Identification and molecular evolution of the GLX genes in 21 plant species: a focus on the Gossypium hirsutum

BACKGROUND

The glyoxalase system includes glyoxalase I (GLXI), glyoxalase II (GLXII) and glyoxalase III (GLXIII), which are responsible for methylglyoxal (MG) detoxification and involved in abiotic stress responses such as drought, salinity and heavy metal.

RESULTS

In this study, a total of 620 GLX family genes were identified from 21 different plant species. The results of evolutionary analysis showed that GLX genes exist in all species from lower plants to higher plants, inferring that GLX genes might be important for plants, and GLXI and GLXII account for the majority. In addition, motif showed an expanding trend in the process of evolution. The analysis of cis-acting elements in 21 different plant species showed that the promoter region of the GLX genes were rich in phytohormones and biotic and abiotic stress-related elements, indicating that GLX genes can participate in a variety of life processes. In cotton, GLXs could be divided into two groups and most GLXIs distributed in group I, GLXIIs and GLXIIIs mainly belonged to group II, indicating that there are more similarities between GLXII and GLXIII in cotton evolution. The transcriptome data analysis and quantitative real-time PCR analysis (qRT-PCR) show that some members of GLX family would respond to high temperature treatment in G.hirsutum. The protein interaction network of GLXs in G.hirsutum implied that most members can participate in various life processes through protein interactions.

CONCLUSIONS

The results elucidated the evolutionary history of GLX family genes in plants and lay the foundation for their functions analysis in cotton.

A spit in time: identification of saliva stains and assessment of total DNA recovery up to 180 days after deposition

The main aim of this work was to validate the detection of saliva samples from denim, cotton, and polyester fabrics aged up to six months, applying rapid immunochromatographic tests resulting in the analysis of nuclear and mitochondrial DNA recovered. A comparison was also carried out between two saliva detection tests, Laboratory and Crime Scene. 50 μl saliva samples (three per time and test) were deposited on denim, cotton, and polyester fabrics. After 1, 3, 7, 14, 21, 30, 60, 90, 150, and 180 days of storage at room temperature, the samples were recovered by swabbing and detected by SERATEC® Amylase (Laboratory) test and SERATEC® SALIVA CS (Crime Scene) test (SERATEC®, Göttingen, Germany). DNA was isolated from the swab extraction buffer applying a silica-based methodology, and quantified based on fluorescent and human-specific quantifications. Then, it was submitted to STR profiling and mtDNA sequencing. According to our results, saliva stains up to six months after deposition remain valid specimens. The intensity of the bands varied among fabric type and time. Total DNA was successfully recovered from all tested samples, though with the limitations of obtaining partial nuclear DNA profiles from the oldest samples. In contrast, complete characterization of mtDNA was achieved from all samples. Lab and CS tests performed similar on the detection of saliva, as well as, DNA yield and profiling. Future research will be able to expand these results, analyzing the stability of other body fluids and the sensitivity of rapid immunochromatographic tests to detect them.

Genome-wide identification and analysis of a cotton secretome reveals its role in resistance against Verticillium dahliae

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.

GhSINA1, a SEVEN in ABSENTIA ubiquitin ligase, negatively regulates fiber development in Upland cotton

Protein ubiquitination is essential for plant growth and responses to the environment. The SEVEN IN ABSENTIA (SINA) ubiquitin ligases have been extensively studied in plants, but information on their roles in fiber development is limited. Here, we identified GhSINA1 in Upland cotton (Gossypium hirsutum), which has a conserved RING finger domain and SINA domain. Quantitative real-time PCR (qRT-PCR) analysis showed that GhSINA1 was preferentially expressed during fiber initiation and elongation, especially during initiation in the fuzzless-lintless cotton mutant. Subcellular localization experiments indicated that GhSINA1 localized to the nucleus. In vitro ubiquitination analysis revealed that GhSINA1 has E3 ubiquitin ligase activity. Ectopic overexpression of GhSINA1 in Arabidopsis thaliana reduced the number and length of root hairs and trichomes. Yeast two-hybrid (Y2H), firefly luciferase complementation imaging (LCI), and bimolecular fluorescence complementation (BiFC) assays demonstrated that the GhSINA1 proteins could interact with each other to form homodimers and heterodimers. Overall, these results suggest that GhSINA1 may act as a negative regulator in cotton fiber development through homodimerization and heterodimerization.

