1 Introduction

The genus Gossypium, commonly known as cotton, encompasses approximately 50 species distributed across tropical and subtropical regions worldwide, excluding Europe. Cotton is not only a vital agricultural commodity but also a significant model for studying plant domestication and evolutionary biology. The domestication of Gossypium species has occurred independently in various ecological zones, leading to the development of economically important cotton species such as Gossypium hirsutum and Gossypium barbadense (Chaudhary et al., 2008; Wang et al., 2017; Viot and Wendel, 2023). This systematic review aims to synthesize current knowledge on the parallel domestication processes of Gossypium species, highlighting the genetic, molecular, and ecological factors that have shaped their evolution and adaptation.

Cotton has been a cornerstone of the global textile industry for centuries, with Gossypium hirsutum (Upland cotton) and Gossypium barbadense (Pima cotton) being the most widely cultivated species due to their superior fiber qualities (Stephens, 1965; Chaudhary et al., 2008). The domestication of these species involved significant genetic and phenotypic changes, driven by both natural and human-mediated selection pressures. Studies have shown that domestication has led to enhanced fiber length, strength, and fineness, which are critical traits for textile production (Rapp et al., 2010; Hu et al., 2013). Moreover, the domestication process has also influenced other agronomic traits such as seed germination and stress resistance, further contributing to the adaptability and productivity of these species (Mehetre, 2010).

The evolutionary history of Gossypium is marked by multiple polyploidization events, which have played a crucial role in the diversification and adaptation of cotton species (Paterson et al., 2012). Polyploidy has conferred emergent properties such as higher fiber productivity and quality, making tetraploid cottons more advantageous compared to their diploid counterparts. Additionally, the study of gene expression and regulatory mechanisms in cotton fibers has provided insights into the molecular basis of domestication and crop improvement (Rapp et al., 2010; Zhu et al., 2012; Wang et al., 2017).

By integrating data from taxonomic investigations, biogeography, molecular genetics, and phylogenetic analyses, this review will elucidate the diversification and polyploid formation in the genus Gossypium. This study will explore the timeline and geographical origins of cotton domestication, highlighting the parallel domestication events in Mesoamerica and South America through analyzing the genetic and molecular changes associated with domestication and investigating the ecological and environmental factors influencing domestication to contribute to a deeper understanding of the complex interplay between genetics, environment, and human intervention in the domestication of Gossypium species, ultimately informing future research and crop improvement strategies.

2 Overview of Gossypium Species

2.1 Taxonomy and classification

The genus Gossypium, commonly known as cotton, comprises approximately 50 species distributed across tropical and subtropical regions worldwide, excluding Europe (Viot and Wendel, 2023). These species are classified into diploid and tetraploid groups, with the latter resulting from polyploidization events that combined genomes from different progenitor species (Paterson et al., 2012). The primary cultivated species include Gossypium hirsutum and Gossypium barbadense, both of which are tetraploids, as well as the diploid species Gossypium herbaceum and Gossypium arboreum (Fang et al., 2017; Grover et al., 2021). The classification within the genus is further refined based on molecular genetics and phylogenetic analyses, which have clarified the relationships among species and their evolutionary history (Zhu et al., 2012; Viot and Wendel, 2023).

2.2 Geographical distribution

Gossypium species are native to diverse ecological zones, ranging from arid to tropical environments. Gossypium hirsutum and Gossypium barbadense were domesticated in the Yucatan Peninsula and northwest South America, respectively, and have since spread throughout the American tropics (Yuan et al., 2021). The diploid species, Gossypium herbaceum and Gossypium arboreum, are primarily found in Africa and Asia, with a significant presence in the Indian subcontinent (Grover et al., 2021). The widespread distribution of these species is a testament to their adaptability and the extensive human-mediated dispersal that has occurred over millennia (Figure 1) (Wang et al., 2022).

Figure 1 Genetic diversity and introduction history of Gossypium barbadense (Adopted from Wang et al., 2022)

2.3 Genetic diversity

The genetic diversity within Gossypium species is substantial, reflecting their complex evolutionary history and multiple domestication events. Studies have shown that Gossypium hirsutum and Gossypium barbadense exhibit significant genetic divergence, with distinct phylogenetic groups corresponding to their wild and domesticated forms (Fang et al., 2017). Despite this divergence, there has been considerable interspecific introgression, particularly from Gossypium hirsutum to Gossypium barbadense, which has contributed to genetic diversity and adaptation (Wang et al., 2022). In diploid species, independent domestication events have led to similar levels of genetic diversity within Gossypium herbaceum and Gossypium arboreum, with notable interspecific gene flow (Grover et al., 2021). The evolutionary rates of genes related to fiber development also vary, with cultivated species showing higher rates of evolution compared to their wild counterparts (Zhu et al., 2012; Zhou et al., 2022). The genus Gossypium encompasses a wide range of species with diverse genetic backgrounds and geographical distributions. The intricate taxonomy, extensive geographical spread, and rich genetic diversity of these species underscore their importance in both natural ecosystems and agricultural systems worldwide. Understanding these aspects is crucial for ongoing efforts in cotton improvement and conservation.

