Cotton Genomics and Genetics 2024, Vol.15, No.2, 66-80 http://cropscipublisher.com/index.php/cgg 67 2 Historical Perspective on Cotton Genome Sequencing 2.1 Early efforts and milestones in cotton genome research Early research on the cotton (Gossypium) genome primarily focused on deciphering the basic structure and function of the genome. Initial genome sequencing efforts used techniques such as Restriction Fragment Length Polymorphism (RFLP) and Simple Sequence Repeat (SSR) markers to construct preliminary maps of the cotton genome. These markers were essential tools for constructing genetic maps and locating genes within the cotton genome. For example, the study by Li et al. (2018) utilized high-throughput sequencing to reveal extensive repetitive sequences in the cotton genome, providing valuable data for subsequent genome assembly and functional genomics research (Li et al., 2018). Early genome research also included preliminary investigations into the genetic basis of key agronomic traits in cotton. For instance, studies on fiber quality, yield, and related traits led to the identification of several Quantitative Trait Loci (QTL). These studies not only highlighted critical regions of the cotton genome that control these important traits but also provided a theoretical foundation and technical support for subsequent molecular breeding efforts (Huang et al., 2021). Additionally, early research focused on the structural features of the cotton genome, such as gene density, repetitive sequences, and chromosomal structural variations. These findings were instrumental in guiding future genome assembly and annotation efforts (Du et al., 2018). With the advancement of sequencing technologies in the 21st century, significant breakthroughs were made in cotton genome research. High-throughput sequencing technologies enabled deep sequencing of the cotton genome, revealing extensive gene sequences and structural variations. This provided crucial data for genome assembly and functional annotation, laying a solid foundation for understanding the complexity and evolutionary processes of the cotton genome. These early studies set the stage for subsequent genomic research, offering valuable resources for future studies (Ma and Cao, 2018). 2.2 Key Discoveries and their impact on cotton genetics Key discoveries in cotton genome research have significantly advanced the field of cotton genetics. One major discovery is the revelation of whole-genome duplication events. Polyploidization is a crucial process in the evolution of the cotton genome, with research uncovering multiple whole-genome duplication events that have profoundly impacted the structure and function of the cotton genome. Through comprehensive genome sequencing and comparative genomics analyses, scientists identified the timing and extent of these duplication events, providing essential insights into the evolutionary history of the cotton genome (Wang et al., 2016; Pan et al., 2020). Another significant discovery is the identification of genes and regulatory mechanisms involved in fiber development. Cotton fiber is a key economic trait, with fiber quality directly affecting the market value of cotton. Genomic studies have identified several critical genes associated with fiber length, strength, and maturity. Functional analyses of these genes have elucidated the molecular mechanisms underlying fiber development, providing a theoretical basis and technical support for improving cotton fiber quality through molecular breeding (Huang et al., 2021). Cotton genome research has uncovered many important metabolic pathways and regulatory networks. For example, studies have identified genes related to stress resistance, which play crucial roles in cotton's response to biotic and abiotic stresses. Functional analyses of these genes have provided deeper insights into the mechanisms by which cotton adapts to environmental stresses such as pests, drought, and salinity. These discoveries have enriched our understanding of cotton genome function and offered new strategies for improving cotton resistance through molecular breeding (He et al., 2021). 2.3 Evolution of sequencing technologies and their adoption in cotton research The continuous advancement of genome sequencing technologies has brought unprecedented opportunities for cotton genome research. Early genome sequencing efforts primarily relied on Sanger sequencing technology, which, despite its high accuracy, was limited by low throughput and high costs, restricting large-scale genome sequencing applications. The emergence of high-throughput sequencing technologies has dramatically increased
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