1 Introduction

Cotton (Gossypium spp.) is the most important natural fiber crop worldwide, playing a crucial role in the global textile industry. Its cultivation dates back thousands of years, and it has been a cornerstone of agricultural economies, particularly in regions with suitable climates for its growth. The economic significance of cotton is underscored by its extensive use in clothing, home furnishings, and industrial products. The domestication and improvement of cotton have been driven by the need for higher fiber yield, better quality, and resilience to environmental stresses (Zhang et al., 2015; Hu et al., 2019; Yang et al., 2020).

The genus Gossypium comprises over 50 species, including both diploid and allotetraploid species. The most widely cultivated species are Gossypium hirsutum (Upland cotton) and Gossypium barbadense (Pima or Egyptian cotton). G. hirsutum is known for its high yield and adaptability to diverse environments, while G. barbadense is prized for its superior fiber quality. The genetic diversity within Gossypium species provides a rich resource for studying polyploid evolution, domestication, and the genetic basis of important agronomic traits (Zhang et al., 2015; Hu et al., 2019; Ma et al., 2021).

Comparative genomics has emerged as a powerful tool in understanding the genetic and molecular mechanisms underlying important traits in crops. In cotton, advances in high-throughput sequencing and bioinformatics have enabled the assembly and annotation of complex genomes, revealing insights into fiber biogenesis, structural variations, and gene expression patterns. These genomic resources facilitate the identification of loci associated with desirable traits such as fiber quality, yield, and stress tolerance, thereby informing breeding strategies aimed at crop improvement (Fang et al., 2017; Yang et al., 2020; Ma et al., 2021; He et al., 2021).

This review aims to provide a comprehensive overview of the recent advancements in the comparative genomics of Gossypium species and their implications for cotton improvement. We will discuss the progress in genome sequencing, the identification of key genetic loci, and the application of genomic data in breeding programs. By synthesizing findings from multiple studies, we seek to highlight the potential of genomics-enabled approaches to enhance fiber yield, quality, and environmental resilience in cotton, ultimately contributing to the sustainability and productivity of this vital crop.

2 Current Status of Genomic Research on Gossypium Species

2.1 Progress in Genome Sequencing of Major Cultivated Species (Gossypium hirsutum, Gossypium barbadense) and Other Species

Significant advancements have been made in the genome sequencing of the major cultivated cotton species, Gossypium hirsutum and Gossypium barbadense. High-quality de novo-assembled genomes for these two species have been reported, proviinsights into their evolutionary history and domestication processes. These assemblies have improved the understanding of species-specific alterations in gene expression, structural variations, and expanded gene families, which are crucial for fiber quality and environmental resilience (Hu et al., 2019). Additionally, reference-grade genome assemblies for G. hirsutum and G. barbadense have been developed using advanced sequencing technologies, revealing extensive structural variations and identifying quantitative trait loci associated with superior fiber quality (Wang et al., 2018).

Other species, such as Gossypium herbaceum and Gossypium arboreum, have also been sequenced, contributing to the understanding of the A-genome evolution in cotton. The assembly of the G. herbaceum genome and improvements in the G. arboreum and G. hirsutum genomes have provided valuable insights into the phylogenetic relationships and origin history of cotton A-genomes (Huang et al., 2020). These genomic resources are essential for cotton genetic improvement and breeding programs.

2.2 Role of Polyploidy in the Cotton Genome

Polyploidy has played a significant role in the evolution and domestication of cotton. The allotetraploid nature of Gossypium species, resulting from polyploidization events, has conferred emergent properties such as higher fiber productivity and quality. The abrupt increase in ploidy levels approximately 60 million years ago and subsequent allopolyploidy events have led to the duplication of ancestral angiosperm genes, contributing to the genetic complexity of elite cottons like G. hirsutum and G. barbadense (Paterson et al., 2012). These polyploidization events have facilitated the recombination of alleles from different progenitor genomes, leading to phenotypic innovations and ecological adaptations.

The role of polyploidy in cotton is further highlighted by the presence of homoeologous gene pairs with biased expression patterns, suggesting abundant gene sub-functionalization. This sub-functionalization has been crucial for the development of superior fiber properties and stress tolerance in cotton (Yuan et al., 2015). The study of polyploidy in cotton provides opportunities to dissect the emergent properties of polyploids and their contributions to crop improvement.

2.3 Similarities and Differences in Genome Structure

The genome structures of Gossypium hirsutum and Gossypium barbadense exhibit both similarities and differences. Comparative genomics analyses have identified extensive structural variations between the two species, including large paracentric and pericentric inversions in several chromosomes. These structural variations likely occurred after polyploidization and have contributed to the divergence in fiber quality and environmental resilience between the two species (Wang et al., 2018). Additionally, the A and D subgenomes of G. hirsutum show asymmetric evolution, with more structural rearrangements, gene loss, and sequence divergence observed in the A subgenome compared to the D subgenome (Zhang et al., 2015).

Despite these differences, there are also significant similarities in the genome structures of G. hirsutum and G. barbadense. Both species share a common allotetraploid origin and exhibit similar patterns of gene expansion and contraction. The presence of homoeologous gene pairs with coordinated expression changes in both species suggests that polyploidization has played a crucial role in shaping their genome structures and functional properties (Yuan et al., 2015). These similarities and differences in genome structure provide valuable insights into the evolutionary history and domestication of cotton.

3 Genome Evolution

3.1 Genome duplication and expansion of gene families

Genome duplication has played a significant role in the evolution of Gossypium species. The complex allotetraploid nature of the cotton genome, particularly in species like Gossypium hirsutum, has resulted from multiple whole-genome duplications. These duplications have led to the presence of two subgenomes, A and D, which have evolved asymmetrically. The A subgenome has undergone more structural rearrangements, gene loss, and sequence divergence compared to the D subgenome, although no genome-wide expression dominance was observed between the subgenomes (Zhang et al., 2015). Additionally, the genome of Gossypium arboreum, a putative contributor to the A subgenome, has experienced two whole-genome duplications before its speciation, contributing to its current genomic complexity (Li et al., 2014).

