1 Introduction

Cotton is a globally significant crop, often referred to as "white gold" due to its substantial economic value. It is cultivated in over 80 countries and serves as the primary natural fiber for the textile industry, making it a critical agricultural commodity (Pei, 2015; Sun et al., 2019; Wang et al., 2021). The quality and yield of cotton fiber directly impact the textile industry, influencing everything from fabric production to global trade dynamics (Sun et al., 2019).

Research into cotton fiber development is scientifically significant for several reasons. Cotton fibers are single-celled trichomes that undergo a complex developmental process, including initiation, elongation, secondary cell wall biosynthesis, and maturation. Understanding the transcriptional regulation of these stages can provide insights into plant cell elongation and differentiation, which are fundamental biological processes (Pei, 2015; Zhang et al., 2018; Lu et al., 2022). Moreover, cotton fiber development serves as an excellent model for studying cell wall expansion and biosynthesis, given the fibers' nearly pure cellulose composition when mature (Cao et al., 2020). Recent studies have identified key transcription factors such as GhWRKY16, GhMYB212, and GhHOX3, which play crucial roles in fiber initiation, elongation, and secondary cell wall formation (Sun et al., 2019; Wang et al., 2021).

This study aims to consolidate current knowledge on the transcriptional regulation of cotton fiber growth, focusing on the roles of various transcription factors and their downstream targets. By examining recent research findings, this study will highlight the molecular mechanisms that control fiber initiation, elongation, and secondary cell wall biosynthesis. The scope includes an analysis of key transcription factors such as GhWRKY16, GhMYB212, GhHOX3, and others, and their interactions with signaling pathways and environmental factors. This comprehensive overview will provide a foundation for future research and potential applications in cotton breeding programs aimed at improving fiber quality and yield.

2 Overview of Cotton Fiber Development

2.1 The Four Stages of Cotton Fiber Development

Cotton fiber development is a complex process that can be divided into four distinct stages: initiation, elongation, secondary cell wall (SCW) synthesis, and maturation. During the initiation stage, fiber cells are committed to their developmental fate, which involves the activation of specific transcription factors and signaling pathways. For instance, the WRKY transcription factor GhWRKY16 plays a crucial role in fiber initiation by binding to the promoters of key genes such as GhHOX3 and GhMYB109, thereby promoting their expression (Wang et al., 2021). Similarly, phytohormones like auxin and gibberellins are essential for the early stages of fiber initiation, as they activate various signaling pathways that mediate cell fate determination (Yang et al., 2006; Lee et al., 2007).

The elongation stage follows initiation and is characterized by rapid cell expansion. This stage relies heavily on the transportation and metabolism of sucrose, which serves as a direct carbon source for fiber growth. The transcription factor GhMYB212 has been identified as a key regulator of sucrose transport into elongating fibers by controlling the expression of the sucrose transporter gene GhSWEET12 (Figure 1) (Sun et al., 2019). Additionally, auxin signaling and wall-loosening enzymes are highly active during this stage, facilitating the rapid elongation of fiber cells (Gou et al., 2007).

2.2 Temporal and Spatial Dynamics of Cotton Fiber Development

The temporal and spatial dynamics of cotton fiber development are tightly regulated by a network of transcription factors and signaling molecules. During the early stages of fiber development, genome-specific transcripts and transcription factors such as MYB and WRKY are selectively enriched in allotetraploid cotton, indicating their crucial roles in fiber cell initiation and elongation (Yang et al., 2006). The spatial distribution of these factors within the ovule epidermis is also critical, as it ensures the proper development of fiber cells from the outer integument of the ovules (Sun et al., 2019).

As fiber development progresses, there is a significant shift in the abundance of transcripts related to gene regulation, cell organization, and metabolism. For example, during the transition from cell elongation to SCW synthesis, the expression of genes involved in cellulose biosynthesis becomes predominant, while other metabolic pathways are downregulated (Gou et al., 2007). This temporal regulation ensures that fiber cells undergo a specialization process, ultimately leading to the deposition of a large amount of cellulose in the SCW (Cao et al., 2020).

