Abundance and diversity of cotton insect pests under repeatedly cultivated cotton fields of Tanzania.

Introduction: Cotton production in Tanzania is facing significant challenges due to insect pests that cause extensive damages to the crop. The most notable pests include the African bollworm (Heliothis armigera Hubner), Spiny bollworm (Earias biplaga Walker), Cotton stainers (Dysdercus sidae (Herrich-Schaeffer), Cotton Aphids (Aphis gossypii Glover), Thrips (Thrips tabaci Lindeman), Jassids (Amrasca biguttula, Bigutula), Leafhoppers (Cicadellidae jassidae), and Whiteflies (Bemisia tabaci Genn). If left uncontrolled, these pests can cause up to 60% damage to the crop. Despite the importance of cotton and the fact that most of these pests are endemic, there are scanty knowledge on the dynamics and distribution of cotton pests across the seasons of the year and crop's phenological growth stages (germination, vegetative growth, flowering and boll formation) in areas under repeated cultivation of the crop in Tanzania. Here we report on the influence of seasons and cotton's phenological stages on the abundance, diversity, distribution and richness of cotton insect pests. Methods: The study was conducted in the Misungwi district for two cotton-growing seasons, using the UKM08 cotton variety. Stick traps and handpicking methods were deployed in catching the cotton insect pests. Results: On average, a total of 8,500 insect specimen of diverse families and species were collected every season. The four dominant species among the collected were Aphis gossypii (17.37%), Amrasca biguttula (11.42%), Nezara viridura (10.7%), and Bemisia tabacci (10.68%). Both cotton phenological growth stages and seasons significantly (p<0.05) influenced the abundance, diversity, distribution and richness of cotton insect pests. In particular, the phenological growth stage 3 exhibited greater diversity of insect pests. The pests' distribution patterns remained relatively uniform across the crop growth stages. Discussion: Findings from the present study could contribute to developing sustainable pest management strategies in areas under repeated cotton production in Tanzania and elsewhere.

Cotton Bollworm (H. armigera) Effector PPI5 Targets FKBP17-2 to Inhibit ER Immunity and JA/SA Responses, Enhancing Insect Feeding.

The cotton bollworm causes severe mechanical damage to plants during feeding and leaves oral secretions (OSs) at the mechanical wounds. The role these OSs play in the invasion of plants is still largely unknown. Here, a novel H. armigera effector peptidyl prolyl trans-isomerase 5 (PPI5) was isolated and characterized. PPI5 induces the programmed cell death (PCD) due to the unfolded protein response (UPR) in tobacco leaf. We reveal that PPI5 is important for the growth and development of cotton bollworm on plants, as it renders plants more susceptible to feeding. The GhFKBP17-2, was identified as a host target for PPI5 with peptidyl-prolyl isomerase (PPIase) activity. CRISPR/Cas9 knock-out cotton mutant (CR-GhFKBP17-1/3), VIGS (TRV: GhFKBP17-2) and overexpression lines (OE-GhFKBP17-1/3) were created and the data indicate that GhFKBP17-2 positively regulates endoplasmic reticulum (ER) stress-mediated plant immunity in response to cotton bollworm infestation. We further confirm that PPI5 represses JA and SA levels by downregulating the expression of JA- and SA-associated genes, including JAZ3/9, MYC2/3, JAR4, PR4, LSD1, PAD4, ICS1 and PR1/5. Taken together, our results reveal that PPI5 reduces plant defense responses and makes plants more susceptible to cotton bollworm infection by targeting and suppressing GhFKBP17-2 -mediated plant immunity.

MAPK and phenylpropanoid metabolism pathways involved in regulating the resistance of upland cotton plants to Verticillium dahliae.