The expansion of gene families in Gossypium species is also notable. For instance, the nucleotide-binding site (NBS)-encoding gene family has been identified as playing a key role in resistance to Verticillium dahliae, a significant pathogen in cotton. This expansion is indicative of the adaptive evolution of gene families in response to biotic stress, which is crucial for crop improvement (Li et al., 2014). Moreover, the comparative genomics of Gossypium and Arabidopsis has revealed that ancient and recent polyploidy events, followed by the loss of many duplicated gene copies, have shaped the genomic architecture of these species, further highlighting the importance of genome duplication in the evolution of Gossypium (Rong et al., 2005).

3.2 Evolution of Cis-regulatory elements and regulatory networks

The evolution of cis-regulatory elements and regulatory networks has been a driving force in the domestication and adaptation of Gossypium species. Comparative population genomics studies have shown that domestication has led to significant cis-regulatory divergence in upland cotton (Gossypium hirsutum). This divergence is evident in the asymmetric selection of subgenomes, where directional selection for long fibers has resulted in distinct regulatory changes between the A and D subgenomes (Wang et al., 2017). The identification of DNase I–hypersensitive sites and 3D genome architecture analyses have provided insights into how domestication has influenced gene organization and regulation, linking functional variants to gene transcription (Wang et al., 2017).

Transposable elements (TEs) have also contributed to the evolution of cis-regulatory elements in Gossypium species. TEs can act as enhancers, promoters, silencers, and boundary elements, thereby influencing gene regulation. The amplification of TEs has been associated with changes in chromatin status and the formation of lineage-specific topologically associating domain (TAD) boundaries. This TE-mediated genome expansion has played a role in the evolution of higher-order chromatin structure in cotton, highlighting the dynamic nature of regulatory networks in response to genomic changes (Sundaram and Wysocka, 2020; Wang et al., 2021).

3.3 Role of repetitive sequences and transposons in genome size and evolution

Repetitive sequences and transposons have been major contributors to genome size variation and evolution in Gossypium species. The differential amplification of transposable elements (TEs) among different Gossypium lineages has led to significant genome size differences. For example, Copia-like retrotransposable elements have accumulated in Gossypium raimondii, which has the smallest genome, while gypsy-like sequences have proliferated in lineages with larger genomes. This lineage-specific expansion of TEs has been a key factor in the threefold increase in genome size observed in Gossypium species over the past 5-10 million years (Hawkins et al., 2006).

The role of TEs in genome evolution extends beyond genome size expansion. TEs have been implicated in the formation of new cis-regulatory elements, thereby influencing gene expression and regulatory networks. The recent amplification of TEs has been associated with the establishment of new TAD boundaries, which are crucial for the 3D genomic architecture. This TE-mediated reorganization of the genome has contributed to the evolution of higher-order chromatin structure and gene regulation in cotton (Wang et al., 2021). Additionally, the presence of long-terminal-repeat (LTR) bursts in the A-genome of Gossypium species has been linked to genome size expansion, speciation, and the evolution of important traits such as fiber quality (Figure 1) (Huang et al., 2020).

4 Genome Divergence and Interspecies Hybridization

4.1 Genomic divergence between cultivated cotton and wild species

The genomic divergence between cultivated cotton species, such as Gossypium hirsutum and Gossypium barbadense, and their wild relatives has been a focal point of research due to its implications for crop improvement. High-quality de novo-assembled genomes of these two cultivated allotetraploid species have revealed significant species-specific alterations in gene expression, structural variations, and expanded gene families that have driven their speciation and evolutionary history. These genomic differences are crucial for understanding the domestication and adaptation processes that have enabled G. hirsutum to produce higher fiber yields and better resilience to environmental stresses compared to G. barbadense, which is known for its superior fiber quality (Wang et al., 2018; Hu et al., 2019).

Comparative genomics analyses have identified extensive structural variations, including large paracentric and pericentric inversions in multiple chromosomes, which likely occurred after polyploidization. These structural changes have contributed to the distinct phenotypic traits observed in the two species. The introgression of favorable chromosome segments from G. barbadense into G. hirsutum has been used to identify quantitative trait loci (QTL) associated with superior fiber quality, further highlighting the importance of genomic divergence in breeding programs aimed at improving cotton fiber characteristics(Wang et al., 2018).

4.2 Genetic and genomic studies on interspecies hybridization

Interspecific hybridization between Gossypium species has played a significant role in the evolution and domestication of cotton. The hybridization of G. hirsutum with other polyploid species, such as G. barbadense, has led to the development of multiple genetic lines with improved traits. However, reproductive barriers such as reduced fertility, segregation distortion, and hybrid breakdown are common in later-generation hybrids, complicating the introgression of new allelic variations. Recent molecular genetics research has provided insights into the location and effects of QTLs from wild species that are associated with important traits for cotton production, offering tools for plant breeders to access novel genes for upland cotton improvement (Table 1) (Anwar et al., 2022).

Genome-wide population analyses have revealed that interspecific introgression from G. hirsutum has significantly reorganized the genomic architecture of G. barbadense, contributing to population divergence and increased genetic diversity. Introgression events have been identified that are associated with agronomic trait variation, such as fiber quality and adaptation to high-latitude environments. These findings underscore the potential of interspecific hybridization to drive genetic diversity and trait improvement in cotton breeding programs (Wang et al., 2022).

4.3 Applications of hybrid breeding in cotton improvement

Hybrid breeding has been instrumental in achieving higher yields and better quality in cotton crops. The development of Chromosome Segment Substitution Lines (CSSLs) from G. barbadense in a G. hirsutum background has provided valuable materials for breeding purposes. These CSSLs have been used to study the molecular mechanisms of fiber development and the potential contributions of chromosome substitution segments from G. barbadense to fiber quality improvement in upland cotton. Transcriptome analyses have identified differentially expressed genes involved in cell wall organization and oxidative stress response, which are crucial for fiber development and quality formation (Li et al., 2017).

The breeding potential of introgression lines (ILs) developed from interspecific crossing between G. hirsutum and G. barbadense has been evaluated through diallel analysis. High mid-parent heterosis has been detected in several hybrids, which out-yielded the high-yielding parent cultivars. General combining ability (GCA) variance was found to be predominant for all traits, indicating the potential of ILs as good general combiners for yield and fiber quality improvement. These findings provide useful information for the further utilization of ILs in cotton breeding programs aimed at enhancing both yield and fiber quality (Zhang et al., 2016).

