1 Introduction

The study of evolutionary genomics in Gossypium species has made significant strides, particularly with advancements in high-throughput sequencing and bioinformatics. These technologies have enabled the assembly and comparative analysis of various Gossypium genomes, providing insights into their evolutionary history and genetic diversity. For instance, the genome sequencing of Gossypium herbaceum, Gossypium arboreum, and Gossypium hirsutum has elucidated the origins and phylogenetic relationships of cotton A-genomes, revealing that all existing A-genomes may have originated from a common ancestor (Huang et al., 2020). Additionally, the sequencing of Gossypium barbadense has shed light on the evolution of extra-long staple fibers and specialized metabolites, highlighting the genetic factors underlying fiber elongation and quality (Liu et al., 2015). These genomic resources are invaluable for understanding the complex evolutionary processes that have shaped the Gossypium species and for guiding future cotton breeding programs (Paterson et al., 2012; Yang et al., 2020).

Fiber quality is a critical determinant of the economic value of cotton, influencing its suitability for various textile applications. High-quality cotton fibers are characterized by their length, strength, and fineness, which are essential for producing superior textiles (Wang and Zhang, 2024). The genetic basis of fiber quality traits has been a focal point of research, with studies identifying key genes and genomic regions associated with these traits. For example, genome-wide association studies (GWAS) have uncovered significant single nucleotide polymorphisms (SNPs) and candidate genes related to fiber length and strength in Gossypium hirsutum (Sun et al., 2017). Moreover, comparative transcriptome analyses have revealed that domestication has reprogrammed resource allocation towards increased fiber growth, enhancing fiber quality in cultivated cotton (Yoo and Wendel, 2014). Understanding the genetic architecture of fiber quality is crucial for developing cotton varieties with improved fiber characteristics, thereby meeting the demands of the textile industry and enhancing the competitiveness of cotton producers (Zhang et al., 2015; He et al., 2021).

This study leverages the latest advances in genomics to elucidate the evolutionary history and phylogenetic relationships within the genus Gossypium, identifies key genetic factors and genomic regions linked to fiber quality traits, and explores the effects of polyploidization and domestication on cotton fiber development and quality. The findings aim to provide genomic resources and insights to guide future cotton breeding for improved fiber quality and environmental adaptability.

2 Evolutionary History of Gossypium

2.1 Phylogeny of Gossypium species

The genus Gossypium, commonly known as cotton, comprises approximately 50 species distributed across tropical and subtropical regions worldwide, excluding Europe. Phylogenetic analyses have revealed significant diversification among diploid species and the formation of polyploids through hybridization events. The phylogenetic relationships within Gossypium have been clarified through molecular genetics and biogeographical studies, which have identified multiple cryptic interspecific hybridizations and contributed to the taxonomy of the genus (Figure 1) (Viot and Wendel, 2023). Additionally, the phylogenetic analysis of 147 cotton accessions, including wild relatives and modern cultivars, has shown two divergent groups for G. hirsutum and G. barbadense, suggesting dual domestication processes in tetraploid cottons (Fang et al., 2017a).

2.2 Origin and domestication of cotton species

The domestication of cotton species, particularly G. hirsutum and G. barbadense, has been a complex process involving parallel domestications in Mesoamerica and South America. These domestication events date back to approximately 8 000 years ago for G. barbadense and 5 500 years ago for G. hirsutum. The transformation of wild perennial shrubs into modern annuals with abundant, high-quality fibers was driven by human selection for desirable traits (Viot and Wendel, 2023). Genomic studies have provided insights into the divergence and dual domestication of these species, revealing selective sweeps associated with fiber development and seed germination (Fang et al., 2017a). The high-quality de novo-assembled genomes of G. hirsutum and G. barbadense have further elucidated the evolutionary history and speciation of these species, highlighting species-specific alterations in gene expression and structural variations (Hu et al., 2019).

