Anthocyanin gene enrichment in the distal region of cotton chromosome A07: mechanisms of reproductive organ coloration.

Introduction: The biosynthesis of secondary metabolites like anthocyanins is often governed by metabolic gene clusters (MGCs) in the plant ancestral genome. However, the existence of gene clusters specifically regulating anthocyanin accumulation in certain organs is not well understood. Methods and results: In this study, we identify MGCs linked to the coloration of cotton reproductive organs, such as petals, spots, and fibers. Through genetic analysis and map-based cloning, we pinpointed key genes on chromosome A07, such as PCC/GhTT19, which is involved in anthocyanin transport, and GbBM and GhTT2-3A, which are associated with the regulation of anthocyanin and proanthocyanidin biosynthesis. Our results demonstrate the coordinated control of anthocyanin and proanthocyanidin pathways, highlighting the evolutionary significance of MGCs in plant adaptation. The conservation of these clusters in cotton chromosome A07 across species underscores their importance in reproductive development and color variation. Our study sheds light on the complex biosynthesis and transport mechanisms for plant pigments, emphasizing the role of transcription factors and transport proteins in pigment accumulation. Discussion: This research offers insights into the genetic basis of color variation in cotton reproductive organs and the potential of MGCs to enhance our comprehension of plant secondary metabolism.

Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects.

The Single-cell Assay for Transposase-Accessible Chromatin with high throughput sequencing (scATAC-seq) has gained increasing popularity in recent years, allowing for chromatin accessibility to be deciphered and gene regulatory networks (GRNs) to be inferred at single-cell resolution. This cutting-edge technology now enables the genome-wide profiling of chromatin accessibility at the cellular level and the capturing of cell-type-specific cis-regulatory elements (CREs) that are masked by cellular heterogeneity in bulk assays. Additionally, it can also facilitate the identification of rare and new cell types based on differences in chromatin accessibility and the charting of cellular developmental trajectories within lineage-related cell clusters. Due to technical challenges and limitations, the data generated from scATAC-seq exhibit unique features, often characterized by high sparsity and noise, even within the same cell type. To address these challenges, various bioinformatic tools have been developed. Furthermore, the application of scATAC-seq in plant science is still in its infancy, with most research focusing on root tissues and model plant species. In this review, we provide an overview of recent progress in scATAC-seq and its application across various fields. We first conduct scATAC-seq in plant science. Next, we highlight the current challenges of scATAC-seq in plant science and major strategies for cell type annotation. Finally, we outline several future directions to exploit scATAC-seq technologies to address critical challenges in plant science, ranging from plant ENCODE(The Encyclopedia of DNA Elements) project construction to GRN inference, to deepen our understanding of the roles of CREs in plant biology.

GhTPPA_2 enhancement of tobacco sugar accumulation and drought tolerance.

Trehalose metabolism plays an important role in plant growth and response to abiotic stress. Trehalose-6-phosphate (Tre6P) can help regulate sugar homeostasis and act as an indication signal for intracellular sugar levels. Crop productivity can be greatly increased by altering the metabolic level of endogenous trehalose in plants, which can optimize the source-sink connection. In this study, the upland cotton GhTPP protein family was first homologously compared and 24 GhTPP genes were found. Transcriptome analysis revealed that GhTPP members had obvious tissue expression specificity. Among them, GhTPPA_2 (Gh_A12G223300.1) was predominantly expressed in leaves and bolls. The results of subcellular localization showed that GhTPPA_2 is localized in the chloroplast. Via PlantCare, we analyzed the promoters and found that the expression of GhTPPA_2 may be induced by light, abiotic stress, and hormones such as abscisic acid, ethylene, salicylic acid and jasmonic acid. In addition, GhTPPA_2 was overexpressed (TPPAoe) in tobacco, and we found that the TPPase activity of TPPAoe tobacco increased by 66 %. Soluble sugar content increased by 39 % and starch content increased by 27 %. Whereas, the transgenic tobacco had obvious growth advantages under 100 mM mannitol stress. Transcriptome sequencing results showed that the differential genes between TPPAoe and control were considerably enriched in functions related to photosynthesis, phosphate group metabolism, and carbohydrate metabolism. This study shows that GhTPPA_2 is involved in regulating sugar metabolism, improving soluble sugar accumulation and drought stress tolerance of tobacco, which provides theoretical basis for research on high yield and drought tolerance of crops.