5 Comparative Genomics Technologies and Methods

5.1 Key tools and algorithms for comparative genomic analysis

Comparative genomics involves the use of various computational tools and algorithms to analyze and compare the genomes of different species. One of the primary tools used in this field is the VISTA suite, which includes multiple tools designed to align long genomic sequences and visualize these alignments with associated functional annotations. The VISTA Browser, for instance, allows users to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms, facilitating detailed comparative analysis (Frazer et al., 2004). Another significant tool is CrimeStatII, which has been used to infer gene order in Gossypium species, providing insights into the consequences of ancient large-scale duplications in cotton (Rong et al., 2005).

Additionally, the use of high-throughput genotyping arrays, such as the CottonSNP63K, has revolutionized comparative genomics in cotton. This array contains assays for thousands of single nucleotide polymorphism (SNP) markers, enabling high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. The CottonSNP63K array has been validated with numerous samples, generating cluster positions to facilitate automated analysis of polymorphic markers, thus providing a standardized resource for the global cotton research community (Hulse-Kemp et al., 2015).

5.2 Application of new technologies (e.g., single-cell sequencing, gene editing)

The advent of new technologies such as single-cell sequencing and gene editing has significantly advanced the field of comparative genomics. Single-cell sequencing allows for the analysis of genomic information at the resolution of individual cells, providing unprecedented insights into cellular heterogeneity and the genetic basis of complex traits. This technology has the potential to uncover the genetic diversity within Gossypium species at a much finer scale, aiding in the identification of key genes involved in fiber quality and yield (Yang et al., 2020).

Gene editing technologies, particularly CRISPR-Cas9, have opened new avenues for functional genomics and crop improvement. By enabling precise modifications of specific genomic regions, gene editing can be used to validate the function of candidate genes identified through comparative genomics. For instance, the improved genome assemblies of Gossypium hirsutum and Gossypium barbadense have facilitated the identification of quantitative trait loci (QTL) associated with superior fiber quality. These QTLs can be targeted using gene editing to develop cotton varieties with enhanced traits, thereby accelerating breeding programs (Wang et al., 2018).

6 Genomic Basis of Stress Resistance Traits in Cotton

6.1 Discovery and functional validation of disease resistance genes

The identification and functional validation of disease resistance genes in cotton have been significantly advanced through genomic studies. For instance, a comprehensive meta-QTL analysis has identified numerous QTLs associated with disease resistance, fiber quality, and yield traits in tetraploid cotton. This study mapped 1,223 QTLs from 42 different studies, revealing clusters and hotspots of QTLs that are crucial for marker-assisted breeding programs aimed at improving disease resistance in cotton (Said et al., 2013). Additionally, the role of ethylene in plant stress resistance has been highlighted through the identification of 1-aminocyclopropane-1-carboxylic acid synthase (ACS) genes in Gossypium species. These genes, particularly GhACS10 and GhACS12, show differential expression in response to various abiotic stresses, indicating their potential roles in enhancing disease resistance (Li et al., 2022).

Functional validation of these genes has been achieved through various molecular techniques. For example, the transient expression of Gh_D12G2017-GFP fusion protein in protoplasts demonstrated the nuclear localization of the CDKF4 gene, which is strongly induced by drought and salt stresses. Transgenic Arabidopsis lines expressing this gene exhibited higher levels of antioxidant enzymes and improved tolerance to drought and salt stress, underscoring the gene's role in stress resistance (Magwanga et al., 2018). These findings provide a robust foundation for the development of disease-resistant cotton cultivars through genetic engineering and marker-assisted selection.

6.2 Genomic mechanisms of resistance to abiotic stresses such as drought and salinity

Abiotic stress tolerance in cotton, particularly to drought and salinity, is governed by complex genetic networks. Transcriptome meta-analysis has identified key regulatory hub genes such as NSP2, DRE1D, ERF61, CDF1, and TLP3 that are associated with drought stress, and TLP1, TLP, ERF109, ELF4, and ATHB7 that are linked to salt stress. These genes play significant roles in nodulation signaling, ethylene response, and dehydration response, providing potential targets for enhancing stress tolerance in cotton (Bano et al., 2022). Similarly, genome-wide association studies (GWAS) have identified quantitative trait nucleotides (QTNs) associated with drought tolerance. Notably, genes such as RD2, HAT22, PIP2, and PP2C have been proposed as key players in drought tolerance, offering valuable markers for breeding programs (Hou et al., 2018).

Further insights into the genomic mechanisms of abiotic stress resistance have been provided by the identification of gene families involved in stress responses. For example, the trehalose-6-phosphate phosphatase (TPP) gene family has been shown to play a crucial role in drought tolerance. Virus-induced gene silencing (VIGS) of GhTPP22 resulted in increased sensitivity to drought stress, highlighting its importance in stress resistance (Wang et al., 2022). Additionally, the glycerol-3-phosphate dehydrogenase (GPDH) gene family has been implicated in drought stress response, with GhGPDH5 playing a positive role in enhancing drought tolerance through mechanisms such as stomatal closure (Sun et al., 2022).

6.3 Breeding for stress tolerance using genomic information

Breeding for stress tolerance in cotton has been significantly enhanced by leveraging genomic information. The integration of QTL mapping and GWAS has facilitated the identification of key genetic loci associated with stress tolerance traits. For instance, a meta-QTL analysis has identified clusters and hotspots of QTLs that are consistent across different environments and populations, providing valuable markers for breeding programs aimed at improving stress tolerance (Said et al., 2013). Similarly, GWAS has identified SNP markers closely related to salt tolerance traits, offering a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties (Zheng et al., 2021).

The application of genomic information in breeding programs has also been demonstrated through the functional validation of stress-responsive genes. For example, the overexpression of CDKF4 in transgenic Arabidopsis lines has resulted in enhanced tolerance to drought and salt stress, providing a proof-of-concept for the use of genetic engineering in developing stress-tolerant cotton cultivars (Magwanga et al., 2018). Additionally, the identification and expression analysis of the NPF gene family have provided insights into the role of these genes in abiotic stress resistance, further informing breeding strategies (Liu et al., 2023). These advancements underscore the potential of genomic information to accelerate the development of cotton cultivars with improved stress tolerance, thereby enhancing crop productivity and resilience.

