GhWRKY1-like enhances cotton resistance to Verticillium dahliae via an increase in defense-induced lignification and S monolignol content

Cotton is one of the most important economic crops and is cultivated globally. Verticillium wilt, caused by the soil-borne hemibiotrophic fungus Verticillium dahliae, is the most destructive disease in cotton production for its infection strategies and great genetic plasticity. Recent studies have identified the accumulation of lignin is a general and basal defense reaction in plant immunity and cotton resistance to V. dahliae. However, the functions and regulatory mechanisms of transcription factors in cotton defense-induced lignification and lignin composition alteration were less reported. Here, we identified a WRKY transcription factor GhWRKY1-like from upland cotton (Gossypium hirsutum) as a positive regulator in resistance to V. dahliae via directly manipulating lignin biosynthesis. Further analysis revealed that GhWRKY1-like interacts with the promoters of lignin biosynthesis related genes GhPAL6 and GhCOMT1, and activates the expression of GhPAL6 and GhCOMT1, which led to enhanced total lignin especially S monomers biosynthesis. These results demonstrate that GhWRKY1-like enhances Verticillium wilt resistance via an increase in defense-induced lignification and broaden our knowledge of the roles of lignification and the lignin composition in plant defense responses.

GhGSTF12, a glutathione S-transferase gene, is essential for anthocyanin accumulation in cotton (Gossypium hirsutum L.)

Anthocyanins are flavonoid pigments providing plants a range of colors from red, pink, orange to blue. Anthocyanins are synthesized in the cytosol but accumulate predominantly in the vacuoles through vacuolar sequestration involving glutathione S-transferases (GSTs) and multidrug and toxic compound extrusion (MATE) and the ATP binding cassette (ABC) transporters. However, little is known about anthocyanin-related GSTs in Upland cotton (Gossypium hirsutum L.). In this study, we performed genome-wide identification of GST genes in Upland cotton and identified GST genes functioning in accumulation of anthocyanins. We demonstrated that GhGSTF12 was able to complement the defective leaf color phenotypes of the Arabidopsis tt19 mutant caused by mutation in a GSTF gene. Virus-induced silencing of GhGSTF12 in the red leaf cultivar turned its red color to green and transient overexpression of GhGSTF12 accelerated anthocyanin accumulation in the red leaf cultivar but not in the green leaf cultivar. Collectively, GhGSTF12 may be involved in transport of anthocyanins from cytosol to vacuoles in cotton. These results also demonstrated a conserved function of plant GSTF genes in anthocyanin accumulation and provide a candidate gene for manipulating pigmentation in cotton tissues.

Impact of dyes and finishes on the aquatic biodegradability of cotton textile fibers and microfibers released on laundering clothes: Correlations between enzyme adsorption and activity and biodegradation rates

The presence and biodegradability of textile microfibers shed during laundering or use is an important environmental issue. In this research, the influence of common textile finishes on the persistence of cotton fibers in an aerobic aquatic environment was assessed. The biodegradation of cotton knitted fabrics with different finishes, silicone softener, durable press, water repellent, and a blue reactive dye was evaluated. The rate of biodegradation decreased with durable press and water repellant finishing treatments. In terms of the final extent of biodegradation, there was no significant difference between the samples. All samples reached more than 60% biodegradation in 102 days. The biodegradation rates were in agreement with observed trends of the same samples for cellulase mediated hydrolysis and cellulase adsorption experiments, indicating the finishes impact the initial adsorption of enzymes excreted by the microorganisms and the initial rates of biodegradation, however despite this the cellulosic material maintains its biodegradability.

