An Efficient Agrobacterium-Mediated Genetic Transformation System for Gene Editing in Strawberry (Fragaria × ananassa).

The octoploid-cultivated strawberry variety Benihope (Fragaria × ananassa Duch cv. Benihope) is an important commercial plant. It is highly susceptible to different diseases, which ultimately leads to a reduction in yield. Gene-editing methods, such as CRISPR/Cas9, demonstrate potential for improving disease resistance in the strawberry cv. Benihope. Establishing a plant regeneration system suitable for CRISPR/Cas9 gene editing is crucial for obtaining transgenic plants on a large scale. This research established a callus induction and plant regeneration system for Agrobacterium-mediated CRISPR/Cas9 gene editing in strawberry cv. Benihope by evaluating multiple types of explants and various plant growth regulators throughout the entire tissue culture process. The results showed that the efficiency of callus induction is strongly influenced by the type of explant and is highly sensitive to the combination of plant growth regulators. Among the different plant growth regulators employed, thidiazuron (TDZ), in combination with 2,4-dichlorophenoxyacetic acid (2,4-D), effectively induced callus formation and plant regeneration from explants derived from nutrient tissues such as runner tips and crowns. In addition, the regeneration experiment demonstrated that the addition of polyvinylpyrrolidone (PVPP) to the shoot regeneration medium could inhibit tissue browning. The gene-edited plants in which some or all of the Fvb7-1, Fvb7-2, Fvb7-3, and Fvb7-4 genes in the MLO (Mildew resistance Locus O) gene family were knocked out by CRISPR/Cas9 system were obtained by applying the plant regeneration system developed in this study.

Tobacco introduced Perilla frutescens and Ocimum basilicum genes attenuates neutrophilic inflammation in lung tissues of COPD rats.

The new-type tobacco varieties "Zisu" and "Luole" were obtained by distant hybridization between N. tabacum L. var. HHY and Perilla frutescens and Ocimum basilicum, with obviously different chemical composition. Smoking is the major risk factor for COPD, characterized by neutrophil-dominant inflammation. In the present study, rat COPD model was established by cigarette exposure, and the health hazard of three varieties was compared by general condition observation, pathological and morphological evaluation, total and differential cell numeration, and characterization of major inflammatory mediators and MAPK/NF-κB pathway, etc. Rats in "HHY" group developed obvious symptoms such as cough, dyspnea, mental fatigue, etc., but these symptoms were obviously mitigated in "Zisu" and "Luole" groups. H&E staining analysis, including score, MLI, MAN, wt% and WA%, showed that "Zisu" and "Luole" significantly alleviated lung injury and the degree of airway remodeling and emphysema compared to "HHY". In BALF, the number of total leukocyte and the percent neutrophils in "Zisu" and "Luole" groups were evidently lower than "HHY" group. The levels of inflammatory mediators, such as IL-8, MPO, MIP-2, LTB4, TNF-α and neutrophil elastase, in "HHY" group were obviously higher than "Zisu" and "Luole" groups. The ROS-mediated NF-κB p65 and p38MAPK pathways may play an important role. Results indicated that tobacco introduced perilla and basil genes could remarkably attenuate recruitment, infiltration and activation of neutrophils and intervene in airway inflammation, retarding disease progression, especially "Zisu". Changes in chemical composition via breeding techniques may be a novel way for tobacco harm reduction.

Different responses of two maize cultivars to Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae infestation provide insights into their differences in resistance.

Spodoptera frugiperda (Lepidoptera: Noctuidae), a pest with an amazing appetite, damages many crops and causes great losses, especially maize. Understanding the differences in different maize cultivars' responses to S. frugiperda infestation is very important for revealing the mechanisms involved in the resistance of maize plants to S. frugiperda. In this study, a comparative analysis of two maize cultivars, the common cultivar 'ZD958' and the sweet cultivar 'JG218', was used to investigate their physico-biochemical responses to S. frugiperda infestation by a pot experiment. The results showed that the enzymatic and non-enzymatic defense responses of maize seedlings were rapidly induced by S. frugiperda. Frist, the hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents of infested maize leaves were significantly increased and then decreased to the level of the control. Furthermore, compared with the control leaves, the puncture force values and the total phenolics, total flavonoids, and 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one contents of infested leaves were significantly increased within a certain time. The superoxide dismutase and peroxidase activities of infested leaves were significantly increased in a certain period of time, while the catalase activities decreased significantly and then increased to the control level. The jasmonic acid (JA) levels of infested leaves were significantly improved, whereas the salicylic acid and abscisic acid levels changed less. Signaling genes associated with phytohormones and defensive substances including PAL4, CHS6, BX12, LOX1, and NCED9 were significantly induced at certain time points, especially LOX1. Most of these parameters changed greater in JG218 than in ZD958. Moreover, the larvae bioassay showed that S. frugiperda larvae weighed more on JG218 leaves than those on ZD958 leaves. These results suggested that JG218 was more susceptible to S. frugiperda than ZD958. Our findings will make it easier to develop strategies for controlling S. frugiperda for sustainable maize production and breeding of new maize cultivars with increased resistance to herbivores.