Introduction: Verticillium dahliae causes a serious decline in cotton yield and quality, posing a serious threat to the cotton industry. However, the mechanism of resistance to V. dahliae in cotton is still unclear, which limits the breeding of resistant cultivars. Methods: To analyze the defense mechanisms of cotton in response to V. dahliae infection, we compared the defense responses of two upland cotton cultivars from Xinjiang (JK1775, resistant; Z8,susceptible) using transcriptome sequencing at different infection stages. Results: The results revealed a significant differential expression of genes in the two cotton cultivars post V. dahliae infection, with the number of DEGs in JK1775 being higher than that in Z8 at different infection stages of V. dahliae. Interestingly, the DEGs of both JK1775 and Z8 were enriched in the MAPK signaling pathway in the early and late stages of infection. Importantly, the upregulated DEGs in both cultivars were significantly enriched in all stages of the phenylpropanoid metabolic pathway. Some of these DEGs were involved in the regulation of lignin and coumarin biosynthesis, which may be one of the key factors contributing to the resistance of upland cotton cultivars to V. dahliae in Xinjiang. Lignin staining experiments further showed that the lignin content increased in both resistant and susceptible varieties after inoculation with V. dahliae. Discussion: This study not only provides insights into the molecular mechanisms of resistance to Verticillium wilt in Xinjiang upland cotton but also offers important candidate gene resources for molecular breeding of resistance to Verticillium wilt in cotton.

Investigation of thermal, acoustic, mechanical, and radiation shielding performance of waste and natural fibers.

It is crucial to address two pressing global issues, energy shortage and environmental pollution, when producing building insulation materials. Using waste and natural fiber groups can be part of the solution. The insulation material was produced using pumpkin fiber, chicken fiber, cotton waste, vermiculite, and epoxy as binders. The samples were tested for thermal conductivity coefficient, ultrasonic sound transmission rate, density, water absorption rate, compressive and bending strength, and fire resistance at temperatures of 75, 100, 125, and 150C. The samples produced using natural and waste materials yielded a thermal conductivity value of 0.041 W/mK, an ultrasonic sound transmission speed of 0.25 km/s, a compressive strength value of 1.57 MPa, and bending strength values of 0.91 MPa. It has been clearly demonstrated that, with its low volume loss, it can serve as an alternative to the EPS-XPS types available in the market. Furthermore, the linear attenuation coefficients (LAC) were examined to obtain radiation shielding properties of the samples at 1173 and 133 keV energies using a 60Co gamma source. Also, LAC values determined between 0,1167 ± 0,0452 cm-1-0,2315 ± 0,0065 cm-1 for 1173 keV and 0,1042 ± 0,0488 cm-1 - 0,2141 ± 0,0062 cm-1 for 1333 keV. Accordingly, it has been revealed that waste compositions are effective in protecting against radiation.

Biowaste rice husk derived cellulosic hydrogel incorporating industrial cotton waste nonwoven for wound dressing.

Bio-wastes are organic materials achieved through biological sources. The rice crop produces a substantial amount of biowaste in the form of rice husk, which is rich in cellulose. In this research, cellulose was extracted from rice husk by alkalization and bleaching process. The rice husk extracted cellulose was further used to develop cellulose hydrogel by using the sol-gel technique. The nonwoven fabric of industrial cotton waste was developed in three different GSM (50, 100, and 150). The nonwoven fabric was incorporated in the cellulose hydrogel having three different concentrations (1 %, 2 %, and 3 %) to develop the hydrogel non-woven cotton fabric composite for sustainable wound dressing applications. Moreover, prepared rice husk extracted cellulose hydrogel loaded with AgNO3 (0.5 %, 1 %, and 1.5 %) for achieving antibacterial characteristics. The Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) were employed to confirm the existence of cellulose hydrogel layers within the cotton nonwoven composite. The developed hydrogel S12 exhibited a maximum fluid absorbency of 1281.84 % with a tensile strength of 28.6 N and elongation of 40.96 %. The results show successful rice husk extracted cellulose hydrogel formation, exhibiting structural stability, excellent exudate absorbency and moisture management, antimicrobial efficacy, and sustainability.

Natural variation in GhKASI_A05 modulates cottonseed oil content in Gossypium hirsutum L.

Cotton is of great economic value because of its fiber that is used in natural textile commodities and its seeds that contain an edible oil with a high content of unsaturated fatty acids and biodiesel applications. Here, we reported that GhKASI_A05 was associated with the cottonseed oil content (SOC) in a natural population via candidate gene association analysis. An 11-bp Indel located in the GhKASI_A05 promoter was found to contribute to SOC and differential expression in upland cotton inbred accessions. Interaction analysis showed that GhWRI1, an AP2/EREBP family transcription factor, that reportedly functions in plant seed oil and fatty acids (FAs) accumulation, directly bound to AW-box cis-elements in two haplotypes of the GhKASI_A05 promoter and activated the expression of GhKASI_A05 at different levels. The seed-specific overexpression of GhKASI_A05 resulted in increased seed size, weight, and protein content, and C16:0 and C18:1 contents but reduced SOC. Our results provide new insights into the biological function of GhKASI in SOC and effective strategies for cotton breeding in the future.

