Search

Establishing a sustainable industrial structure system is imperative for transforming the society to high-quality development and achieve the ''carbon peak'' and ''carbon neutrality'' goals. In this study, we explored a low-carbon pathway of regional industrial structure optimization to achieve a balance among economic growth, social security, and environmental conservation. A multi-objective optimization model of industrial structure of economic-social-environmental system was constructed by minimizing carbon emissions and maximizing economic benefits and social employment. In this study, we explored the scientific allocation path for industrial structure and set various scenarios to meet the diverse preferences and development requirements of decision-makers. Southwest China was used as a practical case to validate the model's efficacy, offering a decision-making framework for the sustainable development of the regional economy. After optimization, carbon emissions reduced by 0.9 %∼3.2 %, economic benefits increased by 2.5 %∼4.8 %, and employment levels nearly doubled. The proportion of the transportation industry in southwest China decreased by 11.58 %. The raw coal was the energy source with the highest contribution to carbon emissions, 2494.2 × 108 kgCO2eq.

Abstract The disaster caused by landslide is huge. To prevent the spread of the disaster to the maximum extent, it is particularly important to carry out landslide disaster treatment work. The selection of landslide disaster treatment alternative is a large scale group decision-making (LSGDM) problem. Because of the wide application of social media, a large number of experts and the public can participate in decision-making process, which is conducive to improving the efficiency and correctness of decision-making. A IF-TW-LSGDM method based on three-way decision (TWD) and intuitionistic fuzzy set (IFS) is proposed and applied to the selection of landslide treatment alternatives. First of all, considering that experts and the public participate in the evaluation of LSGDM events, respectively, the method of obtaining and handling the public evaluation information is given, and the information fusion approach of the public and experts evaluation information is given. Second, evaluation values represented by fuzzy numbers are converted into intuitionistic fuzzy numbers (IFNs), and the intuitionistic fuzzy evaluation decision matrix described by IFNs is obtained. Then, a new LSGDM method of alternatives classification and ranking based on IFS and TWD is proposed, the calculation steps and algorithm description are given. In this process, we first cluster the experts, then consider the identification and management of non-cooperative behavior of expert groups. This work provides an effective method based on LSGDM for the selection of landslide treatment alternatives. Finally, the sensitivity of parameters is analyzed, and the feasibility and effectiveness of this method are compared and verified.

Abstract Background The cotton industry suffers significant yield losses annually due to Verticillium wilt, which is considered the most destructive disease affecting the crop. However, the precise mechanisms behind this disease in cotton remain largely unexplored. Methods Our approach involved utilizing transcriptome data from G. australe which was exposed to Verticillium dahliae infection. From this data, we identified ethylene-responsive factors and further investigated their potential role in resistance through functional validations via Virus-induced gene silencing (VIGS) in cotton and overexpression in Arabidopsis. Results A total of 23 ethylene response factors (ERFs) were identified and their expression was analyzed at different time intervals (24 h, 48 h, and 72 h post-inoculation). Among them, GauERF105 was selected based on qRT-PCR expression analysis for further investigation. To demonstrate the significance of GauERF105, VIGS was utilized, revealing that suppressing GauERF105 leads to more severe infections in cotton plants compared to the wild-type. Additionally, the silenced plants exhibited reduced lignin deposition in the stems compared to the WT plants, indicating that the silencing of GauERF105 also impacts lignin content. The overexpression of GauERF105 in Arabidopsis confirmed its pivotal role in conferring resistance against Verticillium dahliae infection. Our results suggest that WT possesses higher levels of the oxidative stress markers MDA and H2O2 as compared to the overexpressed lines. In contrast, the activities of the antioxidant enzymes SOD and POD were higher in the overexpressed lines compared to the WT. Furthermore, DAB and trypan staining of the overexpressed lines suggested a greater impact of the disease in the wild-type compared to the transgenic lines. Conclusions Our findings provide confirmation that GauERF105 is a crucial candidate in the defense mechanism of cotton against Verticillium dahliae invasion, and plays a pivotal role in this process. These results have the potential to facilitate the development of germplasm resistance in cotton.

