Transcriptomics and virus-induced gene silencing identify defence-related genes during Ralstonia solanacearum infection in resistant and susceptible tobacco.

Bacterial wilt (BW) caused by Ralstonia solanacearum is a globally prevalent bacterial soil-borne disease. In this study, transcriptome sequencing were subjected to roots after infection with the R. solanacearum in the resistant and susceptible tobacco variety. DEGs that responded to R. solanacearum infection in both resistant and susceptible tobacco contributed to pectinase and peroxidase development and were enriched in plant hormone signal transduction, signal transduction and MAPK signalling pathway KEGG terms. Core DEGs in the resistant tobacco response to R. solanacearum infection were enriched in cell wall, membrane, abscisic acid and ethylene terms. qRT-PCR indicated that Nitab4.5_0004899g0110, Nitab4.5_0004234g0080 and Nitab4.5_0001439g0050 contributed to the response to R. solanacearum infection in different resistant and susceptible tobacco. Silencing the p450 gene Nitab4.5_0001439g0050 reduced tobacco resistance to bacterial wilt. These results improve our understanding of the molecular mechanism of BW resistance in tobacco and solanaceous plants.

Genome-wide identification of the TIFY gene family in tobacco and expression analysis in response to Ralstonia solanacearum infection.

The TIFY gene family plays an essential role in plant development and abiotic and biotic stress responses. In this study, genome-wide identification of TIFY members in tobacco and their expression pattern analysis in response to Ralstonia solanacearum infection were performed. A total of 33 TIFY genes were identified, including the TIFY, PPD, ZIM&ZML and JAZ subfamilies. Promoter analysis results indicated that a quantity of light-response, drought-response, SA-response and JA-response cis-elements exist in promoter regions. The TIFY gene family exhibited expansion and possessed gene redundancy resulting from tobacco ploidy change. In addition, most NtTIFYs equivalently expressed in roots, stems and leaves, while NtTIFY1, NtTIFY4, NtTIFY18 and NtTIFY30 preferentially expressed in roots. The JAZ III clade showed significant expression changes after inoculation with R. solanacearum, and the expression of NtTIFY7 in resistant varieties, compared with susceptible varieties, was more stably induced. Furthermore, NtTIFY7-silenced plants, compared with the control plants, were more susceptible to bacterial wilt. These results lay a foundation for exploring the evolutionary history of TIFY gene family and revealing gene function of NtTIFYs in tobacco bacterial wilt resistance.

Local in Time Conservative Binary Dynamics at Fourth Post-Minkowskian Order.

Leveraging scattering information to describe binary systems in generic orbits requires identifying local and nonlocal in time tail effects. We report here the derivation of the universal (nonspinning) local in time conservative dynamics at fourth post-Minkowskian order, i.e., O(G^{4}). This is achtieved by computing the nonlocal-in-time contribution to the deflection angle, and removing it from the full conservative value in [C. Dlapa et al., Phys. Rev. Lett. 128, 161104 (2022).PRLTAO0031-900710.1103/PhysRevLett.128.161104; C. Dlapa et al., Phys. Rev. Lett. 130, 101401 (2023).PRLTAO0031-900710.1103/PhysRevLett.130.101401]. Unlike the total result, the integration problem involves two scales-velocity and mass ratio-and features multiple polylogarithms, complete elliptic and iterated elliptic integrals, notably in the mass ratio. We reconstruct the local radial action, center-of-mass momentum and Hamiltonian, as well as the exact logarithmic-dependent part(s), all valid for generic orbits. We incorporate the remaining nonlocal terms for ellipticlike motion to sixth post-Newtonian order. The combined Hamiltonian is in perfect agreement in the overlap with the post-Newtonian state of the art. The results presented here provide the most accurate description of gravitationally bound binaries harnessing scattering data to date, readily applicable to waveform modeling.

Climate-associated variation in the drivers of benthic macroinvertebrate species-area relationships across shallow freshwater lakes.

