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Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (UGA230, UA48 and CSX8308) and updating the TM-1 cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from Pima cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

SUMMARY Long non‐coding RNAs (lncRNAs) play an important role in various biological processes in plants. However, there have been few reports on the evolutionary signatures of lncRNAs in closely related cotton species. The lncRNA transcription patterns in two tetraploid cotton species and their putative diploid ancestors were compared in this paper. By performing deep RNA sequencing, we identified 280 429 lncRNAs from 21 tissues in four cotton species. lncRNA transcription evolves more rapidly than mRNAs, and exhibits more severe turnover phenomenon in diploid species compared to that in tetraploid species. Evolutionarily conserved lncRNAs exhibit higher expression levels, and lower tissue specificity compared with species‐specific lncRNAs. Remarkably, tissue expression of homologous lncRNAs in Gossypium hirsutum and G. barbadense exhibited similar patterns, suggesting that these lncRNAs may be functionally conserved and selectively maintained during domestication. An orthologous lncRNA, lncR4682, was identified and validated in fibers of G. hirsutum and G. barbadense with the highest conservatism and expression abundance. Through virus‐induced gene silencing in upland cotton, we found that lncR4682 and its target genes GHPAS2 and GHKCS19 positively regulated fiber elongation. In summary, the present study provides a systematic analysis of lncRNAs in four closely related cotton species, extending the understanding of transcriptional conservation of lncRNAs across cotton species. In addition, LncR4682‐PAS2‐KCS19 contributes to cotton fiber elongation by participating in the biosynthesis of very long‐chain fatty acids. [ABSTRACT FROM AUTHOR]

Introduction The material of a bandage plays an important role in wound management. Microorganisms can colonize the dressing and release toxins, which create dead cells in the wound. This allows the microorganisms to bind the dead cells and infect the wound. Thus, a dressing is needed that kills bacteria in the bandage. To combat health care–associated infections, antimicrobial treatment of medical textiles, such as gauze, uniforms, curtains, bed sheets, gowns, and masks, is required. Besides, antimicrobial resistance is another major problem of this century. Antibacterial overuse has contributed to drug-resistant bacteria. To combat these two problems, we synthesized new organo-selenium compounds that can be attached to the cotton of the dressing. We then used an in vivo wound model, which allowed us to measure the effectiveness of selenium attached to a cotton dressing, to prevent bacteria from infecting a wound. Materials and Methods Organo-selenium was attached to cotton fabric, resulting in a fabric with 0.1% selenium covalently attached to it. Staphylococcus aureus (as well as methicillin-resistant S. aureus [MRSA]), Stenotrophomonas maltophilia , Enterococcus faecalis , Staphylococcus epidermidis , and Pseudomonas aeruginosa were chosen for the wound infection study. All the bacteria were enumerated in the wound dressing and in the wound tissue under the dressing. Wounds were made on the backs of mice. The material was used as a bandage over the wound. Bacteria were injected into the wound under the bandage. The amount of bacteria in the wound after 5 days was determined. A similar study was performed using dressing material that was soaked in phosphate buffered saline at 37 °C for 3 months before use. Results Cotton dressing with selenium attached showed complete inhibition (7 logs, as compared with control dressing) of different bacterial strains, in both the dressing and "the tissue" of the wound. Similar results were obtained using selenium cotton dressing that was soaked for 3 months before use. Control cotton with no selenium showed complete infiltration of bacteria into the wound and the dressing. In addition, a study was performed under Food and Drug Administration standard methods to show the ability of the selenium to kill bacteria in the fabric, using material that was washed 5 times in detergent. This also showed complete killing of bacteria in the fabric. Conclusions The results show that the selenium remains in the dressing after washing and is able to completely protect the wound from bacterial infection. In the selenium bandage, no bacteria were found in the bandage or the wound after 5 days. [ABSTRACT FROM AUTHOR]

Surgical resection of the stenotic segment with end-to-end anastomosis is considered the gold standard in postintubation tracheal stenosis. However, outcomes of this concrete aetiology are not well described. With the aim to examine the extent, range and characteristics of the existing evidence, a scoping review was performed. Data sources included MEDLINE, Scopus, Ovid and the Cochrane databases. Inclusion criteria consisted of studies in adult patients with postintubation tracheal stenosis that reported characteristics, surgical management and outcomes. A total of 125 articles were identified, of which 10 were included in the final analysis. All studies were case reports or case series (level 4 evidence) grouping 110 patients, 75 males and 35 females. The age ranged from 15 to 71 years. Cotton–Myer stenosis grade was 1 [1 (0.9%)], 2 [25 (22.7%)], 3 [70 (63.6%)] and 4 [14 (12.7%)]. Stenosis location was in the tracheal upper-third in 108 (98.2%), in the middle-third in 1 (0.9%) and in the lower-third in 1 (0.9%). Stenosis length ranged from 1 to 5.6 cm. Follow-up ranged from 1 to 60 months (2 years for the most). Most frequent complications were transitory dysphagia in 13 (11.3%), granuloma formation in 8 (7.3%), dehiscence or air leak in 5 (4.5%) and wound infection in 4 (3.6%). Restenosis rate ranged from 2% to 25%. There was no perioperative mortality. Tracheal resection and primary anastomosis in postintubation tracheal stenosis appear to be safe and effective in the short and mid-terms; however, the very low level of evidence found prevents definitive conclusions. [ABSTRACT FROM AUTHOR]

Abstract Background Cotton (Gossypium hirsutum L.) is one of the most significant fibre and cash crops and plays an important role in Indian industrial and agricultural economies. However, over the years quantity and quality have been hampered by the pest leafhopper. Leafhopper alone has been shown to cause yield losses of up to 40%. In this study, screening and evaluation were performed to identify and categorize 100 cotton genotypes along with 5 checks as resistant, moderately resistant, sensitive and highly sensitive to leafhoppers. Results A total of hundred genotypes were evaluated along with five checks for leafhopper resistance. Based on the screening results, a total of 19 genotypes were resistant to leafhoppers, which was on par with the findings of the check KC 3. The contents of total soluble sugar, total soluble protein, and total free amino acids were significantly positively correlated with the mean grade, whereas total phenols content and trichome density were significantly negatively correlated with the susceptibility grade. However, based on screening and biochemical analysis, the genotypes KC 2, JR-23, Samaru-26-T, D 4, TCH 1728, RS 253, and B-61-1862 exhibited high resistance to leafhopper. Conclusion According to the findings of this study, choosing genotypes with high total phenolics content together with high trichome density and low contents of total soluble sugar, total soluble protein, and free amino acids may aid in the development of resistant genotypes.