Unraveling genomic regions and candidate genes for multiple disease resistance in upland cotton using meta-QTL analysis

Verticillium wilt (VW), Fusarium wilt (FW) and Root-knot nematode (RKN) are the main diseases affecting cotton production. However, many reported quantitative trait loci (QTLs) for cotton resistance have not been used for agricultural practices because of inconsistencies in the cotton genetic background. The integration of existing cotton genetic resources can facilitate the discovery of important genomic regions and candidate genes involved in disease resistance. Here, an improved and comprehensive meta-QTL analysis was conducted on 487 disease resistant QTLs from 31 studies in the last two decades. A consensus linkage map with genetic overall length of 3006.59 cM containing 8650 markers was constructed. A total of 28 Meta-QTLs (MQTLs) were discovered, among which nine MQTLs were identified as related to resistance to multiple diseases. Candidate genes were predicted based on public transcriptome data and enriched in pathways related to disease resistance. This study used a method based on the integration of Meta-QTL, known genes and transcriptomics to reveal major genomic regions and putative candidate genes for resistance to multiple diseases, providing a new basis for marker-assisted selection of high disease resistance in cotton breeding.

Durable and rechargeable antimicrobial cotton driven by enhanced UV stability and real-time detection of biocidal factors

In this study, graphene oxide/N-halamine nanocomposite was synthesized through Pickering miniemulsion polymerization, which was then coated on cotton surface. The modified cotton exhibited excellent superhydrophobicity, which could effectively prevent microbial infestation and reduce the probability of hydrolysis of active chlorine, with virtually no active chlorine released in water after 72 h. Deposition of reduced graphene oxide nanosheets endowed cotton with ultraviolet-blocking properties, attributing to enhanced UV adsorption and long UV paths. Moreover, encapsulation of polymeric N-halamine resulted in improved UV stability, thus extending the life of N-halamine-based agents. After 24 h of irradiation, 85 % of original biocidal component (active chlorine content) was retained, and approximately 97 % of initial chlorine could be regenerated. Modified cotton has been proven to be an effective oxidizing material against organic pollutants and a potential antimicrobial substance. Inoculated bacteria were completely killed after 1 and 10 min of contact time, respectively. An innovative and simple scheme for determination of active chlorine content was also devised, and real-time inspection of bactericidal activity could be achieved to assure antimicrobial sustainability. Moreover, this method could be utilized to evaluate hazard classification of microbial contamination in different locations, thus broadening the application scope of N-halamine-based cotton fabrics.

Genome-wide analysis of the serine carboxypeptidase-like protein family reveals Ga09G1039 is involved in fiber elongation in cotton

The Gossypium is a model genus for understanding polyploidy and the evolutionary pattern of inheritance. This study aimed to investigate the characteristics of SCPLs in different cotton species and their role in fiber development. A total of 891 genes from one typical monocot and ten dicot species were naturally divided into three classes based on phylogenetic analysis. The SCPL gene family in cotton has undergone intense purifying selection with some functional variation. Segmental duplication and whole genome duplication were shown to be the two main reasons for the increase in the number of genes during cotton evolution. The identification of Gh_SCPL genes exhibiting differential expression in particular tissues or response to environmental stimuli provides a new measure for the in-depth characterization of selected genes of importance. Ga09G1039 was involved in the developmental process of fibers and ovules, and it is significantly different from proteins from other cotton species in terms of phylogenetic, gene structure, conserved protein motifs and tertiary structure. Overexpression of Ga09G1039 significantly increased the length of stem trichomes. Ga09G1039 may be a serine carboxypeptidase protein with hydrolase activity, according to functional region, prokaryotic expression, and western blotting analysis. The results provide a comprehensive overview of the genetic basis of SCPLs in Gossypium and further our knowledge in understanding the key aspects of SCPLs in cotton with their potential role in fiber development and stress resistance.

Hydrogen peroxide mediates high-intensity blue light-induced hypocotyl phototropism of cotton seedlings

Phototropism is a classic adaptive growth response that helps plants to enhance light capture for photosynthesis. It was shown that hydrogen peroxide (H2O2) participates in the regulation of blue light-induced hypocotyl phototropism; however, the underlying mechanism is unclear. In this study, we demonstrate that the unilateral high-intensity blue light (HBL) could induce asymmetric distribution of H2O2 in cotton hypocotyls. Disruption of the HBL-induced asymmetric distribution of H2O2 by applying either H2O2 itself evenly on the hypocotyls or H2O2 scavengers on the lit side of hypocotyls could efficiently inhibit hypocotyl phototropic growth. Consistently, application of H2O2 on the shaded and lit sides of the hypocotyls led to reduced and enhanced hypocotyl phototropism, respectively. Further, we show that H2O2 inhibits hypocotyl elongation of cotton seedlings, thus supporting the repressive role of H2O2 in HBL-induced hypocotyl phototropism. Moreover, our results show that H2O2 interferes with HBL-induced asymmetric distribution of auxin in the cotton hypocotyls. Taken together, our study uncovers that H2O2 changes the asymmetric accumulation of auxin and inhibits hypocotyl cell elongation, thus mediating HBL-induced hypocotyl phototropism.