7 Genomic Studies on Yield and Quality-Related Traits

7.1 Key genes affecting fiber quality and their regulatory networks

Recent genomic studies have identified several key genes and regulatory networks that significantly impact fiber quality in Gossypium species. For instance, a comprehensive genome-wide association study (GWAS) conducted on 719 diverse accessions of upland cotton identified 46 significant single nucleotide polymorphisms (SNPs) associated with five fiber quality traits. These SNPs were linked to 612 unique candidate genes involved in polysaccharide biosynthesis, signal transduction, and protein translocation, which are crucial for fiber development (Sun et al., 2017). Additionally, another study highlighted the importance of structural variations in the D-subgenome, which were found to be associated with fiber quality traits such as fiber length and strength (Ma et al., 2021).

Moreover, the integration of quantitative trait loci (QTL) mapping and multi-omics approaches, including RNA sequencing, has facilitated the identification of differentially expressed genes that contribute to fiber quality. This approach has enabled the validation of candidate genes and the application of marker-assisted selection (MAS) in breeding programs aimed at improving fiber quality (Ijaz et al., 2019). These findings underscore the complexity of fiber quality traits and the necessity of employing advanced genomic tools to dissect their genetic basis.

7.2 Genetic basis of high yield traits

The genetic basis of high yield traits in Gossypium species has been extensively studied through various genomic approaches. A genome-wide association study (GWAS) on Indian upland cotton identified 205 SNPs and 134 QTLs significantly associated with six fiber yield-related traits. These QTLs were enriched for genes involved in plant cell wall synthesis, nutrient metabolism, and vegetative growth, highlighting the multifaceted genetic architecture underlying yield traits (Joshi et al., 2023; Wu, 2024). Similarly, another study on upland cotton revealed that structural variations in the A-subgenome were predominantly associated with yield traits, suggesting that this subgenome undergoes stronger selection during species formation and variety development (Ma et al., 2021).

Furthermore, the resequencing of a core collection of upland cotton accessions identified approximately 3.66 million SNPs and conducted a GWAS for 13 fiber-related traits across 12 environments. This study found that more associated loci were detected for fiber quality than for fiber yield, indicating that fiber yield traits may have a more complex genetic basis (Ma et al., 2018). These insights provide valuable targets for molecular selection and genetic manipulation aimed at enhancing yield traits in cotton breeding programs.

7.3 Strategies for yield improvement based on genomic selection

Genomic selection (GS) has emerged as a promising strategy for yield improvement in Gossypium species. By leveraging high-throughput sequencing and bioinformatics tools, researchers can now predict the genetic potential of breeding lines more accurately. For instance, the development of high-density linkage maps and QTL fine mapping has enabled the precise identification of loci associated with yield traits, facilitating the application of marker-assisted selection (MAS) in breeding programs (Ijaz et al., 2019; Ding, 2024). Additionally, the integration of GWAS and transcriptome analysis has identified key candidate genes and regulatory networks that can be targeted for yield improvement (Sun et al., 2017).

One innovative approach involves the introgression of favorable alleles from wild or less domesticated species into cultivated varieties. A study on Gossypium arboreum, the putative progenitor of the At-subgenome of Gossypium hirsutum, demonstrated the potential of this species in improving yield traits through the development of chromosome segment introgression lines (ILs). This approach revealed several QTLs with positive additive effects on yield traits, indicating that G. arboreum harbors valuable genetic resources for enhancing yield in G. hirsutum (Feng et al., 2021). These strategies underscore the importance of utilizing diverse genetic resources and advanced genomic tools to achieve sustainable yield improvement in cotton.

8 Application of Bioinformatics and Data Integration in Cotton Genomics

8.1 Integration and analysis of large-scale genomic data

The integration and analysis of large-scale genomic data have revolutionized cotton genomics, enabling researchers to overcome the challenges posed by the complex and large genome of Gossypium species. Advances in high-throughput sequencing technologies and bioinformatics tools have facilitated the generation and assembly of high-quality genome sequences for various cotton species, including Gossypium hirsutum and Gossypium barbadense. These efforts have led to significant improvements in the contiguity and completeness of genome assemblies, particularly in regions with high repeat content such as centromeres (Wang et al., 2018; Ma et al., 2021). Comparative genomics analyses have further identified extensive structural variations and quantitative trait loci (QTL) associated with important agronomic traits, providing valuable insights into the genomic basis of fiber quality and environmental resilience (Wang et al., 2018; Ma et al., 2021).

Moreover, large-scale genomic surveys of cotton germplasm have elucidated the genetic architecture underlying favorable traits and geographic differentiation in cultivated cotton. For instance, the analysis of 3 248 tetraploid cotton genomes revealed critical genomic signatures generated by historical breeding effects and identified new fiber quality-related loci through introgression and association analyses He et al., 2021). These findings underscore the importance of integrating large-scale genomic data to enhance our understanding of cotton evolution, domestication, and trait improvement, ultimately informing precision breeding strategies for crop improvement (Yang et al., 2020; He et al., 2021).

8.2 Development and use of databases and resource platforms

The development of comprehensive databases and resource platforms has been instrumental in managing and utilizing the vast amount of genomic data generated in cotton research. One notable example is the Gossypium Resource And Network Database (GRAND), which integrates multiple cotton genome sequences, annotations, variations, and transcriptomes. GRAND provides a suite of tools for data exploration and mining, including flexible search systems, BLAST and BLAT suites, co-expressed gene networks, and primer design tools (Zhang et al., 2022). Such platforms enable researchers to efficiently access and analyze genomic data, accelerating the discovery of genes and molecular markers associated with desirable traits.

Additionally, the NBRI-Comprehensive Cotton Genomics database offers access to a wealth of cotton-related genomic resources, including gene models, transcription factors, promoter sequences, and molecular markers. This database supports the large-scale development of genomic resources through genic-enriched sequencing, facilitating the identification of novel simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) (Rai et al., 2015). These databases and resource platforms play a crucial role in advancing cotton genomics research by providing the necessary infrastructure for data integration, analysis, and dissemination (Rai et al., 2015; Zhang et al., 2022).

8.3 Data-driven precision breeding platforms

Data-driven precision breeding platforms leverage genomic data to enhance the efficiency and accuracy of breeding programs. High-throughput genotyping arrays, such as the CottonSNP63K, have been developed to provide standardized resources for genetic mapping, genome-wide association studies (GWAS), and genomic selection (GS). The CottonSNP63K array, for instance, contains assays for thousands of SNP markers, facilitating the construction of high-density genetic maps and the dissection of complex traits (Hulse-Kemp et al., 2015). These platforms enable breeders to identify and select for favorable alleles with greater precision, thereby accelerating the development of improved cotton varieties.