The island species-area relationship (ISAR) describes how species richness increases with increasing area of a given island or island-like habitat, such as freshwater lakes. While the ISAR is one of the most common phenomena observed in ecology, there is variation in both the form of the relationship and its underlying mechanisms. We compiled a global data set of benthic macroinvertebrates from 524 shallow freshwater lakes, ranging from 1 to 293,300 ha in area. We used individual-based rarefaction to determine the degree to which ISAR was influenced by mechanisms other than passive sampling (larger islands passively sample more individuals from the regional pool and, therefore, have more species than smaller islands), which would bias results away from expected relationships between rarefied species richness (and other measures that capture relative abundances) and lake area. We also examined how climate may alter the shape of the ISARs. We found that both rarefied species richness (the number of species standardized by area or number of individuals) and a measure of evenness emphasizing common species exhibit shallow slopes in relationships with lake area, suggesting that the expected ISARs in these lakes most likely result from passive sampling. While there was considerable variation among ISARs across the investigated lakes, we found an overall positive rarefied ISAR for lakes in warm (i.e. tropical/subtropical) regions (n = 195), and in contrast, an overall negative rarefied ISAR in cool (i.e. north temperate) lakes (n = 329). This suggested that mechanisms beyond passive sampling (e.g. colonization-extinction dynamics and/or heterogeneity) were more likely to operate in warm lakes. One possible reason for this difference is that the area-dependent intensity of fish predation, which can lead to flatter ISARs, is weaker in warmer relative to cooler lakes. Our study illustrates the importance of understanding both the pattern and potential processes underlying the ISARs of freshwater lakes in different climatic regions. Furthermore, it provides a baseline for understanding how further changes to the ecosystem (i.e. in lake area or climate) might influence biodiversity patterns.

The effects of different doses of lanthanum-modified bentonite in combination with a submerged macrophyte (Vallisneria denseserrulata) on phosphorus inactivation and macrophyte growth: A mesocosm study.

The combination of chemical phosphorus (P) inactivation and submerged macrophyte transplantation has been widely used in lake restoration as it yields stronger effects than when applying either method alone. However, the dose effect of chemical materials on P inactivation when used in combination with submerged macrophytes and the influences of the chemicals used on the submerged macrophytes growth remain largely unknown. In this study, we investigated P inactivation in both the water column and the sediment, and the responses of submerged macrophytes to Lanthanum modified bentonite (LMB) in an outdoor mesocosm experiment where Vallisneria denseserrulata were transplanted into all mesocosms and LMB was added at four dosage levels, respectively: control (LMB-free), low dosage (570 g m-2), middle dosage (1140 g m-2), and high dosage (2280 g m-2). The results showed that the combination of LMB dosage and V. denseserrulata reduced TP in the water column by 32%-38% compared to V. denseserrulata alone, while no significant difference was observed among the three LMB treatments. Porewater soluble reactive P, two-dimensional diffusive gradient in thin films (DGT)-labile P concentrations, and P transformation in the 0-1 cm sediment layer exhibited similar trends along the LMB dosage gradient. Besides, LMB inhibited plant growth and reduced the uptake of mineral elements (i.e., calcium, manganese, iron, and magnesium) in a dosage-dependent manner with LMB. LMB may reduce plant growth by creating a P deficiency risk for new ramets and by interfering with the uptake of mineral elements. Considering both the dose effect of LMB on P inactivation and negative effect on macrophyte growth, we suggest a "small dosage, frequent application" method for LMB application to be used in lake restoration aiming to recover submerged macrophytes and clear water conditions.

Composition regulates dissolved organic matter adsorption onto iron (oxy)hydroxides and its competition with phosphate: Implications for organic carbon and phosphorus immobilization in lakes.