Calcium-dependent protein kinase GhCDPK4 plays a role in drought and abscisic acid stress responses

Drought is an important factor limiting the yield and quality of cotton. In the present study, the gene encoding the cotton calcium-dependent protein kinase GhCDPK4 was identified and characterized in the transcriptome of cotton under PEG-induced drought stress. In RT-qPCR experiments, GhCDPK4 expression was found to be up-regulated under drought and abscisic acid (ABA) stress. Under drought conditions, heterologous overexpression of GhCDPK4 in tobacco showed a better phenotypic status, higher antioxidant enzyme activity, and lower relative electrolyte leakage (REL) and malondialdehyde (MDA) content. Meanwhile, ghcdpk4-silenced cotton plants, which were extremely sensitive to drought, exhibited higher levels of O^2-，H₂O₂, and MDA contents compared to the control. Meanwhile, silenced lines showed impaired stomatal closure under drought stress, resulting in increased water loss from transpiration in silenced lines. GhCDPK4 expression was induced by ABA, and there are five ABA-responsive elements in its promoter. and C2-DOMAIN ABA-RELATED 4(CAR4, Gh_D09G1653) were found to interact and be co-expressed in the GhCDPK4 interaction network. Therefore, GhCDPK4 may reduce the extent of water loss and oxidative damage in cotton under drought by positively regulating ABA-controlled stomatal closure and reactive oxygen species (ROS) scavenging systems. This study demonstrates the great potential of GhCDPK4 in improving drought resistance in crops.

Species composition, seasonal abundance and population dynamics of predatory spiders from cotton field plots of irrigated and semi-arid regions of Punjab, Pakistan

The purpose of the current study was to document the variety of predatory spider species present in the cotton fields of two major cotton-producing districts in Punjab, Pakistan, as well as the population dynamics of those spiders. The research was carried out between May and October 2018 and 2019. Manual picking, visual counting, pitfall traps, and sweep netting were the procedures used to collect samples on a biweekly basis. A total of 10,684 spiders comprising 39 species, 28 genera, and 12 families were documented. Araneidae and Lycosidae families contributed a major share to the overall catch of spiders, accounting for 58.55 percent of the total. The Araneidae family's Neoscona theisi ) was the most dominating species, accounting for 12.80% of the total catch and being the dominant species. The estimated spider species diversity was 95%. Their densities were changed over time in the study, but they were highest in the second half of September and the first half of October of both years. The cluster analysis distinguished the two districts and the sites chosen. There was a relationship between humidity and rainfall and the active density of spiders; however, this association was not statistically significant. It is possible to increase the population of spiders in an area by reducing the number of activities detrimental to spiders and other useful arachnids. Spiders are considered effective agents of biological control throughout the world. The findings of the current study will help in the formulation of pest management techniques that can be implemented in cotton growing regions all over the world.

Changes in terpene biosynthesis and submergence tolerance in cotton

BACKGROUND

Flooding is among the most severe abiotic stresses in plant growth and development. The mechanism of submergence tolerance of cotton in response to submergence stress is unknown.

RESULTS

The transcriptome results showed that a total of 6,893 differentially expressed genes (DEGs) were discovered under submergence stress. Gene Ontology (GO) enrichment analysis showed that DEGs were involved in various stress or stimulus responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs related to plant hormone signal transduction, starch and sucrose metabolism, glycolysis and the biosynthesis of secondary metabolites were regulated by submergence stress. Eight DEGs related to ethylene signaling and 3 ethylene synthesis genes were identified in the hormone signal transduction. For respiratory metabolism, alcohol dehydrogenase (ADH, GH_A02G0728) and pyruvate decarboxylase (PDC, GH_D09G1778) were significantly upregulated but 6-phosphofructokinase (PFK, GH_D05G0280), phosphoglycerate kinase (PGK, GH_A01G0945 and GH_D01G0967) and sucrose synthase genes (SUS, GH_A06G0873 and GH_D06G0851) were significantly downregulated in the submergence treatment. Terpene biosynthetic pathway-related genes in the secondary metabolites were regulated in submergence stress.