Furthermore, the integration of genomic data with advanced breeding techniques has led to the creation of introgression lines that combine favorable traits from different cotton species. For example, introgression lines developed by integrating genomic data from G. barbadense into G. hirsutum have been used to identify QTL associated with superior fiber quality (Wang et al., 2018). Such precision breeding platforms harness the power of genomic data to inform breeding decisions, ultimately contributing to the development of cotton varieties with enhanced yield, quality, and resilience (Hulse-Kemp et al., 2015; Wang et al., 2018).

9 Prospects of Genomics in Crop Improvement

9.1 Potential of genome editing

The advent of CRISPR/Cas genome editing has revolutionized the field of crop improvement by enabling precise and efficient modifications of plant genomes. This technology allows for targeted gene editing, which can lead to the development of crops with desirable traits such as increased yield, improved nutritional content, and enhanced resistance to diseases and environmental stresses. For instance, CRISPR/Cas9 has been successfully used to improve crop quality by modulating traits like appearance, palatability, and nutritional components (Liu et al., 2018). Additionally, the versatility of CRISPR/Cas systems, including base editors and prime editors, has expanded the scope of genome editing, allowing for precise single-nucleotide changes without the need for double-strand breaks (Li et al., 2023).

Moreover, CRISPR/Cas technology has facilitated the development of non-genetically modified (Non-GMO) crops by enabling precise modifications without the introduction of foreign DNA. This has significant implications for regulatory approval and public acceptance of genome-edited crops. The ability to fine-tune gene regulation and develop high-throughput mutant libraries further underscores the potential of CRISPR/Cas systems in accelerating crop breeding and improving agricultural productivity (Jaganathan et al., 2018; Chen et al., 2019). The ongoing advancements in delivery systems and editing specificity are expected to enhance the efficiency and applicability of genome editing in crop improvement (Ahmar et al., 2021).

9.2 Future developments in precision breeding based on genomic data

Precision breeding, leveraging genomic data, represents the future of crop improvement. The integration of high-throughput sequencing technologies and advanced bioinformatics tools has enabled the identification of key genetic loci associated with desirable traits. This genomic information can be used to design precise breeding strategies that target specific genes or genomic regions. For example, the use of CRISPR/Cas9 in precision breeding has shown promise in developing crops with enhanced resistance to biotic and abiotic stresses, improved yield, and better quality traits (Nerkar et al., 2021).

The development of high-throughput gene editing pipelines, such as those being optimized at Texas A&M AgriLife Research, exemplifies the potential of precision breeding. These pipelines enable rapid testing and validation of candidate genes, facilitating the development of nutritious, high-yielding, and stress-tolerant crops (Thomson, 2019). Furthermore, the integration of genomic data from various sources, including genome-wide association studies (GWAS) and transcriptomics, can help predict the most beneficial target modifications for crop improvement. This holistic approach to precision breeding is expected to accelerate the development of climate-resilient and high-performing crop varieties (Nascimento et al., 2023).

9.3 Prospects for the application of comparative genomics in other economic crops

Comparative genomics, which involves the analysis of genomic similarities and differences between species, holds significant promise for the improvement of various economic crops. By comparing the genomes of closely related species, researchers can identify conserved and divergent genetic elements that contribute to important agronomic traits. This information can be used to transfer beneficial traits from one species to another through targeted breeding or genome editing. For instance, the insights gained from comparative genomics studies in model plants like Arabidopsis thaliana can be applied to improve crop species such as rice and tomato (Nascimento et al., 2023).

The application of comparative genomics extends beyond traditional crop species to include other economically important plants. For example, the knowledge gained from the comparative genomics of Gossypium species can be leveraged to enhance the quality and yield of cotton. Similarly, comparative genomics can be used to improve the resilience and productivity of other staple crops, thereby contributing to global food security. The integration of comparative genomics with advanced genome editing tools like CRISPR/Cas9 is expected to further enhance the precision and efficiency of crop improvement efforts (Zhang et al., 2017).

10 Concluding Remarks

Comparative genomics has significantly advanced our understanding of the genetic and molecular bases of cotton species, leading to substantial improvements in cotton breeding programs. High-quality genome assemblies and whole-genome comparative analyses have elucidated the evolutionary history and domestication processes of Gossypium species, providing critical insights into fiber quality and environmental resilience. The identification of structural variations and gene families specific to different cotton species has enabled breeders to target specific traits for improvement, such as fiber yield and stress tolerance. Additionally, the development of genotype-independent transformation systems has accelerated the generation of transgenic and gene-edited cotton plants, overcoming previous bottlenecks in cotton genetic transformation.

Despite the progress made, several challenges and research directions remain. One major challenge is the complexity of the cotton genome, which includes large-scale structural variations and repetitive DNA sequences that complicate genomic analyses. Future research should focus on refining genome assemblies and improving the accuracy of gene annotations to better understand the functional roles of these genomic elements. Additionally, there is a need for more comprehensive studies on the genetic basis of agronomic traits, particularly those related to fiber quality and yield, to facilitate the development of superior cotton varieties. Integrating multi-omics approaches, such as transcriptomics, proteomics, and metabolomics, with comparative genomics will provide a more holistic understanding of cotton biology and its response to environmental stresses.

The application of genomics in cotton production holds great promise for enhancing global cotton yields and quality. Genomic tools and resources, such as high-quality reference genomes and genome-wide association studies, have already identified key genetic loci and candidate genes associated with important traits. These findings can be leveraged to develop marker-assisted selection strategies and genomic selection models, enabling more efficient and targeted breeding programs. Furthermore, the integration of genomic data with advanced breeding techniques, such as CRISPR/Cas9-mediated genome editing, offers the potential to create cotton varieties with enhanced fiber quality, disease resistance, and environmental adaptability. As genomic technologies continue to evolve, their application in cotton breeding will play a crucial role in meeting the growing demand for high-quality cotton fiber in the textile industry worldwide.

Acknowledgments

Thank you to the anonymous peer review for providing targeted revision suggestions for the manuscript.

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.

