Cotton Genomics and Genetics 2024, Vol.15, No.2, 66-80 http://cropscipublisher.com/index.php/cgg 73 desirable traits, accelerating the development of new varieties. For example, MAS has been used to select cotton varieties with improved disease resistance and higher yields, enhancing both productivity and resistance to environmental stresses. 5.3 Development of disease-resistant and high-yielding varieties Genome sequencing offers new possibilities for developing disease-resistant and high-yielding cotton varieties. By deeply analyzing the cotton genome, researchers can identify and edit key genes associated with disease resistance and yield. For example, CRISPR/Cas9 genome editing technology has been successfully applied to the cotton genome for targeted mutations, creating new cotton varieties with improved traits (Li et al., 2017). The application of genome editing technologies enables precise modifications to the cotton genome, enhancing the accuracy and efficiency of breeding. By knocking out or introducing specific genes through genome editing, significant improvements in disease resistance and yield can be achieved. Moreover, genome sequencing has revealed genes associated with fiber quality, plant architecture, and stress tolerance, providing new strategies for comprehensive trait improvement in cotton (Peng et al., 2020). 6 Case Study: Application of Genome Sequencing in Cotton Breeding 6.1 Case study onVerticillium wilt resistance Verticillium wilt, caused by the soil-borne pathogen Verticillium dahliae, is a significant disease affecting cotton, leading to substantial yield losses globally. Traditional breeding methods for identifying and utilizing resistance genes are time-consuming and complex. With the advancement of genome sequencing technologies, researchers can precisely locate and identify genes associated with disease resistance, thereby accelerating the development of resistant varieties. Li et al. (2017) conducted a genome-wide association study (GWAS) on 299 cotton accessions using 85 630 single nucleotide polymorphism (SNP) markers. They identified 17 SNP markers significantly associated with Verticillium wilt resistance. Further haplotype block structure analysis predicted 22 candidate genes linked to the significant SNP A10_99672586 on chromosome A10. Among these genes, CG02 was significantly upregulated in resistant genotypes and downregulated in susceptible ones. Quantitative real-time PCR and virus-induced gene silencing (VIGS) analyses revealed that silencingCG02 increased the susceptibility of cotton plants to Verticillium wilt, indicating CG02 as a crucial resistance gene (Li et al., 2017). Zhao et al. (2021) further validated these results by combining GWAS, QTL-seq, and transcriptome sequencing. Using the Cotton 63K Illumina Infinium SNP array on 120 core cotton accessions, they identified five significant QTLs that overlapped with previously reported QTLs. Integrating GWAS, QTL-seq, and transcriptome sequencing, they identified eight candidate genes with genomic DNA sequence variations and expression differences between resistant and susceptible accessions. Most of these genes were involved in transcription factor activity, flavonoid biosynthesis, and plant innate immunity. Additionally, they developed 10 KASP markers, which were successfully validated in different cotton varieties and can be used for marker-assisted selection (MAS) to enhance Verticillium wilt resistance (Zhao et al., 2021). 6.2 Case study on fiber quality improvement inGossypium barbadense Gossypium barbadense is widely cultivated for its superior fiber quality, with key attributes such as length, strength, and fineness. Advances in genome sequencing have enabled researchers to gain deeper insights into the genetic factors influencing these fiber traits, providing new breeding strategies for fiber quality improvement. Liu et al. (2015) sequenced the genome of G. barbadense, revealing genes associated with fiber development and secondary cell wall biosynthesis. Through genome sequencing and transcriptome analysis, they identified candidate genes playing key roles in fiber elongation and cell wall thickening. These genes included enzymes involved in cellulose and lignin synthesis, as well as transcription factors regulating fiber development. Functional validation of these genes showed that overexpression or silencing of specific genes could significantly impact fiber length and strength (Liu et al., 2015).
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