CONCLUSIONS

Regulation of terpene biosynthesis by respiratory metabolism may play a role in enhancing the tolerance of cotton to submergence under flooding. Our findings showed that the mevalonate pathway, which occurs in the cytoplasm of the terpenoid backbone biosynthesis pathway (ko00900), may be the main response to submergence stress.

Response of in situ root phenotypes to potassium stress in cotton

Potassium plays a significant role in the basic functions of plant growth and development. Potassium uptake is closely associated with morphological characteristics of the roots. However, the dynamic characteristics of phenotype and lifespan of cotton (Gossypium hirsutum L.) lateral roots and root hairs under low and high potassium stress remain unclear. In this study, potassium stress experiments (low and high potassium, medium potassium as control) were conducted using RhizoPot (an in situ root observation device) to determine the response characteristics of lateral roots and root hairs in cotton under potassium stress. The plant morphology, photosynthetic characteristics, root phenotypic changes, and lifespan of lateral roots and root hairs were measured. Potassium accumulation, aboveground phenotype, photosynthetic capacity, root length density, root dry weight, root diameter, lateral root lifespan, and root hair lifespan under low potassium stress were significantly decreased compared to medium potassium treatment. However, the root hair length of the former was significantly increased than that of the latter. Potassium accumulation and the lateral root lifespan were significantly increased under high potassium treatment, while root length density, root dry weight, root diameter, root hair length, and root hair lifespan were significantly decreased compared to the medium potassium treatment. Notably, there were no significant differences in aboveground morphology and photosynthetic characters. Principal component analysis revealed that lateral root lifespan, root hair lifespan of the first lateral root, and root hair length significantly correlated with potassium accumulation. The root had similar regularity responses to low and high potassium stress except for lifespan and root hair length. The findings of this study enhance the understanding of the phenotype and lifespan of cotton's lateral roots and root hairs under low and high potassium stress.

Effects of practicing long-term mulched drip irrigation on soil quality in Northwest China

Assessing soil quality variation during the prolonged application of mulched drip irrigation (MDI) is critical to comprehend the sustainability of arid agriculture. To investigate the dynamics of crucial soil-quality indicators caused by the long-term application of MDI, the "space instead of time" methodology was adopted, and six fields were selected to represent the primary successional sequence in Northwest China. A total of 21 vital soil attributes from 18 samples were used as soil quality indicators. Based on the soil quality index calculated from the entire datasets, it was observed that long-term MDI practice enhanced soil quality by 28.21 %-74.36 % due to improvements in soil structure (e.g., soil bulk density, three-phase ratio, and aggregates stability) and nutrients (including total carbon, organic carbon, total nitrogen, and available phosphorus). Compared to natural unirrigated soil, soil salinity in 0-200 cm depth significantly decreased by 51.34 %-92.39 % in cotton fields with increasing years of practicing MDI. In addition, long-term MDI practice restructured soil microbial communities and augmented microbial activity by 259.48 %-502.90 % relative to the natural salt-affected soil. However, soil quality stabilized after 12-14 years of MDI application due to accumulated residual plastic fragments, increased bulk density, and reduced microbial diversity. Overall, practicing long-term MDI promotes soil quality and crop yield by promoting soil microbiome structure and function and soil structure. However, long-term mono-cropping with MDI would result in soil compaction and impair microbial activity.

GhPYL9-5D and GhPYR1-3 A positively regulate Arabidopsis and cotton responses to ABA, drought, high salinity and osmotic stress

BACKGROUND

Abscisic acid (ABA) receptor pyrabactin resistance 1/PYR1-like/regulatory components of ABA receptor proteins (PYR/PYL/RCARs) have been demonstrated to play pivotal roles in ABA signaling and in response to diverse environmental stimuli including drought, salinity and osmotic stress in Arabidopsis. However, whether and how GhPYL9-5D and GhPYR1-3A, the homologues of Arabidopsis PYL9 and PYR1 in cotton, function in responding to ABA and abiotic stresses are still unclear.