3 Historical Perspectives on Gossypium Domestication

3.1 Early evidence of cotton domestication

The domestication of Gossypium species is a remarkable example of parallel evolution driven by human selection. The earliest evidence of cotton domestication dates back to approximately 8 000 years ago for Gossypium barbadense and 5 500 years ago for Gossypium hirsutum. These species were initially wild perennial shrubs with small capsules and seeds covered by short, tan-colored trichomes. Over millennia, they were transformed into modern annuals bearing abundant, fine, strong white fibers through human-mediated selection (Yuan et al., 2021; Viot and Wendel, 2023). The domestication process involved significant morphological changes, including the elongation of cotton fibers, which were crucial for their use in textiles (Chaudhary et al., 2008).

3.2 Archaeological and historical records

Archaeological records provide substantial evidence of the early use and domestication of cotton. In the Americas, Gossypium hirsutum was domesticated in the Yucatan Peninsula, while Gossypium barbadense was domesticated in northwest South America. These domesticated species spread across the American tropics over several millennia, driven by human cultivation and selection (Yuan et al., 2021). The archaeological history of cotton in the Old World is equally significant, with Gossypium arboreum and Gossypium herbaceum being independently domesticated in Africa and Asia. These species have been cultivated for thousands of years, contributing to the textile industries in their respective regions (Renny-Byfield et al., 2016; Grover et al., 2021).

3.3 Comparative timeline of domestication events

The timeline of cotton domestication events reveals a pattern of parallel and independent domestication across different ecological zones. In the New World, Gossypium hirsutum and Gossypium barbadense were domesticated independently but later came into contact, leading to interspecific introgression and further genetic diversity (Yuan et al., 2021; Viot and Wendel, 2023). In the Old World, Gossypium arboreum and Gossypium herbaceum were also domesticated independently, with evidence suggesting that they did not share a common domestication history but rather evolved separately under human selection (Wendel and Grover, 2015; Renny-Byfield et al., 2016).

The domestication of these species involved not only morphological changes but also significant genomic alterations. For instance, the up-regulation of the profilin gene family in both diploid and allopolyploid cottons is a notable example of parallel genetic changes driven by domestication (Bao et al., 2011). These genetic modifications have been crucial for the development of cotton as a major crop, providing insights into the evolutionary forces shaping domesticated species (Peng et al., 2022). The historical perspectives on Gossypium domestication highlight the complex interplay of human selection, ecological adaptation, and genetic evolution that has shaped the cotton species we rely on today. The parallel domestication events in diverse ecological zones underscore the importance of understanding both the historical and genetic contexts of crop domestication for future agricultural improvements.

4 Ecological Zones and Their Impact on Gossypium Domestication

4.1 Tropical and subtropical regions

The tropical and subtropical regions have played a significant role in the domestication of Gossypium species. Gossypium hirsutum and Gossypium barbadense, the two primary cultivated cotton species, were initially domesticated in these regions. G. hirsutum was domesticated in the Yucatan Peninsula, while G. barbadense originated in northwest South America (Yuan et al., 2021; Viot and Wendel, 2023). These regions provided the necessary climatic conditions for the growth and development of wild cotton species, which later underwent significant morphological transformations under human selection. The tropical and subtropical climates facilitated the growth of perennial wild cotton plants, which were eventually transformed into annualized row crops through domestication.

4.2 Arid and semi-arid regions

Arid and semi-arid regions have also contributed to the domestication and adaptation of Gossypium species. The domestication process in these regions involved significant genetic modifications to enhance the plants' tolerance to drought and other environmental stresses. For instance, the introgression from G. hirsutum to G. barbadense has been identified as a key driver for population divergence and genetic diversity, particularly in traits related to environmental adaptation (Wang et al., 2022). These genetic changes have enabled Gossypium species to thrive in arid and semi-arid conditions, thereby expanding their cultivation range and improving their agronomic traits.