Abstract Background The cyclic nucleotide-gated channel (CNGC) gene family plays a significant role in the uptake of both essential and toxic cations, and has a role in enhancing tolerance to various forms of abiotic stresses as well as the modulation of the heavy metal toxicity to plant through the absorption of heavy metals. Results A complete genome-wide identification and functional characterization of the cotton CNGC genes was carried out, in which 55, 28, and 29 CNGC genes were identified in Gossypium hirsutum, G. raimondii, and G. arboreum, respectively. The protein encoded by the CNGC genes exhibited GRAVY value below zero, indicating their hydrophilic property. CNGC genes were unevenly distributed in 19 out of 26 chromosomes, in which the highest density were observed on Ah05, with 8 genes. High gene coverage was observed among the diploid cotton species, with CNGC genes mapped on all A chromosomes and on 11 out of 13 of D chromosomes. The majority of CNGC proteins were localized in the endoplasmic reticulum, nucleus, and plasma membrane. Gene expression analysis revealed the up-regulation of Gh_A01G0520 (CNGC4) and Gh_D13G1974 (CNGC5) across various forms of abiotic stresses. Moreover, down-regulation of Gh_A01G0520 (CNGC4) and Gh_D13G1974 (CNGC5) in CNGC s silenced plants caused the significantly reduced ability to tolerate drought and salt stresses. All CNGCs silenced plants were recorded to have significantly low content of antioxidants but relatively higher content of oxidant, including MDA and H2O2. Furthermore, SPAD, CMS (cell membrane stability), ELWL (excised leaf water loss), SDW (shoot dry matter weight), and RDW (root dry matter weight) were all lower in CNGCs silenced plants compared with the wild type plants. Conclusion Significant reduction in antioxidant content and negative effects of physiological and morphological characters in CNGCs silenced plants has revealed the novel role of CNGC genes in enhancing cell integrity under abiotic stress conditions. These results provide vital information that will expand our understanding of the CNGC gene family in cotton and other plants, thus promoting the integration of these genes in the development of the environmental resilient plants.

Summary: The 5′-deoxyadenosine deaminase (DADD), a member of the amidohydrolase family regulates biological purine metabolism. In this study, bioinformatic analysis, overexpression and knockdown of GhdadD gene were detected to identify its potential role in drought and salt stress tolerance. The results revealed that GhdadD was induced by ABA, Auxin, MBS and light responsive elements. In transgenic Arabidopsis, seed germination rate and root length were increased under drought or salt stress. GhdadD overexpressed seedlings resulted in higher plant height, less leaf damage and lower ion permeability. The expression of osmotic stress and ABA-responsive genes were up regulated. While in GhdadD-silenced cotton seedlings, CAT, SOD activity and soluble sugar content were reduced, MDA content was increased, and the stoma opening was depressed under drought or salt stress. Some osmics stress marker genes were also up regulated. These data indicating that GhdadD enhanced plant resistance to drought and salt stress through ABA pathways.

Abstract Background Plant pollen has diverse morphological characteristics that can be consistently passed down from generation to generation. Information on pollen morphology is thus immensely important for plant classification and identification. In the genus Gossypium, however, in-depth research on pollen morphology is lacking, with only few reports on limited cotton species. To evaluate the diversity of pollen in Gossypium, we therefore conducted a comprehensive analysis of the pollen morphology of 33 cotton species and varieties using scanning electron microscopy. Results The 33 analyzed cotton samples exhibited common pollen morphological features, including spherical shapes, radial symmetry, echination, panporation, and operculation, while the pollen size, spine shape, spine density and length showed distinctive features. Pollen size varied significantly among species, with diameters ranging from 62.43 μm in G. harknessii to 103.41 μm in G. barbadense. The exine had an echinate sculptural texture, and spines were mostly conical or sharply conical but occasionally rod-like. Spine density varied from 173 in G. incanum to 54 in G. gossypioides, while spine length ranged from 3.53 μm in G. herbaceum to 9.47 μm in G. barbadense. In addition, the 33 cotton species and varieties were grouped at a genetic distance of 3.83 into three clusters. Cluster I comprised five allotetraploid AD-genome cotton species, four D-genome species, and one K-genome species. Cluster II included 13 diploid species from A, B, D, E, and G genomes, whereas Cluster III only consisted one E-genome species G. incanum. Conclusions Although pollen characteristics alone are not enough to resolve taxonomic and systematic relationships within the genus Gossypium, our results add to knowledge on palynomorphology and contribute to phenological information on these taxa. Our findings should aid future systematic and phylogenetic studies of the Gossypium genus.