Dissolved organic matter (DOM) is a heterogeneous pool of compounds and exhibits diverse adsorption characteristics with or without phosphorous (P) competition. The impacts of these factors on the burial and mobilization of organic carbon and P in aquatic ecosystems remain uncertain. In this study, an algae-derived DOM (ADOM) and a commercially available humic acid (HA) with distinct compositions were assessed for their adsorption behaviors onto iron (oxy)hydroxides (FeOx), both in the absence and presence of phosphate. ADOM contained less aromatics but more protein-like and highly unsaturated structures with oxygen compounds (HUSO) than HA. The adsorption capacity of FeOx was significantly greater for ADOM than for HA. Protein-like and HUSO compounds in ADOM and humic-like compounds and macromolecular aromatics in HA were preferentially adsorbed by FeOx. Moreover, ADOM demonstrated a stronger inhibitory effect on phosphate adsorption than HA. This observation suggests that the substantial release of autochthonous ADOM by algae could elevate internal P loading and pose challenges for the restoration of restore eutrophic lakes. The presence of phosphate suppressed the adsorption of protein-like compounds in ADOM onto FeOx, resulting in an increase in the relative abundance of protein-like compounds and a decrease in the relative abundance of humic-like compounds in post-adsorption ADOM. In contrast, phosphate exhibited no discernible impact on the compositional fractionation of HA. Collectively, our results show the source-composition characters of DOM influence the immobilization of both DOM and P in aquatic ecosystems through adsorption processes. The preferential adsorption of proteinaceous compounds within ADOM and aromatics within HA highlights the potential for the attachment with FeOx to diminish the original source-specific signatures of DOM, thereby contributing to the shared DOM characteristics observed across diverse aquatic environments.

Aspartate aminotransferase to platelet ratio at admission can predict the prognosis of patients with hemorrhagic fever with renal syndrome.

Early indicators are needed to predict the prognosis of patients with hemorrhagic fever with renal syndrome (HFRS). Aspartate aminotransferase to platelet ratio index (APRI) has been shown to be related to mortality risk of patients with various diseases. This study evaluated the prognostic value of APRI and other inflammatory scores in HFRS patients. Data of hospitalized HFRS patients from a tertiary hospital in northwest China were collected and the inflammatory scores such as APRI and neutrophil to lymphocyte count ratio (NLR) were calculated at the day of patient admission. Independent factors related to the survival of patients were determined by multivariate logistic regression. Receiver operating characteristic curve was used to analyze the predictive value, and area under the curve (AUC) and 95% confidence interval (CI) were calculated for quantification. Of the 317 HFRS patients included in study, 15 patients died. Age (OR: 1.10, 95% CI: 1.04-1.16, p = 0.001), NLR (OR: 1.11, 95% CI: 1.02-1.19, p = 0.01), and APRI (OR: 1.06, 95% CI: 1.03-1.10, p = 0.001) were quantitative objective factors independently associated with the survival of patients. APRI had an AUC of 0.95 (95% CI: 0.91-1.00, p < 0.001) for predicting the prognosis of patients, with a sensitivity of 93.3% and a specificity of 86.8%. The performance of APRI was better than that of age or NLR. Patients with an APRI ≥ 6.15 had significantly decreased survival compared with those with an APRI < 6.15. In conclusion, this simple index APRI calculated at admission can serve as a biomarker to identify HFRS patients at risk of poor prognosis.

Clinical and laboratory features and factors predicting disease severity in pediatric patients with hemorrhagic fever with renal syndrome caused by Hantaan virus.

