Cotton Genomics and Genetics 2024, Vol.15, No.2, 66-80 http://cropscipublisher.com/index.php/cgg 71 14 A1 accessions and 30 (AD)1 accessions, respectively. The percentage value indicates the percentage of ancestral alleles for each species that were identical to those of the D5-genome. (f) Number of nucleotide variations in A1 or A2 compared with At1 across the chromosomes. (g) A model for the formation of allotetraploid cotton showing fiber phenotypes from the (AD)1 (accession TM-1), the D5, the A1 (var. africanum) and the A2 (cv. Shixiya1). Scale bar, 5 mm. h, A schematic map of the evolution of cotton genomes. Major evolutionary events are shown in dashed boxes (Adapted from Huang et al., 2020) Comparative genomics studies using these reference genomes have provided valuable insights into the evolution and domestication of cotton. These studies have revealed the asymmetric evolution between the A and D subgenomes of tetraploid cotton, highlighting the genetic basis of fiber improvement and stress tolerance (Zhang et al., 2015). 4.3 Advances in CRISPR/Cas9 genome editing The advent of CRISPR/Cas9 genome editing technology has opened new avenues for genetic improvement in cotton. This technology allows for precise, targeted modifications of the cotton genome, enabling the introduction of desirable traits and the elimination of undesirable ones. The high efficiency and specificity of CRISPR/Cas9 make it an invaluable tool for cotton breeding. In recent years, significant progress has been made in applying CRISPR/Cas9 to edit the genomes of allotetraploid cotton species. Researchers have successfully used CRISPR/Cas9 to target and modify multiple sites within the cotton genome, achieving high rates of gene editing efficiency. For example, studies have demonstrated the successful editing of genes involved in fiber development and stress response, resulting in improved fiber quality and enhanced resistance to biotic and abiotic stresses (Lu et al., 2019). CRISPR/Cas9 technology has also been used for gene knockout and introduction of specific mutations in cotton, providing valuable insights into gene function and regulation. The ability to accurately edit cotton genes accelerates functional genomics research, enabling researchers to analyze complex genetic pathways and identify key regulatory genes. Wang et al. (2017) introduced a mutation in the DsRed2 gene in cotton variety YZ1 using the CRISPR/Cas9 system. Figure 2 shows the experimental process and results. The upper row (a) displays wild-type cotton seeds (upper row) and DsRed2 overexpressing lines (lower row). By comparing the two, it can be observed that the mutant exhibits differences in performance under different lighting conditions. In addition, the development of multiple CRISPR/Cas9 systems has made it possible to edit multiple genes simultaneously, further improving the efficiency of cotton genome editing. This method performs well in targeting gene families and regulatory networks, promoting the engineering improvement of complex cotton traits (Wang et al., 2017). 5 Implications for Cotton Breeding 5.1 Enhancements in genetic diversity and trait selection Genome sequencing technology provides powerful tools for enhancing genetic diversity and trait selection in cotton. High-throughput sequencing technologies enable comprehensive analysis of the complex structure and variation within the cotton genome. These technologies make it possible to dissect the genome in detail, revealing genes and regulatory networks associated with important agronomic traits. For example, a study on the cotton genome revealed extensive structural variations that significantly impact fiber quality and disease resistance (Wang et al., 2018). Genome sequencing has highlighted the loss of genetic diversity during cotton domestication. Through comprehensive genomic variation analysis, researchers have identified significant differences between cultivated and wild cotton, particularly in gene loss and retention. These findings provide new perspectives on the selective pressures during domestication and improvement processes, aiding in the development of more effective breeding strategies to increase genetic diversity in cotton (Li et al., 2021). 5.2 Marker-Assisted selection and its benefits Marker-assisted selection (MAS) is a significant application of genome sequencing in cotton breeding. MAS uses genomic markers to track and select genes associated with specific traits, making the breeding process more efficient and precise. Genome sequencing has provided a vast array of single nucleotide polymorphism (SNP)
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