4.3 Temperate regions

The expansion of Gossypium cultivation into temperate regions required further genetic adaptations. The domestication process in these regions involved the selection of traits that allowed cotton plants to grow in cooler climates with shorter growing seasons. The transformation of wild perennial shrubs into daylength-neutral annuals was a crucial adaptation that facilitated the spread of cotton cultivation into temperate zones (Viot and Wendel, 2023). Additionally, the prolonged fiber growth and enhanced modulation of cellular processes in domesticated G. barbadense compared to its wild ancestors indicate significant genetic modifications that supported its adaptation to diverse ecological zones, including temperate regions (Chaudhary et al., 2008).

In summary, the domestication of Gossypium species has been profoundly influenced by the ecological zones in which they were cultivated. Tropical and subtropical regions provided the initial conditions for domestication, while arid and semi-arid regions necessitated genetic adaptations for environmental stress tolerance. The expansion into temperate regions required further modifications to support growth in cooler climates. These diverse ecological zones have collectively shaped the genetic architecture and agronomic traits of modern cotton species, making them resilient and adaptable to a wide range of environmental conditions.

5 Genetic Mechanisms Underlying Domestication

5.1 Key genetic traits selected during domestication

The domestication of Gossypium species, particularly G. hirsutum and G. barbadense, involved the selection of several key genetic traits that transformed wild perennial plants into annualized crops with desirable fiber qualities. One of the primary traits selected was the enhancement of fiber length and quality. For instance, G. barbadense is known for its extra-long staple cotton with superior luster and silkiness, traits that were selected during its domestication from an agronomically inferior wild ancestor. Additionally, domestication led to the modulation of cellular redox levels and the avoidance or delay of stress-like processes, which contributed to prolonged fiber growth in cultivated varieties (Chaudhary et al., 2008).

Another significant trait is the transformation of the plants from short-day perennials with small capsules and seeds covered by short, tan-colored trichomes into daylength-neutral annuals bearing abundant, fine, strong white fibers (Viot and Wendel, 2023). This transformation was crucial for the adaptation of cotton to diverse ecological zones and for meeting the demands of agricultural practices.

5.2 Genomic approaches to studying domestication

Genomic approaches have been pivotal in unraveling the complexities of cotton domestication. Deep resequencing of accessions spanning the wild-to-domesticated continuum has provided insights into species relationships and the genetic diversity within and between domesticated and wild cotton species (Figure 2) (Yuan et al., 2021). Phylogenomic analyses have been employed to resolve infraspecific relationships and to quantify genetic diversity, revealing genetic bottlenecks associated with domestication and subsequent diffusion.

Figure 2 Putative regions of selection on the AT chromosomes (top) and DT chromosomes (bottom). For each set of chromosomes, G. hirsutum regions are depicted above each line, whereas G. barbadense regions are placed below each line. Although pictured here on identical scales, the AT chromosomes are about twice the length of DT chromosomes (Adopted from Yuan et al., 2021)

Comparative expression profiling using microarray platforms has also been utilized to study the cotton fiber transcriptome at different developmental stages. This approach has identified approximately 4 200 genes that are differentially expressed between wild and domesticated accessions, providing clues into the processes and genes selected during domestication (Chaudhary et al., 2008). Additionally, chloroplast genome sequences have been used to determine evolutionary rates, domestication selection, and genetic relationships among cotton genotypes, highlighting the higher nucleotide diversity in semi-wild races compared to cultivated genotypes (Zhou et al., 2022).

5.3 Comparative genomics of domesticated and wild cotton

Comparative genomics has revealed significant insights into the evolutionary divergence and genetic mechanisms underlying the domestication of cotton. High-quality reference genomes of domesticated G. hirsutum and its wild relatives have clarified evolutionary relationships and documented genomic changes that characterize these species (Peng et al., 2022). These studies have highlighted the potential for introgression of favorable genes from wild relatives into domesticated cotton, which could enhance resilience to environmental challenges and improve crop varieties.

Diversity scans have identified genomic regions and genes targeted during domestication, revealing subgenomic asymmetries and pervasive genome-wide bidirectional introgression between domesticated and wild cotton species (Yuan et al., 2021). These findings underscore the complex interplay of natural and artificial selection in shaping the genomic architecture of domesticated cotton and provide a rich resource for future cotton improvement efforts. The genetic mechanisms underlying the domestication of Gossypium species involve the selection of key traits such as fiber quality and growth patterns, the use of advanced genomic approaches to study domestication processes, and comparative genomics to understand the evolutionary divergence between domesticated and wild cotton. These insights are crucial for enhancing our understanding of cotton domestication and for guiding future breeding programs aimed at improving cotton varieties.

