Identification and characterization of the plasma membrane H+-ATPase genes in Brassica napus and functional analysis of BnHA9 in salt tolerance.

As a primary proton pump, plasma membrane (PM) H+-ATPase plays critical roles in regulating plant growth, development, and stress responses. PM H+-ATPases have been well characterized in many plant species. However, no comprehensive study of PM H+-ATPase genes has been performed in Brassica napus (rapeseed). In this study, we identified 32 PM H+-ATPase genes (BnHAs) in the rapeseed genome, and they were distributed on 16 chromosomes. Phylogenetical and gene duplication analyses showed that the BnHA genes were classified into five subfamilies, and the segmental duplication mainly contributed to the expansion of the rapeseed PM H+-ATPase gene family. The conserved domain and subcellular analyses indicated that BnHAs encoded canonical PM H+-ATPase proteins with 14 highly conserved domains and localized on PM. Cis-acting regulatory element and expression pattern analyses indicated that the expression of BnHAs possessed tissue developmental stage specificity. The 25 upstream open reading frames with the canonical initiation codon ATG were predicted in the 5' untranslated regions of 11 BnHA genes and could be used as potential target sites for improving rapeseed traits. Protein interaction analysis showed that BnBRI1.c associated with BnHA2 and BnHA17, indicating that the conserved activity regulation mechanism of BnHAs may be present in rapeseed. BnHA9 overexpression in Arabidopsis enhanced the salt tolerance of the transgenic plants. Thus, our results lay a foundation for further research exploring the biological functions of PM H+-ATPases in rapeseed.

Prognostic value of diffuse reduction of spleen density on postoperative survival of pancreatic ductal adenocarcinoma: A retrospective study.

PURPOSE: It is difficult to predict the prognosis of patients with pancreatic ductal adenocarcinoma (PDAC) before radical operation. The purpose of this study was to explore the connection between the diffuse reduction of spleen density on computed tomography (DROSD) and the postoperative prognosis of patients with PDAC. PATIENTS AND METHODS: A total of 160 patients with PDAC who underwent radical surgery in the First Affiliated Hospital of Wenzhou Medical University were enrolled. Cox regression analysis was used to cast the overall survival (OS) and evaluate the prognostic factors. Nomogram was used to forecast the possibility of 1-year, 3-year, and 5-year OS. The prediction accuracy and clinical net benefit are performed by concordance index (C-index), calibration curve, time-dependent receiver operating characteristics (tdROC), and decision curve analysis. RESULTS: In multivariable Cox analysis, DROSD is independently related to OS. Advanced age, TNM stage, neutrophil/lymphocyte ratio, and severe complications were also independent prognostic factors. The calibration curves of nomogram showed optimal agreement between prediction and observation. The C-index of nomogram is 0.662 (95%CI, 0.606-0.754). The area under tdROC curve for a 3-year OS of nomogram is 0.770. CONCLUSION: DROSD is an independent risk factor for an OS of PDAC. We developed a nomogram that combined imaging features, clinicopathological factors, and systemic inflammatory response to provide a personalized risk assessment for patients with PDAC.

Gut microbiome as a biomarker for predicting early recurrence of HBV-related hepatocellular carcinoma.

To investigate the potential of the gut microbiome as a biomarker for predicting the early recurrence of HBV-related hepatocellular carcinoma (HCC), we enrolled 124 patients diagnosed with HBV-associated HCC and 82 HBV-related hepatitis, and 86 healthy volunteers in our study, collecting 292 stool samples for 16S rRNA sequencing and 35 tumor tissue samples for targeted metabolomics. We performed an integrated bioinformatics analysis of gut microbiome and tissue metabolome data to explore the gut microbial-liver metabolite axis associated with the early recurrence of HCC. We constructed a predictive model based on the gut microbiota and validated its efficacy in the temporal validation cohort. Dialister, Veillonella, the Eubacterium coprostanoligenes group, and Lactobacillus genera, as well as the Streptococcus pneumoniae and Bifidobacterium faecale species, were associated with an early recurrence of HCC. We also found that 23 metabolites, including acetic acid, glutamate, and arachidonic acid, were associated with the early recurrence of HCC. A comprehensive analysis of the gut microbiome and tissue metabolome revealed that the entry of gut microbe-derived acetic acid into the liver to supply energy for tumor growth and proliferation may be a potential mechanism for the recurrence of HCC mediated by gut microbe. We constructed a nomogram to predict early recurrence by combining differential microbial species and clinical indicators, achieving an AUC of 78.0%. Our study suggested that gut microbes may serve as effective biomarkers for predicting early recurrence of HCC, and the gut microbial-tumor metabolite axis may explain the potential mechanism by which gut microbes promote the early recurrence of HCC.