Effects of Interface Morphology on the Shear Mechanical Properties of Sand-Concrete Interfaces.

The morphology of the contact surface between cast-in-place engineering structures and soil is generally random. Previous research focusing on the shear mechanical properties of soil-concrete interfaces has predominantly concentrated on the role of interface roughness by constructing regular concrete surface types, largely neglecting the potential impact of the roughness morphology (i.e., the morphology of the concrete surface). In this study, concrete blocks with the same interface roughness and different roughness morphologies were constructed based on the sand-cone method, including random rough surface, triangular groove surface, rectangular groove surface, trapezoid groove surface, and semicircular groove surface. A series of direct shear tests were conducted on the rough and smooth sand-concrete interfaces, as well as on natural sand. Through these tests, we examined the shear mechanical behavior and strength of the sand-concrete interfaces, and analyzed the underlying shear mechanisms. The results showed that: (i) the interface morphology had little effect on the variation in the shear stress-displacement curve of sand-concrete interfaces, and it had a significant influence on the shear strength of the interfaces; (ii) under the same normal stress, the shear strength of the sand-concrete interfaces with a random rough surface was the greatest, followed by the triangular groove surface, while the shear strength of the rectangular groove surface proved the lowest; (iii) the shear strength of the sand-concrete interfaces with the same roughness was affected by the size of the contact area between the concrete plane and the sand, that is, a larger contact area correlated with a decrease in shear strength. It can be concluded that the shear strength value of a sand-concrete surface with the triangular groove is the closest to the shear strength of a random rough interface. By gaining a deep understanding of the effects of different contact surface morphologies on shear strength and shear behavior, significant insights can be provided for optimizing engineering design and enhancing engineering performance.

UAV-based time-series phenotyping reveals the genetic basis of plant height in upland cotton.

Plant height (PH) is an important agronomic trait affecting crop architecture, biomass, resistance to lodging and mechanical harvesting. Elucidating the genetic governance of plant height is crucial because of the global demand for high crop yields. However, during the rapid growth period of plants the PH changes a lot on a daily basis, which makes it difficult to accurately phenotype the trait by hand on a large scale. In this study, an unmanned aerial vehicle (UAV)-based remote-sensing phenotyping platform was applied to obtain time-series PHs of 320 upland cotton accessions in three different field trials. The results showed that the PHs obtained from UAV images were significantly correlated with ground-based manual measurements, for three trials (R2 = 0.96, 0.95 and 0.96). Two genetic loci on chromosomes A01 and A11 associated with PH were identified by genome-wide association studies (GWAS). GhUBP15 and GhCUL1 were identified to influence PH in further analysis. We obtained a time series of PH values for three field conditions based on remote sensing with UAV. The key genes identified in this study are of great value for the breeding of ideal plant architecture in cotton.

Natural variation in Beauty Mark is associated with UV-based geographical adaptation in Gossypium species.

BACKGROUND: Anthocyanins, a class of specialized metabolites that are ubiquitous among plant species, have attracted a great deal of attention from plant biologists due to their chemical diversity. They confer purple, pink, and blue colors that attract pollinators, protect plants from ultraviolet (UV) radiation, and scavenge reactive oxygen species (ROS) to facilitate plant survival during abiotic stress. In a previous study, we identified Beauty Mark (BM) in Gossypium barbadense as an activator of the anthocyanin biosynthesis pathway; this gene also directly led to the formation of a pollinator-attracting purple spot. RESULTS: Here, we found that a single nucleotide polymorphism (SNP) (C/T) within the BM coding sequence was responsible for variations in this trait. Transient expression assays of BM from G. barbadense and G. hirsutum in Nicotiana benthamiana using luciferase reporter gene also suggested that SNPs in the coding sequence could be responsible for the absent beauty mark phenotype observed in G. hirsutum. We next demonstrated that the beauty mark and UV floral patterns are associated phenotypes and that UV exposure resulted in increased ROS generation in floral tissues; BM thus contributed to ROS scavenging in G. barbadense and wild cotton plants with flowers containing the beauty mark. Furthermore, a nucleotide diversity analysis and Tajima's D Test suggested that there have been strong selective sweeps in the GhBM locus during G. hirsutum domestication. CONCLUSIONS: Taken together, these results suggest that cotton species differ in their approaches to absorbing or reflecting UV light and thus exhibit variations in floral anthocyanin biosynthesis to scavenge reactive ROS; furthermore, these traits are related to the geographic distribution of cotton species.