The clinical features and factors associated with disease severity in children with hemorrhagic fever with renal syndrome (HFRS) have not been well characterized. This study analyzed the clinical and laboratory factors associated with disease severity in children with HFRS caused by Hantaan virus. Data in pediatric patients with HFRS were retrospectively collected from Xi'an Children's Hospital over a 9-year period. Independent factors associated with disease severity were identified. Nomogram predicting disease severity was constructed based on variables filtered by feature selection. In total, 206 children with HFRS were studied. Fever, digestive tract symptoms, headache, backache, bleeding, and renal injury signs were the common symptoms. Elevated white blood cell, reduced platelet, hematuria, proteinuria, coagulation abnormalities, increased blood urea nitrogen (BUN) and procalcitonin (PCT), decreased estimated glomerular filtration rate and low serum Na+ , Cl- , and Ca2+ were the common laboratory findings. In the 206 patients, 21 patients had critical type disease and 4 patients (1.9%) died. Hydrothorax, hypotension and cerebral edema/cerebral herniation at hospital admission were independent clinical characteristics, and neutrophil %, prothrombin activity, PCT, BUN, and Ca2+ at hospital admission were independent laboratory factors associated with critical disease. Feature selection identified BUN, PCT and prothrombin time as independent factors related to critical disease. A nomogram integrating BUN and PCT at admission was constructed and calibration showed high accuracy for the probability prediction of critical disease. In conclusion, this study characterized the clinical and laboratory features and constructed a nomogram predicting disease severity in pediatric HFRS, providing references for disease severity evaluation in managing children HFRS.

Radiation Reaction and Gravitational Waves at Fourth Post-Minkowskian Order.

We obtain the total impulse in the scattering of nonspinning binaries in general relativity at fourth post-Minkowskian order, i.e., O(G^{4}), including linear, nonlinear, and hereditary radiation-reaction effects. We derive the total radiated spacetime momentum as well as the associated energy flux. The latter can be used to compute gravitational-wave observables for generic (un)bound orbits. We employ the ("in-in") Schwinger-Keldysh worldline effective field theory framework in combination with modern "multiloop" integration techniques from collider physics. The complete results are in agreement with various partial calculations in the post-Minkowskian and post-Newtonian expansion.

Extensive Carbon Contribution of Inundated Terrestrial Plants to Zooplankton Biomass in a Eutrophic Lake.

Organic carbon derived from terrestrial plants contributes to aquatic consumers, e.g., zooplankton in lakes. The degree of the contribution depends on the availability of terrestrial organic carbon in lake organic pool and the transfer efficiency of the carbon. Terrestrial organic carbon is poor-quality food for zooplankton with a mismatch of nutrition content and was incorporated to zooplankton with much lower efficiency than phytoplankton. Contributions of terrestrial carbon to zooplankton generally decrease with an increase in phytoplankton production, indicating a preferential incorporation of phytoplankton in previous investigations. However, in eutrophic lakes, the dominating cyanobacteria were of poor quality and incorporated to consumers inefficiently too. In that case, zooplankton in eutrophic wetlands, where cyanobacteria dominate the phytoplankton production and massive terrestrial plants are inundated, may not preferentially incorporate poor food-quality phytoplankton resource to their biomass. Therefore, we hypothesize that carbon contributions of terrestrial vegetation to zooplankton and to lake particulate organic pool should be similar in such aquatic ecosystems. We tested this hypothesis by sampling zooplankton and carbon sources in Ming Lake (Jinan University Campus, southern China) which was overgrown by terrestrial plants after drying and re-flooded. After 60 days of observations at weekly (or biweekly) intervals, applying stable carbon (13C), nitrogen (15 N), and hydrogen (2H) isotopic analysis and a stable isotope mixing model, we estimated the occurrence of extensive carbon contribution (≥ 50%) of flooded terrestrial plants to cladocerans and copepods. Contribution of inundated terrestrial plants to cladocerans was similar to that to lake particulate organic pool. Thus, our study quantified the role of terrestrial carbon in eutrophic wetlands, enhancing our understanding of cross-ecosystem interactions in food webs with an emphasis on the resource quality.

Food quality upgrade of carbon from submerged macrophytes by flagellates via a heterotrophic pathway can stimulate growth of Daphnia magna.