References

Ahmar S., Saeed S., Khan M., Khan S., Mora-Poblete F., Kamran M., Faheem A., Maqsood A., Rauf M., Saleem S., Hong W., and Jung K., 2020, A revolution toward gene-editing technology and its application to crop improvement, International Journal of Molecular Sciences, 21(16): 5665.

https://doi.org/10.3390/ijms21165665

Anwar M., Iqbal M., Abro A., Memon S., Bhutto L., Memon S., and Peng Y., 2022, Inter-specific hybridization in cotton (Gossypium hirsutum) for crop improvement, Agronomy, 12(12): 3158.

https://doi.org/10.3390/agronomy12123158

Bano N., Fakhrah S., Mohanty C., and Bag S., 2022, Transcriptome meta-analysis associated targeting hub genes and pathways of drought and salt stress responses in cotton (Gossypium hirsutum): a network biology approach, Frontiers in Plant Science, 13: 818472.

https://doi.org/10.3389/fpls.2022.818472

Chen K., Wang Y., Zhang R., Zhang H., and Gao C., 2019, CRISPR/Cas genome editing and precision plant breeding in agriculture, Annual Review of Plant Biology, 70(1): 667-697.

https://doi.org/10.1146/annurev-arplant-050718-100049

Ding D.Y., 2024 The role of gwas in cotton fiber quality improvement Cotton Genomics and Genetics 15(1): 9-19

Fang L., Wang Q., Hu Y., Jia Y., Chen J., Liu B., Zhang Z., Guan X., Chen S., Zhou B., Mei G., Sun J., Pan Z., He S., Xiao S., Shi W., Gong W., Liu J., Ma J., Cai C., Zhu X., Guo W., Du X., and Zhang T., 2017, Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits, Nature Genetics, 49(7): 1089-1098.

https://doi.org/10.1038/ng.3887

Feng L., Chen Y., Xu M., Yang Y., Yue H., Su Q., Zhou C., Feng G., Ai N., Wang N., and Zhou B., 2021, Genome-wide introgression and quantitative trait locus mapping reveals the potential of asian cotton (Gossypium arboreum) in improving upland cotton (Gossypium hirsutum), Frontiers in Plant Science, 12: 719371.

https://doi.org/10.3389/fpls.2021.719371

Frazer K., Pachter L., Poliakov A., Rubin E., and Dubchak I., 2004, VISTA: computational tools for comparative genomics, Nucleic acids research, 32(suppl_2): W273-W279.

https://doi.org/10.1093/NAR/GKH458

Hawkins J., Kim H., Nason J., Wing R., and Wendel J., 2006, Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium, Genome Research, 16(10): 1252-61.

https://doi.org/10.1101/GR.5282906

He S., Sun G., Geng X., Gong W., Dai P., Jia Y., Shi W., Pan Z., Wang J., Wang L., Xiao S., Chen B., Cui S., You C., Xie Z., Wang F., Sun J., Fu G., Peng Z., Hu D., Wang L., Pang B., and Du X., 2021, The genomic basis of geographic differentiation and fiber improvement in cultivated cotton, Nature Genetics, 53: 916-924.

https://doi.org/10.1038/s41588-021-00844-9

Hou S., Zhu G., Li Y., Li W., Fu J., Niu E., Li L., Zhang D., and Guo W., 2018, Genome-wide association studies reveal genetic variation and candidate genes of drought stress related traits in cotton (Gossypium hirsutum L.), Frontiers in Plant Science, 9: 1276.

https://doi.org/10.3389/fpls.2018.01276

Hu Y., Chen J., Fang L., Zhang Z., Ma W., Niu Y., Ju L., Deng J., Zhao T., Lian J., Baruch K., Fang D., Liu X., Ruan Y., Rahman M., Han J., Wang K., Wang Q., Wu H., Mei G., Zang Y., Han Z., Xu C., Shen W., Yang D., Si Z., Dai F., Zou L., Huang F., Bai Y., Zhang Y., Brodt A., Ben-Hamo H., Zhu X., Zhou B., Guan X., Zhu S., Chen X., and Zhang T., 2019, Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton, Nature Genetics, 51: 739-748.

https://doi.org/10.1038/s41588-019-0371-5

Huang G., Wu Z., Percy R., Bai M., Li Y., Frelichowski J., Hu J., Wang K., Yu J., and Zhu Y., 2020, Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution, Nature Genetics, 52: 516-524.

https://doi.org/10.1038/s41588-020-0607-4

Hulse-Kemp A., Lemm J., Plieske J., Ashrafi H., Buyyarapu R., Fang D., Frelichowski J., Giband M., Hague S., Hinze L., Kochan K., Riggs P., Scheffler J., Udall J., Ulloa M., Wang S., Zhu Q., Bag S., Bhardwaj A., Burke J., Byers R., Claverie M., Gore M., Harker D., Islam M., Jenkins J., Jones D., Lacape J., Llewellyn D., Percy R., Pepper A., Poland J., Rai K., Sawant S., Singh S., Spriggs A., Taylor J., Wang F., Yourstone S., Zheng X., Lawley C., Ganal M., Deynze A., Wilson I., and Stelly D., (2015)., Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp, G3: Genes Genomes Genetics, 5: 1187-1209.

https://doi.org/10.1534/g3.115.018416

Ijaz B., Zhao N., Kong J., and Hua J., 2019, Fiber quality improvement in upland cotton (Gossypium hirsutum L.): quantitative trait loci mapping and marker assisted selection application, Frontiers in Plant Science, 10: 1585.

https://doi.org/10.3389/fpls.2019.01585

Jaganathan D., Ramasamy K., Sellamuthu G., Jayabalan S., and Venkataraman G., 2018, CRISPR for crop improvement: an update review, Frontiers in Plant Science, 9: 985.

https://doi.org/10.3389/fpls.2018.00985

Joshi B., Singh S., Tiwari G., Kumar H., Boopathi N., Jaiswal S., Adhikari D., Kumar D., Sawant S., Iquebal M., and Jena S., 2023, Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.), Frontiers in Plant Science, 14.,

https://doi.org/10.3389/fpls.2023.1252746

Li F., Fan G., Wang K., Sun F., Yuan Y., Song G., Li Q., Ma Z., Lu C., Zou C., Chen W., Liang X., Shang H., Liu W., Shi C., Xiao G., Gou C., Ye W., Xu X., Zhang X., Wei H., Li Z., Zhang G., Wang J., Liu K., Kohel R., Percy R., Yu J., Zhu Y., Wang J., and Yu S., 2014, Genome sequence of the cultivated cotton Gossypium arboreum, Nature Genetics, 46: 567-572.