Changes in Soil Bacterial and Nematode Communities during Long-term Continuous Cotton Cropping in an Arid Region.

larifying the effects of continuous cotton cropping (CC) on soil biological communities is essential for maintaining agricultural productivity. In this study, high-throughput sequencing was used to study the effects of different CC durations (0-yr, 5-yr, 10-yr, 15-yr, 20-yr, and 25-yr CC treatments) on soil microbial and nematode communities. The results showed that the dominant bacterial phyla were Actinobacteria and Proteobacteria, and the dominant nematode genus was Helicotylenchus in all CC treatments. The richness indexes (ACE and Chao1 index) and diversity index (Shannon index) of bacterial and nematode communities were the highest in the 15-yr and 10-yr CC treatments, respectively. Bacterial community was significantly correlated with soil pH and available potassium (AK), and nematode abundance was significantly correlated with microbial biomass carbon (MBC). Soil bacterial PICRUSt analysis results showed that carbon metabolism and amino acid metabolism were the main metabolic functions of bacteria in the CC treatments. The composition and diversity of soil nematode communities were significantly related to the structure of soil bacterial communities, and the niche breadth of soil bacteria was negatively correlated with that of nematodes. Panagrolaimus and Acrobeles were the main genera of bacterialfeeding nematodes affecting bacterial communities, and their relative abundances were significantly positively correlated with the relative abundance of bacterial communities. Overall, long-term (10-15 years) continuous cotton cropping negatively impacts soil biota and the microecological environment of cotton fields in arid regions.

The genome sequence of the Cotton Bollworm moth, Helicoverpa armigera (Hübner, 1808).

We present a genome assembly from an adult female Cotton Bollworm moth, Helicoverpa armigera (Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 362.20 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length.

Natural variation at the cotton HIC locus increases trichome density and enhances resistance to aphids.

Plant trichomes are an excellent model for studying cell differentiation and development, providing crucial defenses against biotic and abiotic stresses. There is a well-established inverse relationship between trichome density and aphid prevalence, indicating that higher trichome density leads to reduced aphid infestations. Here we present the cloning and characterization of a dominant quantitative trait locus, HIC (hirsute cotton), which significantly enhances cotton trichome density. This enhancement leads to markedly improved resistance against cotton aphids. The HIC encodes an HD-ZIP IV transcriptional activator, crucial for trichome initiation. Overexpression of HIC leads to a substantial increase in trichome density, while knockdown of HIC results in a marked decrease in density, confirming its role in trichome regulation. We identified a variant in the HIC promoter (-810 bp A to C) that increases transcription of HIC and trichome density in hirsute cotton compared with Gossypium hirsutum cultivars with fewer or no trichomes. Interestingly, although the -810 variant in the HIC promoter is the same in G. barbadense and hirsute cotton, the presence of a copia-like retrotransposon insertion in the coding region of HIC in G. barbadense causes premature transcription termination. Further analysis revealed that HIC positively regulates trichome density by directly targeting the EXPANSIN A2 gene, which is involved in cell wall development. Taken together, our results underscore the pivotal function of HIC as a primary regulator during the initial phases of trichome formation, and its prospective utility in enhancing aphid resistance in superior cotton cultivars via selective breeding.

Characterization and expression analysis of the MADS-box gene AGL8 in cotton: insights into gene function differentiation in plant growth and stress resistance.