Background: Cotton (Gossypium hirsutum L.) is one of the most significant fibre and cash crops and plays an important role in Indian industrial and agricultural economies. However, over the years quantity and quality have been hampered by the pest leafhopper. Leafhopper alone has been shown to cause yield losses of up to 40%. In this study, screening and evaluation were performed to identify and categorize 100 cotton genotypes along with 5 checks as resistant, moderately resistant, sensitive and highly sensitive to leafhoppers. Results: A total of hundred genotypes were evaluated along with five checks for leafhopper resistance. Based on the screening results, a total of 19 genotypes were resistant to leafhoppers, which was on par with the findings of the check KC 3. The contents of total soluble sugar, total soluble protein, and total free amino acids were significantly positively correlated with the mean grade, whereas total phenols content and trichome density were significantly negatively correlated with the susceptibility grade. However, based on screening and biochemical analysis, the genotypes KC 2, JR-23, Samaru-26-T, D 4, TCH 1728, RS 253, and B-61-1862 exhibited high resistance to leafhopper. Conclusion: According to the findings of this study, choosing genotypes with high total phenolics content together with high trichome density and low contents of total soluble sugar, total soluble protein, and free amino acids may aid in the development of resistant genotypes. [ABSTRACT FROM AUTHOR]

SUMMARY: Cotton is a globally cultivated crop, producing 87% of the natural fiber used in the global textile industry. The pigment glands, unique to cotton and its relatives, serve as a defense structure against pests and pathogens. However, the molecular mechanism underlying gland formation and the specific role of pigment glands in cotton's pest defense are still not well understood. In this study, we cloned a gland‐related transcription factor GhHAM and generated the GhHAM knockout mutant using CRISPR/Cas9. Phenotypic observations, transcriptome analysis, and promoter‐binding experiments revealed that GhHAM binds to the promoter of GoPGF, regulating pigment gland formation in cotton's multiple organs via the GoPGF‐GhJUB1 module. The knockout of GhHAM significantly reduced gossypol production and increased cotton's susceptibility to pests in the field. Feeding assays demonstrated that more than 80% of the cotton bollworm larvae preferred ghham over the wild type. Furthermore, the ghham mutants displayed shorter cell length and decreased gibberellins (GA) production in the stem. Exogenous application of GA3 restored stem cell elongation but not gland formation, thereby indicating that GhHAM controls gland morphogenesis independently of GA. Our study sheds light on the functional differentiation of HAM proteins among plant species, highlights the significant role of pigment glands in influencing pest feeding preference, and provides a theoretical basis for breeding pest‐resistant cotton varieties to address the challenges posed by frequent outbreaks of pests. Significance Statement: Pigment glands are essential for cotton's pest defense, but their formation mechanisms remained unclear. We demonstrated that the GhHAM transcription factor, through the GoPGF‐GhJUB1 pathway, is pivotal for gland development and pest resistance, offering new insights into breeding pest‐resistant cotton. [ABSTRACT FROM AUTHOR]

Approximately 10-15 million years ago, this genus experienced rapid global radiation, leading to the emergence of eight major genome groups (A through G and K) consisting of 13 chromosomes in each group. Moreover, over the past 1-2 million years, the transoceanic dispersal of an A-genome taxon to the New World and subsequent hybridization with a native D-genome diploid resulted in the rise of allopolyploid cotton. This evolutionary process led to the diversification of three modern lineages encompassing seven described species, including the economically significant G. hirsutum L. and G. barbadense L. A parallel evolution, driven by human intervention, unfolded as these two allopolyploids were domesticated. Simultaneously, the independent domestication of two A-genome diploids, G. arboreum L. and G. herbaceum L., originally from Africa-Asia occurred. Recent genomic investigations have unlocked its paleopolyploid history of diploid species and shed light on the surprisingly high frequency of natural interspecific hybridization within and between genome groups. Furthermore, these studies have elucidated the diverse molecular mechanisms underlying allopolyploid genome evolution and provided a more refined understanding of the evolutionary association among the gene pools of each of the four cultivated species. Gossypium is an exceptionally diverse group, encompassing variations in fiber morphology, stress tolerance, and other agronomic characteristics, and represents a vast resource for breeders striving to develop improved cotton varieties. This comprehensive understanding of Gossypium genome evolution and its implications for targeted breeding paves the way for advancements in sustainable cotton agriculture. [ABSTRACT FROM AUTHOR]

BACKGROUND: The extracellular space between the cell wall and plasma membrane is a battlefield in plant-pathogen interactions. Within this space, the pathogen employs its secretome to attack the host in a variety of ways, including immunity manipulation. However, the role of the plant secretome is rarely studied for its role in disease resistance. RESULTS: Here, we examined the secretome of Verticillium wilt-resistant Gossypium hirsutum cultivar Zhongzhimian No.2 (ZZM2, encoding 95,327 predicted coding sequences) to determine its role in disease resistance against the wilt causal agent, Verticillium dahliae. Bioinformatics-driven analyses showed that the ZZM2 genome encodes 2085 secreted proteins and that these display disequilibrium in their distribution among the chromosomes. The cotton secretome displayed differences in the abundance of certain amino acid residues as compared to the remaining encoded proteins due to the localization of these putative proteins in the extracellular space. The secretome analysis revealed conservation for an allotetraploid genome, which nevertheless exhibited variation among orthologs and comparable unique genes between the two sub-genomes. Secretome annotation strongly suggested its involvement in extracellular stress responses (hydrolase activity, oxidoreductase activity, and extracellular region, etc.), thus contributing to resistance against the V. dahliae infection. Furthermore, the defense response genes (immunity marker NbHIN1, salicylic acid marker NbPR1, and jasmonic acid marker NbLOX4) were activated to varying degrees when Nicotina benthamiana leaves were agro-infiltrated with 28 randomly selected members, suggesting that the secretome plays an important role in the immunity response. Finally, gene silencing assays of 11 members from 13 selected candidates in ZZM2 displayed higher susceptibility to V. dahliae, suggesting that the secretome members confer the Verticillium wilt resistance in cotton. CONCLUSIONS: Our data demonstrate that the cotton secretome plays an important role in Verticillium wilt resistance, facilitating the development of the resistance gene markers and increasing the understanding of the mechanisms regulating disease resistance.

Verticillium wilt caused by Verticillium dahliae is a notorious soil-borne fungal disease and seriously threatens the yield of economic crops worldwide. During host infection, V. dahliae secretes many effectors that manipulate host immunity, among which small cysteine-rich proteins (SCPs) play an important role. However, the exact roles of many SCPs from V. dahliae are unknown and varied. In this study, we show that the small cysteine-rich protein VdSCP23 inhibits cell necrosis in Nicotiana benthamiana leaves, as well as the reactive oxygen species (ROS) burst, electrolyte leakage and the expression of defense-related genes. VdSCP23 is mainly localized in the plant cell plasma membrane and nucleus, but its inhibition of immune responses was independent of its nuclear localization. Site-directed mutagenesis and peptide truncation showed that the inhibition function of VdSCP23 was independent of cysteine residues but was dependent on the N-glycosylation sites and the integrity of VdSCP23 protein structure. Deletion of VdSCP23 did not affect the growth and development of mycelia or conidial production in V. dahliae. Unexpectedly, VdSCP23 deletion strains still maintained their virulence for N. benthamiana, Gossypium hirsutum and Arabidopsis thaliana seedlings. This study demonstrates an important role for VdSCP23 in the inhibition of plant immune responses; however, it is not required for normal growth or virulence in V. dahliae.

Abstract The enzyme glutamine synthetase (GLN) is mainly responsible for the assimilation and reassimilation of nitrogen (N) in higher plants. Although the GLN gene has been identified in various plants, there is little information about the GLN family in cotton (Gossypium spp.). To elucidate the roles of GLN genes in cotton, we systematically investigated and characterized the GLN gene family across four cotton species (G. raimondii, G. arboreum, G. hirsutum, and G. barbadense). Our analysis encompassed analysis of members, gene structure, cis-element, intragenomic duplication, and exploration of collinear relationships. Gene duplication analysis indicated that segmental duplication was the primary driving force for the expansion of the GhGLN gene family. Transcriptomic and quantitative real-time reverse-transcription PCR (qRT-PCR) analyses indicated that the GhGLN1.1a gene is responsive to N induction treatment and several abiotic stresses. The results of virus-induced gene silencing revealed that the accumulation and N use efficiency (NUE) of cotton were affected by the inactivation of GhGLN1.1a. This study comprehensively analyzed the GhGLN genes in Gossypium spp., and provides a new perspective on the functional roles of GhGLN1.1a in regulating NUE in cotton.

