Crop chemical regulation using plant growth regulators (PGRs) represents a key strategy for achieving high-efficiency cotton production in China. This review synthesizes four decades of research on mepiquat chloride (MC), an inhibitory PGR pivotal to optimizing cotton growth architecture, stress resilience, and yield-quality parameters. We detail MC's stage-specific roles—from root development and flowering acceleration to canopy optimization and assimilate partitioning—and its mechanistic interactions with hormones (e.g., gibberellin suppression, cytokinin enhancement) under biotic/abiotic stresses. Furthermore, we conceptualize MC deployment into three evolutionary tiers: (1) symptom-guided remedial application, (2) systemic growth-stage programming, and (3) integrated management with agronomic practices. These paradigms, supported by field validation across China's cotton belts, offer a roadmap for precision regulation. Future advancements in nano-formulations, digital agriculture, and PGR synergism are discussed to unlock next-generation yield frontiers.

Background Thidiazuron (TDZ) is a widely used chemical defoliant in commercial cotton production and is often combined with the herbicide Diuron to form the commercial defoliant mixture known as TDZ·Diuron (T·D, 540 g·L^-1 suspension). However, due to increasing concerns about the environmental and biological risks posed by Diuron, there is an urgent need to develop safer and more effective alternatives. Jasmonic acid (JA) and its derivatives are key phytohormones in organ senescence and abscission.
Results Greenhouse experiments at the seedling stage revealed that Me-JA (0.8 mmol·L^-1) alone did not induce defoliation. However, its co-application with TDZ (0.45 mmol·L^-1) at concentrations of 0.6, 0.8, and 1.0 mmol·L^-1 significantly enhanced defoliation efficacy. The most effective combination—TDZ with 0.8 mmol·L^-1 Me-JA—achieved a 100% defoliation rate at 5 days after treatment (DAT), 23.7 percentage points higher than TDZ alone, and comparable to the commercial TDZ·Diuron formulation with equivalent TDZ content. Field trials conducted in Beijing (Shangzhuang), Hebei (Hejian), and Xinjiang (Shihezi) confirmed that the combination of 0.6 mmol·L^-1 Me-JA with 1.70 mmol·L^-1 TDZ provided optimal defoliation performance. At 21 DAT, the defoliation rate increased by 13.5-16.3 percentage points compared with TDZ alone. Furthermore, boll opening rates improved by 5.7-12.7 percentage points relative to TDZ-only treatments. Phytohormonal analyses from the Shangzhuang site showed that the combined treatment significantly altered hormone levels in both leaves and petioles. Compared with TDZ alone, the mixture reduced concentrations of auxin (IAA), cytokinins (Z + ZR, iP + iPA, DHZ + DHZR), and gibberellic acid (GA₃), while increasing levels of JA, abscisic acid (ABA), and brassinosteroids (BR). These hormonal shifts may underlie the enhanced defoliation observed with the combined treatment. Importantly, the TDZ-Me-JA combination did not adversely affect cotton yield, yield components, or fiber quality.
Conclusion The combination of Me-JA and TDZ has a good defoliation effect without affecting crop yield or fiber quality. And it provides a promising foundation for the development of novel, environmentally friendly cotton defoliants.