Effects of seasonal variation on the biology and morphology of the dusky cotton bug, Oxcarenus laetus (Kirby)

The dusky cotton bug (Oxycarenus laetus, KIRBY) a pest of several crops. The effects of winter and summer on the biology and morphology was investigated. The sampled eggs of dusky cotton bug (DCB) were kept under controlled environment for biological and morphological investigations. In winter, the mating duration of DCB was observed longer significantly (74.2 days), egg development period (3.93 days), an egg laying period (3.6 days) and hatching period (6.66 days) noted longer in winter season. Interestingly, average number of hatched egg (16.8 days) observed significantly higher in summer and the percentage of the hatching of eggs (81.95%) were also observed higher in summer as compare to winter. Whereas, the longevity of all nymph stages in winter longer days as compare to summer nymph stages. Moreover, differences were also observed between male and female development days between winter and summer. In the winter, female DCB development was suggestively higher as compare to summer (24 days). Whereas, the developmental days were noted considerably more in winter for males as compare to summer (14.93 days). On other hand, for morphological parameters, no differences were observed between winter and summer population of DCB.

Roles of the 14-3-3 gene family in cotton flowering

BACKGROUND

In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein-protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown.

RESULTS

In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering.

CONCLUSIONS

Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

Genome-wide identification of cotton GRAM family proteins reveals that GRAM31 regulates fiber length

The glucosyltransferases, Rab-like GTPase activators and myotubularins (GRAM) domain is highly conserved in eukaryotic cells and is found in proteins involved in membrane-associated processes. GRAM domain proteins have not yet been functionally characterized in cotton. In this study, we identified 164 genes encoding GRAM domain proteins in four cotton species, comprising two subfamilies. In Gossypium hirsutum, our transcriptome data showed that GhGRAM31 was predominantly expressed during the rapid elongation stage of fiber development and that it might control fiber length. GhGRAM31-RNAi transgenic cotton lines showed inhibition of fiber elongation and produced shorter mature fibers, and this was coupled with expression changes of genes related to fiber development. In addition, lint percentage and seed size were also decreased in the RNAi lines. Further examination revealed that GhGRAM31 directly interacts with two other GRAM-domain proteins, GhGRAM5 and GhGRAM35. GhGRAM5 also interacts with the transcription factor GhTTG1, while GhGRAM35 interacts with the transcription factors GhHOX1 and GhHD1. Co-expression of GhGRAM31 and GhGRAM35 was able to promote GhHD1 transcription activity in cotton protoplasts. Our results provide new insights into the biological function of the GRAM-domain protein family in cotton, and selected genes have the potential to be utilized in future programs for the genetic improvement of fibers.

Characterization of cotton ARF factors and the role of GhARF2b in fiber development

BACKGROUND

Cotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored.

RESULTS

Here, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cotton G. hirsutum, which has 73 ARF genes, and its putative extent parental diploids G. arboreum and G. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that in G. hirsutum ARF genes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate that GhARF2b, a homolog of the Arabidopsis AtARF2, was preferentially expressed in developing ovules and fibers. Overexpression of GhARF2b by a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes.

CONCLUSION

Our results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.

Linking exogenous foliar application of glycine betaine and stomatal characteristics with salinity stress tolerance in cotton (Gossypium hirsutum L.) seedlings

BACKGROUND

Glycine betaine (GB) plays a crucial role in plants responding to abiotic stresses. Studying the physiological response of cotton seedlings to exogenous GB under salt stress provides a reference for the application of GB to improve the resistance of cotton seedlings under salt stress. The purpose of this research is to examine the impacts of foliar-applied GB on leaf stomatal structure and characteristics, gas exchange and chlorophyll fluorescence characteristics and plant growth indicators of Gossypium hirsutum L. under NaCl stress conditions.

RESULTS

Under the salinity of 150 mM, the four concentrations of GB are 0, 2.5, 5, and 7.5 mM, and the control (CK) was GB-untreated non-saline. Salt stress negatively affected leaf stomata as well as gas exchange and chlorophyll fluorescence and decreased plant growth parameters of cotton seedlings. The treatment with 5 mM GB significantly increased the evolution of photosynthetic rate (P_n), transpiration rate (T_r), intracellular CO₂ concentration (C_i) and stomatal conductance (g_s) compared to the GB-untreated saline treatment. The Exogenous foliar-applied GB has sustainably decreased the carboxylation efficiency (P_n/C_i) and water use efficiency (WUE). The concentration of 5 mM GB leads to a significant improvement of leaf stomatal characteristics. The leaf gas exchange attributes correlated positively with stomatal density (SD), stomatal length (SL) and stomatal with (SW).