A Set of Molecular Markers to Accelerate Breeding and Determine Seed Purity of CMS Three-Line Hybrids in Brassica napus.

Cytoplasmic male sterility (CMS) is the main mechanism employed to utilize the heterosis of Brassica napus. CMS three-line rapeseed hybrids have dramatically enhanced yield and brought about the global revolution of hybrid varieties, replacing conventional crop varieties. Over the last half century, China has led the development of hybrid Brassica napus varieties. Two sterile lines, polima (pol) and shaan 2A, were of particular importance for the establishment of three-line hybrid systems in rapeseed, which has opened up a new era of heterosis utilization. However, in current breeding practices, it takes up to three years to identify the restorer or maintainer relationship and the cytoplasmic type of any inbred material. This greatly affects the breeding speed of new varieties and inhibits the rapid development of the rapeseed industry. To address this problem, we developed a set of molecular markers for the identification of fertile cytoplasmic gene N and sterile cytoplasmic gene S, as well as for the fertile nucleus gene R and sterile nucleus gene r, based on differences in the gene sequences between the CMS line, maintainer line and restorer line of Brassica napus. Combining these markers can accurately identify the CMS line, maintainer and restorer of both the pol and shaan systems, as well as their hybrids. These markers can not only be used to identify of the maintainer and restorer relationship of inbred materials; they can also be used as general molecular markers to identify the CMS-type hybrid purity of pol and shaan systems.

Sarcopenia negatively affects postoperative short-term outcomes of patients with non-cirrhosis liver cancer.

BACKGROUND: Literature review have shown that sarcopenia substantially alters the postoperative outcomes after liver resection for malignant tumors. However, these retrospective studies do not distinguish cirrhotic and non-cirrhotic liver cancer patients, nor combine the assessment of muscle strength in addition to muscle mass. The purpose of this study is to study the relationship between sarcopenia and short-term outcomes after hepatectomy in patients with non-cirrhotic liver cancer. METHODS: From December 2020 to October 2021, 431 consecutive inpatients were prospectively enrolled in this study. Muscle strength and mass were assessed by handgrip strength and the skeletal muscle index (SMI) on preoperative computed tomographic scans, respectively. Based on the SMI and the handgrip strength, patients were divided into four groups: group A (low muscle mass and strength), group B (low muscle mass and normal muscle strength), group C (low muscle strength and normal muscle mass), and group D (normal muscle mass and strength). The main outcome was major complications and the secondary outcome was 90-d Readmission rate. RESULTS: After strictly exclusion, 171 non-cirrhosis patients (median age, 59.00 [IQR, 50.00-67.00] years; 72 females [42.1%]) were selected in the final analysis. Patients in group A had a statistically significantly higher incidence of major postoperative complications (Clavien-Dindo classification ≥ III) (26.1%, p = 0.032), blood transfusion rate (65.2%, p < 0.001), 90-day readmission rate (21.7%, p = 0.037) and hospitalization expenses (60,842.00 [IQR, 35,563.10-87,575.30], p < 0.001) than other groups. Sarcopenia (hazard ratio, 4.21; 95% CI, 1.44-9.48; p = 0.025) and open approach (hazard ratio, 2.56; 95% CI, 1.01-6.49; p = 0.004) were independent risk factors associated with major postoperative complications. CONCLUSIONS: Sarcopenia is closely related to poor short-term postoperative outcomes in non-cirrhosis liver cancer patients and the assessment that combines muscle strength and muscle mass can simply and comprehensively identify it. TRIAL REGISTRATION: ClinicalTrials.gov identifiers NCT04637048 . (19/11/2020).