Background Mepiquat chloride (MC) is a widely used plant growth regulator in cotton (Gossypium hirsutum L.). It regulates endogenous hormone content and crosstalk to control plant height and promote lateral root (LR) development. However, the roles of cytokinins (CTKs) in the MC-induced increase in LR number in cotton seedlings remain unclear. Therefore, in this study, whole-genome transcriptome analysis was performed to elucidate the molecular mechanisms, CTK transformation, and CTK signaling pathway response to MC in cotton roots.
Results In the present study, MC reduced the contents of the active CTK trans-zeatin (tZ) and N⁶-isopentenyladenine (iP) but increased the levels of the nucleoside CTK trans-zeatin riboside (tZR) and N⁶-isopentenyladenine riboside (iPR). RNA-seq data showed that the CTK biosynthesis genes GhIPTs and active CTK catabolism genes GhCKXs were obviously upregulated after MC treatment. The CTK-activating enzyme gene GhLOGs was repressed compared with the control. Furthermore, MC inhibited the expression of GhAHK4 and GhARR2/12, which are involved in the CTK signaling pathway, and activated the IAA-IAA14-ARF7/19 signaling module. Meanwhile, MC increased the expression levels of genes involved in sucrose synthesis, the cell cycle, cell division, and cell wall biosynthesis pathways. Silencing the GhCKX family separately decreased the LR number and active indole-3-acetic acid (IAA) level. The expression levels of GhPIN1, GhARF7, GhARF19, GhLBD16, GhLBD18, GhLBD29, and GhLBD33 were downregulated, but GhARR2/12 and GhIAA14 were upregulated. The total content of active CTKs was noticeably increased. The results of silencing the GhLOGs family were opposite to those of silencing GhCKXs. Silencing GhARR12 could upregulate GhPIN1 expression and increase LR number. In addition, the silenced GhCKXs, GhLOGs, and GhARR12 were less responsive to MC-induced LR growth than the control.
Conclusion These results suggested that MC treatment could upregulate CTK-nucleoside biosynthesis and CTK metabolism genes to decrease active CTK levels, promoting crosstalk between CTKs and auxin signaling pathways to enhance LR initiation.

Background Aquaporins (AQPs) are integral membrane proteins belonging to the major intrinsic protein (MIP) family, playing a crucial role in water transport, cell elongation, and stress responses. However, their evolutionary dynamics and functional roles in Gossypium species remain poorly characterized.
Results In the present study, a total of 55, 54, 54, 103, 106, 108, and 104 AQP genes were found in G. herbaceum, G. arboreum, G. raimondii, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii, respectively. Phylogenetic analysis classified them into five conserved subfamilies (PIP, TIP, NIP, SIP, and XIP), with 95 genes showing synteny across species and 17 displaying divergence, suggesting subgenome differentiation. Transcriptome analysis revealed that specific GbAQP genes are involved in early salt stress responses and fiber development. Physiological assays demonstrated stronger salt tolerance in tetraploid cottons, particularly G. darwinii, compared with diploids. Co-expression network analysis linked AQPs to abiotic stress and fiber traits, and virus-induced gene silencing (VIGS) confirmed four AQP genes as critical for salt tolerance.
Conclusion This study provides comprehensive insights into the evolution, expression, and functional roles of AQPs in cotton, identifying key candidate genes for improving salt tolerance and fiber quality in Gossypium species.

One of the solutions to the global warming risk and other climate issues is to concentrate on research and development of utilizing biomass as a fossil fuel alternative. The current estimate of cotton residue waste in the world is about 50 million tons. This massive volume of biomass waste should be turned into clean energy to avert burning the stalks in open fields after cotton harvesting. Therefore, harmful emissions such as CO₂ will be reduced. This study aims to investigate the published literature to comprehend the bioenergy production from the thermal treatment of cotton stalks, including combustion, pyrolysis, carbonization, torrefaction, liquefaction, and gasification. Furthermore, the future outlook, utilization, and prospective challenges of agricultural biomass for biofuel production are discussed. According to the literature, biochar and bio-oil derived from cotton stalks have high heating values of about 27.5 and 37.2 MJ·kg^-1, respectively. These values are double those of cotton stalk raw materials, which make it a good candidate for bioenergy production. This article offers valuable insight into cotton stalk utilization via thermochemical treatment and provides a solid reference for researchers, policymakers, and other stakeholders in this field.

