Cotton Genomics and Genetics 2024, Vol.15, No.2, 103-111 http://cropscipublisher.com/index.php/cgg 103 Feature Review Open Access Cytogenetic Markers and Their Importance inGossypiumBreeding Programs Huijuan Xu, Xiaoyan Chen Modern Agriculture Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding author: xianyan.chen@cuixi.org Cotton Genomics and Genetics, 2024, Vol.15, No.2 doi: 10.5376/cgg.2024.15.0010 Received: 27 Feb., 2024 Accepted: 01 Apr., 2024 Published: 14 Apr., 2024 Copyright © 2024 Xu and Chen, 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: Xu H.J., and Chen X.Y., 2024, Cytogenetic markers and their importance in gossypiumbreeding programs, Cotton Genomics and Genetics, 15(2): 103-111 (doi: 10.5376/cgg.2024.15.0010) Abstract The primary goal of this study is to explore the significance of cytogenetic markers in the breeding programs of Gossypiumspecies, particularly focusing on their application in enhancing genetic diversity, improving fiber quality, and increasing yield. The study highlights several key findings from recent research. Simple Sequence Repeat (SSR) markers have been effectively used to analyze genetic diversity and DNA fingerprinting in Gossypium hirsutum, revealing significant polymorphisms and genetic variations among cultivars. High-density genetic maps constructed using various molecular markers, such as SSRs, SNPs, and others, have facilitated the identification of numerous quantitative trait loci (QTLs) associated with important agronomic traits, including fiber quality and yield. The integration of advanced genomic techniques, such as single-molecule real-time sequencing and high-throughput chromosome conformation capture, has led to the development of reference-grade genome assemblies for Gossypiumspecies, providing deeper insights into cotton evolution and aiding in the identification of loci associated with superior fiber quality. Additionally, marker-assisted selection (MAS) and genome-wide association studies (GWAS) have been instrumental in identifying elite alleles and stable QTLs, which are crucial for modern cotton breeding programs. The findings underscore the critical role of cytogenetic markers in Gossypiumbreeding programs. These markers not only enhance our understanding of genetic diversity and genome structure but also enable the precise identification of valuable traits for cotton improvement. The integration of these markers into breeding strategies promises to accelerate the development of high-yielding, superior fiber quality cotton cultivars, thereby meeting the demands of the textile industry and contributing to sustainable agricultural practices. Keywords Gossypium; Cytogenetic markers; SSR markers; Genetic diversity; QTL mapping; Fiber quality; Marker-assisted selection; Genome sequencing 1 Introduction Gossypium, commonly known as cotton, is a genus of flowering plants that holds significant economic importance due to its fiber, which is a primary raw material for the textile industry. The two most widely cultivated species, Gossypium hirsutum and Gossypium barbadense, are known for their high yield and superior fiber quality, respectively. Breeding programs in Gossypium aim to combine these desirable traits to enhance both yield and fiber quality. Traditional breeding methods, while effective, are time-consuming and labor-intensive. The advent of molecular markers has revolutionized plant breeding by enabling marker-assisted selection (MAS), which accelerates the breeding process and increases precision (He et al., 2007; Han et al., 2006). Cytogenetic markers, including simple sequence repeats (SSRs), sequence-related amplified polymorphism (SRAP), random amplified polymorphic DNA (RAPD), and retrotransposon-microsatellite amplified polymorphism (REMAP), play a crucial role in the genetic mapping and marker-assisted breeding of Gossypium. These markers facilitate the identification and mapping of quantitative trait loci (QTLs) associated with economically important traits such as lint yield, fiber strength, and seed index. For instance, a high-density molecular marker linkage map constructed using SSRs, SRAPs, RAPDs, and REMAPs has been instrumental in detecting 52 distinct QTLs related to various phenotypic traits in cotton (He et al., 2007). Additionally, the development of EST-SSR markers from expressed sequence tags (ESTs) has further enriched the genetic maps, aiding in the identification of QTLs and comparative genomics studies (Han et al., 2006).
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