Glyphosate, one of the most widely used and effective herbicides worldwide, plays a critical role in weed management. However, its application can indirectly compromise crop yield and fiber quality while controlling weeds. Consequently, breeding crop varieties that simultaneously exhibit high herbicide tolerance, high yield, and excellent quality has become a major goal in current crop breeding. To address this critical gap, we successfully developed a transgenic upland cotton line, designated as L397-1, by co-transforming the elite cultivar ZM24 with two functional genes: the herbicide-resistant g10evo-epsps and the high-yield csRRM2. Phenotypic analysis showed that L397–1 plants exhibited significantly enhanced tolerance to glyphosate, as well as increased yield and fiber length, indicating that this strategy effectively pyramids high-yield, high-quality, and high-herbicide-resistance traits. Furthermore, comprehensive environmental safety assessments were conducted on the transgenic plants, covering their competitive fitness in both wasteland and cultivated habitats, field arthropod community structure, incidence of major diseases, and the population density and species richness of harmful pests. The results revealed no significant differences between the transgenic L397–1 and its recipient ZM24 across all evaluated ecological parameters, supporting the ecological safety and application potential of L397–1 for future breeding utilization. In summary, this study establishes an integrated chain from “trait pyramiding technology development—germplasm innovation—multidimensional evaluation of breeding value”, providing new insights for the synergistic improvement of multiple traits and their utilization in crop breeding.

[This corrects the article DOI: 10.3389/fpls.2026.1841757.].

IntroductionCotton fiber development is a critical biological process underlying fiber quality, and its regulation involves multiple molecular layers, including transcription, translation, and metabolism.MethodsTo systematically elucidate the molecular basis of fiber development in Gossypium hirsutum, we selected two cultivars with contrasting fiber quality, Sumian 11 (SM11) and Yumian 5 (YM5), and conducted integrated transcriptomic, proteomic, and metabolomic analyses of fibers collected at 15, 20, 25, and 30 days post anthesis (DPA).ResultsAs fiber development progressed, the numbers of differentially expressed genes, proteins, and accumulated metabolites increased in both cultivars, indicating extensive molecular reprogramming during the later stages of development. Cross-omics comparisons identified plant hormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, cutin, suberin and wax biosynthesis, and ABC transporters as core pathways commonly involved in fiber development. SM11 exhibited stronger enrichment of phenylpropanoid metabolism, cytochrome P450, and MAPK signaling, whereas YM5 showed more pronounced enrichment of ribosome-related processes, fatty acid elongation, and nitrogen metabolism. Proteomic and metabolomic analyses further confirmed substantial differences between the two cultivars in phenylpropanoid and flavonoid metabolism, sugar metabolism, and lipid metabolism. Integrated multi-omics analysis further demonstrated that phenylpropanoid and flavonoid biosynthesis constitute key coordinated modules across the three omics layers. Metabolites such as taxifolin, dihydromyricetin, and sinapaldehyde were closely associated with candidate genes and proteins, together forming an interconnected regulatory network.DiscussionThese findings provide mechanistic insights into the molecular regulation of cotton fiber development and identify candidate molecular targets for fiber quality improvement in G. hirsutum.

Cotton Verticillium wilt seriously threatens global cotton production, necessitating the development of resistant cultivars through molecular breeding. Members of the ethylene response factor (ERF) family function as pivotal transcriptional regulators of the ethylene signaling pathway, orchestrating plant defensive responses against pathogen invasion. Here, through comprehensive phenotypic and transcriptional analyses of lignin biosynthesis genes in AtERF49-overexpressing lines, loss-of-function mutants, dominant repressor plants, and GhERF49-silenced cotton plants (TRV-VIGS), we demonstrate that AtERF49 functions as a negative regulator of Verticillium wilt resistance. Overexpression of AtERF49 significantly compromised defense responses in Arabidopsis thaliana, whereas GhERF49 silencing enhanced cotton resistance to Verticillium wilt. Transcription analysis showed that ERF49-mediated susceptibility correlates with suppression of lignin biosynthesis-related genes following pathogen challenge, suggesting that ERF49 interferes with inducible cell wall fortification. These findings elucidate a previously unrecognized negative regulatory node linking ethylene signaling to lignin-mediated disease resistance, providing promising biotechnological targets for engineering durable Verticillium wilt resistance in cotton and related crops.