2.3 Uniqueness of cotton fiber

Cotton fiber is unique among plant fibers due to its single-cell origin and its highly elongated structure, which is almost entirely composed of cellulose when mature. This uniqueness is partly attributed to the specific transcriptional and post-transcriptional regulatory mechanisms that govern fiber development. For instance, the transcription factor GhTCP4 plays a pivotal role in balancing fiber cell elongation and SCW synthesis by interacting with GhHOX3 to repress cell elongation and promote SCW deposition (Cao et al., 2020). Additionally, small interfering RNAs (siRNAs) derived from natural antisense transcripts (NATs) have been shown to regulate fiber development by mediating mRNA self-cleavage, highlighting the complexity of post-transcriptional regulation in cotton fiber growth (Wan et al., 2016).

Moreover, the conservation of certain molecular mechanisms across different fiber-producing plants suggests that some aspects of cotton fiber development are shared with other species. For example, MYB transcription factors, which are known to regulate leaf trichome development in Arabidopsis, also play a role in cotton fiber development (Lee et al., 2007). This conservation underscores the evolutionary significance of these regulatory pathways in plant cell differentiation and growth.

3 Transcriptional Regulatory Network in Cotton Fiber Development

3.1 Role of MYB Transcription Factors in Cotton Fiber

MYB transcription factors are crucial in regulating various stages of cotton fiber development, from initiation to secondary cell wall synthesis and maturity. The R2R3-MYB transcription factors, such as GhMYB25-like, play a significant role in the early stages of fiber cell differentiation. GhMYB25-like is expressed predominantly in the epidermal layers of cotton ovules before anthesis and is crucial for the initiation of fiber cells. Suppression of GhMYB25-like results in fiberless seeds, indicating its essential role in fiber initiation (Walford et al., 2011). Additionally, GhMYB3, another R2R3-MYB transcription factor, has been shown to interact with bHLH proteins and is involved in trichome development, which is analogous to fiber development in cotton (Shangguan et al., 2021).

Furthermore, genome-wide studies have identified numerous R2R3-MYB genes that are highly expressed during the secondary cell wall thickening stage of fiber development. For instance, GhMYB46_D13 and GhMYB46_D9 are two MYB genes that activate the expression of cellulose synthase genes, which are critical for secondary cell wall biosynthesis in cotton fibers (Huang et al., 2019). These findings highlight the diverse roles of MYB transcription factors in different stages of cotton fiber development.

3.2 Functions of bHLH, NAC, and Other Transcription Factors in Cotton Fiber

bHLH transcription factors also play pivotal roles in cotton fiber development. GhFP2 and GhACE1 are two bHLH proteins that antagonistically regulate fiber elongation. GhFP2, which lacks a DNA binding domain, hinders fiber elongation when overexpressed, while GhACE1 promotes fiber elongation by activating the expression of genes such as GhPIP2;7 and GhEXP8. The interaction between GhFP2 and GhACE1 modulates the transcriptional activation of these target genes, illustrating a complex regulatory mechanism involving bHLH proteins (Figure 2) (Lu et al., 2022).

Image caption: A, The potential E-box (CANNTG) elements in the promoters of GhPIP2;7 and GhEXP8. The upright lines indicate position of E-boxes. The Chip lines indicate fragments detected in ChIP assay. The probe1/2/3/4 lines indicate fragments used in EMSA. The red bold bases in the probe1/2/3/4 sequences are E-boxes. B, ChIP-qPCR assay of GhACE1 proteins binding to the promoters of GhPIP2;7 and GhEXP8 in vivo. GhACE1-bound chromatin DNA fragments were isolated from nine DPA fibers of WT cotton, and qPCR analysis was performed with the primer sets listed in Supplemental Table S3 (see “Materials and methods”). Error bars represent sd of three biological replicates. Data were analyzed with prism7.0. CK, the control sample without anti-GhACE1 antibody. C-F, EMSA showing that GhACE1 protein binds to the E-box elements (probe1/2/3/4) of GhPIP2;7 and GhEXP8 promoters in vitro. Biotin-labeled DNA fragments (probes) were incubated with His-GhACE1 protein. An excess of the unlabeled probes or mutated probes was used to compete with the labeled probes. mCold-probe represents 200× mutated probe. a, 20×probe; b, 200×probe. G, Dual-LUC assay of transcriptional activation of GhACE1 to the target genes and inhibitive effects of GhFP2 on GhACE1 activating GhPIP2;7 and GhEXP8 promoters (pGhPIP2;7 and pGhEXP8). GhPIP2;7 and GhEXP8 promoters were fused to the LUC reporter, respectively, and the promoter activities were determined in leaves of N. benthamiana by transient dual-LUC transcriptional activation assay. The relative LUC activities were normalized to the reference REN luciferase. The corresponding effector (+) and empty vector (-) were co-filtrated. Error bars represent sd of three biological replicates. Data were analyzed with Microsoft Excel. Independent t tests demonstrated significant (P < 0.05) or very significant (P < 0.01) difference between two groups (Adopted from Lu et al., 2022)