2.3 Hybridization events and polyploidy in cotton evolution

Polyploidy has played a crucial role in the evolution of Gossypium, conferring emergent properties such as higher fiber productivity and quality. An abrupt ploidy increase approximately 60 million years ago and subsequent allopolyploidy events around 1~2 million years ago have resulted in significant genetic complexity in elite cottons like G. hirsutum and G. barbadense (Paterson et al., 2012). Interspecific hybridization has also contributed to the genetic diversity and evolution of cotton species. For instance, the hybridization of the A-genome with the D-genome led to the evolution of spinnable lint fibers, which were maintained in subsequent evolution (Anwar et al., 2022). The genomic diversification of five allopolyploid cotton species has shown that polyploidy induces recombination suppression, which can be overcome by wild introgression, providing opportunities for crop improvement (Chen et al., 2020). Molecular evolutionary studies have revealed that human domestication has altered the evolutionary patterns of genes related to fiber development, with G. hirsutum experiencing greater selective pressures than G. barbadense during domestication (Zhu et al., 2012).

3 Genomic Structure of Gossypium

3.1 Chromosome structure and organization

The genomic structure of Gossypium, particularly in allotetraploid species such as Gossypium hirsutum and Gossypium barbadense, is characterized by a complex organization resulting from polyploidization events. These species have undergone significant structural rearrangements, including inversions and translocations, which have contributed to their genomic diversity and adaptability. For instance, large paracentric and pericentric inversions have been identified in 14 chromosomes of these species, highlighting the extensive structural variations that occurred post-polyploidization (Wang et al., 2018). Additionally, the A and D subgenomes exhibit different evolutionary patterns, with the A subgenome showing more structural rearrangements and gene loss compared to the D subgenome (Zhang et al., 2015). This asymmetric evolution is indicative of the distinct roles each subgenome plays in the overall genomic architecture and function of cotton.

3.2 Comparative genomics of diploid and polyploid cotton species

Comparative genomics between diploid and polyploid cotton species reveals significant insights into the evolutionary history and functional adaptations of Gossypium. Polyploidization has led to the duplication of ancestral angiosperm genes, resulting in a genetic complexity that is unparalleled among sequenced angiosperms, except for Brassica (Paterson et al., 2012). The comparison of diploid genomes, such as Gossypium herbaceum (A genome) and Gossypium raimondii (D genome), with their polyploid counterparts, has elucidated the evolutionary processes that have shaped fiber development and other phenotypic traits. Notably, the D subgenome, despite originating from a non-fiber-producing ancestor, contains numerous quantitative trait loci (QTLs) that influence fiber quality and yield in tetraploid cottons. This suggests that the merger of the A and D genomes has created unique avenues for phenotypic innovation and response to selection.

3.3 Key genomic regions related to fiber development

Key genomic regions associated with fiber development in Gossypium have been identified through various genomic studies. The A subgenome is particularly enriched with positively selected genes (PSGs) related to fiber improvement, while the D subgenome harbors genes associated with stress tolerance (Zhang et al., 2015). Additionally, introgression and association analyses have pinpointed new loci related to fiber quality, demonstrating the significant impact of introgressed alleles from diploid cottons on fiber improvement (He et al., 2021). The coordinated expression changes in proximal groups of functionally distinct genes, including those within nuclear mitochondrial DNA blocks, are believed to account for clusters of cotton-fiber QTLs affecting diverse traits (Paterson et al., 2012). These findings underscore the importance of specific genomic regions in the enhancement of fiber properties and provide valuable targets for future breeding programs aimed at improving cotton fiber quality and yield.

4 Gene Families and Fiber Traits

4.1 Gene families involved in fiber development

The development of cotton fiber is a complex process involving various gene families, notably the cellulose synthase (CesA) genes. In Gossypium barbadense, 29 CesA genes have been identified, with most being expressed during fiber development. These genes are crucial for secondary cell wall biosynthesis, which is essential for fiber elongation and strength. The delayed and higher degree of up-regulation of these genes in G. barbadense compared to G. hirsutum contributes to the extended elongation stage and enhanced fiber quality in G. barbadense (Liu et al., 2015). Additionally, the GRAM domain gene family, particularly GhGRAM31, has been shown to regulate fiber length by interacting with other proteins and influencing the expression of genes related to fiber development (Ye et al., 2020).