Microtubules (MTs) are crucial for cell division, growth, development and morphogenesis in plants. Cotton fibres are single-celled trichomes that originate from the epidermal cells of the ovule, making them an excellent model for studying plant cell differentiation and rapid elongation. However, the roles of MTs in cotton fibre development remain incompletely understood. In this study, we identified GhTTLL12, a tubulin-tyrosine ligase-like protein 12, as a positive regulator of fibre initiation and elongation via Gh-Gb introgression analysis. GhTTLL12 was preferentially expressed during the rapid elongation stage of cotton fibres. Overexpression of GhTTLL12 enhanced plant height, root length, fibre cell protrusion number and fibre length in cotton. Conversely, CRISPR/Cas9-mediated knockout of GhTTLL12 led to opposite phenotypes, thereby significantly reducing fibre quality. MT co-sedimentation and immunofluorescence assays demonstrated that GhTTLL12 binds directly to MTs and promotes their assembly while facilitating the formation of transverse MT arrays in elongating fibres. Further investigation of the molecular mechanisms revealed that after GhTTLL12 is recruited into the nucleus by GhTUB8, it promotes mitosis in ovule epidermal cells upon activation by GhMML3, increasing the number of fibre cell protrusions. GhMYB86, a negative regulator of cotton fibre elongation, represses GhTTLL12 transcription in the nucleus, leading to attenuated mitotic activity. Cytoplasmic GhTTLL12 modulates fibre cell elongation by regulating MT assembly and ordered arrangement. Collectively, our findings define a GhMML3/GhMYB86-GhTTLL12-GhTUB8 regulatory module that links stage-specific transcriptional regulation to MT remodelling during cotton fibre development, providing new insights into the improvement of fibre quality and yield.

The origin and evolutionary dynamics of long non-coding RNAs (lncRNAs) represent a pivotal frontier in plant functional genomics. Here, we investigated pseudo-GhFAD2-1 (pGhFAD2-1), a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum, delineating its evolutionary origin and structural dynamics through a comprehensive cross-genomic comparative strategy. Homologous sequence identification, phylogenetic reconstruction, and molecular evolutionary analyses were conducted across 27 Gossypium species representing the A, B, D, E, F, G, K, and AD genomes. Our findings reveal that pGhFAD2–1 originated from a tandem duplication event of GhFAD2-1D in the D-genome ancestor approximately 5 million years ago (MYA). This duplicated locus was subsequently disrupted by a 1,221-bp exogenous sequence insertion, which abolished its protein-coding capacity and catalyzed the emergence of this novel lncRNA transcript. Subjected to strong purifying selection, this reorganized locus retained its core functional domain and exhibited high-fidelity inheritance (sequence identity>85%) across D-genome diploids and AD-genome allotetraploids. Conversely, only fragmented remnants or complete deletions of this locus were detected in non-D genome Gossypium species. This study systematically characterizes the evolutionary trajectory and subgenomic conservation of pGhFAD2-1, elucidating its adaptive significance as a D-lineage-specific lncRNA. These findings provide novel insights into how lineage-specific structural variations rewire epigenetic regulatory networks to drive adaptive diversification in allopolyploid crops, establishing an evolution-informed molecular target for the synergistic genetic improvement of cotton fiber and seed oil traits.

The soil-borne fungal pathogen Verticillium dahliae (V. dahliae) is the causal agent of Verticillium wilt (VW), a vascular disease that severely threatens global cotton production. Although cell wall lignification represents a cornerstone of plant immunity, the precise regulatory circuits that bridge this structural reinforcement with Verticillium dahliae resistance in cotton have yet to be fully elucidated. Here, we demonstrate that the NAC transcription factor GhNAC043 is a key positive regulator of this defense. GhNAC043 expression was rapidly induced upon V. dahliae infection. Silencing GhNAC043 in cotton compromised resistance, reducing lignin accumulation and downregulating lignin biosynthesis genes. Conversely, heterologous overexpression of GhNAC043 in Arabidopsis enhanced VW tolerance. We further identified GhBPM2 as a nuclear interaction partner of GhNAC043. Profiling of the transcriptome demonstrated that the GhNAC043-GhBPM2 module alters the expression profile of genes pivotal for jasmonic acid (JA) and abscisic acid (ABA) signal transduction. Collectively, these results highlight a previously unknown regulatory pathway in which the GhNAC043-GhBPM2 complex drives lignin deposition through the modulation of JA and ABA signaling, thereby fortifying cotton against VW infection.