RESULTS

GhPYL9-5D and GhPYR1-3A were targeted to the cytoplasm and nucleus. Overexpression of GhPYL9-5D and GhPYR1-3A in Arabidopsis wild type and sextuple mutant pyr1pyl1pyl2pyl4pyl5pyl8 plants resulted in ABA hypersensitivity in terms of seed germination, root growth and stomatal closure, as well as seedling tolerance to water deficit, salt and osmotic stress. Moreover, the VIGS (Virus-induced gene silencing) cotton plants, in which GhPYL9-5D or GhPYR1-3A were knocked down, showed clearly reduced tolerance to polyethylene glycol 6000 (PEG)-induced drought, salinity and osmotic stresses compared with the controls. Additionally, transcriptomic data revealed that GhPYL9-5D was highly expressed in the root, and GhPYR1-3A was strongly expressed in the fiber and stem. GhPYL9-5D, GhPYR1-3A and their homologs in cotton were highly expressed after treatment with PEG or NaCl, and the two genes were co-expressed with redox signaling components, transcription factors and auxin signal components. These results suggest that GhPYL9-5D and GhPYR1-3A may serve important roles through interplaying with hormone and other signaling components in cotton adaptation to salt or osmotic stress.

CONCLUSIONS

GhPYL9-5D and GhPYR1-3A positively regulate ABA-mediated seed germination, primary root growth and stomatal closure, as well as tolerance to drought, salt and osmotic stresses likely through affecting the expression of multiple downstream stress-associated genes in Arabidopsis and cotton.

First Report of Alternaria alternata Causing Leaf Spot Diseases of Cotton in Türkiye

Cotton (Gossypium hirsutum L.) is a crucial crop for the textile industry. Sanliurfa is the major cotton production area in southeast Türkiye (USDA 2021). In the summers of 2021 and 2022, the mid to late season desiccation of leaves, stems and bolls as well as severe defoliation were observed in different cotton fields and cultivars in a 30-ha area centered around 36°51'15.7"N, 39°07'12.2"E. Approximately 45% of the plants were severely affected or completely desiccated. Initially, symptoms were circular, pinhead, necrotic lesions surrounded by a purple halo, scattered all around the infected leaves. As the disease progressed, it spread to bracts, petioles, stem and bolls. The necrotic lesions continued to expand, and formed irregular shapes by coalescing, occupied the whole tissue . Finally, severe infection resulted in premature defoliation. A secondary host (Prosopis farcta) of the inoculum of A. alternata is found in the field where the symptoms of pathogen was seen. The disease symptoms were similar to those described in cotton by Macauley (1982). Infected leaf samples with mycelia were collected (n=35) from 25 diseased plants. The samples derived from lesions on infected leaves were cut into 4- to 5- mm pieces, treated in 2% sodium hypochlorite, dipped in water, plated on potato dextrose agar (PDA) amended with 30 mg/L of streptomycin sulphate, and kept at 27°C in the dark. All the isolated fungal samples formed dark olive-green colonies. For morphological characterization, the colonies were examined under light microscopy at ×400 magnification. Conidia formed both cross or longitudinal septa, and were obclavate to elliptical and measured 16.2 to 30.5 µm long and 7.5 to 10.6 µm wide (n=14). The morphological characters were consistent with the genus Alternaria using a taxonomic key (Barnett and Hunter 1972). For pathogenicity test, healthy cotton plants were grown at 15 to 29°C in greenhouse. Conidial suspension (10 6 per mL) was sprayed on 30-d old plants (n=16) while control plants were sprayed with water. Then, the plants were covered with plastic bags (28x45 cm) at nights, opened in the morning. The disease symptoms were seen 20 days after artificial inoculation. However, the control group showed no symptoms. The pathogen was re-isolated from infected leaves. To confirm the result, the pathogenicity test was conducted twice. Then, DNA was extracted from conidia and mycelia using CTAB method with slight modification (Doyle and Doyle 1990). The nuclear rDNA internal transcribed spacer (ITS) and plasma membrane ATPase regions were (Lawrence et al. 2014; White et al. 1990) amplified, using primers ITS4/ITS5 and ATPDF1/ATPDR1, respectively. The PCR products were Sanger-sequenced and were uploaded to GenBank (accession nos. ITS: OP615138.1, ATPase: OP612816.1). The sequenced parts of the genes were 554 bp and 1025 bp, and showed 100% (ITS) and 97.99% (ATPase) nucleotide identity with the corresponding sequences (MT446176.1, ON442363.1) of the reference strains of A. alternata. To the best of our knowledge, this is the first report of A. alternata causing leaf blight of cotton in Türkiye. In several cotton-growing regions, A. alternata leaf spot epidemics have caused yield loss from 25% (Israel) to 37% (India) (Padaganur et al. 1989; Rotem et al. 1988). Although yield loss caused by the pathogen depends on environmental conditions, observations in Türkiye cotton fields suggest A. alternata has the potential to cause yield loss up to 30% under severe infection.