Genome-wide identification and expression analysis of the cotton patatin-related phospholipase A genes and response to stress tolerance.

MAIN CONCLUSION: Patatin-related phospholipase A genes were involved in the response of Gossypium hirsutum to drought and salt tolerance. pPLA (patatin-related phospholipase A) is a key enzyme that catalyzes the initial step of lipid hydrolysis, which is involved in biological processes, such as drought, salt stress, and freezing injury. However, a comprehensive analysis of the pPLA gene family in cotton, especially the role of pPLA in the response to drought and salt tolerance, has not been reported so far. A total of 33 pPLA genes were identified in this study using a genome-wide search approach, and phylogenetic analysis classified these genes into three groups. These genes are unevenly distributed on the 26 chromosomes of cotton, and most of them contain a few introns. The results of the collinear analysis showed that G. hirsutum contained 1-5 copies of each pPLA gene found in G. arboreum and G. raimondii. The subcellular localization analysis of Gh_D08G061200 showed that the protein was localized in the nucleus. In addition, analysis of published upland cotton transcriptome data revealed that six GhPLA genes were expressed in various tissues and organs. Two genes (Gh_A04G142100.1 and Gh_D04G181000.1) were highly expressed in all tissues under normal conditions, showing the expression characteristics of housekeeping genes. Under different drought and salt tolerance stresses, we detected four genes with different expression levels. This study helps to clarify the role of pPLA in the response to drought and salt tolerance.

Genetic and transcriptome analysis of a cotton leaf variegation mutant.

In eukaryotic photosynthetic organisms, chloroplast is not only a site for photosynthesis, but it also have a vital role in signal transduction mechanisms. Plants exhibit various colors in nature with various mutants induced by EMS, whose traits are regulated by developmental and environmental factors, making them ideal for studying the regulation of chloroplast development. In this study, the cotton leaf variegated mutant (VAR) induced by EMS was used for this experiment. Genetic analysis revealed that VAR phenotype was a dominant mutation and by performing freehand section inspection, it was noticed that the vascular bundles of VAR were smaller. Chloroplast ultrastructure showed that the stacking of grana thylakoid was thinner and the starch granules were increased significantly in VAR comparedto wild type (WT). Transcriptome analysis found that the KEGG was enriched in photosynthesis pathway, and GO was abundant in zinc ion transmembrane transport, electron transporter and cation binding terms. In addition, GhFTSH5 expression in VAR was significantly higher than WT and the promoter sequence of GhFTSH5 had differences. The results showed that the VAR plant had altered GhFTSH5 expression and disrupted chloroplast structure, which in turn affects plant photosynthesis. More importantly, this study lays a foundation for further analyzing molecular mechanism of cotton variegated phenotypes.

Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway.

Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.

A Rapid and Efficient Method for Isolation and Transformation of Cotton Callus Protoplast.

Protoplasts, which lack cell walls, are ideal research materials for genetic engineering. They are commonly employed in fusion (they can be used for more distant somatic cell fusion to obtain somatic hybrids), genetic transformation, plant regeneration, and other applications. Cotton is grown throughout the world and is the most economically important crop globally. It is therefore critical to study successful extraction and transformation efficiency of cotton protoplasts. In the present study, a cotton callus protoplast extraction method was tested to optimize the ratio of enzymes (cellulase, pectinase, macerozyme R-10, and hemicellulase) used in the procedure. The optimized ratio significantly increased the quantity and activity of protoplasts extracted. We showed that when enzyme concentrations of 1.5% cellulase and 1.5% pectinase, and either 1.5% or 0.5% macerozyme and 0.5% hemicellulase were used, one can obtain increasingly stable protoplasts. We successfully obtained fluorescent protoplasts by transiently expressing fluorescent proteins in the isolated protoplasts. The protoplasts were determined to be suitable for use in further experimental studies. We also studied the influence of plasmid concentration and transformation time on protoplast transformation efficiency. When the plasmid concentration reaches 16 µg and the transformation time is controlled within 12-16 h, the best transformation efficiency can be obtained. In summary, this study presents efficient extraction and transformation techniques for cotton protoplasts.