The VILLIN (VLN) protein plays a crucial role in regulating the actin cytoskeleton, which is involved in numerous developmental processes, and is crucial for plant responses to both biotic and abiotic factors. Although various plants have been studied to understand the VLN gene family and its potential functions, there has been limited exploration of VLN genes in Gossypium and fiber crops. In the present study, we characterized 94 VLNs from Gossypium species and 101 VLNs from related higher plants such as Oryza sativa and Zea mays and some fungal, algal, and animal species. By combining these VLN sequences with other Gossypium spp., we classified the VLN gene family into three distinct groups, based on their phylogenetic relationships. A more in-depth examination of Gossypium hirsutum VLNs revealed that 14 GhVLNs were distributed across 12 of the 26 chromosomes. These genes exhibit specific structures and protein motifs corresponding to their respective groups. GhVLN promoters are enriched with cis-elements related to abiotic stress responses, hormonal signals, and developmental processes. Notably, a significant number of cis-elements were associated with the light responses. Additionally, our analysis of gene-expression patterns indicated that most GhVLNs were expressed in various tissues, with certain members exhibiting particularly high expression levels in sepals, stems, and tori, as well as in stress responses. The present study potentially provides fundamental insights into the VLN gene family and could serve as a valuable reference for further elucidating the diverse functions of VLN genes in cotton.

Verticillium dahliae is a soilborne plant fungal pathogen that causes Verticillium wilt, a disease that reduces the yields of many economically important crops. Despite its worldwide distribution and harmful impacts, much remains unknown regarding how the numerous effectors of V. dahliae modulate plant immunity. Here, we identified the intracellular effector VdCE11 that induces cell death and defense responses in Nicotiana benthamiana to counter leaf pathogens such as Sclerotinia sclerotiorum and Botrytis cinerea. VdCE11 also contributes to the virulence of V. dahliae in cotton and Arabidopsis. Yeast two-hybrid library screening and immunoprecipitation revealed that VdCE11 interacts physically with the cotton aspartic protease GhAP1. GhAP1 and its Arabidopsis homolog AtAP1 are negative regulators of plant immunity, since disruption of either increased the resistance of cotton or Arabidopsis to V. dahliae. Further, VdCE11 plays a role in promoting the accumulation of the AP1 proteins and increasing its hydrolase activity. Taken together, these results indicate a novel mechanism regulating virulence whereby the secreted effector VdCE11 increases cotton susceptibility to V. dahliae by promoting the accumulation and activity of GhAP1. IMPORTANCE Verticclium dahliae is a plant fungal pathogen that causes a destructive vascular disease on a large number of plant hosts, resulting in great threat to agricultural production. In this study, we identified a V. dahliae effector VdCE11 that induces cell death and defense responses in Nicotiana benthamiana. Meanwhile, VdCE11 contributes to the virulence of V. dahliae in cotton and Arabidopsis. Yeast two-hybrid library screening and immunoprecipitation revealed that VdCE11 interacts physically with the cotton aspartic protease GhAP1. GhAP1 and its Arabidopsis homolog AtAP1 are negative regulators of plant immunity since disruption of either increased the resistance of cotton or Arabidopsis to V. dahliae. Further research showed that VdCE11 plays a role in promoting the accumulation of the AP1 proteins and increasing its hydrolase activity. These results suggested that a novel mechanism regulating virulence whereby VdCE11 increases susceptibility to V. dahliae by promoting the accumulation and activity of GhAP1 in the host.

Cotton is an important cash crop for the textile industry. However, the understanding of natural genetic variation of fiber elongation in relation to miRNA is lacking. A miRNA gene (miR477b) was found to co‐localize with a previously mapped fiber length (FL) quantitative trait locus (QTL). The miR477b was differentially expressed during fiber elongation between two backcross inbred lines (BILs) differing in FL and its precursor sequences. Bioinformatics and qRT‐PCR analysis were further used to analyse the miRNA genes, which could produce mature miR477b. Cotton plants with virus‐induced gene silencing (VIGS) constructs to over‐express the allele of miR477b from the BIL with longer fibers had significantly longer fibers as compared with negative control plants, while the VIGS plants with suppressed miRNA expression had significantly shorter fibers. The expression level of the target gene (DELLA) and related genes (RDL1 and EXPA1 for DELLA through HOX3 protein) in the two BILs and/or the VIGS plants were generally congruent, as expected. This report represents one of the first comprehensive studies to integrate QTL linkage mapping and physical mapping of small RNAs with both small and mRNA transcriptome analysis, followed by VIGS, to identify candidate small RNA genes affecting the natural variation of fiber elongation in cotton. [ABSTRACT FROM AUTHOR]

The enzyme glutamine synthetase (GLN) is mainly responsible for the assimilation and reassimilation of nitrogen (N) in higher plants. Although the GLN gene has been identified in various plants, there is little information about the GLN family in cotton (Gossypium spp.). To elucidate the roles of GLN genes in cotton, we systematically investigated and characterized the GLN gene family across four cotton species (G. raimondii, G. arboreum, G. hirsutum, and G. barbadense). Our analysis encompassed analysis of members, gene structure, cis-element, intragenomic duplication, and exploration of collinear relationships. Gene duplication analysis indicated that segmental duplication was the primary driving force for the expansion of the GhGLN gene family. Transcriptomic and quantitative real-time reverse-transcription PCR (qRT-PCR) analyses indicated that the GhGLN1.1a gene is responsive to N induction treatment and several abiotic stresses. The results of virus-induced gene silencing revealed that the accumulation and N use efficiency (NUE) of cotton were affected by the inactivation of GhGLN1.1a. This study comprehensively analyzed the GhGLN genes in Gossypium spp., and provides a new perspective on the functional roles of GhGLN1.1a in regulating NUE in cotton. [ABSTRACT FROM AUTHOR]

Reniform nematode (Rotylenchulus reniformis) is an important microparasite for Upland cotton (Gossypium hirsutum L.) production. Growing resistant cultivars is the most economical management method, but only a few G. barbadense genotypes and some diploid Gossypium species confer high levels of resistance. This study conducted a transcriptome analysis of resistant genotypes to identify genes involved in host plant defense. Seedlings of G. arboreum accessions PI 529728 (A2-100) and PI 615699 (A2-190), and G. barbadense genotypes PI 608139 (GB 713) and PI 163608 (TX 110), were inoculated with the reniform nematode population MSRR04 and root samples were collected on the fifth (D5) and ninth (D9) day after inoculation. Differentially expressed genes (DEGs) were identified by comparing root transcriptomes from inoculated plants with those from non-inoculated plants. Accessions A2-100 and A2-190 showed 52 and 29 DEGs on D5, respectively, with 14 DEGs in common, and 18 DEGs for A2-100 and 11 DEGs for A2-190 on chromosome 5. On D9, four DEGs were found in A2-100 and two DEGs in A2-190. For GB 713, 52 and 43 DEGs were found, and for TX 110, 29 and 117 DEGs were observed on D5 and D9, respectively. Six DEGs were common at the two sampling times for these genotypes. Some DEGs were identified as Meloidogyne-induced cotton (MIC) 3 and 4, resistance gene analogs, or receptor-like proteins. Other DEGs have potential roles in plant defense, such as peroxidases, programmed cell death, pathogenesis related proteins, and systemic acquired resistance. Further research on these DEGs will aid in understanding the mechanisms of resistance to explore new applications for the development of resistant cultivars. [ABSTRACT FROM AUTHOR]

Abstract Background Gene expression pattern is associated with biological phenotype and is widely used in exploring gene functions. Its evolution is also crucial in understanding species speciation and divergence. The genus Gossypium is a bona fide model for studying plant evolution and polyploidization. However, the evolution of gene expression during cotton species divergence has yet to be extensively discussed. Results Based on the seedling leaf transcriptomes, this work analyzed the transcriptomic content and expression patterns across eight cotton species, including six diploids and two natural tetraploids. Our findings indicate that, while the biological function of these cotton transcriptomes remains largely conserved, there has been significant variation in transcriptomic content during species divergence. Furthermore, we conducted a comprehensive analysis of expression distances across cotton species. This analysis lends further support to the use of G. arboreum as a substitute for the A-genome donor of natural cotton polyploids. Moreover, our research highlights the evolution of stress-responsive pathways, including hormone signaling, fatty acid degradation, and flavonoid biosynthesis. These processes appear to have evolved under lower selection pressures, presumably reflecting their critical role in the adaptations of the studied cotton species to diverse environments. Conclusions In summary, this study provided insights into the gene expression variation within the genus Gossypium and identified essential genes/pathways whose expression evolution was closely associated with the evolution of cotton species. Furthermore, the method of characterizing genes and pathways under unexpected high or slow selection pressure can also serve as a new strategy for gene function exploration.