The cotton protein GhIQD21 interacts with GhCaM7 and modulates organ morphogenesis in Arabidopsis by influencing microtubule stability

KEY MESSAGE

GhIQD21, a cotton IQ67-domain protein, interacts with GhCaM7 and alters organ shape in Arabidopsis by modulating microtubule stability. Calcium ion (Ca²⁺) and the calcium sensor calmodulin play crucial roles in the growth and development of plants. GhCaM7, a calmodulin in upland cotton (Gossypium hirsutum L.), is highly expressed in cotton fiber cells during the rapid elongation period and plays an important role in fiber cell development. In this study, we screened for GhCaM7-interacting proteins and identified GhIQD21, which contains a typical IQ67-domain. GhIQD21 was preferentially expressed at the fiber rapid elongation stage, and the protein localized to microtubules (MTs). Ectopic expression of GhIQD21 in Arabidopsis resulted in shorter leaves, petals, siliques, and plant height, thicker inflorescences, and more trichomes when compared with wild type (WT). Further investigation indicated that the morphogenesis of leaf epidermal cells and silique cells was altered. There was less consistency in the orientation of cortical microtubules in cotyledon and hypocotyl epidermal cells. Furthermore, compared with WT, transgenic seedling hypocotyls were more sensitive to oryzalin, a MT depolymerization drug. These results indicated that GhIQD21 is a GhCaM7-interacting protein located in MTs and that it plays a role in plant growth and potentially cotton fiber development. This study provides a foundation for further studies of the function and regulatory mechanism of GhIQD21 in fiber cell development.

Ca2+-responsive phospholipid-binding BONZAI genes confer a novel role for cotton resistance to Verticillium wilt

Verticillium wilt which produced by the soil-borne fungus Verticillium dahliae is an important biotic threat that limits cotton (Gossypium hirsutum) growth and agricultural productivity. It is very essential to explore new genes for the generation of V. dahliae resistance or tolerance cotton varieties. Ca²⁺ signaling as a secondary messenger is involved in pathogen stress response. Despite Ca²⁺-responsive phospholipid-binding BONZAI (BON) genes have intensively been investigated in Arabidopsis, their function has not still been characterized in cotton. Here, we showed that three copies of GhBON1, two copies of GhBON2 and GhBON3 were found from the genome sequences of upland cotton. The expression of GhBON1 was inducible to V. dahliae. Knocking down of GhBON1, GhBON2 and GhBON3 using virus induced gene silencing (VIGS) each increased up-regulation of defense responses in cotton. These GhBON1, GhBON2 and GhBON3-silenced plants enhanced resistance to V. dahliae accompanied by higher burst of hydrogen peroxide and decreased cell death and had more effect on the up-regulation of defense response genes. Further analysis revealed that GhBON1 could interacts with BAK1-interacting receptor-like kinase 1 (GhBIR1) and pathogen-associated molecular pattern (PAMP) receptor regulator BAK1 (GhBAK1) at plasma membrane. Our study further reveals that plant Ca²⁺ -responsive phospholipid-binding BONZAI genes negatively regulate Verticillium wilt with the conserved function in response to disease resistance or plant immunity.

Experimental Growth Conditions affect Direct and Indirect Defences in two Cotton Species

Cotton has been used as a model plant to study direct and indirect plant defence against herbivorous insects. However, the plant growing conditions could have an important effect on the outcome of such plant defence studies. We examined how common experimental growth conditions influence constitutive and inducible defences in two species of cotton, Gossypium hirsutum and G. herbaceum. We induced plants by applying caterpillar regurgitant to mechanical wounds to compare the induction levels between plants of both species grown in greenhouse or phytotron conditions. For this we measured defence metabolites (gossypol and heliocides) and performance of Spodoptera frugiperda caterpillars on different leaves, the emission of plant volatiles, and their attractiveness to parasitic wasps. Induction increased the levels of defence metabolites, which in turn decreased the performance of S. frugiperda larvae. Constitutive and induced defence levels were the highest in plants grown in the phytotron (compared to greenhouse plants), G. hirsutum and young leaves. Defence induction was more pronounced in plants grown in the phytotron and in young leaves. Also, the differences between growing conditions were more evident for metabolites in the youngest leaves, indicating an interaction with plant ontogeny. The composition of emitted volatiles was different between plants from the two growth conditions, with greenhouse-grown plants showing more variation than phytotron-grown plants. Also, G. hirsutum released higher amounts of volatiles and attracted more parasitic wasps than G. herbaceum. Overall, these results highlight the importance of experimental abiotic factors in plant defence induction and ontogeny of defences. We therefore suggest careful consideration in selecting the appropriate experimental growing conditions for studies on plant defences.

