights into the genetic structure, functional genomics, and breeding strategies for this economically important crop. This study systematically explores the transformative impact of NGS on cotton genomics and its key advancements. NGS has enabled the construction of high-quality reference genomes and de novo assemblies, facilitating detailed studies on genetic diversity, population genomics, and phylogenetic relationships. The integration of NGS with genome editing technologies such as CRISPR/Cas9 has paved the way for precise genetic modifications, accelerating the development of superior cotton varieties. Despite technical challenges, data management complexities, and cost barriers, the continuous evolution of NGS technology promises to overcome these limitations. The future of cotton genomics lies in the integration of NGS with other omics approaches, promoting sustainable cotton production through advanced breeding programs and comprehensive genetic analyses. Keywords Next-generation sequencing; Cotton genomics; Genetic variations; Precision breeding; Genomic analysis 1 Introduction Cotton (Gossypiumspp.) is a globally vital crop, fundamental to the textile industry and a significant agricultural commodity. Its economic importance is underscored by its use in clothing, household items, and industrial products. Beyond its economic value, cotton also plays a crucial role in food production and sustainable agriculture, providing seed oil and animal feed. Cotton is a cornerstone of the global textile industry, serving as the primary source of natural fiber. The economic and agricultural importance of cotton cannot be overstated, as it supports the livelihoods of millions of farmers and contributes significantly to the economies of many countries. The complexity of the cotton genome, characterized by its large size and polyploid nature, has historically posed significant challenges to genomic research. The study of cotton genomics is essential for advancing our understanding of this complex crop, enabling the development of improved varieties with enhanced yield, fiber quality, and resistance to biotic and abiotic stresses. This knowledge is critical for addressing the challenges of climate change, pest and disease management, and the increasing demand for sustainable agricultural practices. However, recent advancements in high-throughput sequencing and bioinformatics have begun to unravel the intricacies of the cotton genome, providing valuable insights into fiber biogenesis, genetic diversity, and the evolutionary history of Gossypium species. These developments have paved the way for genomics-enabled breeding strategies aimed at improving fiber yield, quality, and environmental resilience, thereby addressing the pressing needs of modern agriculture (Pavlovic et al., 2020). Next-Generation Sequencing (NGS) technologies have revolutionized the field of genomics by enabling the rapid and cost-effective sequencing of entire genomes and transcriptomes. Unlike traditional Sanger sequencing, NGS platforms can generate massive amounts of data in a relatively short period, democratizing access to genomic information and facilitating large-scale genetic studies (Kumar et al., 2019; Yang et al., 2021). The primary advantages of NGS include its high throughput, accuracy, and the ability to detect a wide range of genetic variations, from single nucleotide polymorphisms (SNPs) to large structural variants (Levy and Boone, 2019).
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