CONCLUSION

The overall results suggested that exogenous foliar supplementation with GB can effectively alleviate the damage of salt stress to cotton seedlings. The effect of applying 5 mM GB could be an optional choice for protecting cotton seedlings from NaCl stress through promoting the stomatal functions, photosynthetic activities and growth characteristics.

Interactive effect of nitrogen fertilizer and plant density on photosynthetic and agronomical traits of cotton at different growth stages

Individual effects of application of nitrogen (N) and plant densities (PD) were reported in various studies; however an interactive effect of N and PD in cotton was not studied. To explore the benefits of interactive effects of N fertilizer and PD to increase the quality of cotton. This study was carried out in randomized complete block design (RCBD) with split plot arrangement. In split plot arrangement, main plot was consisted of N application rate and in sub plots different PD were done. There were two nitrogen levels; low N level (F1) 120 kg ha^-1 and high N level (F2) 180 kg ha^-1 and three planting densities; 8 plants m^-2 as low density (LD), 10 plants m^-2 as medium density (MD) and 12 plants m^-2 as high density (HD). In this study we observed the interactive effect of N application levels and PD on cotton photosynthetic and agronomic traits of various stages of development. Results showed that cotton growth and N contents was varied among treatments on different development stages. Plant biomass production, photosynthetic rate (Pn), intercellular CO₂ (C_i), water use efficiency (WUE) and N contents were unaffected at the seedling stage by N application rate and PD, however, the highest Pn, C_i and N contents was at squaring stage followed by blooming stage. Higher seed cotton yield and lint yield were obtained F1 with HD, and F2 with MD yielded the highest N contents and cotton yield among treatments. We found that the squaring stage was more critical, followed by the blooming stage when considering N rate and PD.

Identification of hub genes through co-expression network of major QTLs of fiber length and strength traits in multiple RIL populations of cotton

The present study demonstrated a de novo correlation among fiber quality genes in multiple RIL populations including sGK9708 × 0-153, LMY22 × LY343 and Lumianyan28 × Xinluzao24. The current study was conducted to identify the major common QTLs including fiber length and strength, and to identify the co-expression networks of fiber length and strength QTLs harbored genes to target the hub genes. The RNA-seq data of sGK9708 × 0-153 population highlighted 50 and 48 candidate genes of fiber length and fiber strength QTLs. A total of 29 and 21 hub genes were identified in fiber length and strength co-expression network modules. The absolute values of correlation coefficient close to 1 resulted highly positive correlation among hub genes. Results also suggested that the gene correlation significantly influence the gene expression at different fiber development stages. These results might provide useful reference for further experiments in multiple RIL populations and suggest potential candidate genes for functional studies in cotton.

Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress

Alkaline stress is one of the abiotic stresses limiting cotton production. Though RNA-Seq analyses, have been conducted to investigate genome-wide gene expression in response to alkaline stress in plants, the response of sodium bicarbonate (NaHCO₃) stress-related genes in cotton has not been reported. To explore the mechanisms of cotton response to this alkaline stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under NaHCO₃ alkaline stress. A total of 18,230 and 11,177 differentially expressed genes (DEGs) were identified in cotton roots and leaves, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, amino acid biosynthesis, and biosynthesis of secondary metabolites were regulated in response to the NaHCO₃ stress. We further analyzed genes enriched in secondary metabolic pathways and found that secondary metabolites were regulated to eliminate the reactive oxygen species (ROS) and improve the cotton tolerance to the NaHCO₃ stress. In this study, we learned that the toxic effect of NaHCO₃ was more profound than that of NaOH at the same pH. Thus, Na⁺, HCO₃^- and pH had a great impact on the growth of cotton plant. The novel biological pathways and candidate genes for the cotton tolerance to NaHCO₃ stress identified from the study would be useful in the genetic improvement of the alkaline tolerance in cotton.