Genome-wide identification and functional analysis of ICE genes reveal that Gossypium thurberi "GthICE2" is responsible for cold and drought stress tolerance

Cold stress has been found to have a negative impact on cotton growth and annual production. To address this issue, the utilization of cold-tolerant gene resources from wild species of Gossypium is crucial for genetic improvements in cultivated cotton. ICE (inducer of CBF expression) are the key regulators of cold tolerance in plants, however, there is relatively little information on ICE genes in cotton. Herein, we performed comprehensive bioinformatics analyses of the ICE gene family in eight cotton species. Phylogenetic analysis showed that 52 ICE genes were clustered into four subgroups. Cis-regulatory elements analysis suggests that the expression of ICE genes might be regulated by light, plant hormones, and various environment stresses. Higher expression of GthICE2 was observed in leaves as compared to roots and stems, in response to cold, drought, and exogenous hormone ABA. Furthermore, overexpression of GthICE2 in A. thaliana led to higher germination and survival rates, longer root length, lower ion leakage, and induction under cold and drought stress. Histochemical staining showed that oxidative damage in transgenic lines was much lower compared to wild-type plants. Lower MDA contents and higher SOD and POD activities were observed in overexpressed plants. Y1H and LUC assays revealed that GthICE2 might activate the expression of GthCBF4, a cold-responsive gene, by connecting with the MYC cis-element present in the promoter of GthCBF4. GthICE2 confers cold and drought stress tolerance in cotton. Our findings add significantly to the existing knowledge regarding cold stress tolerance and helps to elucidate cold response mechanisms in cotton.

N6-methyladenosine RNA modification regulates cotton drought response in a Ca2+ and ABA-dependent manner

N⁶ -methyladenosine (m⁶ A) is the most prevalent internal modification present in mRNAs, and is considered to participate in a range of developmental and biological processes. Drought response is highly regulated at the genomic, transcriptional and post-transcriptional levels. However, the biological function and regulatory mechanism of m⁶ A modification in the drought stress response is still poorly understood. We generated a transcriptome-wide m⁶ A map using drought-resistant and drought-sensitive varieties of cotton under different water deficient conditions to uncover patterns of m⁶ A methylation in cotton response to drought stress. The results reveal that m⁶ A represents a common modification and exhibit dramatic changes in distribution during drought stress. More 5'UTR m⁶ A was deposited in the drought-resistant variety and was associated with a positive effect on drought resistance by regulating mRNA abundance. Interestingly, we observed that increased m⁶ A abundance was associated with increased mRNA abundance under drought, contributing to drought resistance, and vice versa. The demethylase GhALKBH10B was found to decrease m⁶ A levels, facilitating the mRNA decay of ABA signal-related genes (GhZEP, GhNCED4 and GhPP2CA) and Ca²⁺ signal-related genes (GhECA1, GhCNGC4, GhANN1 and GhCML13), and mutation of GhALKBH10B enhanced drought resistance at seedling stage in cotton. Virus-induced gene silencing (VIGS) of two Ca²⁺ -related genes, GhECA1 and GhCNGC4, reduced drought resistance with the decreased m⁶ A enrichment on silenced genes in cotton. Collectively, we reveal a novel mechanism of post-transcriptional modification involved in affecting drought response in cotton, by mediating m⁶ A methylation on targeted transcripts in the ABA and Ca²⁺ signalling transduction pathways.

Macro- and microplastic leachates show a slightly toxic effect on seed germination of cotton

Utilizing degradable mulching film effectively decreases the accumulation of plastic residuals in agriculture fields and their impacts on plant growth. However, the chemical risks to plants raised by leached substances from different microplastics are still unknown. This work determined the characteristics of macro- and microplastic leachates from different degradation (PE, PO, and Bio) and size (1 × 1 cm, 450-600 μm and <355 μm), as well as their impact on the germination of two varieties of cotton seeds. Our study revealed that degradable characteristics of macro-plastic significantly affect its leachates. Leachates of Bio gained higher dissolved organic carbon (DOC) concentration, aromatic, and values of slope ratios (S_R) compared with PO and PE. The particle size of Bio macro- and microplastics also influences indicators such as S_R, E₂₅₀/E₃₆₅, E₂₅₃/E_203, and Fmax value; however, fluctuations of those indicators were significantly lower than that induced by different degradable traits. Leachates of PE, PO, and Bio seem to have little impact on the germination of two varieties of cotton seeds, only mean germination time (MGT) and shoot height were slightly different among each treatment. A slight fluctuation of enzyme activities also indicates that plastic leachate did not generate excessive oxidative stress in cotton during germination. Leachates of macro- and microplastic under the tested concentration exhibited a slight toxic impact on cotton, which has high-stress tolerance. Thus, further studies should concentrate on the effects of plastic leachate on sensitive plants.