4.2 Role of transcription factors in fiber elongation and strength

Transcription factors (TFs) play a pivotal role in regulating fiber elongation and strength. For instance, the bHLH/HLH transcription factors GhFP2 and GhACE1 have been found to antagonistically regulate fiber elongation. GhACE1 promotes fiber elongation by activating the expression of genes such as GhPIP2;7 and GhEXP8, while GhFP2, which is modulated by brassinosteroids, hinders this process by interacting with GhACE1 and suppressing its activity (Lu et al., 2022). Another significant TF, Gh14-3-3, has been shown to modulate brassinosteroid signaling, thereby influencing fiber initiation and elongation. Overexpression of Gh14-3-3L promotes fiber elongation, whereas its suppression results in shorter fibers (Zhou et al., 2015). Furthermore, the transcription factor PRE1, which is At biased and fiber-specific, has been implicated in the regulation of cell elongation in G. barbadense, highlighting the genetic factors underlying fiber elongation (Liu et al., 2015).

4.3 Genetic regulation of fiber fineness and length

The genetic regulation of fiber fineness and length involves multiple quantitative trait loci (QTLs) and gene expression networks. Genome-wide association studies (GWAS) have identified numerous SNPs and QTLs associated with fiber quality traits. For example, 342 quantitative trait nucleotides (QTNs) have been detected for fiber quality traits, including fiber length, strength, and micronaire. Among these, specific QTNs such as TM80185 (D13) for fiber length and TM1386 (A1) for fiber strength have been identified as potential markers for breeding programs (Li et al., 2018). Additionally, the MIR160 gene family, particularly miR160a_A05, has been shown to regulate fiber length by downregulating its target gene ARF17 and several GH3 genes, which are involved in auxin signaling and fiber elongation (Liu et al., 2019). The identification of new alleles (ENAs) and extremely expressed genes (eGenes) during fiber elongation further elucidates the genetic factors influencing fiber length, with genes such as GhFLA9 playing a significant role (Ma et al., 2022).

5 Functional Genomics and Transcriptomics

5.1 Advances in transcriptome analysis of fiber cells

Recent advancements in transcriptome analysis have significantly enhanced our understanding of fiber cell development in cotton. Comparative transcriptome profiling using RNA-Seq has revealed that a substantial portion of the cotton genome is expressed during fiber development. For instance, in Gossypium hirsutum, at least one-third to one-half of the genes are active at any given stage of fiber development, with around 5 000 genes showing differential expression between wild and domesticated cottons during primary and secondary cell wall synthesis. This comprehensive analysis has highlighted the reprogramming of resource allocation towards increased fiber growth in domesticated cotton, suggesting that human selection has prolonged fiber elongation in modern cultivated forms (Yoo and Wendel, 2014). Additionally, the use of RNA sequencing in recombinant inbred lines has identified numerous differentially expressed genes associated with high-quality fiber traits, providing valuable insights for fiber improvement (Zou et al., 2019).

5.2 Differential gene expression in developing fibers

Differential gene expression plays a crucial role in the development of cotton fibers. Studies have shown that the fiber transcriptome of domesticated cotton is far more dynamic than that of wild cotton, with over twice as many genes being differentially expressed during development (Rapp et al., 2010). For example, in Upland cotton, thousands of genes are upregulated or downregulated at various stages of fiber development, with significant changes observed at 0, 5, 10, 15, 20, and 25 days post-anthesis (He et al., 2023). This differential expression is crucial for understanding the molecular mechanisms underlying fiber development and the impact of domestication on fiber traits. Furthermore, the identification of key modules and hub genes through co-expression network analysis has provided deeper insights into the genetic regulation of fiber quality (Zou et al., 2019; He et al., 2023).