Submerged macrophytes play crucial roles in maintaining the stability of clear-water states in shallow lakes. Recent stable isotope studies have shown that crustacean zooplankton can utilize submerged macrophyte carbon, but macrophytes alone cannot support the growth and reproduction of such grazers, being deficient in highly unsaturated fatty acids (HUFA). We hypothesized that flagellates feeding on macrophytes can synthesize HUFA and thereby support crustacean zooplankton. To test this hypothesis, we conducted a feeding experiment in which Daphnia magna were provided with a diet of submerged macrophyte Hydrilla verticillata detritus which had been degraded by lake microbes. The chlorophyte Scenedesmus bijuga and undegraded macrophyte detritus were used as controls for comparison of Daphnia's performance. Using biochemical analysis, we examined how the degradation process affected the food quality of the macrophyte. Flagellates were subsequently isolated from the degraded macrophyte and cultured heterotrophically to detect their HUFA synthesis. The 5-day degraded H. verticillata showed significantly higher HUFA concentrations than undegraded macrophyte detritus. They supported better Daphnia performance than undegraded macrophyte, being comparable with S. bijuga. Two isolated flagellates (SL-1 and SL-2), identified as Ochromonas sp. and Poterioochromonas sp., were found to contain HUFA when cultured heterotrophically without dietary sources of fatty acids, suggesting their HUFA synthesis ability. Our results demonstrate that submerged macrophytes may thus indirectly support crustacean zooplankton via flagellate mediation. As crustacean zooplanktons are of key importance for water quality in the grazer control of phytoplankton, this microbial facilitation may contribute to the maintenance of macrophyte clear-water conditions in shallow lakes.

Transcriptome, Ectopic Expression and Genetic Population Analysis Identify Candidate Genes for Fiber Quality Improvement in Cotton.

Comparative transcriptome analysis of fiber tissues between Gossypium barbadense and Gossypium hirsutum could reveal the molecular mechanisms underlying high-quality fiber formation and identify candidate genes for fiber quality improvement. In this study, 759 genes were found to be strongly upregulated at the elongation stage in G. barbadense, which showed four distinct expression patterns (I-IV). Among them, the 346 genes of group IV stood out in terms of the potential to promote fiber elongation, in which we finally identified 42 elongation-related candidate genes by comparative transcriptome analysis between G. barbadense and G. hirsutum. Subsequently, we overexpressed GbAAR3 and GbTWS1, two of the 42 candidate genes, in Arabidopsis plants and validated their roles in promoting cell elongation. At the secondary cell wall (SCW) biosynthesis stage, 2275 genes were upregulated and exhibited five different expression profiles (I-V) in G. barbadense. We highlighted the critical roles of the 647 genes of group IV in SCW biosynthesis and further picked out 48 SCW biosynthesis-related candidate genes by comparative transcriptome analysis. SNP molecular markers were then successfully developed to distinguish the SCW biosynthesis-related candidate genes from their G. hirsutum orthologs, and the genotyping and phenotyping of a BC3F5 population proved their potential in improving fiber strength and micronaire. Our results contribute to the better understanding of the fiber quality differences between G. barbadense and G. hirsutum and provide novel alternative genes for fiber quality improvement.

Tissue-specific expression of GhnsLTPs identified via GWAS sophisticatedly coordinates disease and insect resistance by regulating metabolic flux redirection in cotton.