https://doi.org/10.1038/ng.2987

Li J., Zou X., Chen G., Meng Y., Ma Q., Chen Q., Wang Z., and Li F., 2022, Potential Roles of 1-Aminocyclopropane-1-carboxylic Acid Synthase Genes in the Response of Gossypium Species to Abiotic Stress by Genome-Wide Identification and Expression Analysis, Plants, 11(11): 1524.

https://doi.org/10.3390/plants11111524

Li P., Wang M., Lu Q., Ge Q., Rashid M., Liu A., Gōng J., Shang H., Gǒng W., Li J., Song W., Guo L., Su W., Li S., Guo X., Shi Y., and Yuan Y., 2017, Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and chromosome segment substitution lines from G. hirsutum×G. barbadense, BMC Genomics, 18: 1-17.

https://doi.org/10.1186/s12864-017-4077-8

Li Y., Liang J., Deng B., Jiang Y., Zhu J., Chen L., Li M., and Li J., 2023, Applications and prospects of CRISPR/Cas9-mediated base editing in plant breeding, Current Issues in Molecular Biology, 45: 918-935.

https://doi.org/10.3390/cimb45020059

Liu J., Wang C., Peng J., Ju J., Li Y., Li C., and Su J., 2023, Genome-wide investigation and expression profiles of the NPF gene family provide insight into the abiotic stress resistance of Gossypium hirsutum, Frontiers in Plant Science, 14: 1103340.

https://doi.org/10.3389/fpls.2023.1103340

Liu Q., Yang F., Zhang J., Liu H., Rahman S., Islam S., Ma W., and She M., 2021, Application of CRISPR/Cas9 in crop quality improvement, International Journal of Molecular Sciences, 22(8): 4206.

https://doi.org/10.3390/ijms22084206

Ma Z., He S., Wang X., Sun J., Zhang Y., Zhang G., Wu L., Li Z., Liu Z., Sun G., Yan Y., Jia Y., Yang J., Pan Z., Gu Q., Li X., Sun Z., Dai P., Liu Z., Gong W., Wu J., Wang M., Liu H., Feng K., Ke H., Wang J., Lan H., Wang G., Peng J., Wang N., Wang L., Pang B., Peng Z., Li R., Tian S., and Du X., 2018, Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield, Nature Genetics, 50: 803-813.

https://doi.org/10.1038/s41588-018-0119-7

Ma Z., Zhang Y., Wu L., Zhang G., Sun Z., Li Z., Jiang Y., Ke H., Chen B., Liu Z., Gu Q., Wang Z., Wang G., Yang J., Wu J., Yan Y., Meng C., Li L., Li X., Mo S., Wu N., Ma L., Chen L., Zhang M., Si A., Yang Z., Wang N., Wu L., Zhang D., Cui Y., Cui J., Lv X., Li Y., Shi R., Duan Y., Tian S., and Wang X., 2021, High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement, Nature Genetics, 53: 1385-1391.

https://doi.org/10.1038/s41588-021-00910-2

Magwanga R., Lu P., Kirungu J., Cai X., Zhou Z., Wang X., Diouf L., Xu Y., Hou Y., Hu Y., Dong Q., Wang K., and Liu F., 2018, Whole genome analysis of Cyclin dependent kinase (CDK) gene family in cotton and functional evaluation of the role of CDKF4 gene in drought and salt stress tolerance in plants, International Journal of Molecular Sciences, 19(9): 2625.

https://doi.org/10.3390/ijms19092625

Nascimento F., Rocha A., Soares J., Mascarenhas M., Ferreira M., Lino L., Ramos A., Diniz L., Mendes T., Ferreira C., Santos-Serejo J., and Amorim E., 2023, Gene editing for plant resistance to abiotic factors: a systematic review, Plants, 12(2): 305.

https://doi.org/10.3390/plants12020305

Nerkar G., Devarumath S., Purankar M., Kumar A., Valarmathi R., Devarumath R., and Appunu C., 2022, Advances in crop breeding through precision genome editing, Frontiers in Genetics, 13: 880195.

https://doi.org/10.3389/fgene.2022.880195

Paterson A., Wendel J., Gundlach H., Guo H., Jenkins J., Jin D., Llewellyn D., Showmaker K., Shu S., Udall J., Yoo M., Byers R., Chen W., Doron-Faigenboim A., Duke M., Gong L., Grimwood J., Grover C., Grupp K., Hu G., Lee T., Li J., Lin L., Liu T., Marler B., Page J., Roberts A., Romanel E., Sanders W., Szadkowski E., Tan X., Tang H., Xu C., Wang J., Wang Z., Zhang D., Zhang L., Ashrafi H., Bedon F., Bowers J., Brubaker C., Chee P., Das S., Gingle A., Haigler C., Harker D., Hoffmann L., Hovav R., Jones D., Lemke C., Mansoor S., Rahman M., Rainville L., Rambani A., Reddy U., Rong J., Saranga Y., Scheffler B., Scheffler J., Stelly D., Triplett B., Deynze A., Vaslin M., Waghmare V., Walford S., Wright R., Zaki E., Zhang T., Dennis E., Mayer K., Peterson D., Rokhsar D., Wang X., and Schmutz J., 2012, Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres, Nature, 492: 423-427.

https://doi.org/10.1038/nature11798

Rai K., Singh S., Bhardwaj A., Kumar V., Lakhwani D., Srivastava A., Jena S., Yadav H., Bag S., and Sawant S., 2013, Large-scale resource development in Gossypium hirsutum L., by 454 sequencing of genic-enriched libraries from six diverse genotypes, Plant Biotechnology Journal, 11(8): 953-63.

https://doi.org/10.1111/pbi.12088

Rong J., Bowers J., Schulze S., Waghmare V., Rogers C., Pierce G., Zhang H., Estill J., and Paterson A., 2005, Comparative genomics of Gossypium and Arabidopsis: unraveling the consequences of both ancient and recent polyploidy, Genome research 15(9): 1198-210.

https://doi.org/10.1101/GR.3907305

Said J., Lin Z., Zhang X., Song M., and Zhang J., 2013, A comprehensive meta QTL analysis for fiber quality yield yield related and morphological traits drought tolerance and disease resistance in tetraploid cotton, BMC Genomics, 14: 776-776.