Abstract Background Cotton, being extensively cultivated, holds immense economic significance as one of the most prominent crops globally. The SET (Su(var), E, and Trithorax) domain-containing protein is of significant importance in plant development, growth, and response to abiotic stress by modifying the lysine methylation status of histone. However, the comprehensive identification of SET domain genes (SDG) have not been conducted in upland cotton (Gossypium hirsutum L.). Results A total of 229 SDGs were identified in four Gossypium species, including G. arboretum, G. raimondii, G. hirsutum, and G. barbadense. These genes could distinctly be divided into eight groups. The analysis of gene structure and protein motif revealed a high degree of conservation among the SDGs within the same group. Collinearity analysis suggested that the SDGs of Gossypium species and most of the other selected plants were mainly expanded by dispersed duplication events and whole genome duplication (WGD) events. The allopolyploidization event also has a significant impact on the expansion of SDGs in tetraploid Gossypium species. Furthermore, the characteristics of these genes have been relatively conserved during the evolution. Cis-element analysis revealed that GhSDGs play a role in resistance to abiotic stresses and growth development. Furthermore, the qRT-PCR results have indicated the ability of GhSDGs to respond to salt stress. Co-expression analysis revealed that GhSDG51 might co-express with genes associated with salt stress. In addition, the silencing of GhSDG51 in cotton by the virus-induced gene silencing (VIGS) method suggested a potential positive regulatory role of GhSDG51 in salt stress. Conclusions The results of this study comprehensively analyze the SDGs in cotton and provide a basis for understanding the biological role of SDGs in the stress resistance in upland cotton.

The arms race between fungal pathogens and plant hosts involves recognition of fungal effectors to induce host immunity. Although various fungal effectors have been identified, the effector functions of ribonucleases are largely unknown. Herein, we identified a ribonuclease secreted by Verticillium dahliae (VdRTX1) that translocates into the plant nucleus to modulate immunity. The activity of VdRTX1 causes hypersensitive response (HR)-related cell death in Nicotiana benthamiana and cotton. VdRTX1 possesses a signal peptide but is unlikely to be an apoplastic effector because its nuclear localization in the plant is necessary for cell death induction. Knockout of VdRTX1 significantly enhanced V. dahliae virulence on tobacco while V. dahliae employs the known suppressor VdCBM1 to escape the immunity induced by VdRTX1. VdRTX1 homologs are widely distributed in fungi but transient expression of 24 homologs from other fungi did not yield cell death induction, suggesting that this function is specific to the VdRTX1 in V. dahliae. Expression of site-directed mutants of VdRTX1 in N. benthamiana leaves revealed conserved ligand-binding sites that are important for VdRTX1 function in inducing cell death. Thus, VdRTX1 functions as a unique HR-inducing effector in V. dahliae that contributes to the activation of plant immunity.

Background: Gene expression pattern is associated with biological phenotype and is widely used in exploring gene functions. Its evolution is also crucial in understanding species speciation and divergence. The genus Gossypium is a bona fide model for studying plant evolution and polyploidization. However, the evolution of gene expression during cotton species divergence has yet to be extensively discussed. Results: Based on the seedling leaf transcriptomes, this work analyzed the transcriptomic content and expression patterns across eight cotton species, including six diploids and two natural tetraploids. Our findings indicate that, while the biological function of these cotton transcriptomes remains largely conserved, there has been significant variation in transcriptomic content during species divergence. Furthermore, we conducted a comprehensive analysis of expression distances across cotton species. This analysis lends further support to the use of G. arboreum as a substitute for the A-genome donor of natural cotton polyploids. Moreover, our research highlights the evolution of stress-responsive pathways, including hormone signaling, fatty acid degradation, and flavonoid biosynthesis. These processes appear to have evolved under lower selection pressures, presumably reflecting their critical role in the adaptations of the studied cotton species to diverse environments. Conclusions: In summary, this study provided insights into the gene expression variation within the genus Gossypium and identified essential genes/pathways whose expression evolution was closely associated with the evolution of cotton species. Furthermore, the method of characterizing genes and pathways under unexpected high or slow selection pressure can also serve as a new strategy for gene function exploration. [ABSTRACT FROM AUTHOR]

Summary: Gossypol and the related terpenoids are stored in the pigment gland to protect cotton plants from biotic stresses, but little is known about the synthetic sites of these metabolites.Here, we showed that GoPGF, a key gene regulating gland formation, was expressed in gland cells and roots. The chromatin immunoprecipitation sequencing (ChIP‐seq) analysis demonstrated that GoPGF targets GhJUB1 to regulate gland morphogenesis.RNA‐sequencing (RNA‐seq) showed high accumulation of gossypol biosynthetic genes in gland cells. Moreover, integrated analysis of the ChIP‐seq and RNA‐seq data revealed that GoPGF binds to the promoter of several gossypol biosynthetic genes. The cotton callus overexpressing GoPGF had dramatically increased the gossypol levels, indicating that GoPGF can directly activate the biosynthesis of gossypol. In addition, the gopgf mutant analysis revealed the existence of both GoPGF‐dependent and ‐independent regulation of gossypol production in cotton roots.Our study revealed that the pigment glands are synthetic sites of gossypol in aerial parts of cotton and that GoPGF plays a dual role in regulating gland morphogenesis and gossypol biosynthesis. The study provides new insights for exploring the complex relationship between glands and the metabolites they store in cotton and other plant species. [ABSTRACT FROM AUTHOR]

Extremely high temperatures affecting cotton plants at various stages of ontogenesis. Oxidative damage of cell structures inflicted by moderately high temperatures is a main cause for the deleterious effect of heat stress. However, the status of the protective antioxidant system (AOS) in cotton plants has been studied mainly at the generative stages of development, while peculiarities of its functioning in the juvenile plants of various genotypes remains underexplored. The work was done to study the reaction of growth and the AOS response to the heat stress in the 7-8-day seedlings of various cotton cultivars obtained by various selection methods differing in economically valuable features. Surkhan-103 and Bukhara-102, the cultivars generated by classical selection, as well as those generated by biotechnological methods with higher fiber quality, to cultivars Porlok-1, Porlok-2, Ravnak-1 and Ravnak-2, were the objects of experiments. The 7-day seedlings were exposed to the 6-hour effect of high temperature (45°C) to subsequently assess the increment of control and stressinflicted plants and to determine parameters of the AOS state and development of oxidative damages. Surkhan-103, Porlok-4 and Ravnak-2 cultivars were found to distinguish by significantly lower post-stress inhibition of growth of both seedlings and roots than those of Bukhara-102, Ravnak-1 and Porlok-1. The sensitive cultivars affected by heat stress demonstrated higher post-stress contents of hydrogen peroxide and malondialdehyde (MDA), a product of lipid peroxidation, in the leaves. At the same time, the resistant cultivars demonstrated higher activity of catalase and superoxide dismutase. The higher post-stress content of proline were typical of the resistant cultivars. A close direct correlation between inhibition of growth of seedlings and higher contents of hydrogen peroxide and MDA was demonstrated. In addition, high-level inverse correlation was demonstrated between the growth inhibition and higher catalase activity and proline content. The juvenile cotton plants were concluded to be promising in assessment of heat resistance and its dependence on the AOS state. [ABSTRACT FROM AUTHOR]