5.3 Role of non-coding RNAs in fiber improvement

Non-coding RNAs, particularly long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), have emerged as important regulators in cotton fiber development. A comprehensive identification of lncRNAs in Gossypium spp. has revealed over 30 000 long intergenic noncoding RNA (lincRNA) loci and 4 718 long noncoding natural antisense transcript (lncNAT) loci, which are preferentially expressed in a tissue-specific manner and exhibit biased expression patterns towards the At or Dt subgenomes (Wang et al., 2015). These lncRNAs are involved in various regulatory processes, including fiber initiation and elongation. Additionally, miRNAs have been shown to play a significant role in fiber development. For instance, differentially expressed miRNAs (DEmiRs) have been identified in domesticated cotton species, with functional annotations revealing their involvement in hormone-signaling, calcium-signaling, and reactive oxygen species (ROS) signaling during fiber initiation and elongation (Arora and Chaudhary, 2021). The integration of lncRNA and miRNA data has provided a more comprehensive understanding of the regulatory networks governing fiber development and offers potential targets for genetic improvement of cotton fibers.

6 Genomic Tools and Techniques for Fiber Improvement

6.1 Marker-assisted selection (MAS) in cotton breeding

Marker-assisted selection (MAS) has become a pivotal tool in cotton breeding, particularly for improving fiber quality traits. MAS leverages molecular markers linked to desirable traits, allowing breeders to select plants with superior fiber characteristics more efficiently than traditional phenotypic selection methods. The development of high-density linkage maps and quantitative trait loci (QTL) fine mapping has significantly enhanced the precision of MAS. For instance, QTL mapping combined with multi-omics approaches, such as RNA sequencing, has facilitated the identification of differentially expressed genes associated with fiber quality traits in upland cotton (Gossypium hirsutum) (Ijaz et al., 2019). Additionally, genome-wide association studies (GWAS) have identified numerous quantitative trait nucleotides (QTNs) controlling fiber quality traits, further supporting the application of MAS in breeding programs (Li et al., 2018). The construction of comprehensive PCR-based marker linkage maps has also been instrumental in identifying QTLs for fiber quality traits, thereby aiding MAS (Zhang et al., 2009). Functional markers developed through kompetitive allele-specific PCR (KASP) assays have proven effective in differentiating cotton accessions with superior fiber length and strength, underscoring the practical value of MAS in cotton breeding (Li et al., 2022).

6.2 CRISPR-Cas genome editing in Gossypium

CRISPR-Cas genome editing has emerged as a revolutionary tool for precise genetic modifications in Gossypium species, offering new avenues for fiber improvement. This technology allows for targeted alterations in the cotton genome, enabling the introduction or correction of specific genes associated with fiber quality. The sequencing of the allotetraploid Gossypium hirsutum genome has provided a comprehensive resource for identifying target genes for CRISPR-Cas editing (Zhang et al., 2015). By leveraging this genomic information, researchers can design CRISPR-Cas systems to enhance fiber traits such as length, strength, and fineness. The potential of CRISPR-Cas to create targeted mutations or insertions in key genes holds promise for accelerating the development of cotton varieties with superior fiber qualities. Moreover, the integration of CRISPR-Cas with other genomic tools, such as QTL mapping and GWAS, can further refine the selection of target genes for editing (Han, 2024), thereby maximizing the impact of this technology on cotton breeding.

6.3 Application of genomic selection (GS) in fiber quality improvement

Genomic selection (GS) is a cutting-edge approach that utilizes genome-wide marker data to predict the breeding value of individuals, thereby enhancing the efficiency of selection for complex traits like fiber quality. GS models, such as Bayes Ridge Regression and BayesB, have been evaluated for their performance in predicting fiber quality phenotypes across multiple environments in cotton breeding programs (Gapare et al., 2018). These models have demonstrated high prediction accuracies, particularly when accounting for genotype × environment interactions, which are crucial for identifying stable breeding lines with superior fiber traits. The use of historical datasets and large-scale genomic surveys has further enriched the genomic resources available for GS, enabling the identification of new fiber quality-related loci and the assessment of haplotypic diversity in cultivated cotton (He et al., 2021). By integrating GS with traditional breeding methods and other genomic tools, cotton breeders can achieve more rapid and precise improvements in fiber quality, ultimately leading to the development of high-yielding, superior fiber varieties.