BACKGROUND: AGAMOUS-LIKE 8 (AGL8) belongs to the MADS-box family, which plays important roles in transcriptional regulation, sequence-specific DNA binding and other biological processes and molecular functions. The genome of cotton, a representative polyploid plant, contains multiple AGL8 genes. However, their functional differentiation is still unclear. METHODS AND RESULTS: In this study, a comprehensive genomic analysis of AGL8 genes was conducted. Cotton AGL8s were subdivided into four subgroups (Groups 1, 2, 3, and 4) based on phylogenetic analysis, and different subgroups of AGL8s presented different characteristics, including different structures and conserved motifs. With respect to the promoter regions of the GhAGL8 genes, we successfully predicted cis-elements that respond to phytohormone signal transduction and the stress response of plants. Transcriptome data and real-time quantitative PCR validation indicated that three genes, namely, GH_D07G0744, GH_A03G0856 and GH_A07G0749, were highly induced by methyl jasmonate (MeJA), salicylic acid (SA), and abscisic acid (ABA), which indicated that they function in plant resistance to abiotic and biotic stresses. CONCLUSIONS: The information from the gene structure, number and types of conserved domains, tissue-specific expression levels, and expression patterns under different treatments highlights the differences in sequence and function of the cotton AGL8 genes. Different AGL8s play roles in vegetative growth, reproductive development, and plant stress resistance. These results lay a foundation for further study of GhAGL8s in cotton.

Optimizing nitrogen fertilizer for improved root growth, nitrogen utilization, and yield of cotton under mulched drip irrigation in southern Xinjiang, China.

The root system plays a crucial role in water and nutrient absorption, making it a significant factor affected by nitrogen (N) availability in the soil. However, the intricate dynamics and distribution patterns of cotton (Gossypium hirsutum L.) root density and N nutrient under varying N supplies in Southern Xinjiang, China, have not been thoroughly understood. A two-year experiment (2021 and 2022) was conducted to determine the effects of five N rates (0, 150, 225, 300, and 450 kg N ha-1) on the root system, shoot growth, N uptake and distribution, and cotton yield. Compared to the N0 treatment (0 kg N ha-1), the application of N fertilizer at a rate of 300 kg N ha-1 resulted in consistent and higher seed cotton yields of 5875 kg ha-1 and 6815 kg ha-1 in 2021 and 2022, respectively. This N fertilization also led to a significant improvement in dry matter weight and N uptake by 32.4% and 53.7%, respectively. Furthermore, applying N fertilizer at a rate of 225 kg N ha-1 significantly increased root length density (RLD), root surface density (RSD), and root volume density (RVD) by 49.6-113.3%, 29.1-95.1%, and 42.2-64.4%, respectively, compared to the treatment without N fertilization (0 kg N ha-1). Notably, the roots in the 0-20 cm soil layers exhibited a stronger response to N fertilization compared to the roots distributed in the 20-40 cm soil layers. The root morphology parameters (RLD, RSD, and RVD) at specific soil depths (0-10 cm in the seedling stage, 10-25 cm in the bud stage, and 20-40 cm in the peak boll stage) were significantly associated with N uptake and seed cotton yield. Optimizing nitrogen fertilizer supply within the range of 225-300 kg N ha-1 can enhance root foraging, thereby promoting the interaction between roots and shoots and ultimately improving cotton production in arid areas.

Leveraging transcriptomics-based approaches to enhance genomic prediction: integrating SNPs and gene networks for cotton fibre quality improvement.

Cultivated cotton plants are the world's largest source of natural fibre, where yield and quality are key traits for this renewable and biodegradable commodity. The Gossypium hirsutum cotton genome contains ~80K protein-coding genes, making precision breeding of complex traits a challenge. This study tested approaches to improving the genomic prediction (GP) accuracy of valuable cotton fibre traits to help accelerate precision breeding. With a biology-informed basis, a novel approach was tested for improving GP for key cotton fibre traits with transcriptomics of key time points during fibre development, namely, fibre cells undergoing primary, transition, and secondary wall development. Three test approaches included weighting of SNPs in DE genes overall, in target DE gene lists informed by gene annotation, and in a novel approach of gene co-expression network (GCN) clusters created with partial correlation and information theory (PCIT) as the prior information in GP models. The GCN clusters were nucleated with known genes for fibre biomechanics, i.e., fasciclin-like arabinogalactan proteins, and cluster size effects were evaluated. The most promising improvements in GP accuracy were achieved by using GCN clusters for cotton fibre elongation by 4.6%, and strength by 4.7%, where cluster sizes of two and three neighbours proved most effective. Furthermore, the improvements in GP were due to only a small number of SNPs, in the order of 30 per trait using the GCN cluster approach. Non-trait-specific biological time points, and genes, were found to have neutral effects, or even reduced GP accuracy for certain traits. As the GCN clusters were generated based on known genes for fibre biomechanics, additional candidate genes were identified for fibre elongation and strength. These results demonstrate that GCN clusters make a specific and unique contribution in improving the GP of cotton fibre traits. The findings also indicate that there is room for incorporating biology-based GCNs into GP models of genomic selection pipelines for cotton breeding to help improve precision breeding of target traits. The PCIT-GCN cluster approach may also hold potential application in other crops and trees for enhancing breeding of complex traits.