In addition to bHLH proteins, NAC transcription factors are involved in fiber development. NAC proteins are known to regulate various aspects of plant growth and development, including secondary cell wall formation. Although specific NAC transcription factors involved in cotton fiber development were not detailed in the provided data, their general role in regulating cell wall biosynthesis suggests their potential importance in this process. Other transcription factors, such as those from the WRKY family, have also been implicated in fiber development, particularly during the early stages of fiber cell differentiation (Yang et al., 2006).

3.3 Interaction of transcription factors and regulatory networks

The interaction between different transcription factors forms a complex regulatory network that governs cotton fiber development. The MYB-bHLH-WD40 complex is a well-characterized regulatory module in Arabidopsis trichome development and is also implicated in cotton fiber development. For instance, GhMYB3 interacts with bHLH proteins and WD40 proteins to form a regulatory complex that controls fiber development (Shangguan et al., 2016; 2021). Similarly, GhMML4_D12, a MYB-like protein, interacts with the WD40 protein GhWDR, forming a complex that regulates fiber development in a manner analogous to the MYB-bHLH-WD40 complex (Tian et al., 2020).

Moreover, the brassinosteroid (BR) signaling pathway also interacts with transcription factors to regulate fiber elongation. GhBES1.4, a BR-responsive transcription factor, promotes fiber elongation by regulating the expression of target genes involved in cell elongation. The interplay between BR signaling and transcription factors such as GhBES1.4 highlights the integration of hormonal and transcriptional regulation in cotton fiber development (Liu et al., 2022).

4 Hormonal Regulation of Cotton Fiber Growth

4.1 Role of auxin in cotton fiber development

Auxin is a crucial phytohormone that significantly influences cotton fiber development. It promotes fiber elongation by enhancing gibberellic acid (GA) biosynthesis. Studies have shown that the exogenous application of auxin leads to increased fiber length, indicating its pivotal role in fiber cell elongation. Specifically, auxin-responsive factors such as GhARF18 have been identified as key regulators in this process. GhARF18 binds to the promoters of GA biosynthesis genes, thereby increasing GA content and promoting fiber elongation (Zhu et al., 2021). Additionally, auxin transporters like GhPIN3a are essential for the asymmetric accumulation of auxin in the ovule epidermis, which is critical for fiber cell initiation (Zeng et al., 2019).

Moreover, auxin interacts with other hormones to regulate fiber growth. For instance, the interaction between auxin and strigolactones (SLs) has been shown to influence fiber cell elongation. SL signaling repressors, such as GhSMXL7 and GhSMXL8, negatively regulate fiber elongation by interfering with auxin response factors (ARFs) and gibberellin signaling pathways. This complex interplay highlights the multifaceted role of auxin in cotton fiber development (Sun et al., 2024).

4.2 Effects of Gibberellins (GA), Cytokinins (CK), and Abscisic Acid (ABA) on cotton fiber

Gibberellins (GA) are another group of phytohormones that play a significant role in cotton fiber growth. GA promotes fiber elongation by enhancing cell expansion and division. The application of GA has been shown to improve fiber length, and its biosynthesis is regulated by auxin-responsive factors such as GhARF18. This indicates that GA functions downstream of auxin in the regulatory pathway of fiber development (Zhu et al., 2021). Additionally, the degradation of DELLA proteins, which are negative regulators of GA signaling, further promotes fiber elongation (Sun et al., 2024).

In contrast, cytokinins (CK) and abscisic acid (ABA) have inhibitory effects on cotton fiber growth. CK disrupts the asymmetric accumulation of auxin in the ovule epidermis, thereby inhibiting fiber cell initiation. This antagonistic effect of CK on auxin highlights the complex hormonal interactions that regulate fiber development (Zeng et al., 2019). Similarly, ABA has been reported to inhibit fiber growth, although the exact mechanisms remain to be fully elucidated (Xiao et al., 2019).