Identification of long non-coding RNA-microRNA-mRNA regulatory modules and their potential roles in drought stress response in wheat (Triticum aestivum L.).

Drought is one of the most severe abiotic stresses that influence wheat production across the globe. Understanding the molecular regulatory network of wheat in response to drought is of great importance in molecular breeding. Noncoding RNAs influence plant development and resistance to abiotic stresses by regulating gene expression. In this study, whole-transcriptome sequencing was performed on the seedlings of two wheat varieties with contrasting levels of drought tolerance under drought and control conditions to identify long noncoding RNAs (lncRNAs), micro RNAs (miRNAs), and mRNAs related to drought stress and explore the potential lncRNA-miRNA-mRNA regulatory modules in controlling wheat drought stress response. A total of 1515 differentially expressed lncRNAs (DELs), 209 differentially expressed miRNAs (DEMs), and 20462 differentially expressed genes (DEGs) were identified. Of the 20462 DEGs, 1025 were identified as potential wheat drought resistance-related DEGs. Based on the regulatory relationship and expression patterns of DELs, DEMs, and DEGs, 10 DEL-DEM-DEG regulatory modules related to wheat drought stress response were screened, and preliminary expression verification of two important candidate modules was performed. Our results revealed the possible roles of lncRNA-miRNA-mRNA modules in regulatory networks related to drought tolerance and provided useful information as valuable genomic resources in molecular breeding of wheat.

Quantitative trait loci mapping and candidate gene analysis of stoma-related traits in wheat (Triticum aestivum L.) glumes.

The photosynthesis of wheat glumes makes important contributions to the yield. Stomata play a crucial role in regulating photosynthesis and transpiration in plants. However, the genetic base of wheat glume stomata is not fully understood. In this study, stomatal length (SL), stomatal width (SW), stomatal density (SD), potential conductance index (PCI) of stomata, stomatal area (SA), and stomatal relative area (SRA) were measured in different parts of wheat glumes from a doubled haploid (DH) population and their parents. Quantitative trait loci (QTLs) of these traits were anchored on a high-density genetic linkage map of the DH population. A total of 61 QTLs for stoma-related traits were mapped onto 16 chromosomes, and each one accounted for 3.63 to 19.02% of the phenotypic variations. Two QTL hotspots were detected in two marker intervals, AX-109400932∼AX-110985652 and AX-108972184∼AX-108752564, on chromosome 6A. Five possibly candidate genes (TraesCS6A02G105400, TraesCS6A02G106400, TraesCS6A02G115100, TraesCS6A02G115400, and TraesCS6A02G116200) for stoma-related traits of wheat glumes were screened out , according to their predicted expression levels in wheat glumes or spikes. The expression of these genes may be induced by a variety of abiotic stresses. These findings provide insights for cloning and functional characterization of stoma-related candidate genes in wheat glumes.

Acute kidney injury-attributable mortality in critically ill patients with sepsis.

Background: To assess whether acute kidney injury (AKI) is independently associated with hospital mortality in ICU patients with sepsis, and estimate the excess AKI-related mortality attributable to AKI. Methods: We analyzed adult patients from two distinct retrospective critically ill cohorts: (1) Medical Information Mart for Intensive Care IV (MIMIC IV; n = 15,610) cohort and (2) Wenzhou (n = 1,341) cohort. AKI was defined by Kidney Disease: Improving Global Outcomes (KDIGO) criteria. We applied multivariate logistic and linear regression models to assess the hospital and ICU mortality, hospital length-of-stay (LOS), and ICU LOS. The excess attributable mortality for AKI in ICU patients with sepsis was further evaluated. Results: AKI occurred in 5,225 subjects in the MIMIC IV cohort (33.5%) and 494 in the Wenzhou cohort (36.8%). Each stage of AKI was an independent risk factor for hospital mortality in multivariate logistic regression after adjusting for baseline illness severity. The excess attributable mortality for AKI was 58.6% (95% CI [46.8%-70.3%]) in MIMIC IV and 44.6% (95% CI [12.7%-76.4%]) in Wenzhou. Additionally, AKI was independently associated with increased ICU mortality, hospital LOS, and ICU LOS. Conclusion: Acute kidney injury is an independent risk factor for hospital and ICU mortality, as well as hospital and ICU LOS in critically ill patients with sepsis. Thus, AKI is associated with excess attributable mortality.