Overexpression of LT, an Oncoprotein Derived from the Polyomavirus SV40, Promotes Somatic Embryogenesis in Cotton.

Although genetic transformation has opened up a new era for cotton molecular breeding, it still suffers from the limitation problem of long transformation periods, which slows down the generation of new cotton germplasms. In this study, LT gene (SV40 large T antigen), which promotes the transformation efficiency of animal cells, was codon-optimized. Its overexpression vector was transformed into cotton. It was observed that EC (embryogenic callus) formation period was 33% shorter and transformation efficiency was slightly higher in the LT T0 generation than that of control. RNA-seq data of NEC (non-embryonic callus) and EC from LT and control revealed that more DEGs (differential expression genes) in NEC were identified than that of EC, indicating LT mainly functioned in NEC. Further KEGG, GO, and transcription factor analyses showed that DEGs were significantly enriched in brassinosteroid biosynthesis pathways and that bHLH, MYB, and AP2/ERF were the top three gene families, which are involved in EC formation. In addition, the key genes related to the auxin pathway were differentially expressed only in LT overexpression NEC, which caused early response, biosynthesis, and transportation of the hormone, resulting in EC earlier formation. In summary, the results demonstrated that LT can promote somatic embryogenesis in cotton, which provides a new strategy for improving cotton transformation and shortening EC formation time.

Insights Into MicroRNA-Mediated Regulation of Flowering Time in Cotton Through Small RNA Sequencing.

The timing of flowering is a key determinant for plant reproductive. It has been demonstrated that microRNAs (miRNAs) play an important role in transition from the vegetative to reproductive stage in cotton; however, knowledge remains limited about the regulatory role of miRNAs involved in flowering time regulation in cotton. To elucidate the molecular basis of miRNAs in response to flowering time in cotton, we performed high-throughput small RNA sequencing at the fifth true leaf stage. We identified 56 and 43 miRNAs that were significantly up- and downregulated in two elite early flowering cultivars (EFC) compared with two late flowering cultivars (LFC), respectively. The miRNA targets by RNA sequencing analysis showed that GhSPL4 in SBP transcription factor family targeted by GhmiR156 was significantly upregulated in EFCs. Co-expression regulatory network analysis (WGCNA) revealed that GhSOC1, GhAP1, GhFD, GhCOL3, and GhAGL16 act as node genes in the auxin- and gibberellin-mediated flowering time regulatory networks in cotton. Therefore, elucidation of miRNA-mediated flowering time regulatory network will contribute to our understanding of molecular mechanisms underlying flowering time in cotton.

Multi-Dimensional Molecular Regulation of Trichome Development in Arabidopsis and Cotton.

Plant trichomes are specialized epidermal cells that are widely distributed on plant aerial tissues. The initiation and progression of trichomes are controlled in a coordinated sequence of multiple molecular events. During the past decade, major breakthroughs in the molecular understanding of trichome development were achieved through the characterization of various trichomes defective mutants and trichome-associated genes, which revealed a highly complex molecular regulatory network underlying plant trichome development. This review focuses on the recent millstone in plant trichomes research obtained using genetic and molecular studies, as well as 'omics' analyses in model plant Arabidopsis and fiber crop cotton. In particular, we discuss the latest understanding and insights into the underlying molecular mechanisms of trichomes formation at multiple dimensions, including at the chromatin, transcriptional, post-transcriptional, and post-translational levels. We summarize that the integration of multi-dimensional trichome-associated genes will enable us to systematically understand the molecular regulation network that landscapes the development of the plant trichomes. These advances will enable us to address the unresolved questions regarding the molecular crosstalk that coordinate concurrent and ordered the changes in cotton fiber initiation and progression, together with their possible implications for genetic improvement of cotton fiber.

Overexpression of GhKTI12 Enhances Seed Yield and Biomass Production in Nicotiana Tabacum.