Auxin homeostasis is hypothesized to play an important role in the growth-defense trade-off in plants; however, the potential mechanisms by which auxin metabolism correlates with cell wall dynamics and immune signaling during vascular pathogen infection in cotton warrant further investigation. In this study, we characterized GhGH3.1, an IAA-conjugating candidate belonging to the GH3 class II lineage, and explored its potential involvement in defense responses against Verticillium dahliae (V. dahliae) infection in Gossypium hirsutum. GhGH3.1 appears evolutionarily conserved across Gossypium species, exhibited a root-predominant expression pattern, and was induced upon V. dahliae challenge. Functional investigations via transient virus-induced gene silencing (VIGS) indicated that the knockdown of GhGH3.1 in cotton was associated with an altered host susceptibility; complementarily, its heterologous expression within Arabidopsis thaliana was associated with relative tolerance. Pairwise interaction assays tentatively showed that the GhGH3.1 protein physically associates with the epidermis development-related protein GhPDF1. Comparative transcriptomic and physiological profiling further indicated that GhGH3.1 deficiency was accompanied by transcriptional co-alterations in jasmonic acid (JA) signaling marker genes, secondary cell wall structural components, and reactive oxygen species (ROS) accumulation. Collectively, these findings tentatively present a preliminary working model where GhGH3.1, potentially through its interaction with GhPDF1, may contribute to V. dahliae defense, likely by modulating auxin-amido conjugation and aligning downstream JA signaling, cell wall reinforcement, and redox balance during the immune response.

As an important cash crop, cotton is susceptible to drought stress, which leads to reduced yields. Receptor-like protein kinases are widely distributed in plants and play important roles in plant growth, development and stress response. In this study, 94 L-type LecRLK genes were identified in upland cotton, while 88, 49 and 55 LecRLK genes were identified in 3 additional cotton species, respectively. The LecRLKs were divided into four groups by phylogenetic and evolutionary analysis among Five species (Arabidopsis thaliana and four cotton species). In upland cotton, LecRLK was evenly distributed in the two subgenomes and was mostly localized to the cell membrane. The Ka/Ks values of 90

Alkaline stress causes significant adverse effects that slows down the growth of plants and lowers the yield of crops; hence, it is a major challenge in cotton farming. Spermidine (Spd), a vital polyamine, plays a significant role in enhancing plant resistance to stress caused by various abiotic factors. The molecular mechanism of Spd biosynthesis and especially the role of spermidine synthase (SPDS) in tolerance of alkaline stress in cotton is, however, little known. In this study, a systematic comparative analysis of SPDS-associated genes was performed across four representative cotton cultivars (Gossypium spp.), followed by preliminary functional characterization through promoter cis-acting element profiling. Virus-induced gene silencing (VIGS) was utilized to disrupt GhSPDS11-mediated Spd biosynthesis. Under alkaline stress, GhSPDS11-silenced seedlings exhibited 29.14% and 11.12% reductions in superoxide dismutase (SOD) and catalase (CAT) activities, 31.57% and 15.16% decreases in soluble sugar and proline (Pro) content, along with 42.38% and 38.66% increases in malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) compared to controls. Concurrently, silenced plants showed 44.87% fewer open stomata and significant declines in Spd content, relative water content, and biomass. These results indicate the key importance of Spd, which is composed of GhSPDS11, in improving alkali tolerance in cotton. This research gives good information regarding the molecular processes that take part in the tolerance of cotton to the saline-alkaline soils, and that GhSPDS11 could be a good genetic target in cotton enhancement in this tough agro-climatic condition.

Introduction:Chromatin accessibility is broadly implicated in plant abiotic stress responses; nevertheless, its role under cold stress in upland cotton (Gossypium hirsutum) remains largely unexplored. Methods:Here, we integrated the transcriptomic, metabolomic, and ATAC-seq profiles of a cold-tolerant line, Xinluzao 52 (X52), and a cold-sensitive line, Dai 4554 (D4554), which were sampled before (0 h) and after (6 h) cold treatment. Results:Compared with the respective 0-h controls, the 6-h cold exposure group had specifically enriched differentially expressed genes (DEGs) related to the fatty acid metabolism pathway in X52, while no comparable enrichment was observed in D4554. Among all the DEGs from comparison groups D4554-C vs. X52-C, D4554-C vs. D4554-T, D4554-T vs. X52-T, and X52-C vs. X52-T, a total of 3, 338 differentially expressed transcription factors (TFs) were identified, of which the MYB, bHLH, NAC, and WRKY families were predominated. Coexpression analysis partitioned these TFs into nine modules and identified 24 hub TFs. Metabolomic profiling revealed that fatty acids accounted for ~10% of the differentially expressed metabolites (DEMs), and eight of the nine TF coexpression modules were strongly correlated with fatty acid pathway metabolites (|r| > 0.9, P < 0.01). ATAC-seq detected 92, 356 differentially accessible regions (DARs) in X52 (0 h vs. 6 h). Genes linked to these DARs were significantly enriched for DNA-binding and DNA-templated transcription functions. In addition, DAR-linked genes were annotated to lipid metabolism. Notably, the DARs were enriched for binding motifs of bHLH-, bZIP-, AP2-, and C2H2-type TFs. In summary, we elucidate a chromatin accessibility-TF-enzyme gene-fatty acid metabolite regulatory network and highlight the possible chromatin-mediated transcriptional control of fatty acid metabolism during the adaptation to cold stress in cotton, offering a new perspective on the molecular basis of cold tolerance in upland cotton.