Small RNA and degradome deep sequencing reveals important roles of microRNAs in cotton (Gossypium hirsutum L.) response to root-knot nematode Meloidogyne incognita infection

Investigation of cotton response to nematode infection will allow us to better understand the cotton immune defense mechanism and design a better biotechnological approach for efficiently managing pest nematodes in cotton. In this study, we firstly treated cotton by root knot nematode (RKN, Meloidogyne incognita) infections, then we employed the high throughput deep sequencing technology to sequence and genome-widely identify all miRNAs in cotton; finally, we analyzed the functions of these miRNAs in cotton response to RKN infections. A total of 266 miRNAs, including 193 known and 73 novel miRNAs, were identified by deep sequencing technology, which belong to 67 conserved and 66 novel miRNA families, respectively. A majority of identified miRNA families only contain one miRNA; however, miR482 family contains 14 members and some others contain 2-13 members. Certain miRNAs were specifically expressed in RKN-infected cotton roots and others were completely inhibited by RKN infection. A total of 50 miRNAs were differentially expressed after RKN infection, in which 28 miRNAs were up-regulated and 22 were inhibited by RKN treatment. Based on degradome sequencing, 87 gene targets were identified to be targeted by 57 miRNAs. These miRNA-targeted genes are involved in the interaction of cotton plants and nematode infection. Based on GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, 466 genes from all 636 miRNA targets were mapped to 6340 GO terms, 181 genes from 228 targets of differentially expressed miRNAs were mapped to 1588 GO terms. The GO terms were then categorized into the three main GO classes: biological processes, cellular components, and molecular functions. The targets of differentially expressed miRNAs were enriched in 43 GO terms, including 22 biological processes, 10 cellular components, and 11 molecular functions (p < 0.05). Many identified processes were associated with organism responses to the environmental stresses, including regulation of nematode larval development, response to nematode, and response to flooding. Our results will enhance the study and application of developing new cotton cultivars for nematode resistance.

Cotton seedling drought tolerance is improved via salt preconditioning

In this study, 12 upland cotton seedlings were used as the material, and four treatments were designed (15% PEG for 6 h, 250 mM NaCl for 3 h, 15% PEG for 6 h after 250 mM NaCl pretreatment, and blank control). Various physiological indicators, including the malondialdehyde (MDA) and proline (Pro) contents and superoxide dismutase (SOD) and peroxidase (POD) activities, and the relative electrolyte leakage (REL), were measured during exposure to the aforementioned stresses, and three stress-related transcription factors (GhHsfA, GhbZIP, and GhNAC) were used to assess the differences in the drought resistance of cotton during exposure to PEG stress and NaCl/PEG combined stress. The analyses of the physiological and biochemical indicators revealed that the cotton seedlings exposed to NaCl/PEG combined stress exhibited the highest relative changes in the SOD and POD enzyme activities, while the relative changes in the MDA content and REL were relatively small. The cluster analysis showed that the treatments could be ranked as follows based on degree of damage exhibited by the exposed cotton seedlings: PEG > NaCl > NaCl/PEG. The exposure of cotton to NaCl/PEG combined stress resulted in a lower degree of damage than that obtained after exposure to PEG alone, which indicated that an appropriate amount of NaCl could partially relieve the adverse effects of drought on cotton seedlings. In addition, the relative expression levels of GhHsfA, GhbZIP, and GhNAC were significantly correlated with multiple physiological and biochemical indicators under different stresses, and the principal component analysis identified these transcription factors as important indicators. Based on these findings, these three transcription factors can be used as molecular indicators for the identification of drought resistance. A comprehensive D value cluster analysis ranked the 12 cotton varieties based on their drought resistance, and the most drought-resistant variety was ND359-5. This study provides new methods and materials for research on drought resistance in cotton.