7 Environmental and Epigenetic Factors Affecting Fiber Development

7.1 Impact of environmental stressors on fiber traits

Environmental stressors such as drought, temperature extremes, and soil salinity significantly impact cotton fiber traits. Gossypium hirsutum, for instance, has evolved to produce higher fiber yields and better withstand harsh environments compared to Gossypium barbadense, which is known for superior fiber quality but less resilience to environmental stress (Hu et al., 2019). The genomic basis of these adaptations includes structural variations and gene expression changes that enhance stress tolerance (Zhang et al., 2015; Hu et al., 2019). Additionally, wild cotton species allocate more resources to stress response pathways, which are reprogrammed during domestication to favor fiber growth (Yoo and Wendel, 2014).

7.2 Epigenetic modifications and fiber development

Epigenetic modifications play a crucial role in regulating gene expression during fiber development. Studies have shown that genes involved in fiber elongation and secondary cell wall synthesis are differentially expressed between wild and domesticated cotton, suggesting that epigenetic changes have been selected for during domestication to enhance fiber traits (Yoo and Wendel, 2014). The identification of stress-tolerant and light-responsive cis-acting elements in promoter regions of fiber-related genes further underscores the importance of epigenetic regulation in fiber development (Ashraf et al., 2022).

7.3 Plasticity of fiber traits under varying environmental conditions

The plasticity of fiber traits under varying environmental conditions is a key factor in cotton's adaptability. Comparative genomic analyses have revealed that Gossypium species exhibit significant genetic diversity, which contributes to their ability to adapt to different environments (Yang et al., 2020; He et al., 2021). This plasticity is also evident in the differential expression of fiber-related genes under various environmental conditions, which allows for the optimization of fiber traits such as length and strength (Sun et al., 2017; Li et al., 2018). The ability to modulate fiber development in response to environmental cues is a critical aspect of cotton's evolutionary success and ongoing improvement efforts.

8 Case Study: Genomic Improvement in Commercial Cotton Varieties

8.1 Case study: development of a pest-resistant, high-fiber-quality cotton variety

The development of pest-resistant, high-fiber-quality cotton varieties has been significantly advanced through genomic research. For instance, the sequencing of the allotetraploid Gossypium hirsutum L. acc. TM-1 genome has provided a comprehensive resource for fiber improvement. This genome sequencing revealed structural rearrangements and gene loss, which are crucial for understanding the genetic basis of fiber quality and stress tolerance (Zhang et al., 2015). Additionally, the identification of quantitative trait nucleotides (QTNs) controlling fiber quality traits through genome-wide association studies (GWASs) has highlighted the potential for marker-assisted selection in breeding programs (Li et al., 2018). These genomic insights have enabled the development of cotton varieties that not only produce high-quality fiber but also exhibit resistance to pests and environmental stresses.

8.2 Success stories of utilizing genomics in cotton breeding

Several success stories illustrate the impact of genomics on cotton breeding. One notable example is the identification of new fiber quality-related loci through large-scale genomic surveys of tetraploid cotton genomes. These loci, derived from introgressed alleles of diploid cottons, have significantly improved fiber quality, overcoming previous bottlenecks in cotton breeding (Figure 2) (He et al., 2021). Another success story involves the construction of introgression lines from Gossypium barbadense to Gossypium hirsutum, which identified 13 quantitative trait loci associated with superior fiber quality (Figure 3) (Wang et al., 2018). These advancements underscore the power of genomics in enhancing cotton breeding programs, leading to the development of superior cotton lines with improved fiber quality and resilience.