Cotton (Gossypium hirsutum) is constantly attacked by pathogens and insects. The most efficient control strategy is to develop resistant varieties using broad-spectrum gene resources. Several resistance loci harboured by superior varieties have been identified through genome-wide association studies. However, the key genes and/or loci have not been functionally identified. In this study, we identified a locus significantly associated with Verticillium wilt (VW) resistance, and within a 145.5-kb linkage disequilibrium, two non-specific lipid transfer protein genes (named GhnsLTPsA10) were highly expressed under Verticillium pathogen stress. The expression of GhnsLTPsA10 significantly increased in roots upon Verticillium dahliae stress but significantly decreased in leaves under insect attack. Furthermore, GhnsLTPsA10 played antagonistic roles in positively regulating VW and Fusarium wilt resistance and negatively mediating aphid and bollworm resistance in transgenic Arabidopsis and silenced cotton. By combining transcriptomic, histological and physiological analyses, we determined that GhnsLTPsA10-mediated phenylpropanoid metabolism further affected the balance of the downstream metabolic flux of flavonoid and lignin biosynthesis. The divergent expression of GhnsLTPsA10 in roots and leaves coordinated resistance of cotton against fungal pathogens and insects via the redirection of metabolic flux. In addition, GhnsLTPsA10 contributed to reactive oxygen species accumulation. Therefore, in this study, we elucidated the novel function of GhnsLTP and the molecular association between disease resistance and insect resistance, balanced by GhnsLTPsA10. This broadens our knowledge of the biological function of GhnsLTPsA10 in crops and provides a useful locus for genetic improvement of cotton.

Novel insights into water-deficit-responsive mRNAs and lncRNAs during fiber development in Gossypium hirsutum.

BACKGROUND: The fiber yield and quality of cotton are greatly and periodically affected by water deficit. However, the molecular mechanism of the water deficit response in cotton fiber cells has not been fully elucidated. RESULTS: In this study, water deficit caused a significant reduction in fiber length, strength, and elongation rate but a dramatic increase in micronaire value. To explore genome-wide transcriptional changes, fibers from cotton plants subjected to water deficit (WD) and normal irrigation (NI) during fiber development were analyzed by transcriptome sequencing. Analysis showed that 3427 mRNAs and 1021 long noncoding RNAs (lncRNAs) from fibers were differentially expressed between WD and NI plants. The maximum number of differentially expressed genes (DEGs) and lncRNAs (DERs) was identified in fibers at the secondary cell wall biosynthesis stage, suggesting that this is a critical period in response to water deficit. Twelve genes in cotton fiber were differentially and persistently expressed at ≥ five time points, suggesting that these genes are involved in both fiber development and the water-deficit response and could potentially be used in breeding to improve cotton resistance to drought stress. A total of 540 DEGs were predicted to be potentially regulated by DERs by analysis of coexpression and genomic colocation, accounting for approximately 15.76% of all DEGs. Four DERs, potentially acting as target mimics for microRNAs (miRNAs), indirectly regulated their corresponding DEGs in response to water deficit. CONCLUSIONS: This work provides a comprehensive transcriptome analysis of fiber cells and a set of protein-coding genes and lncRNAs implicated in the cotton response to water deficit, significantly affecting fiber quality during the fiber development stage.

Conservative Dynamics of Binary Systems at Fourth Post-Minkowskian Order in the Large-Eccentricity Expansion.

We compute the conservative dynamics of nonspinning binaries at fourth post-Minkowskian order in the large-eccentricity limit, including both potential and radiation-reaction tail effects. This is achieved by obtaining the scattering angle in the worldline effective field theory approach and deriving the bound radial action via analytic continuation. The associated integrals are bootstrapped to all orders in velocities through differential equations, with boundary conditions in the potential and radiation regions. The large angular momentum expansion captures all the local-in-time effects as well as the trademark logarithmic corrections for generic bound orbits. Agreement is found in the overlap with the state of the art in post-Newtonian theory.

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.

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.

A large-scale genomic association analysis identifies a fragment in Dt11 chromosome conferring cotton Verticillium wilt resistance.