Excessive salt content in soil has adverse effects on cotton production, especially during the germination and seedling stages. γ-aminobutyric acid (GABA) is an important active substance that is expected to improve the resistance of plants to abiotic stresses. This study focused on two cotton cultivars (Gossypium hirsutum L.: Tahe 2 and Xinluzhong 62) and investigated the impact of exogenous GABA (0, 1, 2, 3, and 4 mM) on seed germination, seedling growth, and related morphological, physiological, and biochemical indicators under salt stress (150 mM NaCl). The results showed that salt stress significantly reduced the germination rate and germination index of cotton seeds (decreased by 20.34% and 32.14% for Tahe 2 and Xinluzhong 62, respectively), leading to decreased seedling height and biomass and causing leaf yellowing. Salt stress induced osmotic stress in seedlings, resulting in ion imbalance (marked reduction in K+/Na+ ratio) and oxidative damage. Under salt stress conditions, exogenous GABA increased the germination rate (increased by 10.64~23.40% and 2.63~31.58% for Tahe 2 and Xinluzhong 62, respectively) and germination index of cotton seeds, as well as plant height and biomass. GABA treatment improved leaf yellowing. Exogenous GABA treatment increased the content of proline and soluble sugars, with varying effects on betaine. Exogenous GABA treatment reduced the Na+ content in seedlings, increased the K+ content, and increased the K+/Na+ ratio (increased by 20.44~28.08% and 29.54~76.33% for Tahe 2 and Xinluzhong 62, respectively). Exogenous GABA treatment enhanced the activities of superoxide dismutase and peroxidase, and reduced the accumulation of hydrogen peroxide and malondialdehyde, but had a negative impact on catalase activity. In conclusion, exogenous GABA effectively improved cotton seed germination. By regulating osmoprotectant levels, maintaining ion homeostasis, and alleviating oxidative stress, GABA mitigated the adverse effects of salt stress on cotton seedling growth. [ABSTRACT FROM AUTHOR]

Background: Cotton, being extensively cultivated, holds immense economic significance as one of the most prominent crops globally. The SET (Su(var), E, and Trithorax) domain-containing protein is of significant importance in plant development, growth, and response to abiotic stress by modifying the lysine methylation status of histone. However, the comprehensive identification of SET domain genes (SDG) have not been conducted in upland cotton (Gossypium hirsutum L.). Results: A total of 229 SDGs were identified in four Gossypium species, including G. arboretum, G. raimondii, G. hirsutum, and G. barbadense. These genes could distinctly be divided into eight groups. The analysis of gene structure and protein motif revealed a high degree of conservation among the SDGs within the same group. Collinearity analysis suggested that the SDGs of Gossypium species and most of the other selected plants were mainly expanded by dispersed duplication events and whole genome duplication (WGD) events. The allopolyploidization event also has a significant impact on the expansion of SDGs in tetraploid Gossypium species. Furthermore, the characteristics of these genes have been relatively conserved during the evolution. Cis-element analysis revealed that GhSDGs play a role in resistance to abiotic stresses and growth development. Furthermore, the qRT-PCR results have indicated the ability of GhSDGs to respond to salt stress. Co-expression analysis revealed that GhSDG51 might co-express with genes associated with salt stress. In addition, the silencing of GhSDG51 in cotton by the virus-induced gene silencing (VIGS) method suggested a potential positive regulatory role of GhSDG51 in salt stress. Conclusions: The results of this study comprehensively analyze the SDGs in cotton and provide a basis for understanding the biological role of SDGs in the stress resistance in upland cotton. [ABSTRACT FROM AUTHOR]

Salinity stress significantly hampers cotton seed germination and seedling growth. Employing plant growth regulators stands out as an effective strategy to mitigate salt stress. In this study, we assessed the impact of varying concentrations of natural composite salt conditions (0%, 0.6%, and 1.2%) on cotton seed germination, seedling growth, and physiology. Additionally, we explored the effects of compound sodium nitrophenolate (CSN: 2 mg·L−1 and 10 mg·L−1), 24-epibrassinolide (EBR: 0.02 mg·L−1 and 0.1 mg·L−1), and gibberellic acid (GA: 60 mg·L−1 and 300 mg·L−1), against a control (CK: distilled water) group. The results indicate that with an increase in the composite salt concentration, the germination potential (GP) and germination rate (GR) of cotton seeds gradually decrease. Simultaneously, the fresh weight and root vitality of seedlings also correspondingly decrease, while the degree of membrane lipid peroxidation increases. Under high-salt (1.2%) conditions, soaking treatments with CSN and EBR significantly enhance both GP (45–59% and 55–64%) and GR (30–33% and 39–36%) compared to the CK. However, the GA treatment does not increase the GP and GR of cotton. Moreover, under high-salt (1.2%) conditions, CSN and EBR treatments result in the increased activities of superoxide dismutase (56–66% and 71–80%), peroxidase (20–24% and 37–51%), and catalase (26–32% and 35–46%). Consequently, cotton exhibits a relatively good tolerance to natural composite salts. Soaking treatments with CSN and EBR effectively improve cotton germination by enhancing antioxidant enzyme activities, thereby strengthening cotton's tolerance to salt stress. These findings offer new insights for enhancing the salt tolerance of cotton. [ABSTRACT FROM AUTHOR]

A new invasive pest, Amrasca biguttula (Ishida) (Hemiptera: Cicadellidae), has recently been detected in southern Puerto Rico. This is the first time that this species has been officially reported in the Western Hemisphere. The species was observed affecting cotton, both cultivated and wild, and eggplant. More research is needed to understand the potential impacts of this species on the island. Recientemente se ha encontrado una nueva plaga invasiva en el sur de Puerto Rico. Este es el primer registro de la especie en el hemisferio occidental. Se observó el mismo afectando líneas de algodón, berenjenas y algodón silvestre. Se necesita más investigación para comprender los impactos potenciales de A. bigutulla en la isla. [ABSTRACT FROM AUTHOR]

Summary: Verticillium dahliae, one of the most destructive fungal pathogens of several crops, challenges the sustainability of cotton productivity worldwide because very few widely‐cultivated Upland cotton varieties are resistant to Verticillium wilt (VW). Here, we report that REVEILLE2 (RVE2), the Myb‐like transcription factor, confers the novel function in resistance to VW by regulating the jasmonic acid (JA) pathway in cotton. RVE2 expression was essentially required for the activation of JA‐mediated disease‐resistance response. RVE2 physically interacted with TPL/TPRs and disturbed JAZ proteins to recruit TPL and TPR1 in NINJA‐dependent manner, which regulated JA response by relieving inhibited‐MYC2 activity. The MYC2 then bound to RVE2 promoter for the activation of its transcription, forming feedback loop. Interestingly, a unique truncated RVE2 widely existing in D‐subgenome (GhRVE2D) of natural Upland cotton represses the ability of the MYC2 to activate GhRVE2A promoter but not GausRVE2 or GbRVE2. The result could partially explain why Gossypium barbadense popularly shows higher resistance than Gossypium hirsutum. Furthermore, disturbing the JA‐signalling pathway resulted into the loss of RVE2‐mediated disease‐resistance in various plants (Arabidopsis, tobacco and cotton). RVE2 overexpression significantly enhanced the resistance to VW. Collectively, we conclude that RVE2, a new regulatory factor, plays a pivotal role in fine‐tuning JA‐signalling, which would improve our understanding the mechanisms underlying the resistance to VW. [ABSTRACT FROM AUTHOR]

