Cotton Genomics and Genetics 2025, Vol.16, No.5, 249-258 249 Review and Progress Open Access High-Throughput Genotyping and Its Role in Accelerating Cotton Breeding Xian Zhang, Pingping Yang, 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.5 doi: 10.5376/cgg.2025.16.0025 Received: 13 Aug., 2025 Accepted: 25 Sep., 2025 Published: 18 Oct., 2025 Copyright © 2025 Zhang 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: Zhang X., Yang P.P., and Zhang J., 2025, High-throughput genotyping and its role in accelerating cotton breeding, Cotton Genomics and Genetics, 16(5): 249-258 (doi: 10.5376/cgg.2025.16.0025) Abstract Cotton, as a globally significant economic crop, has long been the core goal of breeding improvement in terms of its yield and fiber quality. However, traditional breeding methods are characterized by long cycles and low efficiency, making it difficult to meet the increasingly complex breeding demands. The rise of High-Throughput Genotyping (HTG) technology has provided strong technical support for cotton molecular breeding, especially showing broad application prospects in quantitative trait localization, molecular marker development, genomic selection, etc. This study systematically reviews the characteristics and applicability of the current mainstream HTG technology platforms (such as SNP chips, GBS, RAD-seq, DArT, etc.), and analyzes their application progress in the genetic basis research of important agronomic traits such as yield, quality, and resistance. The practical role of HTG in QTL localization, GWAS analysis, marker-assisted selection and other links was discussed. Through typical breeding practice cases, evaluate its breeding acceleration efficiency in the context of multiple environments and varieties, and further look forward to the prospects of its deep integration with phenomics, genomic selection and intelligent decision-making platforms. This research provides theoretical basis and technical support for accelerating the genetic improvement and molecular breeding of cotton. Keywords Cotton breeding; High-throughput genotyping; Molecular marker; Genomic selection; QTL positioning 1 Introduction Cotton (Gossypiumspp.) is not only an indispensable raw material in the global textile industry, but also plays an important role as an oil crop at the same time. More than 90% of the world's cotton production actually comes from one variety-terrestrial cotton (G. hirsutum). For many countries, it is not only related to economic development, but more often it is also about people's food security and job opportunities. Nowadays, however, the direction of breeding is no longer solely focused on yield as in the past. Fiber quality, stress resistance, and environmental adaptability have gradually become unavoidable goals-climate change, tight land resources, and the textile industry's demand for high-performance fibers have all brought this matter to the forefront (Wang et al., 2024). But when it comes to the speed of traditional breeding, it is not very satisfactory. The method of observing traits and conducting field experiments is not only slow but also labor-intensive, and is further limited by the reality that the genetic diversity of modern cotton varieties is not rich enough. Breeders often encounter the embarrassing situation of "seeing good traits but not being able to select them". Fortunately, with the introduction of molecular techniques, especially the gradual application of methods such as DNA labeling and QTL localization, breeding has finally begun to move from the "visible" to the "invisible" level. Nowadays, with the help of high-throughput typing platforms such as SNP chips and next-generation sequencing, we can screen for variations among tens of thousands of markers. It is not only fast but also very accurate, and the cost is acceptable. Their addition has made GWAS, MAS and even genetic analysis of complex traits feasible, and has indeed significantly improved the efficiency of cotton breeding (Kushanov et al., 2021). This study first reviews the economic and biological background of cotton breeding, then explores the limitations of traditional methods and the transformative impact of high-throughput genotyping, and outlines the latest technological developments, their applications in genetic mapping and breeding, as well as the integration of genotype data with phenotypic and environmental information. This study emphasizes how high-throughput
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