Cotton Genomics and Genetics 2024, Vol.15, No.2, 112-126 http://cropscipublisher.com/index.php/cgg 118 important agronomic trait genes, which are directly related to cotton's drought, salt, and disease resistance. For example, some methylation sites on chromosome D13 were closely associated with drought resistance, suggesting that specific methylation patterns might respond to environmental stress by affecting gene expression or suppression. Figure 3 Phenotype of CRI-12 and synteny relation of different cotton genomes (Adopted from Lu et al., 2022) Image caption: A: Phenotype of CRI-12; B: Hi-C map of CRI-12. From left to right, each square represents a chromosome from chromosome 1 to 26; C: Synteny analysis of different cotton species; D: Whole-genome duplications in Malvales through 4DTv analysis. The percentages of the orthologous gene pairs between CRI-12 and other species and 4DTv values were calculated. Fourfold degenerate synonymous site (4DTV) is used as an evolutionary parameter to evaluate whether a genome-wide replication event has occurred. The site of a codon at which all nucleotides encode the same amino acid is a quadruple degenerate site (Adopted from Lu et al., 2022) The application of WGBS technology provides new insights into the genetic regulation of cotton under complex environmental conditions and highlights the importance and function of methylation in plant adaptation to environmental changes. 3.3.2 Applications in cotton breeding The application of NGS technologies in epigenomics has significant implications for cotton breeding. By integrating epigenetic data with genomic and transcriptomic information, breeders can gain a deeper understanding of the factors influencing trait expression and inheritance. This knowledge can be used to develop epigenetic markers for selection and to design breeding strategies that exploit epigenetic variation to enhance desirable traits (Isobe et al., 2020). The ability to manipulate epigenetic modifications through breeding or biotechnological approaches holds great promise for improving cotton yield, quality, and stress tolerance. Next-generation sequencing technologies have revolutionized cotton genomics by enabling high-resolution genome sequencing, comprehensive transcriptome analysis, and detailed epigenomic studies. These advancements have provided valuable insights into the genetic and epigenetic mechanisms underlying important traits in cotton, paving the way for more effective breeding strategies and crop improvement efforts.
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