Cotton Genomics and Genetics 2024, Vol.15, No.2, 112-126 http://cropscipublisher.com/index.php/cgg 121 region, reflecting the genetic diversity and complexity. Additionally, despite the geographical clustering, the samples from different regions exhibit some degree of crossover and genetic connectivity, indicating genetic exchanges and relationships between these regions. This phylogenetic analysis provides insights into the genetic diversity and evolutionary relationships among upland cotton varieties from different geographical backgrounds (Adapted from Wang et al., 2022) 4.2.2 Genomic selection strategies Genomic selection (GS) strategies in cotton have benefited from the advancements in NGS technologies. GS involves using genome-wide markers to predict the breeding value of individuals, allowing for the selection of superior genotypes based on their genetic potential rather than phenotypic performance alone. NGS provides the high-density marker data required for accurate genomic predictions, improving the efficiency and effectiveness of selection in breeding programs (Sahu et al., 2020; Kushanov et al., 2021). The integration of NGS data with advanced bioinformatics tools has enabled the development of robust genomic selection models, which can be used to accelerate the breeding of high-yielding, stress-resistant cotton cultivars (Le Nguyen et al., 2019). NGS technologies have transformed the study of genetic diversity and the application of marker-assisted selection in cotton genomics. By enabling the discovery of SNPs, elucidating phylogenetic relationships, identifying QTLs, and supporting genomic selection strategies, NGS has become a game changer in cotton breeding and genetic research. The continued development and application of NGS technologies hold great promise for the future of cotton improvement. 5 Functional Genomics in Cotton Using NGS 5.1 Gene discovery and annotation Next-Generation Sequencing (NGS) technologies have significantly advanced the field of cotton genomics by enabling comprehensive gene discovery and annotation. The high-throughput nature of NGS allows for the rapid sequencing of entire cotton genomes, facilitating the identification of novel genes and the annotation of their functions. Computational tools and pipelines have been developed to assist in the structural and functional annotation of these sequences, which are crucial for understanding gene functions and genome evolution. The integration of NGS with advanced computational methods has also improved the accuracy and efficiency of genome annotations, reducing the likelihood of misannotations and enhancing our understanding of the cotton genome (Ejigu and Jung, 2020). 5.2 Functional characterization of genes The functional characterization of genes in cotton has been greatly enhanced by NGS technologies. By providing detailed insights into gene expression patterns and regulatory networks, NGS enables researchers to elucidate the roles of specific genes in various biological processes. For instance, the development of genome editing tools such as CRISPR/Cas9 has allowed for precise manipulation of target genes, facilitating functional studies in cotton. These tools have been used to create targeted mutations in key genes, such as GhMYB25-like A and GhMYB25-like D, which are involved in important developmental processes (Li and Zhang, 2019). Additionally, base-editing techniques using modified CRISPR/Cas9 systems have enabled the creation of specific point mutations, further aiding in the functional analysis of genes in the allotetraploid cotton genome (Qin et al., 2020). 5.3 CRISPR/Cas9 and genome editing technologies CRISPR/Cas9 and other genome editing technologies have revolutionized cotton genomics by providing powerful tools for precise genetic modifications. The CRISPR/Cas9 system has been optimized for use in cotton, allowing for efficient and targeted gene editing with high specificity and minimal off-target effects. This technology has been employed to generate site-specific mutations, enabling the study of gene function and the development of improved cotton varieties. For example, the CRISPR/Cas9 system has been used to create transgene-free genetically engineered cotton plants with desired traits, such as enhanced resistance to diseases and improved fiber quality (Li and Zhang, 2019). Moreover, the development of novel CRISPR/Cas9 variants, such as Cas9-NG, has expanded the targeting scope of genome editing tools, offering greater flexibility in selecting target sites within the cotton genome (Ren et al., 2019). These advancements in genome editing technologies hold great promise for the future of cotton breeding and functional genomics research.
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