Abstract Geological hazards caused by strong earthquakes have caused continuous social and economic losses and destruction of the ecological environment in the hazard area, and are mostly manifested in the areas with frequent occurrence of geological hazards or the clustering of geological hazards. Considering the long-term nature of earthquakes and geological disasters in this region, this paper takes ten earthquake-stricken areas in Wenchuan earthquake zone as examples to collect shallow landslide data in 2010, combined with the spatial location of landslides and other factors. Kernel density estimation (KDE) method is used to analyze the spatial characteristics of shallow landslide. Taking the space of shallow landslide as the characteristic variable and fully considering the regulating factors of earthquake-induced landslide: terrain complexity, distance to river, distance to fault, distance to road, lithology, normalized vegetation difference index (NDVI) and ground peak acceleration (PGA) as independent variables, based on KDE and polynomial logistic regression (MLR), A quantitative model of shallow landslide in the earthquake area is constructed. The results show that: (1) PGA has the greatest impact on landslide in the study area. (2) Compared with the two-category logistic regression (two-category LR) model, the susceptibility map of landslide prediction results based on the KDE-MLR landslide susceptibility prediction model is more consistent with the actual situation. (3) The prediction accuracy of the model validation set is 70.7%, indicating that the landslide susceptibility prediction model based on KDE-MLR can effectively highlight the spatial characteristics of shallow landslides in 10 extreme disaster areas. The research results can provide decision-making basis for shallow landslide warning and post-disaster reconstruction in earthquake-stricken areas.

Abstract Background Current climate change scenarios are posing greater threats to the growth and development of plants. Thus, significant efforts are required that can mitigate the negative effects of drought on the cotton plant. GDSL esterase/lipases can offer an imperative role in plant development and stress tolerance. However, thesystematic and functional roles of the GDSL gene family, particularly in cotton under water deficit conditions have not yet been explored. Results In this study, 103, 103, 99, 198, 203, 239, 249, and 215 GDSL proteins were identified in eight cotton genomes i.e., Gossypium herbaceum (A1), Gossypium arboretum (A2), Gossypium raimondii (D5), Gossypium hirsutum (AD1), Gossypium barbadense (AD2), Gossypium tomentosum (AD3), Gossypium mustelinum (AD4), Gossypium darwinii (AD5), respectively. A total of 198 GDSL genes of Gossypium hirsutum were divided into eleven clades using phylogenetic analysis, and the number of GhirGDSL varied among different clades. The cis-elements analysis showed that GhirGDSL gene expression was mainly related to light, plant hormones, and variable tense environments. Combining the results of transcriptome and RT-qPCR, GhirGDSL26 (Gh_A01G1774), a highly up-regulated gene, was selected for further elucidating its tole in drought stress tolerance via estimating physiological and biochemical parameters. Heterologous expression of the GhirGDSL26 gene in Arabidopsis thaliana resulted in a higher germination and survival rates, longer root lengths, lower ion leakage and induced stress-responsive genes expression under drought stress. This further highlighted that overexpressed plants had a better drought tolerance as compared to the wildtype plants. Moreover, 3, 3’-diaminobenzidine (DAB) and Trypan staining results indicated reduced oxidative damage, less cell membrane damage, and lower ion leakage in overexpressed plants as compared to wild type. Silencing of GhirGDSL26 in cotton via VIGS resulting in a susceptible phenotype, higher MDA and H2O2 contents, lower SOD activity, and proline content. Conclusion Our results demonstrated that GhirGDSL26 plays a critical role in cotton drought stress tolerance. Current findings enrich our knowledge of GDSL genes in cotton and provide theoretical guidance and excellent gene resources for improving drought tolerance in cotton.