8.3 Lessons learned and challenges encountered in the breeding program

The integration of genomics into cotton breeding programs has provided valuable lessons and highlighted several challenges. One key lesson is the importance of understanding the genetic architecture of fiber quality traits, which has been facilitated by the identification of QTNs and their associated candidate genes (Li et al., 2018). However, challenges remain, such as the complexity of the cotton genome and the need for high-quality genome assemblies to accurately identify structural variations and gene expression patterns (Wang et al., 2018; Ma et al., 2021). Additionally, the dynamic nature of gene expression during fiber development, as observed in domesticated versus wild cotton, emphasizes the need for comprehensive transcriptomic analyses to fully understand the genetic basis of fiber improvement (Rapp et al., 2010). Addressing these challenges will be crucial for the continued success of genomics-enabled cotton breeding programs.

9 Challenges and Future Directions in Cotton Genomics

9.1 Overcoming limitations in genomic resources

The complexity and size of the cotton genome have historically posed significant challenges to genomic research. However, advancements in high-throughput sequencing and bioinformatics have begun to mitigate these obstacles. For instance, the sequencing of the allotetraploid Gossypium hirsutum L. acc. TM-1 genome has provided a valuable resource for fiber improvement by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences, and genotype-by-sequencing genetic maps (Zhang et al., 2015). Additionally, the reference genome sequences of Gossypium hirsutum and Gossypium barbadense have shown considerable improvements in contiguity and completeness, particularly in regions with high repeat content such as centromeres (Wang et al., 2018). Despite these advancements, there remains a need for more comprehensive and high-quality genomic data to fully understand the genetic basis of fiber traits and to facilitate the development of superior cotton lines (Hu et al., 2019; Yang et al., 2020).

9.2 Integrating multi-omics data for fiber trait improvement

The integration of multi-omics data, including genomics, transcriptomics, proteomics, and metabolomics, holds great promise for the improvement of fiber traits in cotton. Recent studies have utilized genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping to identify loci associated with fiber quality and yield traits (Ijaz et al., 2019; Joshi et al., 2023). For example, a comprehensive genomic assessment of modern upland cotton has revealed that lint yield has stronger selection signatures than other traits, and identified ethylene-pathway-related genes associated with increased lint yield (Fang et al., 2017b). Furthermore, the use of RNA sequencing datasets to identify differentially expressed genes has facilitated the validation of candidate genes and the application of marker-assisted selection (MAS) in breeding programs (Ijaz et al., 2019). These multi-omics approaches provide a holistic understanding of the genetic and molecular mechanisms underlying fiber traits, enabling more targeted and efficient breeding strategies (Paterson et al., 2012; He et al., 2021).

9.3 Prospects of sustainable cotton production through genomics

Genomic research in cotton not only aims to improve fiber quality and yield but also to enhance the sustainability of cotton production. The identification of genomic signatures associated with stress tolerance and environmental resilience is crucial for developing cotton varieties that can thrive under changing climatic conditions (Zhang et al., 2015; Hu et al., 2019). For instance, the genomic basis of geographic differentiation in cultivated cotton has been linked to extensive chromosome inversions, which may play a role in adaptive evolution (He et al., 2021). Additionally, the high-quality de novo-assembled genomes of Gossypium hirsutum and Gossypium barbadense have provided insights into the evolution of cotton genomes and their domestication history, which can inform breeding programs aimed at improving resilience to environmental stress (Hu et al., 2019). By leveraging genomic resources and integrating multi-omics data, researchers can develop cotton varieties that are not only high-yielding and of superior quality but also more sustainable and resilient to environmental challenges (Huang et al., 2020; Yang et al., 2020).