4.3 Interaction between hormones in cotton fiber growth

The interaction between different phytohormones is crucial for the regulation of cotton fiber growth. Auxin and gibberellins (GA) work synergistically to promote fiber elongation. Auxin enhances GA biosynthesis by upregulating GA biosynthesis genes, while GA, in turn, promotes cell elongation and division. This synergistic interaction underscores the importance of hormonal balance in fiber development (Zhu et al., 2021).

On the other hand, the interaction between auxin and cytokinins (CK) is antagonistic. CK reduces auxin accumulation in the ovule epidermis, thereby inhibiting fiber cell initiation. This antagonistic relationship highlights the need for a precise hormonal balance to ensure optimal fiber growth (Zeng et al., 2019). Additionally, strigolactones (SLs) integrate both GA and auxin signaling pathways to regulate fiber cell elongation, further illustrating the complex hormonal interplay involved in cotton fiber development (Sun et al., 2024).

5 Epigenetic Regulation of Cotton Fiber Growth

5.1 Role of dna methylation and histone modification in cotton fiber

DNA methylation plays a crucial role in the regulation of cotton fiber growth. Studies have shown that the level of CHH DNA methylation increases during fiber development, which is accompanied by a decrease in RNA-directed DNA methylation (RdDM). This dynamic change is mediated predominantly by an active H3K9me2-dependent pathway rather than the RdDM pathway, which remains inactive during this process. The transition from euchromatin to heterochromatin in developing fibers shapes the DNA methylation landscape, influencing lipid biosynthesis and the modulation of reactive oxygen species during fiber differentiation (Wang et al., 2016).

Histone modifications, particularly histone acetylation and methylation, are also vital in cotton fiber development. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) regulate chromatin structure and gene transcription. Gossypium HATs are differentially expressed in various tissues and stages of fiber development, responding to environmental stresses and hormonal signals. Similarly, HDACs in Gossypium hirsutum are differentially regulated in response to abiotic stresses and phytohormones, indicating their role in fiber development and stress adaptation (Imran et al., 2019; 2020).

5.2 Effects of Non-coding RNAs on cotton fiber development

Non-coding RNAs (ncRNAs), including small RNAs and microRNAs (miRNAs), significantly impact cotton fiber development. Small RNAs regulate the expression of genes involved in cellular growth and development. For instance, miRNAs mediate the degradation of homoeologous mRNAs encoding MYB-domain transcription factors, which are essential for the initiation of seed fibers in cotton. This regulation exemplifies the coevolution between small RNAs and their targets, shaping morphological traits such as fiber length and quality during domestication (Guan et al., 2014).

Additionally, the dynamic roles of small RNAs and DNA methylation during ovule and fiber development have been highlighted. CHH hypermethylation in promoters, induced by siRNAs, up-regulates ovule-preferred genes, while CHH hypermethylation in fibers represses transposable elements and nearby genes, including those related to fiber development. This dual mechanism suggests that ncRNAs and DNA methylation work together to mediate gene expression and facilitate the transition from epidermal to fiber cells (Song et al., 2015).

5.3 Dynamic changes in epigenetic regulation

The dynamic nature of epigenetic regulation in cotton fiber growth is evident through the continuous changes in DNA methylation and histone modifications. DNA methylation levels fluctuate annually, correlating with the expression of DNA demethylases and methyltransferases. These changes affect the promoter regions of key genes regulating cotton fiber growth, such as ERF6, SUR4, and KCS13, demonstrating the importance of temporal regulation in fiber development (Jin et al., 2013; Zhu et al., 2024).

Histone modifications also exhibit dynamic changes during fiber development. The JmjC domain-containing histone demethylase gene family in Gossypium hirsutum shows high expression levels at different developmental stages of fibers. These genes regulate gene transcription and chromatin structure by altering the methylation state of lysine residues, playing a crucial role in fiber development and response to abiotic stresses (Zhang et al., 2020). Furthermore, the regulation of m6A methylation in mRNA affects the stability of fiber elongation-related genes, such as GhMYB44, highlighting the intricate control of gene expression through epitranscriptomic modifications (Xing et al., 2023).