Salinity is a major threat to the yield and productivity of cotton seedlings. In the present study, we developed a BC2F2 population of cotton plants from Gossypium darwinii (5–7) and Gossypium hirsutum (CCRI 12–4) salt-susceptible parents to identify salt-resistant candidate genes. The Illumina HiSeq™ strategy was used with bulked segregant analysis. Salt-resistant and salt-susceptible DNA bulks were pooled by using 30 plants from a BC2F2 population. Next-generation sequencing (NGS) technology was used for the sequencing of parents and both bulks. Four significant genomic regions were identified: the first genomic region was located on chromosome 18 (1.86 Mb), the second and third genomic regions were on chromosome 25 (1.06 Mb and 1.94 Mb, respectively), and the fourth was on chromosome 8 (1.41 Mb). The reads of bulk1 and bulk2 were aligned to the G. darwinii and G. hirsutum genomes, respectively, leading to the identification of 20,664,007 single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels). After the screening, 6,573 polymorphic markers were obtained after filtration of the candidate regions. The SNP indices in resistant and susceptible bulks and Δ(SNP-index) values of resistant and susceptible bulks were measured. Based on the higher Δ(SNP-index) value, six effective polymorphic SNPs were selected in a different chromosome. Six effective SNPs were linked to five candidate genes in four genomic regions. Further validation of these five candidate genes was carried out using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), resulting in an expression profile that showed two highly upregulated genes in the salt-tolerant species G. darwinii, i.e., Gohir.D05G367800 and Gohir.D12G239100; however, the opposite was shown in G. hirsutum, for which all genes, except one, showed partial expression. The results indicated that Gohir.D05G367800 and Gohir.D12G239100 may be salt-tolerant genes. We are confident that this study could be helpful for the cloning, transformation, and development of salt-resistant cotton varieties.

Abstract Background Crops face several environmental stresses (biotic and abiotic), thus resulting in severe yield losses. Around the globe abiotic stresses are the main contributors of plant damages, primarily drought and salinity. Many genes and transcription factors are involved in abiotic and biotic stress responses. NAC TF (Transcription Factors) improves tolerance to stresses by controlling the physiological and enzyme activities of crops. Results In current research, GhNAC072 a highly upregulated TF in RNA-Seq was identified as a hub gene in the co-expression network analysis (WGCNA). This gene was transformed to Arabidopsis thaliana to confirm its potential role in drought and salt stress tolerance. Significant variations were observed in the morpho-physiological traits with high relative leaf water contents, chlorophyll contents, higher germination and longer root lengths of the overexpressed lines and low excised leaf loss and ion leakage as compared to the wildtype plants. Besides, overexpressed lines have higher amounts of antioxidants and low oxidant enzyme activities than the wildtype during the period of stress exposure. Conclusions In summary, the above analysis showed that GhNAC072 might be the true candidate involved in boosting tolerance mechanisms under drought and salinity stress.

The development of resource-based cities faces with stagnation due to the exhaustion of resources. Scientific and rational characterization of the temporal and spatial characteristics of resource environmental carrying capacity (RECC) is conducive to the sustainable development of these cities. In the present study, 8 resource-based cities in Sichuan Province were used as the research objects. A RECC research framework was constructed based on natural resources, environmental resources, economic resources and social resources dimensions (NEES), and a RECC assessment system was then extracted. This paper constructed a RECC calculation method based on the EWM-CPM (EWM: entropy weight method, CPM: catastrophe progression method). Mean and standard deviation were used for statistical analysis of RECC. The temporal trends of the NEES and RECC of resource-based cities in Sichuan Province were analyzed from the perspective of time, and the dynamic characteristics were analyzed combined with the dynamic evaluation measure model. The spatial pattern of RECC in the resource-based cities in Sichuan Province was analyzed from a spatial perspective. The relationship between NEES and RECC was evaluated through a path analysis method. The research results were as follows: (1) In terms of time, the average value of RECC in the resource-based cities in Sichuan Province was 0.628, and the standard deviation was 0.200, indicating that the stability of RECC in the entire region was poor. Natural resources are the main subsystem of RECC impacts in NEES. From the calculation results of the dynamic evaluation measure model, the level of RECC in PZH (Panzhihua) was stable, and the level of RECC in GA (Guang'an) increased with time, whereas the level of RECC in NC (Nanchong) was poor. (2) In terms of space, the eight resource-based cities showed uneven development in regard to RECC from 2010 to 2019, and the urban advantageous industries were related to the types of resources in the NEES. (3) The path analysis method results indicated that the directional impact of natural resources on RECC was the highest (0.658), followed by the effect of social resources, environmental resources and economic resources. The findings of the present study provide a basis for the establishment of methods for the sustainable development of urban areas, effective information extraction and the integrated assessment of factors that affect the development of resource-based cities.