6 Parallel Domestication Processes

6.1 Independent domestication events in different regions

The domestication of Gossypium species is a remarkable example of independent domestication events occurring in different regions. Gossypium hirsutum and Gossypium barbadense, the two primary cultivated allopolyploid cotton species, were independently domesticated in the Yucatan Peninsula and Northwest South America, respectively. These species underwent significant morphological transformations from wild perennial plants to annualized row crops over 4 000~8 000 years, spreading across the American tropics (Yuan et al., 2021; Viot and Wendel, 2023). Similarly, the diploid species Gossypium herbaceum and Gossypium arboreum were independently domesticated in the Old World, with evidence suggesting their domestication occurred several millennia ago (Renny-Byfield et al., 2016; Grover et al., 2021). These independent domestication events highlight the diverse ecological zones and human selection pressures that shaped the evolution of these cotton species.

6.2 Convergent evolution in Gossypium species

Convergent evolution in Gossypium species is evident through the similar phenotypic traits that have arisen independently in different species due to similar selection pressures. For instance, both G. hirsutum and G. barbadense have developed traits such as daylength-neutrality and the production of abundant, fine, strong white fibers, despite their separate domestication events (Hovav et al., 2008; Viot and Wendel, 2023). This convergent evolution is driven by human selection for desirable agronomic traits, leading to similar genetic and phenotypic outcomes in different species. The modulation of homeologous gene expression in response to domestication pressures further supports the occurrence of convergent evolution, with different sets of genes being selected in G. hirsutum and G. barbadense (Hovav et al., 2008).

6.3 Case studies of parallel domestication

Several case studies illustrate the parallel domestication of Gossypium species. The domestication of G. hirsutum and G. barbadense involved significant genetic bottlenecks and subsequent diffusion, with pervasive genome-wide bidirectional introgression occurring as these species became sympatric (Yuan et al., 2021). In the Old World, G. herbaceum and G. arboreum were independently domesticated, with genomic analyses confirming their separate domestication events and documenting the genomic distribution of interspecific genetic exchange (Renny-Byfield et al., 2016; Grover et al., 2021). Additionally, the introgression from G. hirsutum to G. barbadense has been identified as a driver for population divergence and genetic diversity, highlighting the role of interspecific gene flow in the domestication process (Wang et al., 2022). These case studies underscore the complexity and diversity of domestication processes in Gossypium species, shaped by both independent and convergent evolutionary forces.

7 Human Influence on Domestication and Cultivation

7.1 Role of traditional agricultural practices

Traditional agricultural practices have played a significant role in the domestication and cultivation of Gossypium species. The initial domestication of Gossypium hirsutum and Gossypium barbadense occurred in the Yucatan Peninsula and NW South America, respectively, and these species were subsequently spread under domestication over thousands of years to encompass most of the American tropics (Yuan et al., 2021). The domestication process involved human-mediated selection for economically important traits such as fiber length, luster, and yield, transforming wild perennial plants into annualized row crops. This transformation was driven by traditional agricultural practices that selected for desirable traits, leading to the development of modern cotton varieties with superior fiber qualities (Chaudhary et al., 2008).

7.2 Impact of modern breeding techniques

Modern breeding techniques have further influenced the domestication and cultivation of Gossypium species. Advances in genomic technologies have enabled the identification of genetic regions and genes targeted during domestication, providing insights into the evolutionary history and genetic architecture of cotton (Yuan et al., 2021; Viot and Wendel, 2023). For instance, deep resequencing of cotton accessions has revealed genetic bottlenecks associated with domestication and subsequent diffusion, as well as pervasive genome-wide bidirectional introgression between G. hirsutum and G. barbadense (Yuan et al., 2021). Additionally, comparative expression profiling has identified differentially expressed genes between wild and domesticated accessions, highlighting the role of signal transduction and hormone signaling genes in prolonged fiber growth. These modern breeding techniques have facilitated the development of elite cotton lines with enhanced agronomic traits, contributing to the global importance of cotton as a fiber crop (Chaudhary et al., 2008).