The resilient cotton plant: uncovering the effects of stresses on secondary metabolomics and its underlying molecular mechanisms

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.

Agrobacterium-mediated Genetic Transformation of Cotton and Regeneration via Somatic Embryogenesis

Cotton is a significant industrial crop, playing an essential role in the global economy that suffers several setbacks due to biotic and abiotic adversities. Despite such problems, biotechnological advances in cotton are limited because of genetic transformation and regeneration limitations. Here, we present a detailed protocol optimized based on previously published papers, along with our modifications. These involve changes in Agrobacterium concentration, co-cultivation time and temperature, hormones used for regeneration, media manipulation for embryogenic callus production, and efficient rescue of deformed embryos. Further, this protocol has been used in genetic studies on biotic and abiotic stress in cotton. This protocol assures a reproducible stable transgenic cotton development procedure via somatic embryogenesis that can be used by researchers worldwide. This protocol was validated in: Nat Biotechnol (2016), DOI: 10.1038/nbt.3665.

Development and identification of molecular markers of GhHSP70-26 related to heat tolerance in cotton

Heat stress significantly affect plant growth and development, which is an important factor contributing to crop yield loss. However, heat shock proteins (HSPs) in plants can effectively alleviate cell damage caused by heat stress. In order to rapidly and accurately cultivate heat-tolerant cotton varieties, this study conducted correlation analysis between heat tolerance index and insertion/deletion (In/Del) sites of GhHSP70-26 promoter in 39 cotton materials, so as to find markers related to heat tolerance function of cotton, which can be used in molecular marker-assisted breeding. The results showed the natural variation allele (Del22 bp) type at -1590 bp upstream of GhHSP70-26 promoter (haplotype2, Hap2) in cotton (Gossypium spp.) promoted GhHSP70-26 expression under heat stress. The relative expression level of GhHSP70-26 of M-1590-Del22 cotton materials were significantly higher than that of M-1590-In type cotton materials under heat stress (40 ℃). Also, M-1590-Del22 material had lower conductivity and less cell damage after heat stress, indicating that it is a heat resistant cotton material. The Hap1 (M-1590-In) promoter was mutated into Hap1^del22, and Hap1 and Hap1^del22 were fused with GUS to transform Arabidopsis thaliana. Furthermore, Hap1^del22 promoter had higher induction activity than Hap1 under heat stress and abscisic acid (ABA) treatment in transgenic Arabidopsis thaliana. Further analysis confirmed that M-1590-Del22 was the dominant heat-resistant allele. In summary, these results identify a key and previously unknown natural variation in GhHSP70-26 with respect to heat tolerance, providing a valuable functional molecular marker for genetic breeding of cotton and other crops with heat tolerance.

Light induced shoot-sourced transcription factor HY5 regulates the nitrate uptake of cotton by shoot-to-root signal transport

Elongated hypocotyls 5 (HY5) is a transcription factor that can be induced by illumination and promotes nitrate uptake in Arabidopsis. However, whether GhHY5 regulates nitrate uptake in cotton is unknown. In this study, the cotton seedlings growing in light and dark conditions were treated with ¹⁵N-labeled nutrient solution to study whether the GhHY5 regulates nitrate uptake in cotton. The results showed that the ¹⁵N content and GhNRT1.1 expression in the light condition were higher than that in the dark condition, indicating that light induced the expression of GhNRT1.1 and subsequently promoted N uptake. Additionally, the expression of GhHY5 in the leaf and root of cotton was induced by light and the expression pattern of GhHY5 in the root was similar to that of GhNRT1.1. Furthermore, when the GhHY5 expression in the root was reduced, the ¹⁵N content and GhNRT1.1 expression were both decreased, indicating that the GhNRT1.1 expression was regulated by GhHY5. The root expression of GhHY5 was decreased in the grafted seedlings which the GhHY5 in the shoot was silenced by VIGS or the seedlings which the hypocotyl was girdled, but the expression of GhHY5 on one side root of the grafted cotton seedling was not changed if the GhHY5 was silenced on the other side root. Thus, we proposed that the light induced shoot-derived GhHY5 gene or GhHY5 protein may be transported from the xylem to the root, regulating the expression of GhHY5 and GhNRT1.1, and thus regulating N uptake at the root of cotton.