Silver nanoparticles synthesized by Nigrospora oryzae showed antifungal activity

In this investigation, an alternate green-route based on myco-synthesised silver nanoparticles (Ag NPs) was evaluated to control plant disease to reduce the usage of synthetic chemicals. Here, we described biologically synthesised Ag NPs using the corn grain contaminant, Nigrospora oryzae, and were well-characterised by UV-visible spectrophotometer, X-ray powder diffraction (XRD), transmission electron microscopy (TEM), Energy Dispersive Spectroscopy (EDS) and particle size analyzer. The pathogenic behaviour of the Fusarium spp. were checked on Giza 86 and Giza 90 cultivars under greenhouse conditions. F. moniliforme and F. oxysporum exhibited high pathogenecity against Giza 90 and Giza 86 cultivars respectively. The antifungal activity of biosynthesised Ag NPs was evaluated against eight species of Fusaria causing damping-off of cotton seedlings. In vitro treatments with different concentrations of Ag NPs were achieved on Czapek Dox agar and Potato dextrose agar plates. Fungal growth was drastically retarded from 25 to 200 ppm of Ag NPs interaction. The antifungal activity of Ag NPs against the Fusarium spp. was clearly proven.

Impact of dyes and finishes on the microfibers released on the laundering of cotton knitted fabrics

The influence of common textile finishes on cotton fabrics on the generation of microfibers during laundering was assessed. Microfiber release was determined to be in the range of 9000-14,000 particles per gram of cotton fabric. Cotton knitted fabrics treated with softener and durable press generate more microfibers (1.30-1.63 mg/g fabric) during laundering by mass and number than untreated fabric (0.73 mg/g fabric). The fabrics treated with softener generated the longest average microfiber length (0.86 mm), whereas durable press and water repellent treatments produced the shortest average microfiber length (0.62 and 0.63 mm, respectively). In general, the changes in the mechanical properties of the fibers and fabrics due to the finishing treatments are the main factor affecting the microfiber release. The abrasion resistance of the fabrics decreases for durable press treatments and water repellent treatments due to the brittleness in the structure originated by the crosslinking treatment. In the case of the softener treatment, the fabric surface is soft and smooth decreasing the friction coefficient between fibers favoring the fibers loosening from the textile and resulting in a high tendency for fuzz formation and microfiber release. These findings are useful for the textile industry in the design and selection of materials and treatments for the reduction of synthetic or natural microfiber shedding from textiles.

Differentiation in the genetic basis of stem trichome development between cultivated tetraploid cotton species

BACKGROUND

Cotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism. Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood.

RESULTS

In this study, Gossypium hirsutum (Gh) and G. barbadense (Gb) were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore. Gh varieties normally had long singular and clustered trichomes, while Gb varieties had short clustered trichomes. Genetic mapping using five F₂ populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr. 06 and Chr. 24. The twenty- six F₁ generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion of Gh wild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion of Gb primitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in both Gh and Gb primitive accessions and modern varieties.

CONCLUSION

Based on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.

Tolerance of cotton to elevated levels of Pb and its potential for phytoremediation

Two experiments were conducted to determine the cotton plant's tolerance to Pb and its remediation potential. In the first experiment, the phytoremediation potential was determined by exposing the plant to four levels of Pb (0, 500, 750, and 1000 mg kg-1). The cotton plant exhibited an excellent tolerance index at Pb 1000 mg kg-1 (root 78.65% and shoot 93.08%) and lower grade of growth inhibition (root 21.35% and shoot 6.92%). Pb stress resulted in higher leakage of electrolytes and increased the synthesis of higher proline, total phenol, and free amino acid contents to mitigate stress. The plant could not meet the criteria of a hyperaccumulator of Pb. The concentration of Pb in the shoot was a mere 96 μg g-1 dry wt (< the critical judging concentration of 1000 μg g-1 dry wt), and bioconcentration and translocation factors were <1. The study established that cotton exhibited an exclusion mechanism of Pb. Further, the translocation efficiency (TE %) was very low, i.e., <50% (ranged from 49% at 500 mg kg-1 to 42% at 1000 mg kg -1), and the % of Pb removed by the crop was too little (on an average 0.1%). Pb inhibited the dehydrogenase activity (DHA) by 76%, fluorescein diacetate (FDA) hydrolysis by 60%, and β-glucosidase activity by 20%. However, applied Pb increased the population of actinomycetes by 3.21 times, but significantly decreased heterotrophic bacteria by 3.40 times and N2 fixers by over 53% over control. In the second experiment, the plant was exposed to very high Pb (0, 1000, 1500, 2000, 2500, and 3000 mg kg -1) to determine the concentration up to which the plant will survive. The investigation revealed that plants could survive up to Pb 3000 mg kg-1. It confirmed the first experiment in the tolerance index, grade of growth inhibition, bioconcentration factor, translocation factor, and partitioning of Pb. Therefore, it was concluded that the cotton plant was an excluder of Pb and could be effectively cultivated for the phytostabilization of soils polluted with Pb.