Abstract Background Cotton is a valuable economic crop and the main significant source of natural fiber for textile industries globally. The effects of drought and salt stress pose a challenge to strong fiber and large-scale production due to the ever-changing climatic conditions. However, plants have evolved a number of survival strategies, among them is the induction of various stress-responsive genes such as the ribosomal protein large (RPL) gene. The RPL gene families encode critical proteins, which alleviate the effects of drought and salt stress in plants. In this study, comprehensive and functional analysis of the cotton RPL genes was carried out under drought and salt stresses. Results Based on the genome-wide evaluation, 26, 8, and 5 proteins containing the RPL14B domain were identified in Gossypium hirsutum, G. raimondii, and G. arboreum, respectively. Furthermore, through bioinformatics analysis, key cis-regulatory elements related to RPL14B genes were discovered. The Myb binding sites (MBS), abscisic acid-responsive element (ABRE), CAAT-box, TATA box, TGACG-motif, and CGTCA-motif responsive to methyl jasmonate, as well as the TCA-motif responsive to salicylic acid, were identified. Expression analysis revealed a key gene, Gh_D01G0234 (RPL14B), with significantly higher induction levels was further evaluated through a reverse genetic approach. The knockdown of Gh_D01G0234 (RPL14B) significantly affected the performance of cotton seedlings under drought/salt stress conditions, as evidenced by a substantial reduction in various morphological and physiological traits. Moreover, the level of the antioxidant enzyme was significantly reduced in VIGS-plants, while oxidant enzyme levels increased significantly, as demonstrated by the higher malondialdehyde concentration level. Conclusion The results revealed the potential role of the RPL14B gene in promoting the induction of antioxidant enzymes, which are key in oxidizing the various oxidants. The key pathways need to be investigated and even as we exploit these genes in the developing of more stress-resilient cotton germplasms.

Lint percentage is one of the most essential yield components and an important economic index for cotton planting. Improving lint percentage is an effective way to achieve high-yield in cotton breeding worldwide, especially upland cotton (Gossypium hirsutum L.). However, the genetic basis controlling lint percentage has not yet been systematically understood. Here, we performed a genome-wide association mapping for lint percentage using a natural population consisting of 189 G. hirsutum accessions (188 accessions of G. hirsutum races and one cultivar TM-1). The results showed that 274 single-nucleotide polymorphisms (SNPs) significantly associated with lint percentage were detected, and they were distributed on 24 chromosomes. Forty-five SNPs were detected at least by two models or at least in two environments, and their 5 Mb up- and downstream regions included 584 makers related to lint percentage identified in previous studies. In total, 11 out of 45 SNPs were detected at least in two environments, and their 550 Kb up- and downstream region contained 335 genes. Through RNA sequencing, gene annotation, qRT-PCR, protein–protein interaction analysis, the cis-elements of the promotor region, and related miRNA prediction, Gh_D12G0934 and Gh_A08G0526 were selected as key candidate genes for fiber initiation and elongation, respectively. These excavated SNPs and candidate genes could supplement marker and gene information for deciphering the genetic basis of lint percentage and facilitate high-yield breeding programs of G. hirsutum ultimately.

Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.

Drought seriously threats the growth and development of Gossypium hirsutum L. To dissect the genetic basis for drought tolerance in the G. hirsutum L. germplasm, a population, consisting of 188 accessions of G. hirsutum races and a cultivar (TM-1), was genotyped using the Cotton80KSNP biochip, and 51,268 high-quality single-nucleotide polymorphisms (SNPs) were obtained. Based on the phenotypic data of eight drought relative traits from four environments, we carried out association mapping with five models using GAPIT software. In total, thirty-six SNPs were detected significantly associated at least in two environments or two models. Among these SNPs, 8 and 28 (including 24 SNPs in 5 peak regions) were distributed in the A and D subgenome, respectively; eight SNPs were found to be distributed within separate genes. An SNP, TM73079, located on chromosome D10, was simultaneously associated with leaf fresh weight, leaf wilted weight, and leaf dry weight. Another nine SNPs, TM47696, TM33865, TM40383, TM10267, TM59672, TM59675, TM59677, TM72359, and TM72361, on chromosomes A13, A10, A12, A5, D6, and D9, were localized within or near previously reported quantitative trait loci for drought tolerance. Moreover, 520 genes located 200 kb up- and down-stream of 36 SNPs were obtained and analyzed based on gene annotation and transcriptome sequencing. The results showed that three candidate genes, Gh_D08G2462, Gh_A03G0043, and Gh_A12G0369, may play important roles in drought tolerance. The current GWAS represents the first investigation into mapping QTL for drought tolerance in G. hirsutum races and provides important information for improving cotton cultivars.