Background: In recent years, changes in climate conditions and long-term continuous cropping have led to the increased occurrence of Verticillium wilt in various cotton-growing regions, causing significant economic losses in cotton production. Research has shown that volatile substances are closely linked to plant disease resistance; however, studies on their roles in the response of cotton to Verticillium wilt, including their relationship with gene regulation, are limited. Methods: In this study, the transcriptomes and metabolomes of Xinluzao 57 (a highly susceptible Verticillium wilt variety) and 192,868 (a highly resistant Verticillium wilt variety) were sequenced at different time points after inoculation with Verticillium wilt. Results: A total of 21,911 commonly differentially expressed genes (DEGs) were identified within and between the materials, and they were clustered into eight groups. Significant annotations were made in pathways related to amino acids and anthocyanins. Metabolomics identified and annotated 26,200 volatile metabolites across nine categories. A total of 158 differentially accumulated metabolites (DAMs) were found within and between the materials; three clusters were identified, and the 10 metabolites with the most significant fold changes were highlighted. Weighted gene coexpression network analysis (WGCNA) revealed that 13 genes were significantly correlated with guanosine, 6 genes were correlated with 2-deoxyerythritol, and 32 genes were correlated with raffinose. Conclusions: Our results provide a foundation for understanding the role of volatile substances in the response of cotton to Verticillium wilt and offer new gene resources for future research on Verticillium wilt resistance.

Cotton is a kind of cash crop widely planted in arid and semi-arid areas. In this study, we performed multi-omics analysis of two drought resistant extreme materials, Yumian 4 and C460, under drought stress. Transcriptome analysis showed that DY (post-drought stress Yumian 4) had more differentially expressed genes than DC (post-drought stress C460), and there were 10247 DEGs in the two comparison groups. Metabolomics analysis identified 1766 metabolites, which were divided into 12 classes. The up-regulated metabolites mainly included lipid accumulation, phenylpropanoid biosynthesis, and flavonoids. The combined transcriptome and metabolome analysis highlighted the importance of phenylpropanoid biosynthesis in enhancing drought tolerance. Combining the two omics analysis, it was found that the enrichment pathway of differential genes and differential metabolites is mainly in the phenylpropane biosynthesis pathway, which contains 23 related candidate genes. In summary, the results of multi-omics analysis of the two extreme drought resistance cotton materials showed that they enhanced drought resistance by affecting phenylpropanoid biosynthesis pathways. Promote the accumulation of osmotic substances. The results further deepen our understanding of the molecular mechanism of drought tolerance in cotton and provide new insights for molecular breeding of cotton.

Background The diploid cotton species Gossypium thurberi (D1) and Gossypium trilobum (D8) exhibit significant divergence in cold stress tolerance despite their close phylogenetic relationship. Methods To explore the genetic basis of this difference, we conducted a comparative transcriptomic analysis under cold stress at 4 °C, identifying 697 and 311 species-specific differentially expressed genes (DEGs) in G. thurberi and G. trilobum, respectively. Functional enrichment analysis was performed to investigate the biological pathways associated with these DEGs. Additionally, hormone levels, particularly gibberellic acid (GA), were measured to assess their role in cold stress responses. Results The DEGs in both species were significantly enriched in the “hormone signal transduction” pathway, highlighting the importance of hormonal regulation in cold adaptation. Distinct trends in GA levels were observed between G. thurberi and G. trilobum, with GA strongly correlated with species-specific DEGs. G. thurberi demonstrated greater cold tolerance than G. trilobum, likely due to a more robust GA-regulated response. Conclusion These findings indicate that expression divergence in GA-mediated pathways between sister species has driven adaptive evolution in cold stress tolerance. This study not only advances our understanding of cold adaptation mechanisms in cotton but also provides genetic insights for improving cold tolerance in cultivated varieties through targeted breeding and genetic engineering.