Acknowledgments

The authors express deep gratitude to Prof. & Dr. Xuanjun Fang, Director of the Hainan Institute of Tropical Agricultural Resources and Director of the Hainan Provincal Key Laboratory of Crop Molecular Breeding for his thorough review of the manuscript and for providing comprehensive and systematic revision suggestions. The authors also extend thanks to the two anonymous peer reviewers for their valuable comments and constructive recommendations on this 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

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

Arora S., and Chaudhary B., 2021, Global expression dynamics and miRNA evolution profile govern floral/fiber architecture in the modern cotton (Gossypium), Planta, 254: 62.

https://doi.org/10.1007/s00425-021-03711-3

Ashraf F., Khan A., Iqbal N., Mahmood Z., Ghaffar A., and Khan Z., 2022, In silico analysis and expression profiling of Expansin A4, BURP domain protein RD22-like and E6-like genes associated with fiber quality in cotton, Molecular Biology Reports, 49: 5521-5534.

https://doi.org/10.1007/s11033-022-07432-y

Chen Z., Sreedasyam A., Ando A., Song Q., Santiago L., Hulse-Kemp A., Ding M., Ye W., Kirkbride R., Jenkins J., Plott C., Lovell J., Lin Y., Vaughn R., Liu B., Simpson S., Scheffler B., Wen L., Saski C., Grover C., Hu G., Conover J., Carlson J., Shu S., Boston L., Williams M., Peterson D., Mcgee K., Jones D., Wendel J., Stelly D., Grimwood J., and Schmutz J., 2020, Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement, Nature Genetics, 52: 525-533.

https://doi.org/10.1038/s41588-020-0614-5

Fang L., Gong H., Hu Y., Liu C., Zhou B., Huang T., Wang Y., Chen S., Fang D., Du X., Chen H., Chen J., Wang S., Wang Q., Wan Q., Liu B., Pan M., Chang L., Wu H., Mei G., Xiang D., Li X., Cai C., Zhu X., Chen Z., Han B., Chen X., Guo W., Zhang T., and Huang X., 2017a, Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons, Genome Biology, 18: 33.

https://doi.org/10.1186/s13059-017-1167-5

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., 2017b, Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits, Nature Genetics, 49: 1089-1098.

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

Gapare W., Liu S., Conaty W., Zhu Q., Gillespie V., Llewellyn D., Stiller W., and Wilson I., 2018, Historical datasets support genomic selection models for the prediction of cotton fiber quality phenotypes across multiple environments, G3: Genes, Genomes, Genetics, 8: 1721-1732.

https://doi.org/10.1534/g3.118.200140

Han Y.P., 2024, Application of CRISPR/Cas9 technology in editing poplar drought resistance genes, Molecular Plant Breeding, 15(2): 81-89

He J., Xu Z., Azhar M., Zhang Z., Li P., Gong J., Jiang X., Fan S., Ge Q., Yuan Y., and Shang H., 2023, Comparative transcriptional and co-expression network analysis of two upland cotton accessions with extreme phenotypic differences reveals molecular mechanisms of fiber development, Frontiers in Plant Science, 14: 1189490.

https://doi.org/10.3389/fpls.2023.1189490

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

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

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

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: 1252746.

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

Li C., Fu Y., Sun R., Wang Y., and Wang Q., 2018, Single-locus and multi-locus genome-wide association studies in the genetic dissection of fiber quality traits in upland cotton (Gossypium hirsutum L.), Frontiers in Plant Science, 9: 1083.

https://doi.org/10.3389/fpls.2018.01083

Li L., Sun Z., Zhang Y., Ke H., Yang J., Li Z., Wu L., Zhang G., Wang X., and Ma Z., 2022, Development and utilization of functional kompetitive allele-specific PCR markers for key genes underpinning fiber length and strength in Gossypium hirsutum L., Frontiers in Plant Science, 13: 853827.

https://doi.org/10.3389/fpls.2022.853827

Liu G., Liu J., Pei W., Li X., Wang N., Ma J., Zang X., Zhang J., Yu S., Wu M., and Yu J., 2019, Analysis of the MIR160 gene family and the role of MIR160a_A05 in regulating fiber length in cotton, Planta, 250: 2147-2158.