Drought has been identified as a major threat for global crop production worldwide. Phosphofructokinase (PFK) is vital for sugar metabolism. During phosphorylation, plants have two enzymes: ATP-dependent phosphofructokinase (PFK) and pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP). Genome-wide identification led to the identification of 80 PFK genes, 26 genes in G. hirsutum and G. barbadense, and 14 genes in G. arboreum and G. raimondii. Phylogenetic, gene structure, and motif analyses showed that PFK genes were grouped into two main categories, namely, PFK and PFP, with 18 and 8 genes in the allotetraploid species and 10 PFK and 4 PFP genes in the diploid species, respectively. Using the RNA-seq expressions of 26 genes from GhPFK, a co-expression network analysis was performed to identify the hub genes. GhPFK04, GhPFK05, GhPFK09, GhPFK11, GhPFK13, GhPFK14, and GhPFK17 in leaves and GhPFK02, GhPFK09, GhPFK11, GhPFK15, GhPFK16, and GhPFK17 in root tissues were found as hub genes. RT-qPCR analysis validated the expressions of identified hub genes. Interestingly, GhPFK11 and GhPFK17 were identified as common hub genes, and these might be the true candidate genes involved in the drought stress tolerance. In the KEGG enrichment analysis, amino acids such as L-valine, L-histidine, L-glutamine, L-serine, L-homoserine, L-methionine, L-cysteine, and gluconic acid were significantly upregulated, whereas sugars, mainly fructose-1-phosphate, D-mannitol, D-sorbitol, dulcitol, and lactose, were significantly downregulated during drought stress. Genome-wide analysis paves the way for a deeper understanding of the PFK genes and establishes the groundwork for future research into PFK’s role in enhancing drought stress tolerance and sugar metabolism in cotton.

The most devastating abiotic factors worldwide are drought and salinity, causing severe bottlenecks in the agricultural sector. To acclimatize to these harsh ecological conditions, plants have developed complex molecular mechanisms involving diverse gene families. Among them, S-adenosyl-L-methionine synthetase (SAMS) genes initiate the physiological, morphological, and molecular changes to enable plants to adapt appropriately. We identified and characterized 16 upland cotton SAMS genes (GhSAMSs). Phylogenetic analysis classified the GhSAMSs into three major groups closely related to their homologs in soybean. Gene expression analysis under drought and salt stress conditions revealed that GhSAMS2, which has shown the highest interaction with GhCBL10 (a key salt responsive gene), was the one that was most induced. GhSAMS2 expression knockdown via virus-induced gene silencing (VGIS) enhanced transgenic plants’ susceptibility to drought and salt stress. The TRV2:GhSAMS2 plants showed defects in terms of growth and physiological performances, including antioxidative processes, chlorophyll synthesis, and membrane permeability. Our findings provide insights into SAMS genes’ structure, classification, and role in abiotic stress response in upland cotton. Moreover, they show the potential of GhSAMS2 for the targeted improvement of cotton plants’ tolerance to multiple abiotic stresses.

Low temperature is a common biological abiotic stress in major cotton-growing areas. Cold stress significantly affects the growth, yield, and yield quality of cotton. Therefore, it is important to develop more robust and cold stress-resilient cotton germplasms. In response to climate change and erratic weather conditions, plants have evolved various survival mechanisms, one of which involves the induction of various stress responsive transcript factors, of which the C-repeat-binding factors (CBFs) have a positive effect in enhancing plants response to cold stress. In this study, genomewide identification and functional characterization of the cotton CBFs were carried out. A total of 29, 28, 25, 21, 30, 26, and 15 proteins encoded by the CBF genes were identified in seven Gossypium species. A phylogenetic evaluation revealed seven clades, with Clades 1 and 6 being the largest. Moreover, the majority of the proteins encoded by the genes were predicted to be located within the nucleus, while some were distributed in other parts of the cell. Based on the transcriptome and RT-qPCR analysis, Gthu17439 (GthCBF4) was highly upregulated and was further validated through forward genetics. The Gthu17439 (GthCBF4) overexpressed plants exhibited significantly higher tolerance to cold stress, as evidenced by the higher germination rate, increased root growth, and high-induction levels of stress-responsive genes. Furthermore, the overexpressed plants under cold stress had significantly reduced oxidative damage due to a reduction in hydrogen peroxide (H2O2) production. Moreover, the overexpressed plants under cold stress had minimal cell damage compared to the wild types, as evidenced by the Trypan and 3,3′-Diaminobenzidine (DAB) staining effect. The results showed that the Gthu17439 (GthCBF4) could be playing a significant role in enhancing cold stress tolerance in cotton and can be further exploited in developing cotton germplasm with improved cold-stress tolerance.