Background Achieving a synergistic enhancement in both the yield and insect resistance of Bt cotton holds substantial importance for boosting farmers' income and ecological advantages. This study investigated the impact of amino acid foliar fertilizer (AAF) on the yield and Cry1Ac protein (CP) content, providing valuable insights for enhancing its productivity and insect-resistance capabilities. In 2021, Sikang 1 and Sikang 3 were treated with AAF once (A1) and water (CK) during the peak flowering stage. In 2022, AAF was sprayed one (A1), two (A2), and three (A3) times, respectively, with CK serving as the control.
Results Compared with the control, the A3 treatment increased seed cotton yield (SCY) by 16.0% and CP by 40.98% at 30 days after flowering. AAF application enhanced soluble protein content (SP) and glutamate pyruvate transaminase (GPT) activity, while suppressing protease and peptidase activities. Concurrently, AAF improved sucrose metabolism through elevated sucrose content and increased activities of sucrose synthase (SS) and sucrose conversion enzyme (SCE), which were also positively correlated with yield. A lower ratio of carbon-to-nitrogen (C/N) was linked to higher yields and CP content. Path analysis confirmed that SP, GPT, SS, and SCE demonstrated positive effects on CP content and SCY, respectively. Peptidase activity had negative effects on CP and SCY. The C/N ratio had negative effects on SCY and CP, respectively.
Conclusions Triple foliar application of AAF maintained lower C/N ratios with enhanced carbon metabolism and protein synthesis capacity, thereby simultaneously increasing both Cry1Ac protein content and yield in Bt cotton. These findings provide critical insights for improving both pest resistance and agronomic performance in Bt cotton cultivation.

Background Plant natriuretic peptides (PNPs) are a class of peptide hormones that regulate plant responses to salt stress, water balance, and pathogen attacks. However, the precise underlying role of PNPs in plant defense mechanisms remains poorly understood.
Results In this study, we investigated the role of the cotton gene GhEG45 in plant response to Verticillium dahliae infection. GhEG45 overexpression in cotton (Gossypium hirsutum) enhanced resistance to V. dahliae by increasing the expression levels of salicylic acid (SA)-related defense genes and upregulating antioxidant activities. GhEG45 expression was significantly induced by both V. dahliae infection and exogenous treatments with SA, hydrogen peroxide (H₂O₂), and other stress signals, which indicates its potential involvement in modulating plant defense mechanisms via SA signaling, oxidative stress pathways, and cell wall-based defenses. Transcriptomic analysis showed that GhEG45 regulates SA signaling and reactive oxygen species (ROS) metabolism. GhEG45 silencing via virus-induced gene silencing (VIGS) increased susceptibility to V. dahliae, impaired SA signaling, and disrupted ROS regulation.
Conclusions This study provides evidences that GhEG45 plays a pivotal role in defense against V. dahliae infection in cotton, primarily by regulating SA signaling and ROS metabolism. Although GhEG45 shares some functional characteristics with PNPs, further structural and biochemical studies are needed to comprehensively categorize GhEG45 as a natriuretic peptide. Our findings suggest that GhEG45 enhances cotton resistance to V. dahliae by potentiating defense responses.

Background Cotton lodging has become increasingly prevalent due to extreme environmental conditions and agronomic practices, severely compromising yield, fiber quality, and mechanical harvesting efficiency. However, research on cotton lodging remains limited, with most studies focusing on individual or isolated indices rather than a comprehensive system. This study systematically compared four lodging-resistant varieties (LR-1, LR-2, LR-3, LR-4) and four lodging varieties (L-1, L-2, L-3, L-4) across multiple indices: morphological traits, boll distribution, internode filling degree, stem density, mechanical strength, anatomical structure, and chemical composition.
Results The results showed that at the boll-opening stage, lodging-resistant varieties exhibited higher density in the first (increased by 11.6%) and third (increased by 23.5%) basal internodes compared with lodging varieties and significantly greater filling degree in the first (increased by 22.6%), second (increased by 23.1%), and third (increased by 26.1%) basal internodes; significantly higher stem puncture strength (increased by 41.2%) and stem bending resistance (increased by 38.2%); and a significantly lower stem lodging coefficient (19.0% lower in lodging-resistant varieties). Additionally, lodging-resistant varieties showed significantly enhanced anatomical structures, including greater cortex thickness, more mechanical tissue layers, and larger pith cavity, xylem, and phloem areas. Conversely, no significant differences were observed in morphological traits, boll distribution, or chemical composition between the lodging-resistant and lodging types.
Conclusion Lodging-resistant varieties exhibited thicker cortical tissue and mechanical tissue layers, along with larger xylem area and phloem area in basal internodes. These structural characteristics provide superior support for the filling degree and density of basal internodes, thereby enhancing stem puncture strength and bending resistance, and ultimately improving lodging resistance in cotton. These findings provide a theoretical basis for reducing the occurrence of cotton lodging.