6 Functional Validation and Gene Editing of Key Genes in Cotton Fiber

6.1 Application of RNA interference (RNAi) in cotton fiber gene function analysis

RNA interference (RNAi) has emerged as a powerful tool for functional genomics in cotton, enabling the discovery of genetic sequence functions and the biological roles of key genes involved in fiber development. RNAi technology has replaced previous antisense approaches due to its higher efficiency and specificity. It has been instrumental in elucidating the functions of numerous genes related to fiber development, fertility, somatic embryogenesis, and resistance to biotic and abiotic stresses. For instance, RNAi-mediated silencing of GhMYB212 resulted in reduced sucrose and glucose accumulation in developing fibers, leading to shorter fibers and a lower lint index, thereby highlighting the gene's role in sucrose transport and fiber elongation (Abdurakhmonov et al., 2016; Sun et al., 2019).

Moreover, RNAi has facilitated the identification of genes that regulate secondary cell wall (SCW) biosynthesis in cotton fibers. Silencing of GhERF108, a transcription factor involved in ethylene-auxin signaling crosstalk, led to reduced cell wall thickness and defects in SCW formation. This demonstrates the critical role of GhERF108 in fiber SCW biosynthesis and its interaction with other transcription factors like GhARF7-1 and GhARF7-2 (Wang et al., 2023). These examples underscore the utility of RNAi in dissecting the complex regulatory networks governing cotton fiber development.

6.2 Application of CRISPR/Cas9 in cotton fiber growth regulation

The CRISPR/Cas9 gene editing system has revolutionized plant genetics by enabling precise modifications of target genes. In cotton, CRISPR/Cas9 has been employed to validate the functions of key genes involved in fiber development. For instance, the GhImA gene, encoding a pentatricopeptide repeat (PPR) protein, was identified and edited using CRISPR/Cas9. The null allele of GhImA resulted in a non-fluffy fiber phenotype due to impaired mitochondrial nad7 mRNA splicing, reduced Complex I activities, and disrupted ATP supply and ROS balance (Zhang et al., 2020).

Additionally, CRISPR/Cas9 has been used to investigate the role of transcription factors in fiber elongation. Overexpression of GhBES1.4, a brassinosteroid-responsive transcription factor, promoted fiber elongation, while its silencing reduced fiber length. This highlights the importance of GhBES1.4 in regulating fiber elongation through its target genes, such as GhCYP84A1 and GhHMG1, which are involved in brassinosteroid signaling pathways (Liu et al., 2022). These studies demonstrate the potential of CRISPR/Cas9 in advancing our understanding of the genetic mechanisms underlying cotton fiber growth.

6.3 Functional analysis of key genes

Functional analysis of key genes involved in cotton fiber development has provided valuable insights into the molecular mechanisms regulating fiber growth. For example, the transcription factor GhMYB212 has been shown to regulate sucrose transport into expanding fibers. RNAi-mediated silencing of GhMYB212 led to shorter fibers and reduced sucrose and glucose accumulation, indicating its crucial role in fiber elongation (Sun et al., 2019). Similarly, GhWRKY16, a WRKY transcription factor, was found to positively regulate fiber initiation and elongation by binding to the promoters of genes such as GhHOX3 and GhMYB25, which are essential for early fiber development (Wang et al., 2021).

Another key gene, GhERF108, interacts with auxin response factors GhARF7-1 and GhARF7-2 to mediate ethylene-auxin signaling crosstalk, which is vital for SCW biosynthesis in cotton fibers. Silencing of GhERF108 resulted in reduced cell wall thickness and defects in SCW formation, highlighting its role in fiber development (Wang et al., 2021). These functional analyses underscore the importance of transcription factors and their regulatory networks in controlling various aspects of cotton fiber growth.

7 Influence of Environmental Factors on Cotton Fiber Development and Transcriptional Response

7.1 Impact of environmental factors such as temperature and water on cotton fiber

Environmental factors such as temperature and water availability significantly influence cotton fiber development. Drought stress, for instance, has been shown to adversely affect fiber elongation by down-regulating genes involved in cell wall loosening and expansion processes. High-throughput transcriptomic analyses have identified a number of differentially expressed genes (DEGs) during fiber elongation under drought conditions, highlighting the profound impact of water stress on fiber quality and yield (Padmalatha et al., 2011). Additionally, drought stress leads to the up-regulation of genes encoding transcription factors (AP2-EREBP, WRKY, NAC, and C2H2), osmoprotectants, ion transporters, and heat shock proteins, which are crucial for the plant's defense mechanisms.