Verticillium wilt (VW) is a destructive disease that results in great losses in cotton yield and quality. Identifying genetic variation that enhances crop disease resistance is a primary objective in plant breeding. Here we reported a GWAS of cotton VW resistance in a natural-variation population, challenged by different pathogenicity stains and different environments, and found 382 SNPs significantly associated with VW resistance. The associated signal repeatedly peaked in chromosome Dt11 (68 798 494-69 212 808) containing 13 core elite alleles undescribed previously. The core SNPs can make the disease reaction type from susceptible to tolerant or resistant in accessions with alternate genotype compared to reference genotype. Of the genes associated with the Dt11 signal, 25 genes differentially expressed upon Verticillium dahliae stress, with 21 genes verified in VW resistance via gene knockdown and/or overexpression experiments. We firstly discovered that a gene cluster of L-type lectin-domain containing receptor kinase (GhLecRKs-V.9) played an important role in VW resistance. These results proved that the associated Dt11 region was a major genetic locus responsible for VW resistance. The frequency of the core elite alleles (FEA) in modern varieties was significantly higher than the early/middle varieties (12.55% vs 4.29%), indicating that the FEA increased during artificial selection breeding. The current developmental resistant cultivars, JND23 and JND24, had fixed these core elite alleles during breeding without yield penalty. These findings unprecedentedly provided genomic variations and promising alleles for promoting cotton VW resistance improvement.

A stable QTL qSalt-A04-1 contributes to salt tolerance in the cotton seed germination stage.

KEY MESSAGE: A stable QTL qSalt-A04-1 for salt tolerance in the cotton seed germination stage, and two candidate genes, GhGASA1 and GhADC2, that play negative roles by modulating the GA and PA signalling pathways, respectively, were identified. The successful transition of a seed into a seedling is a prerequisite for plant propagation and crop yield. Germination is a vulnerable stage in a plant's life cycle that is strongly affected by environmental conditions, such as salinity. In this study, we identified a novel quantitative trait locus (QTL) qRGR-A04-1 associated with the relative germination rate (RGR) after salt stress treatment based on a high-density genetic map under phytotron and field conditions, with LOD values that ranged from 6.65 to 16.83 and 6.11-12.63% phenotypic variations in all five environmental tests. Two candidate genes with significantly differential expression between the two parents were finally identified through RNA-seq and qRT-PCR analyses. Further functional analyses showed that GhGASA1- and GhADC2-overexpression lines were more sensitive to salt stress than wild-type Arabidopsis based on the regulation of the transcript levels of gibberellic acid (GA)- and polyamine (PA)- related genes in GA and PA biosynthesis and the reduction in the accumulation of GA and PA, respectively, under salt stress. Virus-induced gene silencing analysis showed that TRV:GASA1 and TRV:ADC2 were more tolerant to salt stress than TRV:00 based on the increased expression of GA synthesis genes and decreased H2O2 content, respectively. Taken together, our results suggested that QTL qRGR-A04-1 and its two harboured genes, GhGASA1 and GhADC2, are promising candidates for salt tolerance improvement in cotton.

Scores based on neutrophil percentage and lactate dehydrogenase with or without oxygen saturation predict hospital mortality risk in severe COVID-19 patients.

BACKGROUND: Risk scores are needed to predict the risk of death in severe coronavirus disease 2019 (COVID-19) patients in the context of rapid disease progression. METHODS: Using data from China (training dataset, n = 96), prediction models were developed by logistic regression and then risk scores were established. Leave-one-out cross validation was used for internal validation and data from Iran (test dataset, n = 43) was used for external validation. RESULTS: A NSL model (area under the curve (AUC) 0.932) and a NL model (AUC 0.903) were developed based on neutrophil percentage and lactate dehydrogenase with and without oxygen saturation (SaO2) using the training dataset. AUCs of the NSL and NL models in the test dataset were 0.910 and 0.871, respectively. The risk scoring systems corresponding to these two models were established. The AUCs of the NSL and NL scores in the training dataset were 0.928 and 0.901, respectively. At the optimal cut-off value of NSL score, the sensitivity and specificity were 94% and 82%, respectively. The sensitivity and specificity of NL score were 94% and 75%, respectively. CONCLUSIONS: These scores may be used to predict the risk of death in severe COVID-19 patients and the NL score could be used in regions where patients' SaO2 cannot be tested.