Background The bromodomain (BRD) proteins play a pivotal role in regulating gene expression by recognizing acetylated lysine residues and acting as chromatin-associated post-translational modification-inducing proteins. Although BRD proteins have been extensively studied in mammals, they have also been characterized in plants like Arabidopsis thaliana and Oryza sativa, where they regulate stress-responsive genes related to drought, salinity, and cold. However, their roles in cotton species remain unexplored.
Results In this genome-wide comparative analysis, 145 BRD genes were identified in the tetraploid species (Gossypium hirsutum and G. barbadense), compared with 82 BRD genes in their diploid progenitors (G. arboreum and G. raimondii), indicating that polyploidization significantly influenced BRD gene evolution. Gene duplication analysis revealed 78.85% of duplications were segmental and 21.15% were tandem among 104 in-paralogous gene pairs, contributing to BRD gene expansion. Gene structure, motif, and domain analyses demonstrated that most genes were intron-less and conserved throughout evolution. Syntenic analysis revealed a greater number of orthologous gene pairs in the Dt sub-genome than in the At sub-genome. The abundance of regulatory, hormonal, and defense-related cis-regulatory elements in the promoter region suggests that BRD genes play a role in both biotic and abiotic stress responses. Protein-protein interaction analysis indicated that global transcription factor group E (GTE) transcription factors regulate BRD genes. Expression analysis revealed that BRD genes are predominantly involved in ovule development, with some genes displaying specific expression patterns under heat, cold, and salt stress. Furthermore, qRT-PCR analysis demonstrated significant differential expression of BRD genes between the tolerant and sensitive genotype, underscoring their potential role in mediating drought and salinity stress responses.
Conclusions This study provides valuable insights into the evolution of BRD genes across species and their roles in abiotic stress tolerance, highlighting their potential in breeding programs to develop drought and salinity tolerant cotton varieties.

Cotton is an essential agricultural commodity, but its global yield is greatly affected by climate change, which poses a serious threat to the agriculture sector. This review aims to provide an overview of the impact of climate change on cotton production and the use of genomic approaches to increase stress tolerance in cotton. This paper discusses the effects of rising temperatures, changing precipitation patterns, and extreme weather events on cotton yield. It then explores various genomic strategies, such as genomic selection and marker-assisted selection, which can be used to develop stress-tolerant cotton varieties. The review emphasizes the need for interdisciplinary research efforts and policy interventions to mitigate the adverse effects of climate change on cotton production. Furthermore, this paper presents advanced prospects, including genomic selection, gene editing, multi-omics integration, highthroughput phenotyping, genomic data sharing, climate-informed breeding, and phenomics-assisted genomic selection, for enhancing stress resilience in cotton. Those innovative approaches can assist cotton researchers and breeders in developing highly resilient cotton varieties capable of withstanding the challenges posed by climate change, ensuring the sustainable and prosperous future of cotton production.

Nitrogen (N) and phosphorus (P) are mineral nutrients essential for plant growth and development, playing a crucial role throughout the plant life cycle. Cotton, a globally significant textile crop, has a particularly high demand for N fertilizer across its developmental stages. This review explores the effects of adequate or deficient N and P levels on cotton growth phases, focusing on their influence on physiological processes and molecular mechanisms. Key topics include the regulation of N- and P-related enzymes, hormones, and genes, as well as the complex interplay of N- and P-related signaling pathways from the aspects of N-P signaling integration to regulate root development, N-P signaling integration to regulate nutrient uptake, and regulation of N-P interactions—a frontier in current research. Strategies for improving N and P use efficiency are also discussed, including developing high-efficiency cotton cultivars and identifying functional genes to enhance productivity. Generally speaking, we take model plants as a reference in the hope of coming up with new strategies for the efficient utilization of N and P in cotton.