Temperature also plays a critical role in cotton fiber development. Elevated temperatures can accelerate fiber maturation but may compromise fiber quality. Proteomic studies have revealed that cotton plants have developed sophisticated mechanisms to respond to environmental stresses, including temperature fluctuations, to mitigate detrimental effects on growth and development. These mechanisms involve the regulation of various stress-responsive proteins and pathways, which are essential for maintaining fiber quality under adverse conditions (Zhou et al., 2014).

7.2 Interaction of environmental signals with cotton fiber transcription factors

Environmental signals interact with cotton fiber transcription factors to modulate fiber development. For example, the overexpression of Arabidopsis transcription factors AtRAV1 and AtRAV2 in cotton has been shown to increase fiber length under drought stress conditions. These transcription factors repress the transcription of FLOWERING_LOCUS_T (FT) and promote stomatal opening, which helps the plant to better manage water stress. The transgenic cotton lines expressing AtRAV1 and AtRAV2 exhibited longer fibers and improved yarn quality under drought conditions compared to control plants (Mittal et al., 2015).

Moreover, the interaction between environmental signals and transcription factors such as WRKY, bHLH/HLH, and ARF is crucial for fiber development. WRKY transcription factors, for instance, are phosphorylated by mitogen-activated protein kinases (MAPKs) in response to environmental cues, which enhances their transcriptional activity on downstream genes involved in fiber initiation and elongation (Wang et al., 2021). Similarly, bHLH/HLH transcription factors like GhFP2 and GhACE1 regulate fiber elongation antagonistically, with their activity being modulated by brassinosteroid-related signals (Lu et al., 2022).

7.3 Environmental adaptation mechanisms of cotton fiber

Cotton plants have evolved various adaptation mechanisms to cope with environmental stresses, ensuring sustainable fiber development. One such mechanism involves the differential expression of genes in response to abiotic stresses. Integrative meta-analyses have identified numerous DEGs between normal and stress conditions, with significant enrichment in pathways related to the ubiquitin-dependent process, biosynthesis of secondary metabolites, and plant hormone signal transduction. These findings highlight the complex regulatory networks that cotton plants employ to adapt to environmental challenges (Tahmasebi et al., 2019).

Additionally, the interaction between phytohormones and transcription factors plays a pivotal role in environmental adaptation. For instance, the transcription factor ERF108 interacts with auxin response factors (ARFs) to mediate fiber secondary cell wall biosynthesis under stress conditions. This interaction enhances the activation of MYB transcription factor genes, which are crucial for cellulose biosynthesis and fiber strength. Such regulatory mechanisms enable cotton plants to maintain fiber quality and yield despite environmental stresses (Wang et al., 2023).

8 Future Perspectives on Transcriptional Regulation of Cotton Fiber

8.1 Limitations of current research on cotton fiber

Despite significant advancements in understanding the transcriptional regulation of cotton fiber growth, several limitations persist. Current research often focuses on specific transcription factors or pathways without integrating the broader network of interactions. For instance, while studies have identified key transcription factors such as GhMYB212 and GhWRKY16 that regulate fiber elongation and initiation, the comprehensive regulatory networks involving these factors remain underexplored (Sun et al., 2019; Wang et al., 2021). Additionally, the functional redundancy and compensatory mechanisms among different transcription factors are not fully understood, which complicates the interpretation of gene function and regulation in fiber development (Hao et al., 2012)..

Another limitation is the reliance on model systems and specific genotypes, which may not fully represent the diversity of cotton species. Most studies utilize Gossypium hirsutum, potentially overlooking unique regulatory mechanisms present in other cotton species. Furthermore, environmental factors and their impact on transcriptional regulation are often not adequately considered, despite evidence that abiotic stresses significantly influence fiber growth and quality (Clark et al., 2009; Ding, 2024). This gap highlights the need for more comprehensive studies that incorporate diverse genotypes and environmental conditions to better understand the transcriptional regulation of cotton fiber growth.