7.3 Socio-economic factors

Socio-economic factors have also played a crucial role in the domestication and cultivation of Gossypium species. The historical importance of cotton in various regions, particularly in the Indian subcontinent, has driven human-mediated dispersal and interspecific gene flow between cultivated diploid species such as G. herbaceum and G. arboreum (Grover et al., 2021). The economic value of cotton, driven by its superior fiber qualities and high yield, has led to extensive human-mediated selection and hybridization efforts to improve agronomic traits (Chaudhary et al., 2008). Interspecific introgressions from G. hirsutum to G. barbadense, for example, have been associated with significant phenotypic improvements in yield and fiber qualities, highlighting the potential value of these introgressions in further human-mediated hybridization or precision breeding (Fang et al., 2021). The socio-economic demand for high-quality cotton has thus been a driving force behind the continuous improvement and cultivation of Gossypium species.

The domestication and cultivation of Gossypium species have been profoundly influenced by traditional agricultural practices, modern breeding techniques, and socio-economic factors. These elements have collectively shaped the evolutionary history and genetic architecture of cotton, leading to the development of globally important fiber crops with superior agronomic traits.

8 Environmental Adaptations of Domesticated Gossypium

8.1 Adaptations to climate variability

Domesticated Gossypium species, particularly Gossypium hirsutum and Gossypium barbadense, have demonstrated significant adaptability to diverse climatic conditions. These species were initially domesticated in distinct ecological zones-G. hirsutum in the Yucatan Peninsula and G. barbadense in NW South America-before spreading across the American tropics over several millennia (Yuan et al., 2021; Viot and Wendel, 2023). This extensive geographical spread necessitated adaptations to varying climatic conditions, including temperature fluctuations and differing precipitation patterns. The polyploid nature of these species has contributed to their resilience, as polyploidy often confers emergent properties such as enhanced stress tolerance and ecological adaptability (Paterson et al., 2012). Additionally, the introgression of genetic material between these species has facilitated the exchange of adaptive traits, further enhancing their ability to thrive in diverse environments (Fang et al., 2021; Wang et al., 2022).

8.2 Soil and water requirements

The soil and water requirements of domesticated Gossypium species are critical factors influencing their cultivation and productivity. Gossypium species have evolved to grow in a variety of soil types, ranging from sandy to clayey soils, with a preference for well-drained soils to prevent root diseases. The domestication and subsequent breeding of these species have led to the selection of traits that optimize water use efficiency and drought tolerance. For instance, Gossypium australe, a wild diploid species, possesses traits such as delayed gland morphogenesis and disease resistance, which have been incorporated into domesticated cotton through distant breeding programs (Cai et al., 2019). These traits contribute to the plant's ability to manage water stress and maintain productivity under suboptimal water conditions. Furthermore, the genetic diversity within Gossypium species, as revealed by genome-wide association studies, highlights the presence of loci associated with improved water use efficiency and soil adaptability (Fang et al., 2021; Wang et al., 2022).

8.3 Resistance to pests and diseases

Resistance to pests and diseases is a crucial aspect of the environmental adaptations of domesticated Gossypium species. The evolutionary history of these species includes the selection of genetic traits that confer resistance to various pathogens and pests. For example, Gossypium australe has been identified as possessing excellent disease resistance traits, which have been successfully introgressed into domesticated cotton varieties to enhance their resistance to diseases such as Verticillium wilt (Cai et al., 2019). Additionally, the development of synthetic allotetraploids, such as the novel A1A1G3G3 genotype, has provided new germplasm resources with enhanced disease resistance characteristics (Yin et al., 2020). The repeated polyploidization events in Gossypium have also contributed to the genetic complexity and diversity of these species, enabling them to develop robust defense mechanisms against a wide range of biotic stresses (Paterson et al., 2012). The ongoing introgression and hybridization efforts continue to play a significant role in improving the pest and disease resistance of domesticated cotton, ensuring its sustainability and productivity in various ecological zones (Fang et al., 2021; Wang et al., 2022).

9 Challenges and Future Directions in Gossypium Domestication Research

9.1 Current challenges in domestication studies

One of the primary challenges in Gossypium domestication research is the complexity of the genus itself, which includes approximately 50 species distributed across diverse tropical and subtropical regions (Wendel et al., 2010; Viot and Wendel, 2023). This diversity poses significant difficulties in understanding the evolutionary and domestication processes, particularly given the dual domestication events in different hemispheres for G. hirsutum and G. barbadense (Fang et al., 2017). Additionally, the genetic divergence between these two species, despite their commercial importance, remains largely unexplored, complicating efforts to map their population structure and genetic variations comprehensively (Fang et al., 2017).