https://doi.org/10.1186/1471-2164-14-776

Sun J., Cui H., Wu B., Wang W., Yang Q., Zhang Y., Yang S., Zhao Y., Xu D., Liu G., and Qin T., 2022, Genome-wide identification of cotton (Gossypium spp.) Glycerol-3-Phosphate Dehydrogenase (GPDH) family members and the role of GhGPDH5 in response to drought stress, Plants, 11(5): 592.

https://doi.org/10.3390/plants11050592

Sun Z., Wang X., Liu Z., Gu Q., Zhang Y., Li Z., Ke H., Yang J., Wu J., Wu L., Zhang G., Zhang C., and Ma Z., 2017, Genome‐wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L., Plant Biotechnology Journal, 15: 982-996.

https://doi.org/10.1111/pbi.12693

Sundaram V., and Wysocka J., 2020, Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes, Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1795): 20190347.

https://doi.org/10.1098/rstb.2019.0347

Thomson M., 2019, 230 genome editing applications in plants: high-throughput CRISPR/Cas editing for crop improvement, Journal of Animal Science, 97: 56-56.

https://doi.org/10.1093/jas/skz258.115

Wang M., Li J., Wang P., Liu F., Liu Z., Zhao G., Xu Z., Pei L., Grover C., Wendel J., Wang K., and Zhang X., 2021, Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton, Molecular Biology and Evolution, 38: 3621-3636.

https://doi.org/10.1093/molbev/msab128

Wang M., Tu L., Lin M., Lin Z., Wang P., Yang Q., Ye Z., Shen C., Li J., Zhang L., Zhou X., Nie X., Li Z., Guo K., Ma Y., Huang C., Jin S., Zhu L., Yang X., Min L., Yuan D., Zhang Q., Lindsey K., and Zhang X., 2017, Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication, Nature Genetics, 49: 579-587.

https://doi.org/10.1038/ng.3807

Wang M., Tu L., Yuan D., Zhu D., Shen C., Li J., Liu F., Pei L., Wang P., Zhao G., Ye Z., Huang H., Yan F., Ma Y., Zhang L., Liu M., You J., Yang Y., Liu Z., Huang F., Li B., Qiu P., Zhang Q., Zhu L., Jin S., Yang X., Min L., Li G., Chen L., Zheng H., Lindsey K., Lin Z., Udall J., and Zhang X., 2018, Reference genome sequences of two cultivated allotetraploid cottons Gossypium hirsutum and Gossypium barbadense, Nature Genetics, 51: 224-229.

https://doi.org/10.1038/s41588-018-0282-x

Wang P., Wang M., Dong N., Sun G., Jia Y., Geng X., Liu M., Wang W., Pan Z., Yang Q., Li H., Wei C., Wang L., Zheng H., He S., Zhang X., Wang Q., and Du X., 2022, Introgression from Gossypium hirsutum is a driver for population divergence and genetic diversity in Gossypium barbadense, The Plant Journal: for Cell and Molecular Biology, 110(3): 764-780.

https://doi.org/10.1111/tpj.15702

Wang W., Cui H., Xiao X., Wu B., Sun J., Zhang Y., Yang Q., Zhao Y., Liu G., and Qin T., 2022, Genome-wide identification of cotton (Gossypium spp.) Trehalose-6-phosphate Phosphatase (TPP) gene family members and the role of GhTPP22 in the response to drought stress, Plants, 11(8): 1079.

https://doi.org/10.3390/plants11081079

Wu W.C., 2024, Revealing the genetic differentiation of different geographical populations of Juniperus spp., based on chloroplast genome, Molecular Plant Breeding, 15(1): 1-7.

Yang Z., Qanmber G., Wang Z., Yang Z., and Li F., 2020, Gossypium genomics: trends scope and utilization for cotton improvement, Trends in Plant Science, 25(5): 488-500.

https://doi.org/10.1016/j.tplants.2019.12.011

Yuan D., Tang Z., Wang M., Gao W., Tu L., Jin X., Chen L., He Y., Zhang L., Zhu L., Li Y., Liang Q., Lin Z., Yang X., Liu N., Jin S., Lei Y., Ding Y., Li G., Ruan X., Ruan Y., and Zhang X., 2015, The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres, Scientific Reports, 5(1): 17662.

https://doi.org/10.1038/srep17662

Zhang H., Zhang J., Lang Z., Botella J., and Zhu J., 2017, Genome Editing-Principles and Applications for Functional Genomics Research and Crop Improvement, Critical Reviews in Plant Sciences, 36: 291-309.

https://doi.org/10.1080/07352689.2017.1402989

Zhang J., Wu M., Yu J., Li X., and Pei W., 2016, Breeding potential of introgression lines developed from interspecific crossing between upland cotton (Gossypium hirsutum) and Gossypium barbadense: Heterosis combining ability and genetic effects, PLoS One, 11(1): e0143646.

https://doi.org/10.1371/journal.pone.0143646

Zhang T., Hu Y., Jiang W., Fang L., Guan X., Chen J., Zhang J., Saski C., Scheffler B., Stelly D., Hulse-Kemp A., Wan Q., Liu B., Liu C., Wang S., Pan M., Wang Y., Wang D., Ye W., Chang L., Zhang W., Song Q., Kirkbride R., Chen X., Dennis E., Llewellyn D., Peterson D., Thaxton P., Jones D., Wang Q., Xu X., Zhang H., Wu H., Zhou L., Mei G., Chen S., Tian Y., Xiang D., Li X., Ding J., Zuo Q., Tao L., Liu Y., Li J., Lin Y., Hui Y., Cao Z., Cai C., Zhu X., Jiang Z., Zhou B., Guo W., Li R., and Chen Z., 2015, Sequencing of allotetraploid cotton (Gossypium hirsutum L., acc., TM-1) provides a resource for fiber improvement, Nature Biotechnology, 33: 531-537.

https://doi.org/10.1038/nbt.3207

Zhang Z., Chai M., Yang Z., Yang Z., and Fan L., 2022, GRAND: an integrated genome transcriptome resources and gene network database for Gossypium, Frontiers in Plant Science, 13: 773107.

https://doi.org/10.3389/fpls.2022.773107

Zheng J., Zhang Z., Gong Z., Liang Y., Sang Z., Xu Y., Li X., and Wang J., 2021, Genome-wide association analysis of salt-tolerant traits in terrestrial cotton at seedling stage, Plants, 11(1): 97.

https://doi.org/10.3390/plants11010097