Effects of Bt-cotton cultivation on Helicoverpa armigera activity-density in agricultural landscapes in northwestern China.

BACKGROUND: Cotton bollworm, Helicoverpa armigera (Hübner), threatens many crops. Bacillus thuringiensis (Bt) cotton has been planted to control this severe pest in northern Xinjiang, China. In 2021 and 2022, we monitored the activity densities of H. armigera males using sex pheromone traps in Bt cotton and non-Bt maize fields. We assessed how much of the population variation of cotton bollworm in the fields within the Bt cotton planting area could be explained by (i) landscape composition [including the proportion of Bt cotton among total area of host crops (cotton, maize, wheat and vegetables)], (ii) landscape configuration (patch density - i.e. the number of patches within a given area) across 0.5-2.0 km scales, or (iii) the population density of the previous pest generation. RESULTS: Cotton bollworm activity-density exhibited two distinct peaks annually (mid- to late May and mid-July each year), with the number of males caught during the second peak significantly and positively correlated with the first peak's numbers. The suppressive effect of the proportion of Bt cotton in the landscape on bollworms was more pronounced at larger scales, and patch density had a significant positive effect on bollworm activity density. CONCLUSIONS: These findings support (i) the promotion of Bt cotton in northwestern China has reduced and suppressed the occurrence of cotton bollworms at the landscape scale and (ii) the importance of controlling spring populations for effective summer outbreak management, and (iii) that cotton bollworm control should be coordinated at a large scale across multiple crop fields. © 2024 Society of Chemical Industry.

Dam removal effects on carbon processing in a mountainous Mediterranean stream.

The global prevalence of obsolete or unsafe old dams necessitates the development of effective restoration approaches and expanded knowledge in this field. This study evaluates the effects of dam removal on carbon processing by measuring key ecosystem functions - organic matter decomposition, whole-reach metabolism, and gaseous carbon fluxes - in a mountainous Mediterranean stream. We compared these functions among three reaches: one where a dam was removed (restored), one with an intact dam (impacted), and one in natural conditions (reference). The measurements were conducted throughout the different seasons over the course of one year. Temperature-corrected organic matter decomposition rates and metabolic parameters in the restored reach showed intermediate values between those in the reference and impacted reaches. Additionally, dam removal resulted in carbon dioxide fluxes similar to those in the reference reach, whereas methane fluxes tended to be higher in the restored reach compared to the other reaches. Seasonal variation was high, and the observed effects were inconsistent across seasons for several functions. This inconsistency is likely due to uneven seasonal changes in the hydromorphological and physicochemical characteristics of the studied reaches. Our results indicate that, despite notable improvements, a longer timeframe is necessary for the restored reach to fully emulate the functional characteristics of the reference reach. While restoration by dam removal positively contributes to certain aspects of carbon processing, a more holistic approach, possibly encompassing broader hydromorphological and habitat enhancements, is needed to fully restore ecological processes in stream ecosystems. These insights are critical for informing future dam removal restoration projects, advocating the use of ecosystem function metrics as comprehensive indicators of ecological recovery and restoration success.

Investigation of the microscopic damage mechanisms in cotton fibers induced by mechanical friction.

For the problem of friction damage in cotton fiber processing, a multi-scale combination of investigation methods is proposed. The surface of damaged cotton fiber is detected by relevant test means with damage features such as dislocations, defects and cracks. The internal pyranose ring and glycosidic bond fail, the crystallinity decreases, and the number of hydrogen bonds decreases. Anisotropy exists in the frictional properties of the microscopic surface of the cotton fiber. The results of molecular dynamics simulation showed that the cellulose main chain failed mainly at the glycosidic bond, and the side chain failed mainly at the hydroxymethyl functional group. Its interchain hydrogen bond O3H…O5 was the least damaged. The cellulose crystal (200) surfaces had poor abrasion resistance, and the frictional properties of each crystal surface were anisotropic. The results of the study provide a theoretical basis for improving friction and wear problems in cotton fiber processing.