QTL mapping and candidate gene analysis of seed vigor-related traits during artificial aging in wheat (Triticum aestivum).

High vigor seeds have greater yield potential than those with low vigor; however, long-term storage leads to a decline in this trait. The objective of this study was to identify quantitative trait loci (QTLs) for seed vigor-related traits under artificial aging conditions using a high-density genetic linkage map of wheat (Triticum aestivum) and mine the related candidate genes. A doubled haploid population, derived from a cross between Hanxuan 10 × Lumai 14, was used as the experimental material. Six controlled-environment treatments were set up, i.e. the seeds were aged for 0, 24, 36, 48, 60, and 72 h at a high temperature (48 °C) and under high humidity (relative humidity 100%). Eight traits including seed germination percentage, germination energy, germination index, seedling length, root length, seedling weight, vigor index, and simple vigor index were measured. With the prolongation of artificial aging treatment, these traits showed a continuous downward trend and significant correlations were observed between most of them. A total of 49 additive QTLs for seed vigor-related traits were mapped onto 12 chromosomes (1B, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5B, 5D, 6D, and 7A); and each one accounted for 6.01-17.18% of the phenotypic variations. Twenty-five pairs of epistatic QTLs were detected on all chromosomes, except for 5D, 6A, and 7D, and each epistasis accounted for 7.35-26.06% of the phenotypic variations. Three additive QTL hot spots were found on chromosomes 5A, 5B, and 5D, respectively. 13 QTLs, QGEe5B, QGIe5B, QSLc5B, QSLd5B, QSLf5B, QRLd5B, QRLe5B, QRLf5B, QVId5B, QVIe5B, QVIf5B, QSVId5B, and QSVIe5B, were located in the marker interval AX-94643729 ~ AX-110529646 on 5B and the physical interval 707,412,449-710,959,479 bp. Genes including TRAESCS5B01G564900, TRAESCS5B01G564200, TRAESCS5B01G562600, TraesCS5B02G562700, TRAESCS5B01G561300, TRAESCS5B01G561400, and TRAESCS5B01G562100, located in this marker interval, were found to be involved in regulating the processes of carbohydrate and lipid metabolism, transcription, and cell division during the germination of aging seeds, thus they were viewed as candidate genes for seed viability-related traits. These findings provide the basis for the seed-based cloning and functional identification of related candidate genes for seed vigor.

[Effects of high CO2 concentration, drought, and their interaction on different stay-green wheat seedlings]. / 高CO2æµ“åº¦ã€å¹²æ—±åŠå ¶äº’ä½œå¯¹ä¸åŒæŒç»¿åž‹å°éº¦å¹¼è‹—çš„å½±å“.

In this study, a pot experiment was carried out to examine the effects of high CO2 concentration, drought and interaction on seedling growth traits, biomass accumulation and physiological characteristics of different stay-green wheat seedlings, with a stay-green wheat variety Yannong 19 and a non stay-green wheat variety Hanxuan 3 as test materials. There were four treatments in the Open Top Chamber with factorial of CO2 concentration (370 µmol·mol-1 vs 550 µmol·mol-1) and drought (45%-55% vs. 75%-85% of field water-holding capacity). Drought significantly inhibited the growth and development of wheat seedlings, while CO2 concentration significantly increased the number of tillers and promoted the growth and development of wheat seedlings. Under drought condition, high CO2 concentration increased the number of tillers of Hanxuan 3 and Yannong 19 by 61.0% and 42.3%, respectively. Under both water conditions, high CO2 concentration significantly increased the biomass of wheat seedlings, and decreased the content of peroxidase and proline in leaves. Under drought condition, high CO2 concentration showed stronger "fertilizer effect". Furthermore, different varieties had different responses to high CO2 concentration, with higher sensitivity of Hanxuan 3 to enhancement of CO2 concentration. Under the scenario of increasing CO2 concentration, the amount of irrigation water applied to a field can be appropriately reduced for efficient use of water resources. Meanwhile, it is necessary to pay attention to the selection of suitable wheat varieties.

Dimensionality reduction for single cell RNA sequencing data using constrained robust non-negative matrix factorization.