Cotton (Gossypium spp. L.) is a major origin of natural fiber, and is projected at 117 million bales worldwide for 2021/22. A variety of biotic and abiotic stresses have considerable negative impacts on cotton. The significantly decreased applications of chemical insecticidal sprays in the agro-ecosystem have greatly affected the biodiversity and dynamics of primary and secondary insects. Various control measures were taken around the globe to increase production costs. Temperature, drought, and salinity, and biotic stresses such as bacteria, viruses, fungi, nematodes, insects, and mites cause substantial losses to cotton crops. Here, we summarize a number of biotic and abiotic stresses upsetting Bt cotton crop with present and future biotechnology solution strategies that include a refuge strategy, multi-gene pyramiding, the release of sterile insects, seed mixing, RNAi, CRISPR/Cas9, biotic signaling, and the use of bioagents. Surveillance of insect resistance, monitoring of grower compliance, and implementation of remedial actions can lead to the sustainable use of cotton across the globe. [ABSTRACT FROM AUTHOR]

Cotton (Gossypium species) has received considerable interest from the geneticists, cytologists and evolutionary biologists since the last more than a century. Here, we explore the genetics of petal spot in the interspecific derivatives involving tetraploid and diploid cottons; and confirm the location of gene governing petal spot phenotype on chromosome A7 by demonstrating co-segregation of SSR marker NAU 2186 with petal spot phenotype. The presence of petal spot was observed to be dominant over its absence. Petal spot inheritance showed significant deviation from the expected Mendelian ratio in all the segregating populations indicating segregation distortion. The distortion was biased towards the hirsutum parent which has important implications from introgression point of view. We also report a strong association between petal spot and petal margin coloration phenotypes. Extant American cotton varieties generally lack petal spot and margin coloration phenotypes. These petal characteristics can serve as morphological markers during germplasm characterization.

Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, these functions have not been assessed in Verticillium dahliae, a soil-borne fungal pathogen that causes devastating wilt diseases in many crops. The discovery and identity of novel lncRNAs and their association with virulence may contribute to an increased understanding of the regulation of virulence in V. dahliae. Here, we identified a total of 352 lncRNAs in V. dahliae. The lncRNAs were transcribed from all V. dahliae chromosomes, typically with shorter open reading frames, lower GC content, and fewer exons than protein-coding genes. In addition, 308 protein-coding genes located within 10 kb upstream and 10 kb downstream of lncRNAs were identified as neighboring genes, and which were considered as potential targets of lncRNA. These neighboring genes encode products involved in development, stress responses, and pathogenicity of V. dahliae, such as transcription factors (TF), kinase, and members of the secretome. Furthermore, 47 lncRNAs were significantly differentially expressed in V. dahliae following inoculation of susceptible cotton (Gossyoiumhisutum) cultivar Junmian No.1, suggesting that lncRNAs may be involved in the regulation of virulence in V. dahliae. Moreover, correlations in expression patterns between lncRNA and their neighboring genes were detected. Expression of lncRNA012077 and its neighboring gene was up-regulated 6 h following inoculation of cotton, while the expression of lncRNA007722 was down-regulated at 6 h but up-regulated at 24 h, in a pattern opposite to that of its neighboring gene. Overexpression of lncRNA012077 in wild-type strain (Vd991) enhanced its virulence on cotton while overexpression of lncRNA009491 reduced virulence. Identification of novel lncRNAs and their association with virulence may provide new targets for disease control.

Cotton being the major fiber crop across the world is exposed to numerous biotic and abiotic stresses. Genetic transformation of cotton is vital to meet the world's food, feed and fiber demands. Genetic manipulation by randomly transferring the genes emanate variable gene expression. Targeted gene insertion by latest genome editing tools results in predictable expression of genes at a specified location. Gene stacking technology emerged as an adaptive strategy to combat biotic and abiotic stresses by integrating 2-3 genes simultaneously and at a specific site to avoid variable gene expression at diverse locations. This study explains the development of cotton's founder transformants to be used as a base line for multiple gene stacking projects. We introduced Cre and PhiC31 mediated recombination sites to specify the locus of incoming genes. CRISPR-Cas9 gene was integrated for developing CRISPR based founder lines of cotton. Cas9 gene along with gRNA was integrated to target Rep (replication) region of cotton leaf curl virus. Replication region of virus was specifically targeted to diminish further proliferation and preventing the virus to develop new strains. To successfully develop these primary transformants, a model transformation system has been optimized with the red color visualization (DS-Red). Following red color transformation system, three baselines with recombination specified site (Rec), targeted replication region (Rep) and Cas9 founder lines have been developed. These founder transformants are useful for developing recombinase mediated and CRISPR/Cas9 based originator lines of cotton. Moreover, these transformants will set up a base system for all the recombinase mediated gene stacking projects.

The accumulation of reactive oxygen species (ROS) is a widespread defence mechanism in higher plants against pathogen attack and sometimes is the cause of cell death that facilitates attack by necrotrophic pathogens. Plant pathogens use superoxide dismutase (SOD) to scavenge ROS derived from their own metabolism or generated from host defence. The significance and roles of SODs in the vascular plant pathogen Verticillium dahliae are unclear. Our previous study showed a significant upregulation of Cu/Zn-SOD1 (VdSOD1) in cotton tissues following V. dahliae infection, suggesting that it may play a role in pathogen virulence. Here, we constructed VdSOD1 deletion mutants (ΔSOD1) and investigated its function in scavenging ROS and promoting pathogen virulence. ΔSOD1 had normal growth and conidiation but exhibited significantly higher sensitivity to the intracellular ROS generator menadione. Despite lacking a signal peptide, assays in vitro by western blot and in vivo by confocal microscopy revealed that secretion of VdSOD1 is dependent on the Golgi reassembly stacking protein (VdGRASP). Both menadione-treated ΔSOD1 and cotton roots infected with ΔSOD1 accumulated more O2- and less H2 O2 than with the wildtype strain. The absence of a functioning VdSOD1 significantly reduced symptom severity and pathogen colonization in both cotton and Nicotiana benthamiana. VdSOD1 is nonessential for growth or viability of V. dahliae, but is involved in the detoxification of both intracellular ROS and host-generated extracellular ROS, and contributes significantly to virulence in V. dahliae.

Intercropped systems have agro-ecological and socioeconomic advantages over monocultures. Cotton is used in systems associated with food crops as an option to increase sustainability in family farming. The objective of this research was to evaluate the productivity of cotton in association with food crops, without using any nutritional assistance in the soil. This study was conducted on the rainy season of 2020 in Manabí-Ecuador. Six treatments were performed: four treatments related with the association of cotton with peanut, cowpea bean, field corn, and sweet corn; and two treatments with cotton monoculture (with and without soil fertilization). Agronomic, productive, and phytosanitary variables were evaluated in 60 m2 experimental plots. A randomized complete block design with four replications was used. The results determined that cotton yield in the association with peanut was significantly equal to the monoculture with and without fertilization. In the intercropped food crops, there was a reduction in production in relation to the monocultures. However, it was the peanut in association with cotton with the lowest reduction, in addition to presenting the best Land Equivalence Ratio (1.71) and the best Marginal Rate of Return (120.56%), which suggests that this association is a viable alternative and easy to adopt by the small cotton producer.