Stepwise Empty Nose Syndrome Evaluation (SENSE) test-A modified cotton test for reduced bias in office diagnosis of empty nose syndrome.

INTRODUCTION: Diagnosis of empty nose syndrome (ENS) relies on the ENS six-item questionnaire (ENS6Q) with a score of ≥11, followed by a "positive" cotton test yielding seven-point reduction from baseline ENS6Q score via cotton placement to the inferior meatus (IM). Given the intricacies of diagnosing ENS and the propensity for false positives with the standard cotton test, we modified the classic single-step cotton test into a four-part Stepwise Empty Nose Syndrome Evaluation (SENSE) cotton test to reduce bias and evaluate the placebo effect. METHODS: Individuals diagnosed with ENS underwent the SENSE test, a single-blinded, four-step, office-based cotton test, without topical anesthesia or decongestants. Conditions included: (1) placebo/no cotton placed; (2) complete cotton-blockade of nasal vestibule; (3) cotton placed medially against the nasal septum; and (4) cotton placed laterally in the IM (site of inferior turbinate tissue loss). With each condition, patients completed an ENS6Q. RESULTS: Forty-eight ENS patients were included. Twenty-nine percent demonstrated a placebo effect (p < 0.001), 40.4% had a positive response to complete cotton-blockade (p < 0.001), 64.4% to septum-placed cotton, and 79.1% to IM-placed cotton (p < 0.001), corresponding to a mean ENS6Q reduction of 11.9 points (p < 0.001). Notably, the mean difference in ENS6Q scores between septum and IM placement was 1.7 (p < 0.001). CONCLUSIONS: The SENSE test offers further insight into subtleties of nasal breathing experienced by ENS patients. The placebo effect can be prominent and important to consider with individual patients. While most ENS patients prefer any intranasal cotton placement over baseline, blinded testing reveals these patients can accurately discriminate minimal changes in nasal aerodynamics.

GhCASPL1 regulates secondary cell wall thickening in cotton fibers by stabilizing the cellulose synthase complex on the plasma membrane.

Cotton (Gossypium hirsutum) fibers are elongated single cells that rapidly accumulate cellulose during secondary cell wall (SCW) thickening, which requires cellulose synthase complex (CSC) activity. Here, we describe the CSC-interacting factor CASPARIAN STRIP MEMBRANE DOMAIN-LIKE1 (GhCASPL1), which contributes to SCW thickening by influencing CSC stability on the plasma membrane. GhCASPL1 is preferentially expressed in fiber cells during SCW biosynthesis and encodes a MARVEL domain protein. The ghcaspl1 ghcaspl2 mutant exhibited reduced plant height and produced mature fibers with fewer natural twists, lower tensile strength, and a thinner SCW compared to the wild type. Similarly, the Arabidopsis (Arabidopsis thaliana) caspl1 caspl2 double mutant showed a lower cellulose content and thinner cell walls in the stem vasculature than the wild type but normal plant morphology. Introducing the cotton gene GhCASPL1 successfully restored the reduced cellulose content of the Arabidopsis caspl1 caspl2 mutant. Detergent treatments, ultracentrifugation assays, and enzymatic assays showed that the CSC in the ghcaspl1 ghcaspl2 double mutant showed reduced membrane binding and decreased enzyme activity compared to the wild type. GhCASPL1 binds strongly to phosphatidic acid (PA), which is present in much higher amounts in thickening fiber cells compared to ovules and leaves. Mutating the PA-binding site in GhCASPL1 resulted in the loss of its colocalization with GhCesA8, and it failed to localize to the plasma membrane. PA may alter membrane structure to facilitate protein-protein interactions, suggesting that GhCASPL1 and PA collaboratively stabilize the CSC. Our findings shed light on CASPL functions and the molecular machinery behind SCW biosynthesis in cotton fibers.

GhJUB1_3-At positively regulate drought and salt stress tolerance under control of GhHB7, GhRAP2-3 and GhRAV1 in Cotton.