Single cell RNA-sequencing (scRNA-seq) technology, a powerful tool for analyzing the entire transcriptome at single cell level, is receiving increasing research attention. The presence of dropouts is an important characteristic of scRNA-seq data that may affect the performance of downstream analyses, such as dimensionality reduction and clustering. Cells sequenced to lower depths tend to have more dropouts than those sequenced to greater depths. In this study, we aimed to develop a dimensionality reduction method to address both dropouts and the non-negativity constraints in scRNA-seq data. The developed method simultaneously performs dimensionality reduction and dropout imputation under the non-negative matrix factorization (NMF) framework. The dropouts were modeled as a non-negative sparse matrix. Summation of the observed data matrix and dropout matrix was approximated by NMF. To ensure the sparsity pattern was maintained, a weighted ℓ1 penalty that took into account the dependency of dropouts on the sequencing depth in each cell was imposed. An efficient algorithm was developed to solve the proposed optimization problem. Experiments using both synthetic data and real data showed that dimensionality reduction via the proposed method afforded more robust clustering results compared with those obtained from the existing methods, and that dropout imputation improved the differential expression analysis.

Structure, elastic characteristic, ideal strengths, and phonon stability of binary uranium intermetallic UGe3 of AuCu3-type.

Crystallographic characterization, energy band structure, densities of states and charge density, elastic properties, ideal tensile and shear strengths, lattice dynamics and thermophysical characteristics of UGe3 of AuCu3-type have been studied by employing the first principles method based on Density Functional Theory (DFT). The optimized lattice parameters, such as lattice constant a, equilibrium cell volume V0, U-Ge distance and U-U distance of UGe3, are in favorable agreement with the available experimental results. Three single-crystalline elastic constants of C11, C12, and C44 have been obtained using the "energy-strain" technique by increasingly varying small strains. The polycrystalline elastic moduli including volume modulus B, Young's modulus E, and shear modulus G, Poisson's ratio v, brittle/ductile nature, Debye temperature θD, and the integration of elastic wave velocities over different crystallographic directions have also been successfully calculated. The anisotropy of the three-directional bulk modulus and Young's modulus is systematically explored and analyzed. The calculations indicate that UGe3 of AuCu3-type should be stabilized mechanically, and the system possesses insignificant elastic anisotropy. In particular, the vibrational spectrum, phonon densities of states and the infrared-active and inactive vibration modes at the center of the Brillouin zone are determined using Density Functional Perturbation Theory (DFPT) and group theory for the first time. This study reveals that UGe3 of AuCu3-type is also stable dynamically. Finally, within the calculated phonon densities of states and the quasi-harmonic Debye model, the constant volume heat capacity Cv and the vibration entropy S in the temperature range of 0-1000 K are predicted and analyzed comprehensively. The present investigations are expected to provide some valuable references for further exploring the properties of uranium compounds.

Structural instabilities and mechanical properties of U2Mo from first principles calculations.

We perform detailed first principles calculations of the structural parameters at zero pressure and high pressure, the elastic properties, phonon dispersion relation, and ideal strengths of U2Mo with the C11b structure. In contrast to previous theoretical studies, we show that the I4/mmm structure is indeed a mechanically and dynamically unstable phase, which is confirmed by the negative elastic constant C66 as well as the imaginary phonon modes observed along the Σ1-N-P line. The calculations of ideal strengths for U2Mo are performed along the [100], [001], and [110] directions for tension and on (001)[010] and (010)[100] slip systems for shear load. The ideal shear strength is about 8.1 GPa, much smaller than a tension of 18-28 GPa, which indicates that the ductile U2Mo alloy will fail by shear rather than by tension.

[Drought-resistance of local wheat varieties in Shanxi Province of China: a comprehensive evaluation by using GGE biplot and subordinate function].

Taking 7 local wheat varieties in Shanxi Province of China and two other control varieties as test materials, this paper studied their morphological and physiological traits under normal and water stress field conditions. The drought-resistance coefficient of each index of the traits was calculated. On the basis of principal component analysis, the correlations between the drought-resistance indices and their relationships with the drought-resistance of different varieties were analyzed by GGE biplot, and the drought resistance of the wheat varieties was comprehensively evaluated with the combination of subordinate function and drought resistance index analysis. The main morphological and physiological factors affecting the drought-resistance of the wheat varieties were uppermost internode length, plant height, internode length, leaf area, leaf POD and SOD activities, and leaf relative water content and relative electric conductivity. There existed different degrees of correlation between these indices, and each index had different effects on the drought resistance of the varieties, being the main cause for the different drought resistance of the wheat varieties. Based on the drought-resistance, the test varieties could be classified into three groups, i. e. , drought-resistance group, intermediate group, and sensitive group. Two highly drought-resistance cultivars, Baiheshangtou and Zhuganqing, whose drought-resistance was similar to that of drought-resistant Jinmai 47, could be used as the parent materials for breeding drought-resistance wheat.