Research on fusion modeling of high spatial and temporal resolution images typically uses MODIS products at 500 m and 250 m resolution with Landsat images at 30 m, but the effect on results of the date of reference images and the 'mixed pixels' nature of moderate-resolution imaging spectroradiometer (MODIS) images are not often considered. In this study, we evaluated those effects using the flexible spatiotemporal data fusion model (FSDAF) to generate fusion images with both high spatial resolution and frequent coverage over three cotton field plots in the San Joaquin Valley of California, USA. Landsat images of different dates (day-of-year (DOY) 174, 206, and 254, representing early, middle, and end stages of the growing season, respectively) were used as reference images in fusion with two MODIS products (MOD09GA and MOD13Q1) to produce new time-series fusion images with improved temporal sampling over that provided by Landsat alone. The impact on the accuracy of yield estimation of the different Landsat reference dates, as well as the degree of mixing of the two MODIS products, were evaluated. A mixed degree index (MDI) was constructed to evaluate the accuracy and time-series fusion results of the different cotton plots, after which the different yield estimation models were compared. The results show the following: (1) there is a strong correlation (above 0.6) between cotton yield and both the Normalized Difference Vegetation Index (NDVI) from Landsat (NDVIL30) and NDVI from the fusion of Landsat with MOD13Q1 (NDVIF250). (2) Use of a mid-season Landsat image as reference for the fusion of MODIS imagery provides a better yield estimation, 14.73% and 17.26% higher than reference images from early or late in the season, respectively. (3) The accuracy of the yield estimation model of the three plots is different and relates to the MDI of the plots and the types of surrounding crops. These results can be used as a reference for data fusion for vegetation monitoring using remote sensing at the field scale.

Abstract 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.

Reniform nematode (Rotylenchulus reniformis) is an important microparasite for Upland cotton (Gossypium hirsutum L.) production. Growing resistant cultivars is the most economical management method, but only a few G. barbadense genotypes and some diploid Gossypium species confer high levels of resistance. This study conducted a transcriptome analysis of resistant genotypes to identify genes involved in host plant defense. Seedlings of G. arboreum accessions PI 529728 (A2-100) and PI 615699 (A2-190), and G. barbadense genotypes PI 608139 (GB 713) and PI 163608 (TX 110), were inoculated with the reniform nematode population MSRR04 and root samples were collected on the fifth (D5) and ninth (D9) day after inoculation. Differentially expressed genes (DEGs) were identified by comparing root transcriptomes from inoculated plants with those from non-inoculated plants. Accessions A2-100 and A2-190 showed 52 and 29 DEGs on D5, respectively, with 14 DEGs in common, and 18 DEGs for A2-100 and 11 DEGs for A2-190 on chromosome 5. On D9, four DEGs were found in A2-100 and two DEGs in A2-190. For GB 713, 52 and 43 DEGs were found, and for TX 110, 29 and 117 DEGs were observed on D5 and D9, respectively. Six DEGs were common at the two sampling times for these genotypes. Some DEGs were identified as Meloidogyne-induced cotton (MIC) 3 and 4, resistance gene analogs, or receptor-like proteins. Other DEGs have potential roles in plant defense, such as peroxidases, programmed cell death, pathogenesis related proteins, and systemic acquired resistance. Further research on these DEGs will aid in understanding the mechanisms of resistance to explore new applications for the development of resistant cultivars.

This study aimed to determine the optimal proportion of cottonseed cake (CSC) as an additive in sorghum silage to improve its chemical composition, fermentative profile, microbial populations, losses, dry matter recovery, and aerobic stability. Five treatments were evaluated, varying the inclusion of CSC at ensiling (0, 50, 100, 200, and 200 g kg−1 on fresh matter basis). The results showed that the inclusion of CSC significantly increased the content of dry matter, crude protein, and ether extract in the silages. Water-soluble carbohydrates, buffering capacity, and ammoniacal nitrogen exhibited a linear decrease with increasing CSC inclusion. The populations of lactic acid bacteria and moulds showed a quadratic response to CSC inclusion. The yeast population was completely inhibited with a minimum inclusion of 200 g kg−1 CSC. Aerobic stability and dry matter recovery showed a linear increase with CSC inclusion. These findings indicate that adding CSC to sorghum silage enhances its nutritive value, fermentative profile, dry matter recovery, and effectively inhibits yeast growth, which is recommended to include 200 g kg−1 of CSC for good cost-effectiveness. [ABSTRACT FROM AUTHOR]

Virus-induced gene silencing (VIGS) by deploying viral-based vectors such as tobacco rattle virus (TRV) is a homology-based gene silencing technique in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) to validate the function of particular genes. The study presented here showed the induction of DNA methylation in the promoter regions of three phenotypic marker genes in different cotton accessions, including two endogenous genes such as phytoene desaturase (PDS) and phytoene synthase (PSY), and an exogenous gene, such as green fluorescent protein (GFP). First, DNA methylation was established in transgenic GFP cotton where methylation persisted up to S3 generation. Afterward, the promoter of PSY was targeted following the same conditions. Significant silencing of PSY was observed and methylation of the promoter was found up to S2 generation in red leaf cotton as detected in GFP cotton. Silencing of PDS resulted in a photobleaching phenotype; interestingly, the strength of this phenotype was diverse within the plants and was not observed in the next generation. Bisulfite sequencing results showed methylation percentage of the cytosine residues was high at CG and CHG sites of the targeted promoter sequences in the silenced plants. The findings of this paper suggest that TRV-based vector system can be used to monitor DNA methylation for both exogenous and endogenous gene levels in cotton and offer a very useful tool for plant epigenetic modification. [ABSTRACT FROM AUTHOR]

PHYTOCHROME INTERACTING FACTORS (PIFs) integrate light and temperature signs to control plant growth and development. However, little is known about PIFs in crop plants such as cotton. Here, we identified 68 PIF proteins and their coding genes from an allotetraploid and three diploid ancestors. Cotton PIFs contain typical ACTIVEPHYA-BINDING (APA) and ACTIVE PHYB-BINDING (APB) motifs by which they bind to phytochrome phyA and phyB, respectively, and have a BASIC HELIX-LOOP-HELIX (bHLH) domain and a nuclear localization sequence necessary for bHLH-type transcription factors. Bioinformatics analysis showed that the promoter of each PIF gene contains multiple cis -acting elements and that the evolution of cotton genomes probably underwent loss, recombination, and tandem replication. Further observations indicated that the sensitivity of cotton PIF expression to high temperature was significantly different from that to low temperature. We found that allotetraploid Gossypium hirsutum PIF4a (GhPIF4a) was induced by high temperature. GhPIF4a promotes flowering in cotton and Arabidopsis and binds to the promoter of GhFT (G. hirsutum FLOWERING LOCUS T), and binding increased with increasing temperature. Our work identifies the evolutionary and structural characteristics and functions of PIF family members in cotton. [ABSTRACT FROM AUTHOR]

Cottonseed is an invaluable resource, providing protein, oil, and abundant minerals that significantly contribute to the well-being and nutritional needs of both humans and livestock. However, cottonseed also contains a toxic substance called gossypol, a secondary metabolite in Gossypium species that plays an important role in cotton plant development and self-protection. Herein, genome-wide analysis and characterization of the terpene synthase (TPS) gene family identified 304 TPS genes in Gossypium. Bioinformatics analysis revealed that the gene family was grouped into six subgroups TPS-a, TPS-b, TPS-c, TPS-e, TPS-f, and TPS-g. Whole-genome, segmental, and tandem duplication contributed to the evolution of TPS genes. According to the analysis of selection pressure, it was predicted that TPS genes experience predominantly negative selection, with positive selection occurring subsequently. RT-qPCR analysis in TM-1 and CRI-12 lines revealed GhTPS48 gene as the candidate gene for silencing experiments. To summarize, comprehensive genome-wide studies, RT-qPCR, and gene silencing experiments have collectively demonstrated the involvement of the TPS gene family in the biosynthesis of gossypol in cotton. [ABSTRACT FROM AUTHOR]