Verticillium wilt, caused by the infamous pathogen Verticillium dahliae, presents a primary constraint on cotton cultivation worldwide. The complexity of disease resistance in cotton and the largely unexplored interaction dynamics between the cotton plant host and V. dahliae pathogen pose a crucial predicament for effectively managing cotton Verticillium wilt. Nevertheless, the most cost-effective approach to controlling this disease involves breeding and cultivating resistant cotton varieties, demanding a meticulous analysis of the mechanisms underlying cotton’s resistance to Verticillium wilt and the identification of pivotal genes. These aspects constitute focal points in disease-resistance breeding programs. In this review, we comprehensively discuss genetic inheritance associated with Verticillium wilt resistance in cotton, the advancements in molecular markers for disease resistance, the functional investigation of resistance genes in cotton, the analysis of pathogenicity genes in V. dahliae, as well as the intricate interplay between cotton and this fungus. Moreover, we delve into the future prospects of cutting-edge research on cotton Verticillium wilt, aiming to proffer valuable insights for the effective management of this devastating fungus.

Background Cotton is an industrial crop renowned for its multifaceted applications in the textiles, pharmaceuticals, and biofuel industries. Plant regeneration through somatic embryogenesis (SE) plays a crucial role in the genetic improvement of cotton. There is a strong correlation between SE and zygotic embryogenesis (ZE) in plants. Furthermore, the strategy of ectopic expression of cotton genes into the model plant Arabidopsis has been a widely accepted approach for functional study.
Result Based on previous spatial transcriptomics of cotton somatic embryos, two genes, GhHAT5 and GhCRK29, were identified. They are highly expressed in cotyledon and epidermal cells of cotton cotyledonary embryos, respectively. In this study, GhHAT5 and GhCRK29 were ectopically expressed in Arabidopsis to investigate their functions. The result showed that in Arabidopsis zygotic embryos, the overexpression of GhHAT5 promoted the development of apical embryonic upper-tier cells and embryonic cotyledon, while the overexpression of GhCRK29 promoted the development of apical embryonic lower-tier cells and embryonic radicle. Given the similarities between somatic and zygotic embryogenesis, these findings suggest that GhHAT5 and GhCRK29 are involved in cotton SE. We also speculate that these genes may promote the expression of the Arabidopsis endogenous gene AtSCR, which is crucial for embryonic development.
Conclusion These results revealed that GhHAT5 and GhCRK29 regulate embryonic development and are essential in advancing our understanding of cotton SE and facilitating targeted genetic manipulation strategies to improve industrial crop traits and agricultural sustainability.

Background The geo-traceability of cotton is crucial for ensuring the quality and integrity of cotton brands. However, effective methods for achieving this traceability are currently lacking. This study investigates the potential of explainable machine learning for the geo-traceability of raw cotton.
Results The findings indicate that principal component analysis (PCA) exhibits limited effectiveness in tracing cotton origins. In contrast, partial least squares discriminant analysis (PLS-DA) demonstrates superior classification performance, identifying seven discriminating variables: Na, Mn, Ba, Rb, Al, As, and Pb. The use of decision tree (DT), support vector machine (SVM), and random forest (RF) models for origin discrimination yielded accuracies of 90%, 87%, and 97%, respectively. Notably, the light gradient boosting machine (LightGBM) model achieved perfect performance metrics, with accuracy, precision, and recall rate all reaching 100% on the test set. The output of the LightGBM model was further evaluated using the SHapley Additive exPlanation (SHAP) technique, which highlighted differences in the elemental composition of raw cotton from various countries. Specifically, the elements Pb, Ni, Na, Al, As, Ba, and Rb significantly influenced the model's predictions.
Conclusion These findings suggest that explainable machine learning techniques can provide insights into the complex relationships between geographic information and raw cotton. Consequently, these methodologies enhances the precision and reliability of geographic traceability for raw cotton.