Climate change severely affects crop production. Cotton is one of the primary fiber crops in the world and its production is susceptible to various environmental stresses, especially drought and salinity. Development of stress tolerant genotypes is the only way to escape from these environmental constraints. We identified sixteen homologs of the Arabidopsis JUB1 gene in cotton. Expression of GhJUB1_3-At was significantly induced in the temporal expression analysis of GhJUB1 genes in the roots of drought tolerant (H177) and susceptible (S9612) cotton genotypes under drought. The silencing of the GhJUB1_3-At gene alone and together with its paralogue GhJUB1_3-Dt reduced the drought tolerance in cotton plants. The transgenic lines exhibited tolerance to the drought and salt stress as compared to the wildtype (WT). The chlorophyll and relative water contents of wildtype decreased under drought as compared to the transgenic lines. The transgenic lines showed decreased H2O2 and increased proline levels under drought and salt stress, as compared to the WT, indicating that the transgenic lines have drought and salt stress tolerance. The expression analysis of the transgenic lines and WT revealed that GAI was upregulated in the transgenic lines in normal conditions as compared to the WT. Under drought and salt treatment, RAB18 and RD29A were strongly upregulated in the transgenic lines as compared to the WT. Conclusively, GhJUB1_3-At is not an auto activator and it is regulated by the crosstalk of GhHB7, GhRAP2-3 and GhRAV1. GhRAV1, a negative regulator of abiotic stress tolerance and positive regulator of leaf senescence, suppresses the expression of GhJUB1_3-At under severe circumstances leading to plant death.

CRISPR/dCas13(Rx) Derived RNA N6-methyladenosine (m6A) Dynamic Modification in Plant.

N6-methyladenosine (m6A) is the most prevalent internal modification of mRNA and plays an important role in regulating plant growth. However, there is still a lack of effective tools to precisely modify m6A sites of individual transcripts in plants. Here, programmable m6A editing tools are developed by combining CRISPR/dCas13(Rx) with the methyltransferase GhMTA (Targeted RNA Methylation Editor, TME) or the demethyltransferase GhALKBH10 (Targeted RNA Demethylation Editor, TDE). These editors enable efficient deposition or removal of m6A modifications at targeted sites of endo-transcripts GhECA1 and GhDi19 within a broad editing window ranging from 0 to 46 nt. TDE editor significantly decreases m6A levels by 24%-76%, while the TME editor increases m6A enrichment, ranging from 1.37- to 2.51-fold. Furthermore, installation and removal of m6A modifications play opposing roles in regulating GhECA1 and GhDi19 mRNA transcripts, which may be attributed to the fact that their m6A sites are located in different regions of the genes. Most importantly, targeting the GhDi19 transcript with TME editor plants results in a significant increase in root length and enhanced drought resistance. Collectively, these m6A editors can be applied to study the function of specific m6A modifications and have the potential for future applications in crop improvement.

Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton.

The polyploid genome of cotton has significantly increased the transcript complexity. Recent advances in full-length transcript sequencing are now widely used to characterize the complete landscape of transcriptional events. Such studies in cotton can help us to explore the genetic mechanisms of the cotton seedling growth. Through long-read single-molecule RNA sequencing, this study compared the transcriptomes of three yield contrasting genotypes of upland cotton. Our analysis identified different numbers of spliced isoforms from 31,166, 28,716, and 28,713 genes in SJ48, Z98, and DT8 cotton genotypes, respectively, most of which were novel compared to previous cotton reference transcriptomes, and showed significant differences in the number of exon structures and coding sequence length due to intron retention. Quantification of isoform expression revealed significant differences in expression in the root and leaf of each genotype. An array of key isoform target genes showed protein kinase or phosphorylation functions, and their protein interaction network contained most of the circadian oscillator proteins. Spliced isoforms from the GIGANTEA (GI) protien were differentially regulated in each genotype and might be expected to regulate translational activities, including the sequence and function of target proteins. In addition, these spliced isoforms generate diurnal expression profiles in cotton leaves, which may alter the transcriptional regulatory network of seedling growth. Silencing of the novel spliced GI isoform Gh_A02G0645_N17 significantly affected biomass traits, contributed to variable growth, and increased transcription of the early flowering pathway gene ELF in cotton. Our high-throughput hybrid sequencing results will be useful to dissect functional differences among spliced isoforms in the polyploid cotton genome.