Impact of heat stress responsive factors on growth and physiology of cotton (Gossypium hirsutum L.)

Pakistan ranked highest with reference to average temperatures in cotton growing areas of the world. The heat waves are becoming more intense and unpredictable due to climate change. Identification of heat tolerant genotypes requires comprehensive screening using molecular, physiological and morphological analysis. Heat shock proteins play an important role in tolerance against heat stress. In the current study, eight heat stress responsive factors, proteins and genes (HSFA2, GHSP26, GHPP2A, HSP101, HSC70-1, HSP3, APX1 and ANNAT8) were evaluated morphologically and physiologically for their role in heat stress tolerance. For this purpose, cotton crop was grown at two temperature conditions i.e. normal weather and heat stress at 45 °C. For molecular analysis, genotypes were screened for the presence or absence of heat shock protein genes. Physiological analysis of genotypes was conducted to assess net photosynthesis, stomatal conductance, transpiration rate, leaf-air temperature and cell membrane stability under control as well as high temperature. The traits photosynthesis, cell membrane stability, leaf-air temperature and number of heat stress responsive factors in each genotypes showed a strong correlation with boll retention percentage under heat stress. The genotypes with maximum heat shock protein genes such as Cyto-177, MNH-886, VH-305 and Cyto-515 showed increased photosynthesis, stomatal conductance, negative leaf-air temperature and high boll retention percentage under heat stress condition. These varieties may be used as heat tolerant breeding material.

Pectin lyase enhances cotton resistance to Verticillium wilt by inducing cell apoptosis of Verticillium dahliae

Verticillium wilt caused by Verticillium dahliae Kleb. is a major disease in cotton. We found that pectin lyase can enhance cotton resistance to Verticillium wilt and induce cell apoptosis of V. dahliae strain Vd080. The biocontrol effect of pectin lyase on Vd080 reached 61.9%. Pectin lyase increased ERG4 (Delta (24 (24 (1)))-sterol reductase) expression, the ergosterol content of the cell membrane, the collapse of mitochondrial membrane potential, hydrogen peroxide content, metacaspase activity, and Ca²⁺ content in the cytoplasm in the Vd080 strain and induced endoplasmic reticulum (ER) stress. Pectin lyase also increased the expression levels of the ER molecular chaperone glucose regulating protein Grp78 (BiP), protein disulfide isomerase (PDI) and calnexin (CNX), reduced the expression levels of the protein Hsp40. When the PDI and BiP genes of Vd080 were knocked out, the mutants △BiP and △PDI had reduced sensitivity to pectin lyase. In the absence of external stress, ER stress appeared in mutant △BiP cells. Pectin lyase affects the ergosterol content of the Vd080 cell membrane, which causes ER stress and increases the level of BiP to induce Vd080 cell apoptosis. These results demonstrate that pectin lyase can be used to control Verticillium wilt in cotton.