Cotton is an important fiber crop cultivated around the world under diverse climate conditions and generates billions of dollars in annual revenue globally. Biotic and abiotic stresses have caused reduction in yield and productivity of cotton crops. In this review, we comprehensively analyzed and summarized the effect of biotic and abiotic stress on secondary metabolite production in cotton. The development of cotton varieties with improved tolerance against abiotic and biotic stress can play an important role in sustainable cotton production. Under stress conditions, plants develop a variety of defense mechanisms such as initiating signaling functions to upregulate defense responsive genes and accumulation of secondary metabolites. Understanding the impact of stress on secondary metabolite production in cotton is crucial for developing strategies to alleviate the negative effects of stress on crop yield and quality. Further, the potential industrial applications of these secondary metabolites in cotton, such as gossypol, could provide new opportunities for sustainable cotton production and the development of value-added products. Additionally, transgenic and genome-edited cotton cultivars can be developed to provide tolerance to both abiotic and biotic stress in cotton production. [ABSTRACT FROM AUTHOR]

Intercropped systems have agro-ecological and socioeconomic advantages over monocultures. Cotton is used in systems associated with food crops as an option to increase sustainability in family farming. The objective of this research was to evaluate the productivity of cotton in association with food crops, without using any nutritional assistance in the soil. This study was conducted on the rainy season of 2020 in Manabí-Ecuador. Six treatments were performed: four treatments related with the association of cotton with peanut, cowpea bean, field corn, and sweet corn; and two treatments with cotton monoculture (with and without soil fertilization). Agronomic, productive, and phytosanitary variables were evaluated in 60 m² experimental plots. A randomized complete block design with four replications was used. The results determined that cotton yield in the association with peanut was significantly equal to the monoculture with and without fertilization. In the intercropped food crops, there was a reduction in production in relation to the monocultures. However, it was the peanut in association with cotton with the lowest reduction, in addition to presenting the best Land Equivalence Ratio (1.71) and the best Marginal Rate of Return (120.56%), which suggests that this association is a viable alternative and easy to adopt by the small cotton producer. [ABSTRACT FROM AUTHOR]

Verticillium dahliae is a soil-borne fungus that causes vascular wilt on numerous plants worldwide. The fungus survives in the soil for up to 14 years by producing melanized microsclerotia. The protective function of melanin in abiotic stresses is well documented. Here, we found that the V. dahliae tetraspan transmembrane protein VdSho1, a homolog of the Saccharomyces cerevisiae Sho1, acts as an osmosensor, and is required for plant penetration and melanin biosynthesis. The deletion mutant ΔSho1 was incubated on a cellophane membrane substrate that mimics the plant epidermis, revealing that the penetration of ΔSho1 strain was reduced compared to the wild-type strain. Furthermore, VdSho1 regulates melanin biosynthesis by a signalling mechanism requiring a kinase-kinase signalling module of Vst50-Vst11-Vst7. Strains, ΔVst50, ΔVst7 and ΔVst11 also displayed defective penetration and melanin production like the ΔSho1 strain. Defects in penetration and melanin production in ΔSho1 were restored by overexpression of Vst50, suggesting that Vst50 lies downstream of VdSho1 in the regulatory pathway governing penetration and melanin biosynthesis. Data analyses revealed that the transmembrane portion of VdSho1 was essential for both membrane penetration and melanin production. This study demonstrates that Vst50-Vst11-Vst7 module regulates VdSho1-mediated plant penetration and melanin production in V. dahliae, contributing to virulence.

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. [ABSTRACT FROM AUTHOR]

Background: The semi-domesticated Brazilian perennial cotton (Gossypium spp.) germplasm is considered a source of variability for creating modern upland cotton varieties. Here we used Inter-simple Sequence Repeat (ISSR) markers to detect intra and interspecific genetic polymorphism in Gossypium hirsutum L. r. marie-galante and Gossypium barbadense L. and to use molecular data to assessing genetic diversity and molecular discrimination of these species. Methods and results: The sets contained 12 G. barbadense genotypes and 16 G. hirsutum genotypes from a Brazilian collection. The 11 ISSR primers were used for genotyping yielded 101 bands (polymorphism = 47.5%) and were classified as moderately informative (PIC = 0.304). The ISSR markers exposed a greater diversity in G. hirsutum (P = 24.72%; HE =0.071 and I = 0.111) as compared to G. barbadense (P = 17.98%, HE = 0.043 and I = 0.070). The AMOVA analysis showed that 89.47% of the genetic variation was partitioned within species which is supported by Nei's genetic differentiation (Gst = 0.598) and gene flow (Nm = 0.338), suggesting that strong reproductive barriers between species. The UPGMA Cluster Analysis, Principal Coordinate Analysis and Bayesian Model-Based Structural Analysis divided the 28 genotypes into two main clades consistent with the taxonomical delimitation. Conclusion: The ISSR marker system offers a new approach to determining molecular differences between two cotton species (G. hirsutum L. r. marie-galante and G. barbadense L.). This study can expand the molecular marker resources for the identification and improvement of our knowledge about the genetic diversity and relationships between perennial cotton genotypes. [ABSTRACT FROM AUTHOR]

Cyclic nucleotide-gated ion channels (CNGCs) are channel proteins for calcium ions, and have been reported to play important roles in regulating survival and environmental response of various plants. However, little is known about how the CNGC family works in Gossypium. In this study, 173 CNGC genes, which were identified from two diploid and five tetraploid Gossypium species, were classified into four groups by phylogenetic analysis. The collinearity results demonstrated that CNGC genes are integrally conservative among Gossypium species, but four gene losses and three simple translocations were detected, which is beneficial to analyzing the evolution of CNGCs in Gossypium. The various cis-acting regulatory elements in the CNGCs' upstream sequences revealed their possible functions in responding to multiple stimuli such as hormonal changes and abiotic stresses. In addition, expression levels of 14 CNGC genes changed significantly after being treated with various hormones. The findings in this study will contribute to understanding the function of the CNGC family in cotton, and lay a foundation for unraveling the molecular mechanism of cotton plants' response to hormonal changes. [ABSTRACT FROM AUTHOR]

YTH domain-containing proteins are one kind of RNA-binding protein involved in post-transcriptional regulation and play multiple roles in regulating the growth, development, and abiotic stress responses of plants. However, the YTH domain-containing RNA-binding protein family has not been previously studied in cotton. In this study, a total of 10, 11, 22, and 21 YTH genes were identified in Gossypium arboreum, Gossypium raimondii, Gossypium barbadense, and Gossypium hirsutum, respectively. These Gossypium YTH genes were categorized into three subgroups by phylogenetic analysis. The chromosomal distribution, synteny analysis, structures of Gossypium YTH genes, and the motifs of YTH proteins were analyzed. Furthermore, the cis-element of GhYTH genes promoter, miRNA targets of GhYTH genes, and subcellular localization of GhYTH8 and GhYTH16 were characterized. Expression patterns of GhYTH genes in different tissues, organs, and in response to different stresses were also analyzed. Moreover, functional verifications revealed that silencing GhYTH8 attenuated the drought tolerance in the upland cotton TM-1 line. These findings provide useful clues for the functional and evolutionary analysis of YTH genes in cotton. [ABSTRACT FROM AUTHOR]