Drought and low-temperature stresses are the most prominent abiotic stresses affecting cotton. Wild cotton being exposed to harsh environments has more potential to cope with both biotic and abiotic stresses. Exploiting wild cotton material to induce resistant germplasm would be of greater interest. The candidate gene was identified in the BC2F2 population among Gossypium tomentosum and Gossypium hirsutum as wild male donor parent noted for its drought tolerance and the recurrent parent and a high yielding but drought susceptible species by genotyping by sequencing (GBS) mapping. Golden2-like (GLK) gene, which belongs to the GARP family, is a kind of plant-specific transcription factor (TF) that was silenced by virus-induced gene silencing (VIGS). Silencing of GhGLK1 in cotton results in more damage to plants under drought and cold stress as compared with wild type (WT). The overexpression of GhGLK1 in Arabidopsis thaliana showed that the overexpressing plants showed more adaptability than the WT after drought and cold treatments. The results of trypan blue and 3,3′-diaminobenzidine (DAB) staining showed that after drought and cold treatment, the leaf damage in GhGLK1 overexpressed plants was less as compared with the WT, and the ion permeability was also lower. This study suggested that the GhGLK1 gene may be involved in the regulation of drought and cold stress response in cotton. Our current research findings add significantly to the existing knowledge of cold and drought stress tolerance in cotton.

Cotton is one of the most important fiber crops globally. Despite this, various abiotic stresses, including drought, cause yield losses. We used transcriptome profiles to investigate the co-expression patterns of gene networks associated with drought stress tolerance. We identified three gene modules containing 3,567 genes highly associated with drought stress tolerance. Within these modules, we identified 13 hub genes based on intramodular significance, for further validation. The yellow module has five hub genes (Gh_A07G0563, Gh_D05G0221, Gh_A05G3716, Gh_D12G1438, and Gh_D05G0697), the brown module contains three hub genes belonging to the aldehyde dehydrogenase (ALDH) gene family (Gh_A06G1257, Gh_A06G1256, and Gh_D06G1578), and the pink module has five hub genes (Gh_A02G1616, Gh_D12G2599, Gh_D07G2232, Gh_A02G0527, and Gh_D07G0629). Based on RT-qPCR results, the Gh_A06G1257 gene has the highest expression under drought stress in different plant tissues and it might be the true candidate gene linked to drought stress tolerance in cotton. Silencing of Gh_A06G1257 in cotton leaves conferred significant sensitivity in response to drought stress treatments. Overexpression of Gh_A06G1257 in Arabidopsis also confirms its role in drought stress tolerance. L-valine, Glutaric acid, L-proline, L-Glutamic acid, and L-Tryptophan were found to be the most significant metabolites playing roles in drought stress tolerance. These findings add significantly to existing knowledge of drought stress tolerance mechanisms in cotton.

As one of the pioneer crops widely planted in saline-alkaline areas, Gossypium provides daily necessities, including natural fiber, vegetable proteins, and edible oils. However, cotton fiber yield and quality are highly influenced by salt stress. Therefore, elucidating the molecular mechanisms of cotton in response to salinity stress is importance to breed new cultivars with high tolerance. In this study, we first developed a method for single-cell RNA-seq based on isolating protoplast from cotton root tips; then, we studied the impact of salinity stress on gene expression profiling and their dynamic changes using the developed high-efficiency method for protoplast dissociation suitable for single-cell RNA-seq. A total of 3391 and 2826 differentially expressed genes (DEGs) were identified in salt-treated samples before and after protoplast dissociation, respectively, which were enriched into several molecular components, including response to stimulus, response to stress, and cellular macromolecule metabolic process by gene ontology (GO) analysis. Plant hormone signal transduction, phenylpropanoid biosynthesis, and MAPK signaling pathway were found to be enriched via Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Twenty-two and nine salinity-responsive DEGs participated in plant hormone signaling and MAPK signaling in roots, before and after protoplast dissociation, respectively; six upregulated DEGs were involved in ABA signaling transduction, namely, Ga04G2111, Ga07G0142, Ga09G2061, Ga10G0262, Ga01G0063, and Ga08G1915 which indicates their potential functions on plants adapting to salt stress. Additionally, 384 and 257 transcription factors (TFs) were differentially expressed in salt-stress roots before and after protoplast dissociation, respectively, of which significantly up-regulated TFs mainly belonged to the AP2/ERF-ERF family, which implied their potential roles responding to salt stress. These results not only provide novel insights to reveal the regulatory networks in plant’s root response to salt stress, but also lay the solid foundation for further exploration on cellular heterogeneity by single-cell transcriptome sequencing.