https://doi.org/10.1007/s00425-019-03271-7

Liu X., Zhao B., Zheng H., Hu Y., Lu G., Yang C., Chen J., Chen J., Chen D., Zhang L., Zhou Y., Wang L., Guo W., Bai Y., Ruan J., Shangguan X., Mao Y., Shan C., Jiang J., Zhu Y., Jin L., Kang H., Chen S., He X., Wang R., Wang Y., Chen J., Wang L., Yu S., Wang B., Wei J., Song S., Lu X., Gao Z., Gu W., Deng X., Ma D., Wang S., Liang W., Fang L., Cai C., Zhu X., Zhou B., Chen Z., Xu S., Zhang Y., Wang S., Zhang T., Zhao G., and Chen X., 2015, Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites, Scientific Reports, 5: 14139.

https://doi.org/10.1038/srep14139

Lu R., Li Y., Zhang J., Wang Y., Zhang J., Li Y., Zheng Y., and Li X., 2022, The bHLH/HLH transcription factors GhFP2 and GhACE1 antagonistically regulate fiber elongation in cotton, Plant Physiology, 189(2): 628-643.

https://doi.org/10.1093/plphys/kiac088

Ma J., Jiang Y., Pei W., Wu M., Ma Q., Liu J., Song J., Jia B., Liu S., Wu J., Zhang J., and Yu J., 2022, Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton, Plant Biotechnology Journal, 20: 1940-1955.

https://doi.org/10.1111/pbi.13874

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

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

Rapp R., Haigler C., Flagel L., Hovav R., Udall J., and Wendel J., 2010, Gene expression in developing fibres of upland cotton (Gossypium hirsutum L.) was massively altered by domestication, BMC Biology, 8: 139.

https://doi.org/10.1186/1741-7007-8-139

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

Viot C., and Wendel J., 2023, Evolution of the cotton genus, Gossypium, and its domestication in the Americas, Critical Reviews in Plant Sciences, 42: 1-33.

https://doi.org/10.1080/07352689.2022.2156061

Wang J.M., and Zhang J., 2024, Assessing the impact of various cotton diseases on fiber quality and production, Field Crop, 7(4): 212-221.

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 M., Yuan D., Tu L., Gao W., He Y., Hu H., Wang P., Liu N., Lindsey K., and Zhang X., 2015, Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.), The New Phytologist, 207(4): 1181-1197.

https://doi.org/10.1111/nph.13429

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

Ye Z., Qiao L., Luo X., Chen X., Zhang X., and Tu L., 2020, Genome-wide identification of cotton GRAM family finds GhGRAM31 regulates fiber length, Journal of Experimental Botany, 72(7): 2477-2490.

https://doi.org/10.1093/jxb/eraa597

Yoo M., and Wendel J., 2014, Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome, PLoS Genetics, 10(1): e1004073.

https://doi.org/10.1371/journal.pgen.1004073

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., Hu M., Zhang J., Liu D., Zheng J., Zhang K., Wang W., and Wan Q., 2009, Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.), Molecular Breeding, 24: 49-61.

https://doi.org/10.1007/s11032-009-9271-1

Zhou Y., Zhang Z., Li M., Wei X., Li X., Li B., and Li X., 2015, Cotton (Gossypium hirsutum) 14-3-3 proteins participate in regulation of fibre initiation and elongation by modulating brassinosteroid signalling, Plant Biotechnology Journal, 13(2): 269-280.

https://doi.org/10.1111/pbi.12275

Zhu H., Lv J., Zhao L., Tong X., Zhou B., Zhang T., and Guo W., 2012, Molecular evolution and phylogenetic analysis of genes related to cotton fibers development from wild and domesticated cotton species in Gossypium, Molecular Phylogenetics and Evolution, 63(3): 589-597.

https://doi.org/10.1016/j.ympev.2012.01.025

Zou X., Liu A., Zhang Z., Ge Q., Fan S., Gong W., Li J., Gong J., Shi Y., Tian B., Wang Y., Liu R., Lei K., Zhang Q., Jiang X., Feng Y., Zhang S., Jia T., Zhang L., Yuan Y., and Shang H., 2019, Co-expression network analysis and hub gene selection for high-quality fiber in upland cotton (Gossypium hirsutum) using RNA sequencing analysis, Genes, 10(2): 119.

https://doi.org/10.3390/genes10020119