Crop molecular breeding primarily focuses on increasing the trait of plant yield. An elongator-associated protein, KTI12, is closely associated with plant biomass and yield. KTI12 is involved in developmental processes of most organs, including the leaf, root, flower, and seed, through regulating cell division and differentiation. Previous work has shown that in upland cotton (Gossypium hirsutum), GhKTI12 regulates plant height, flowering, and tolerance to salt and drought stress. However, little is known about the molecular regulation mechanism of GhKTI12 in plant developmental processes. In this study, we identified the main GhKTI12 (Gh_D02G144400) gene and transformed it into tobacco (Nicotonia tabacum cv NC89). From seven transgenic lines, we obtained three (OE5, OE6 and OE8) with high expression of GhKTI12; compared with wild type plants, these three lines exhibited larger plant size, later flowering, and higher seed yield. Microscopic observation revealed that the number of leaf epidermal cells and stem parenchyma cells was increased by ~55%. Biochemical analysis showed that chlorophyll content and starch accumulation were significantly increased in younger leaves at the top canopy of transgenic plants, which may contribute to improved photosynthetic rate and, in turn, increased seed yield. To understand the molecular mechanism of GhKTI12 in transgenic plants development, two lines (OE6 and OE8) with higher expression levels of GhKTI12 were used as representative plants to conduct RNA-seq analysis. Through transcriptome analysis of the plant's shoot apical meristematic tissue of these two lines, we identified 518 upregulated genes and 406 downregulated genes common to both overexpression lines. A large number of cellular component genes associated with cell division and differentiation, such as RD21, TET8, KTN80, AOX1, AOX2, CP1, and KIC, were found to be upregulated, and genes showing the most downregulation included MADS-box genes related to flowering time, such as MADS6, AP1, AP3, AGL8, AGL6, SEP1, and SEP2. Downregulation of these genes caused delayed flowering time and longer vegetative stage during development. Combined with the upregulation of the yield-related gene RD21, the GhKTI12 transgenic plants could produce a higher seed yield. We here show that the overexpression of GhKTI12 could positively improve key agronomic traits in tobacco by regulating cell proliferation, photosynthesis, and organ development, and suggest that homologs of GhKTI12 may also be important in the genetic improvement of other crop plants.

Increasing floral visitation and hybrid seed production mediated by beauty mark in Gossypium hirsutum.

Hybrid crop varieties have been repeatedly demonstrated to produce significantly higher yields than their parental lines; however, the low efficiency and high cost of hybrid seed production has limited the broad exploitation of heterosis for cotton production. One option for increasing the yield of hybrid seed is to improve pollination efficiency by insect pollinators. Here, we report the molecular cloning and characterization of a semidominant gene, Beauty Mark (BM), which controls purple spot formation at the base of flower petals in the cultivated tetraploid cotton species Gossypium barbadense. BM encodes an R2R3 MYB113 transcription factor, and we demonstrate that GbBM directly targets the promoter of four flavonoid biosynthesis genes to positively regulate petal spot development. Introgression of a GbBM allele into G. hirsutum by marker-assisted selection restored petal spot formation, which significantly increased the frequency of honeybee visits in G. hirsutum. Moreover, field tests confirmed that cotton seed yield was significantly improved in a three-line hybrid production system that incorporated the GbBM allele. Our study thus provides a basis for the potentially broad application of this gene in improving the long-standing problem of low seed production in elite cotton hybrid lines.

Computational Drug Repurposing Based on a Recommendation System and Drug-Drug Functional Pathway Similarity.

Drug repurposing identifies new clinical indications for existing drugs. It can be used to overcome common problems associated with cancers, such as heterogeneity and resistance to established therapies, by rapidly adapting known drugs for new treatment. In this study, we utilized a recommendation system learning model to prioritize candidate cancer drugs. We designed a drug-drug pathway functional similarity by integrating multiple genetic and epigenetic alterations such as gene expression, copy number variation (CNV), and DNA methylation. When compared with other similarities, such as SMILES chemical structures and drug targets based on the protein-protein interaction network, our approach provided better interpretable models capturing drug response mechanisms. Furthermore, our approach can achieve comparable accuracy when evaluated with other learning models based on large public datasets (CCLE and GDSC). A case study about the Erlotinib and OSI-906 (Linsitinib) indicated that they have a synergistic effect to reduce the growth rate of tumors, which is an alternative targeted therapy option for patients. Taken together, our computational method characterized drug response from the viewpoint of a multi-omics pathway and systematically predicted candidate cancer drugs with similar therapeutic effects.