IntroductionLipid-transfer proteins (LTPs) are a class of small, alkaline proteins that bind and transport various lipid molecules, including fatty acids, phospholipids, glycolipids, and steroids, between phospholipid bilayers. They play crucial roles in signal transduction, stress tolerance, and plant growth and development.MethodsIn this study, based on pan-genomic data, we identified 107 LTP family members across nine diploid cotton species, comprising 45 core, 43 variable, and 19 specific genes. Synteny and selection pressure analyses clarified the evolutionary relationships among these genes, while structural variation analyses revealed that although structural variants altered gene structures, domains, and cis-acting elements, they did not significantly affect gene expression.ResultsExpression profiling further demonstrated that LTP genes exhibited distinct spatiotemporal expression patterns in cotton ovules and roots at different developmental stages.DiscussionOverall, these findings highlight both conserved and divergent evolutionary patterns of the LTP family among diploid cotton species, providing new insights into their functional diversification, adaptive evolution, and potential involvement in cotton fiber development and stress responses.

Background: High-temperature stress is one of the major abiotic stresses limiting cotton production. Identifying genetic loci and genes for heat tolerance is crucial for breeding heat-tolerant varieties. Methods: Given the complexity of heat tolerance phenotypes in cotton, this study, which focused on resource materials, identified an A/C SNP mutation at position 5486185 on chromosome D06 within the heat tolerance interval through genome-wide association studies (GWAS) of natural Gossypium hirsutum populations. Results: A total of 308 resource materials were identified and evaluated for their heat tolerance phenotypes over two years of field research. Kompetitive allele-specific PCR (KASP) molecular markers were developed on the basis of the D06-5486185 SNP to characterize the heat tolerance phenotypes of these 308 resource materials. Genotyping for heat tolerance-related traits and agronomic traits was also performed. Materials with the C/C haplotype at position D06-5486185 presented increased heat tolerance (higher pollen viability (PV), leaf area (LA), chlorophyll (Chl) and number of bolls on the third fruit branch (FB3) and a lower number of dry buds (DBs) and drop rate (DR)) without negatively impacting key yield traits. This locus is located in the intergenic region of two adjacent bZIP transcription factor genes (GH_D06G0408 and GH_D06G0409). Expression analysis revealed that the expression levels of these two genes were significantly greater in heat-tolerant accessions (C/C type) than in sensitive accessions and that their expression levels were significantly correlated with multiple heat-tolerant phenotypes. Conclusions: In summary, this study developed a Kompetitive Allele Specific PCR (KASP) marker associated with heat tolerance in G. hirsutum and identified two key heat tolerance candidate genes. These results provide an efficient marker selection tool and important genetic resources for the molecular breeding of heat-tolerant G. hirsutum, laying an important foundation for further establishing a molecular marker-assisted breeding system for heat tolerance in G. hirsutum.

The occurrence and spread of Verticillium dahliae (V. dahliae) in cotton depends on the combined effects of pathogens, host plants, and the environment, among which temperature is one of the most important environmental factors. Studying how temperature impacts the occurrence of V. dahliae in cotton and the mechanisms governing host defense responses is crucial for disease prevention and control. Understanding the dual effects of temperature on both pathogens and hosts can provide valuable insights for developing effective strategies to manage this destructive fungal infection in cotton. This study was based on the deciduous V. dahliae Vd-3. Through cultivation at different temperatures, Vd-3 formed the most microsclerotia and had the largest colony diameter at 25 °C. Endospore toxins were extracted, and 48 h was determined to be the best pathogenic time point for endotoxins to infect cotton leaves through a chlorophyll fluorescence imaging system and phenotypic evaluation. Transcriptome sequencing was performed on cotton leaves infected with Vd-3 endotoxins for 48 h at different culture temperatures. A total of 34,955 differentially expressed genes (DEGs) were identified between each temperature and CK (no pathogen inoculation), including 17,422 common DEGs. The results of the enrichment analysis revealed that all the DEGs were involved mainly in photosynthesis and sugar metabolism. Among the 34,955 DEGs, genes in the biosynthesis and signal transduction pathways of jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) were identified, and their expression patterns were determined. A total of 5652 unique DEGs were clustered into six clusters using the k-means clustering algorithm, and the functions and main transcription factors (TFs) of each cluster were subsequently annotated. In addition, we constructed a gene regulatory network via weighted correlation network analysis (WGCNA) and identified twelve key genes related to cotton defense against V. dahliae at different temperatures, including four genes encoding transcription factors. These findings provide a theoretical foundation for investigating temperature regulation in V. dahliae infecting cotton and introduce novel genetic resources for enhancing resistance to this disease in cotton plants.