Another challenge is the limited access to diverse genetic materials. Although some studies have resequenced genomes of various cotton accessions, including wild relatives, landraces, and modern cultivars, the overall genetic diversity and interspecific hybridization events are not fully understood (Fang et al., 2017). This gap in knowledge hinders the ability to leverage genetic diversity for crop improvement and adaptation to changing environmental conditions.

9.2 Technological advances and opportunities

Recent technological advancements offer promising opportunities to overcome these challenges. High-throughput sequencing technologies and comprehensive variation mapping have provided deeper insights into the genomic architecture of Gossypium species (Fang et al., 2017). These technologies enable the identification of selective sweeps and highly expressed genes associated with desirable traits such as fiber development and seed germination, which are crucial for improving cotton production.

Moreover, phylogenetic analysis and molecular genetics have clarified the evolutionary history and interspecific hybridization events within the genus, providing a robust framework for future research (Viot and Wendel, 2023). The integration of biogeography, archaeology, and modern genomic tools has also enriched our understanding of the domestication and diffusion of cotton in the Americas, highlighting the importance of interdisciplinary approaches in domestication studies.

9.3 Future research directions

Future research should focus on expanding the genetic diversity available for study by incorporating more wild relatives and landraces into genomic analyses. This will help to uncover the full extent of genetic variation and facilitate the identification of novel alleles that can be used for crop improvement (Fang et al., 2017). Additionally, there is a need for more detailed studies on the population structure and genetic variations within and between G. hirsutum and G. barbadense to better understand their domestication processes and evolutionary trajectories.

Another important direction is the exploration of interspecific introgression events and their impact on the genetic makeup of modern cultivars. Understanding the patterns and consequences of gene flow between species can provide valuable insights into the mechanisms of adaptation and hybrid vigor (Fang et al., 2017). Finally, leveraging advanced genomic tools and interdisciplinary approaches will be crucial for addressing the complex challenges in Gossypium domestication research and for developing strategies to enhance cotton production in diverse ecological zones (Wendel et al., 2010; Viot and Wendel, 2023).

10 Concluding Remarks

The parallel domestication of Gossypium species in diverse ecological zones has been a remarkable process, characterized by significant genetic, morphological, and agronomic transformations. The domestication of Gossypium hirsutum and Gossypium barbadense in the Americas involved dramatic changes from wild perennial plants to annualized row crops, driven by human selection over thousands of years. Phylogenomic analyses have revealed the independent domestication events of these species, with G. hirsutum originating in the Yucatan Peninsula and G. barbadense in NW South America. These species have undergone extensive genetic bottlenecks and introgression events, which have shaped their current genetic diversity and adaptation.

In the Old World, the diploid species Gossypium herbaceum and G. arboreum also experienced independent domestication, with notable interspecific gene flow and introgression contributing to their evolution and diversity. The genomic architecture of these species has been significantly influenced by introgression from G. hirsutum, which has driven population divergence and increased genetic diversity in G. barbadense. Comparative transcriptomic analyses have highlighted the differential gene expression patterns between wild and domesticated accessions, shedding light on the metabolic and physiological changes associated with domestication.

The insights gained from the parallel domestication of Gossypium species have profound implications for future cotton breeding. Understanding the genetic basis of domestication traits and the role of introgression in shaping genetic diversity can inform breeding strategies aimed at improving cotton yield, fiber quality, and stress tolerance. The identification of selective sweeps and introgressed haplotypes associated with agronomic traits provides valuable targets for marker-assisted selection and genomic selection in cotton breeding programs.

Moreover, the knowledge of interspecific gene flow and its impact on genetic diversity can be leveraged to enhance the genetic base of cultivated cotton. Breeding programs can exploit the genetic variation from wild relatives and introgressed regions to develop new cultivars with improved performance and resilience to environmental stresses. The parallel domestication events also underscore the potential for using comparative genomics to identify conserved genetic pathways and regulatory networks that can be manipulated to achieve desired agronomic traits.

The study of parallel domestication in Gossypium species offers a compelling example of how human-mediated selection and natural evolutionary processes have shaped the genetic and phenotypic diversity of one of the world's most important fiber crops. The integration of genomic, phylogenetic, and transcriptomic data has provided a comprehensive understanding of the domestication history and genetic architecture of cotton. As we move forward, the continued exploration of cotton's genetic diversity and the application of advanced breeding technologies will be crucial in meeting the challenges of sustainable cotton production and improving the livelihoods of cotton farmers worldwide.

Acknowledgments

The author would like to express our gratitude to the two anonymous peer reviewers for their critical assessment and constructive suggestions on themanuscript.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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