8.2 Integration of Multi-Omics Data and Network Construction

The integration of multi-omics data, including genomics, transcriptomics, proteomics, and metabolomics, offers a promising approach to overcome current research limitations. By combining these datasets, researchers can construct more comprehensive regulatory networks that provide insights into the complex interactions governing fiber development. For example, integrating RNA-seq data with chromatin accessibility assays (ATAC-seq) has revealed key transcription factors and their target genes involved in fiber elongation, such as those identified in the short-fiber mutant ligon linless-2 (Li2) (Hao et al., 2012; Yang et al., 2023). This approach allows for the identification of regulatory motifs and the construction of functional regulatory networks that are crucial for understanding fiber development.

Moreover, systems biology approaches, such as weighted gene co-expression network analysis (WGCNA), can identify co-expression modules and hub genes that play central roles in fiber growth. For instance, WGCNA has uncovered distinct co-expression modules associated with stress response and cell wall organization, highlighting potential candidate genes for improving fiber quality (Lu et al., 2022; Clark et al., 2009). By integrating multi-omics data, researchers can develop predictive models and identify key regulatory nodes that can be targeted for genetic improvement of cotton fiber.

8.3 Application potential of gene editing and synthetic biology in cotton fiber improvement

Gene editing technologies, such as CRISPR/Cas9, offer significant potential for improving cotton fiber quality by precisely modifying key regulatory genes. For instance, targeted editing of genes involved in auxin signaling, such as GhAXR2 and GhSHY2, has demonstrated the ability to enhance fiber elongation by modulating their interactions with auxin response factors (ARFs) (Shan et al., 2014). Similarly, editing genes like GhMYB212, which regulates sucrose transport into fibers, can directly impact fiber length and quality by optimizing carbohydrate supply during fiber development (Sun et al., 2019).

Synthetic biology approaches also hold promise for cotton fiber improvement by enabling the design and construction of novel genetic circuits that enhance fiber growth. For example, synthetic promoters and transcription factors can be engineered to precisely control the expression of key genes involved in fiber elongation and secondary cell wall synthesis. The integration of synthetic biology with traditional breeding and gene editing techniques can accelerate the development of cotton varieties with superior fiber qualities. Additionally, the use of synthetic biology tools to manipulate regulatory networks, such as those involving brassinosteroids and their downstream targets, can further enhance fiber elongation and overall plant growth (Lu et al., 2022; Yang et al., 2023).

9 Conclusion

Recent studies have significantly advanced our understanding of the transcriptional regulation of cotton fiber growth. Key transcription factors such as AUX/IAAs, bHLH/HLH, MYB, NAC, and WRKY have been identified as crucial regulators. For instance, GhAXR2 and GhSHY2, two AUX/IAA proteins, exhibit opposing effects on fiber elongation, with GhAXR2 promoting and GhSHY2 inhibiting fiber growth through interactions with specific ARFs. Similarly, the bHLH/HLH transcription factors GhFP2 and GhACE1 antagonistically regulate fiber elongation, with GhFP2 hindering and GhACE1 promoting fiber development.

Moreover, GhMYB212 has been shown to regulate sucrose transportation into expanding fibers, which is essential for fiber elongation. The NAC transcription factor GhFSN1 positively influences secondary cell wall (SCW) biosynthesis, although it reduces fiber length. Additionally, GhWRKY16, phosphorylated by GhMPK3-1, plays a critical role in fiber initiation and elongation by activating downstream genes. These findings collectively highlight the complex regulatory networks and the pivotal roles of various transcription factors in cotton fiber development.

Future research should focus on elucidating the detailed molecular mechanisms underlying the interactions between different transcription factors and their target genes. For example, while the roles of GhAXR2 and GhSHY2 in fiber elongation have been established, the precise mechanisms by which these proteins interact with ARFs and other regulatory elements need further investigation. Similarly, the antagonistic relationship between GhFP2 and GhACE1 warrants deeper exploration to understand how these factors coordinate to regulate fiber elongation.

Additionally, there is a need to explore the potential of genetic manipulation to enhance fiber quality and yield. For instance, overexpression or silencing of key transcription factors such as GhMYB212 and GhFSN1 could be employed to optimize fiber length and SCW thickness. Furthermore, integrating advanced genomic and transcriptomic techniques, such as ATAC-seq and RNA-seq, could provide comprehensive insights into the regulatory networks governing fiber development. This approach could identify novel regulatory elements and pathways that can be targeted for genetic improvement of cotton fiber traits.

Conflict of Interest Disclosure

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

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