Functional genome research, including gene transcriptional and posttranslational modifications of histones, can benefit greatly from a high-quality genome assembly. Histone modification plays a significant role in modulating the responses to abiotic stress in plants. However, there are limited reports on the involvement of dynamic changes in histone modification in cold stress response in upland cotton. In this study, the genome of an elite accession, YM11, with considerable cold stress tolerance was de novo assembled, which yielded a genome of 2343.06 Mb with a contig N50 of 88.96 Mb, and a total of 73,821 protein-coding gene models were annotated. Comparisons among YM11 and five Gossypium allopolyploid cotton assemblies highlighted a large amount of structural variations and presence/absence variations. We analyzed transcriptome and metabolome changes in YM11 seedlings subjected to cold stress. Using the CUT&Tag method, genome-wide H3K4me3 and H3K9ac modification patterns and effect of histone changes on gene expression were profiled during cold stress. Significant and consistently changing histone modifications and the gene expressions were screened, of which transcription factors (TFs) were highlighted. Our results suggest a positive correlation between the changes in H3K4me3, H3K9ac modifications and cold stress-responsive gene activation. This genome assembly and comprehensive analysis of genome-wide histone modifications and gene expression provide insights into the genomic variation and epigenetic responses to cold stress in upland cotton.

Background: DNA methylation is an important part of epigenetic regulation and plays an important role in the response of plants to adverse stress. Methods: In this study, whole-genome bisulfite sequencing (WGBS) was performed on the high-temperature-resistant material Xinluzao 36 and the high-temperature-sensitive material Che 61-72 at 0 h and 12 h under high-temperature stress conditions. Results: The results revealed that the Gossypium hirsutum methylation levels of CG and CHG (H = A, C, or T) decreased after the high-temperature stress treatment, and the methylation level of the A subgenome was significantly greater than that of the D subgenome. The methylation level of CHH increased, and the methylation level of CHH in the D subgenome was significantly greater than that in the A subgenome after high-temperature stress treatment. The methylation density of CG is lower than that of CHG and CHH, and the methylation density of the middle region of chromosomes is greater than that of both ends, which is opposite to the distribution density of genes. There were 124 common differentially methylated genes in the CG, CHG, and CHH groups, and 5130 common DEGs and differentially methylated genes were found via joint analysis with RNA-seq; these genes were significantly enriched in the biosynthesis of plant hormones, thiamine metabolism, glutathione metabolism, and tyrosine metabolism pathways. DNA methylation did not affect the expression of many genes (accounting for 85.68% of the differentially methylated genes), DNA methylation-promoted gene expression was located mainly in the downstream region of the gene or gene body, and the expression of inhibitory genes was located mainly in the upstream region of the gene. Conclusions: This study provides a theoretical basis for further exploration of the gene expression and functional regulatory mechanism of G. hirsutum DNA methylation under high-temperature stress conditions.

Abstract γ -aminobutyric acid (GABA) is closely related to the growth, development and stress resistance of plants. Combined with the previous study of GABA to promote the cotton against abiotic stresses, the characteristics and expression patterns of GABA branch gene family laid the foundation for further explaining its role in cotton stress mechanism. Members of GAD, GAB-T and SSADH (three gene families of GABA branch) were identified from the Gossypium hirsutum, Gossypium barbadense , Gossypium arboreum and Gossypium raimondii genome. The GABA branch genes were 10 GAD genes, 4 GABA-T genes and 2 SSADH genes. The promoter sequences of genes mainly contains response-related elements such as light, hormone and environment.Phylogenetic analysis shows that GAD indicating that even in the same species, the homologous sequences in the family. The GABA-T gene of each cotton genus was in sum the family had gene loss in the process of dicotyledon evolution. SSADH families Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii were closely related to the dicot plants.GABA gene is involved in the regulation of salt stress and high temperature in Gossypium hirsutum.GABA attenuated part of the abiotic stress damage by increasing leaf protective enzyme activity and reducing reactive oxygen species production.This lays the foundation for a thorough analysis of the mechanism of GABA in cotton stress resistance.