Salinity is a major threat to the yield and productivity of cotton seedlings. In the present study, we developed a BC2F2 population of cotton plants from Gossypium darwinii (5-7) and Gossypium hirsutum (CCRI 12-4) saltsusceptible parents to identify salt-resistant candidate genes. The Illumina HiSeq™ strategy was used with bulked segregant analysis. Salt-resistant and salt-susceptible DNA bulks were pooled by using 30 plants from a BC2F2 population. Next-generation sequencing (NGS) technology was used for the sequencing of parents and both bulks. Four significant genomic regions were identified: the first genomic region was located on chromosome 18 (1.86 Mb), the second and third genomic regions were on chromosome 25 (1.06 Mb and 1.94 Mb, respectively), and the fourth was on chromosome 8 (1.41 Mb). The reads of bulk1 and bulk2 were aligned to the G. darwinii and G. hirsutum genomes, respectively, leading to the identification of 20,664,007 single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels). After the screening, 6,573 polymorphic markers were obtained after filtration of the candidate regions. The SNP indices in resistant and susceptible bulks and D(SNP-index) values of resistant and susceptible bulks were measured. Based on the higher D(SNP-index) value, six effective polymorphic SNPs were selected in a different chromosome. Six effective SNPs were linked to five candidate genes in four genomic regions. Further validation of these five candidate genes was carried out using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), resulting in an expression profile that showed two highly upregulated genes in the salt-tolerant species G. darwinii, i.e., Gohir.D05G367800 and Gohir.D12G239100; however, the opposite was shown in G. hirsutum, for which all genes, except one, showed partial expression. The results indicated that Gohir.D05G367800 and Gohir.D12G239100 may be salt-tolerant genes. We are confident that this study could be helpful for the cloning, transformation, and development of salt-resistant cotton varieties. [ABSTRACT FROM AUTHOR]

Drought has been identified as a major threat for global crop production worldwide. Phosphofructokinase (PFK) is vital for sugar metabolism. During phosphorylation, plants have two enzymes: ATP-dependent phosphofructokinase (PFK) and pyrophosphatedependent fructose-6-phosphate phosphotransferase (PFP). Genome-wide identification led to the identification of 80 PFK genes, 26 genes in G. hirsutum and G. barbadense, and 14 genes in G. arboreum and G. raimondii. Phylogenetic, gene structure, and motif analyses showed that PFK genes were grouped into two main categories, namely, PFK and PFP, with 18 and 8 genes in the allotetraploid species and 10 PFK and 4 PFP genes in the diploid species, respectively. Using the RNA-seq expressions of 26 genes from GhPFK, a co-expression network analysis was performed to identify the hub genes. GhPFK04, GhPFK05, GhPFK09, GhPFK11, GhPFK13, GhPFK14, and GhPFK17 in leaves and GhPFK02, GhPFK09, GhPFK11, GhPFK15, GhPFK16, and GhPFK17 in root tissues were found as hub genes. RT-qPCR analysis validated the expressions of identified hub genes. Interestingly, GhPFK11 and GhPFK17 were identified as common hub genes, and these might be the true candidate genes involved in the drought stress tolerance. In the KEGG enrichment analysis, amino acids such as L-valine, L-histidine, L-glutamine, L-serine, L-homoserine, L-methionine, L-cysteine, and gluconic acid were significantly upregulated, whereas sugars, mainly fructose-1-phosphate, D-mannitol, D-sorbitol, dulcitol, and lactose, were significantly downregulated during drought stress. Genomewide analysis paves the way for a deeper understanding of the PFK genes and establishes the groundwork for future research into PFK's role in enhancing drought stress tolerance and sugar metabolism in cotton. [ABSTRACT FROM AUTHOR]