CGG_2024v15n2

2 Overview of Next-Generation Sequencing Technolog	51
2.1 History and development of NGS	51
2.2 Types of NGS technologies	51
2.2.1 Illumina sequencing	51
2.2.2 PacBio sequencing	51
2.2.3 Oxford Nanopore sequencing	53
2.3 Comparison of NGS technologies	53
3 Applications of NGS in Cotton Genomics	53
3.1 Genome sequencing and assembly	53
3.1.1 Reference genome construction	53
3.1.2 de novo genome assembly	53
3.2 Transcriptomics and gene expression analysis	54
3.2.1 RNA-Seq applications	54
3.2.2 Differential gene expression	55
3.3 Epigenomics and methylation studies	55
3.3.1 Whole-Genome bisulfite sequencing	55
3.3.2 Applications in cotton breeding	56
4 NGS and Genetic Diversity in Cotton	57
4.1 Population genomics and phylogenetics	57
4.1.1 SNP discovery and genotyping	57
4.1.2 Phylogenetic relationships	57
4.2 Marker-Assisted selection (MAS)	57
4.2.1 Identification of QTLs	57
4.2.2 Genomic selection strategies	59
5 Functional Genomics in Cotton Using NGS	59
5.1 Gene discovery and annotation	59
5.2 Functional characterization of genes	59
5.3 CRISPR/Cas9 and genome editing technologies	59
6 Challenges and Limitations of NGS in Cotton Geno	60
6.1 Technical challenges	60
6.2 Data management and analysis	60
6.3 Cost and accessibility	60
7 Future Prospects and Directions	60
7.1 Emerging NGS technologies	60
7.2 Integration with other omics technologies	61
7.3 Potential for sustainable cotton production	61
8 Concluding Remarks	61

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