Novel sustainable alternatives for the fashion industry: A method of chemically recycling waste textiles via acid hydrolysis

The fashion industry has a considerable environmental impact, especially due to the increased generation of waste textiles as a result of fast fashion business models. Although fiber-to-fiber recycling processes are being developed, such a process is in reality a downcycling process, in which the mechanical properties of the textile fibers are impoverished with each cycle. Thus, new alternatives are required to completely close the fashion loop through chemically recycling textile fibers unfit for other types of recycling or resale due to their poor quality. We have evaluated the possibility of using acid hydrolysis to directly depolymerize the cotton fibers in waste textiles to produce a glucose solution, which could subsequently be used for the production of chemicals or fuels. Although a one-step procedure with sulfuric acid was unable to deliver high glucose production, it was possible to achieve a glucose yield over 90% through a two-step procedure, in which concentrated and dilute sulfuric acid were combined to exploit the benefits of both concentrations. Glucose concentrations around 40 g/L were achieved by increasing the solids loading in the two-step process, which might be sufficiently high for the fermentation of the solution into high-value products. Thus, this study demonstrates that it would be possible to chemically recycle (cellulose-based) waste textiles via acid hydrolysis, which, if correctly designed, could avoid the need to use enzymes to achieve high conversion efficiencies.

Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes

BACKGROUND

Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton.

RESULTS

In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls.

CONCLUSIONS

These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.

Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton

BACKGROUND

Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering.

RESULTS

To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues.

CONCLUSION

All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

Genome-wide analysis of CBL and CIPK family genes in cotton: conserved structures with divergent interactions and expression

Calcineurin B-like proteins (CBLs) interact with CBL-interacting protein kinases (CIPKs) to form complex molecular modules in response to diverse abiotic stresses. Although previous studies demonstrated that the CBL-CIPK networks play a crucial role in plants response to abiotic stresses, however, little is known about their functions in cotton. In the present study, a total of 22 GhCBL and 79 GhCIPK gene family members were identified in upland cotton (Gossypium hirsutum Linn). Synteny analysis revealed that most genes of GhCBL and GhCIPK exist in pairs between At sub-genome and Dt sub-genome. Interaction analysis between GhCBL and GhCIPK proteins by yeast two-hybrid (Y2H) suggested that the GhCBL-GhCIPK networks were complex, and exhibited functional redundancy in cotton. Quantitative expression analysis by public transcriptome datasets revealed that some GhCBL and GhCIPK genes are differentially expressed under abiotic stress treatments, and especially under drought stress. Our results not only contribute to understanding the structural features of GhCBL and GhCIPK genes but also provide the basis for in-depth functional studies of GhCBL-GhCIPK networks in stress response for plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at (doi:10.1007/s12298-021-00943-1).

Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

BACKGROUND

Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear.

RESULTS

Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA.

CONCLUSION

This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

Genome-Wide Mining of MYB Transcription Factors in the Anthocyanin Biosynthesis Pathway of Gossypium Hirsutum

The MYB family, one of the largest transcription factor (TF) families, plays an important role in plant growth, development, and stress response. Although genome-wide analysis of the MYB family has been performed in many species based on sequence similarity, predicting the potential functions of the MYB genes and classifying the regulators into specific metabolic pathways remains difficult. In this study, using a hidden Markov model search and co-expression regulatory network analysis, we demonstrated a process to screen and identify potential MYB TFs in the anthocyanin biosynthesis pathway of Gossypium hirsutum. As a result, we identified 617 and 784 MYB genes (812 in total) from the previously reported and recently released genomes, respectively. Using 126 structural genes involved in the anthocyanin biosynthesis pathway as targets for several co-expression network analyses, we sorted out 31 R2R3-MYB genes, which are potential regulators in the specific pathway. Phylogenetic and collinearity analyses indicated that 83.9% of the 31 MYB genes originated from whole genome duplication or polyploidization. In addition, we revealed relatively specific regulatory relationships between the MYB TFs and their target structural genes. Approximately, 71% of the MYBs could regulate only a single anthocyanin-related structural gene. Moreover, we found that the A- and D- subgenome homoeologs of MYB TFs in G. hirsutum rarely co-regulate the same target gene. The current study not only demonstrated an easy method to rapidly predict potential TFs in a specific metabolic pathway, but also enhanced our understanding of the evolution, gene characteristics, expression, and regulatory pattern of MYB TFs in G. hirsutum.