Background Cotton is an important crop providing the most natural fibers all over the world. The cotton genomics community has utilized whole genome sequencing data to construct an elite gene pool in which functional genes are related to agronomic traits. However, the functional validation of these genes is hindered by time-consuming and inefficient genetic transformation methods. Thus, establishing a transient transformation system of high efficiency is necessary for cotton genomics.
Results To improve the efficiency of transient transformation, we used the protoplasts isolated from the etiolated cotyledon as recipient. The enzymatic digestion buffer comprised 1.5% (w/v) cellulase, 0.75% (w/v) macerozyme, and 1% hemicellulase, osmotically buffered with 0.4 mol·L⁻¹ mannitol. After 5 h of dark incubation at 25 ˚C, uniform cotton protoplasts were successfully isolated with a yield of 4.6 × 10⁶ protoplasts per gram (fresh weight) and 95% viability. We incubated 100 μL protoplasts (2.5 × 10⁵·mL⁻¹) with 15 μg plasmid in the solution of 0.4 mol·L⁻¹ mannitol and 40% PEG 4000 for 15 min, ultimately achieving an optimal transient transfection efficiency of 71.47%.
Conclusions This transient system demonstrated effective utility in cellular biology research through successful applications in subcellular localization analyses, bimolecular fluorescence complementation (BiFC) verification, and prime editing vector validation. Through systematic optimization, we established an efficient and expedited protoplast-based transient transformation system and successfully applied this platform to cotton functional genomics studies.

Background Soil available phosphorus (AP) deficiency significantly limits cotton production, particularly in arid and saline-alkaline regions. Screening cotton cultivars for low phosphorus (P) tolerance is crucial for the sustainable development of cotton production. However, the effect of different growth media on the screening outcomes remains unclear. To address this, we evaluated the low P tolerance of 25 cotton cultivars through hydroponic culture at two P levels (0.01 and 0.5 mmol•L^-1 KH₂PO₄) in 2018 and field culture with two P rates (0 and 90 kg•hm^-2, in P₂O₅) in 2019.
Results In the hydroponic experiments, principal component analysis (PCA) showed that shoot dry weight (SDW) and P utilization efficiency in shoots (PUES) of cotton seedlings explained over 45% of the genetic variation in P nutrition. Cotton cultivars were subjected to comprehensive cluster analysis, utilizing agronomic traits (SDW and PUES) during the seedling stage (hydroponic) and yield and fiber quality traits during the mature stage (in field). These cultivars were grouped into four clusters: resistant, moderately resistant, moderately sensitive, and sensitive. In low P conditions (0.01 mmol•L^-1 KH₂PO₄ and 4.5 mg•kg^-1 AP), the low-P-resistant cluster showed significantly smaller reductions in SDW (54%), seed cotton yield (3%), lint yield (- 2%), fiber length (- 1%), and fiber strength (- 3%) compared with the low-P-sensitive cluster (75%, 13%, 17%, 7%, and 9%, respectively). The increase in PUES (299%) in the resistant cluster was also significantly higher than in the sensitive cluster (131%). Four of the eight low-P-tolerant cotton cultivars identified in the field and six in the hydroponic screening overlapped in both screenings. Two cultivars overlapped in both screening in the low-P-sensitive cluster.
Conclusion Based on the screenings from both field and hydroponic cultures, ZM-9131, CCRI-79, JM-958, and J-228 were identified as low-P-tolerant cotton cultivars, while JM-169, XM-33B, SCRC-28, and LNM-18 were identified as low-P-sensitive cotton cultivars. The relationship between field and hydroponic screening results for low-P-tolerant cotton cultivars was strong, although field validation is still required. The low P tolerance of these cultivars was closely associated with SDW and PUES.