Macroeconomic Image Analysis and GDP Prediction Based on the Genetic Algorithm Radial Basis Function Neural Network (RBFNN-GA).

The prediction of gross domestic product (GDP) is a research hotspot, and its importance is self-evident. Its complex internal change mechanism also increases the difficulty of analyzing GDP data. The genetic algorithm (GA) is applied to the parameter design of the radial basis function neural network (RBFNN) based on genetic algorithm optimization (RBFNN-GA). An economic zone GDP image prediction model is proposed, which realizes the optimal design of the center vector, the base width vector of the RBFNN node function, and the weight between the hidden layer and output layer. Based on the GDP data over the years, this paper uses the RBFNN-GA prediction model to analyze and predict the GDP image and compares the image prediction results. The results show that the genetic algorithm is used to optimize RBFNN, which gives full play to the advantages of the two algorithms. The relative error of the RBFNN-GA prediction model is only 3.52%. Compared with the prediction results, the prediction accuracy is significantly higher than the ARIMA time series model and GM (1,1) model.

China's COVID-19 Vaccination Strategy and Its Impact on the Global Pandemic.

Public health crises are challenging for governments and health systems. Vaccines are a key solution to viruses, and immunization has always played a critical role during public health crises in the past century. In the context of coronavirus disease 2019 (COVID-19), we explore China's vaccination strategies and challenges. Accordingly, we identify the causes of the high vaccination rate in China, including technical and nontechnical factors. Considering the impact of China's high vaccination rate on the global pandemic, we argue that it has strengthened China's opportunities and capabilities to participate in global development, enhanced the equity of vaccines and given the world community more choices.

Fuzzy Comprehensive Evaluation Model of M&A Synergy Based on Transfer Learning Graph Neural Network.

With the rapid development of modern China and the influx of capital, the number of companies has gradually increased. However, most companies cannot operate for a long time due to various reasons. Therefore, mergers and acquisitions have occurred. Large companies merge small companies to some extent. The number of employees can be guaranteed, and the market can be stabilized. However, mergers and acquisitions also have higher risks. As the pace of mergers and acquisitions accelerates, there are more and more cases of failed mergers and acquisitions. The synergy effect of mergers and acquisitions is an important indicator to judge the performance of mergers and acquisitions. This article measures the synergy obtained by the main enterprise from the perspective of performance changes, establishes an evaluation model through the rate of change of financial indicators and migration learning, estimates it through a neural network model, and conducts an empirical analysis on it. The transfer learning neural network has been studied in depth. The research of this article is to accurately assess the synergy effect obtained after mergers and acquisitions and to analyze whether the company can profit from mergers and acquisitions, so as to provide a reference for subsequent mergers and acquisitions between companies.

Elevation of GhDREB1B transcription by a copy number variant significantly improves chilling tolerance in cotton.

MAIN CONCLUSION: The elevation of transcript levels of GhDREB1B causes the accumulation of osmoregulants and mitigation of reactive oxygen species, which contributes to the enhanced resistance to chilling stress in AiSheng98 cotton. Low temperature is one of the key environmental stresses that impairs cotton growth and restricts fiber productivity. Dehydration responsive element binding (DREB) transcription factors play an important role in cold response in plants by modulating the transcription level of cold-responsive genes to protect the plants from low-temperature stress. Here, we showed that GhDREB1B, a copy number variant in the AiSheng98 (AS98) cotton mutant, significantly improved chilling tolerance in cotton seedlings, while silencing of GhDREB1B made transgenic cotton sensitive to chilling stress in AS98 cotton compared with control plants. Elevated GhDREB1B transcript level activated the expression of major cold-responsive genes. Genome-wide expression profiling by RNA sequencing revealed the upregulation of genes related to fatty acids, lipid proteins, osmoprotection, and anti-oxidative enzymes in AiSheng98. Excessive accumulation of malondialdehyde (MDA) and higher ion leakage rates occurred in wild-type LFH10 plants when compared to those of Aisheng98 during chilling stress, signifying lower chilling tolerance in the wild-type than in Aisheng98. Furthermore, the Aisheng98 mutant under chilling stress accumulated higher levels of free proline and soluble sugar than LFH10 accumulated. These results suggest that GhDREB1B is a positive regulator and its variant can alter the expression patterns of major low-temperature stress-related genes and enhance chilling tolerance in cotton.