Effect of Sarcopenia on Survival and Health-Related Quality of Life in Patients with Hepatocellular Carcinoma after Hepatectomy.

BACKGROUND: Although sarcopenia has been reported as a negative prognostic factor in patients with hepatocellular carcinoma (HCC), the lack of studies with a prospective design utilizing comprehensive sarcopenia assessment with composite endpoints is an important gap in understanding the impact of sarcopenia in patients with HCC. The aim of this study was to investigate the relationship between sarcopenia and postoperative 1-year mortality and health-related quality of life (HRQOL) based on sarcopenia assessment. METHODS: The study cohort, who received resection surgery for HCC between May 2020 and August 2021, was assessed for sarcopenia based on grip strength, the chair stand test, skeletal muscle mass, and gait speed. The primary outcome measures were 1-year mortality and HRQOL determined using the QLQ-C30 questionnaire. In addition, we collected hospital costs, postoperative hospital stays, complications, 30-day and 90-day mortality, and 90- and 180-day readmission rates. Univariate and multivariate linear regression analyses were conducted to examine factors associated with global health status. RESULTS: A total of 153 eligible patients were included in the cohort. One-year mortality was higher in patients with sarcopenia than in those without sarcopenia (p = 0.043). There was a correlation between sarcopenia and the surgical approach to global health status (p = 0.025) and diarrhea (p = 0.003). CONCLUSIONS: Preoperative sarcopenia reduces postoperative survival and health-related quality of life in patients with HCC.

[Responses of plant C:N:P stoichiometry to soil properties on unstable slopes of dry-hot valley]. / 干热河谷失稳性坡面植物碳氮磷化学计量特征对土壤性质的响应.

In this study, we examined plant C:N:P stoichiometry of herbaceous plants in different sections (stable area, unstable area and deposition area) of the unstable slope on both shade and sunny aspects of dry-hot valley with different soil properties. The results showed that C concentration (320.59 g·kg-1), N concentration (12.15 g·kg-1), and N:P ratio (25.37) of shoot on the unstable slope were significantly higher than those of root, with 254.01 g·kg-1, 6.12 g·kg-1 and 13.43, respectively. The average value of the C:N ratio was significantly higher in root (43.09) than shoot (31.90). The C content and N:P ratio of shoot and root in stable and unstable areas were significantly higher than in deposition area, whereas the N content in unstable area was significantly higher than that in deposition area on the sunny slope. In addition, the N and P contents of shoot and the root P content in deposition area were significantly higher than in stable and unstable areas, whereas the C content of root in stable and unstable areas were significantly higher than in deposition area on the shade slope. Moreover, the shoot growth of plants was mainly limited by P, whereas root growth was mainly limited by N and the limitation gradually increased as the section goes down. Soil water content (SWC) was an important factor controlling the C, N, and P contents change of shoot with the relative influence ratios of 28.8%, 20.8%, and 19.9%, respectively. Soil organic carbon (SOC) had a significant impact on the C and P contents of root with the relative influence ratios of 49.5% and 22.1%. The change of root N content was mainly affected by soil pH (24.3%). Our results revealed that nutrient allocation of plant was significantly affected by slope aspects, sections and soil factors, which were mainly constituted by SWC, SOC, and soil pH.

Genome Structures and Evolution Analysis of Hsp90 Gene Family in Brassica napus Reveal the Possible Roles of Members in Response to Salt Stress and the Infection of Sclerotinia sclerotiorum.

Heat shock proteins 90 (Hsp90s) are conserved proteins participating in the responses to heat stress and are found to be involved in different kinds of abiotic and biotic stresses. Brassica napus (B. napus) is an important heteropolyploid crop, producing edible oil. Salt stress is one of the most important hazards to the growth of rape in the world, while Sclerotinia stem rot is one of the most serious diseases, caused by Sclerotinia sclerotiorum (S. sclerotiorum). In this study, the evolution of Hsp90 genes and their responses to these two stresses were elucidated. Bioinformatic analysis through the whole genome of B. napus identified 35 Hsp90 gene family members. Five groups were obtained via phylogenetic analysis with the 35 Hsp genes, Hsps from its two ancestor species Brassica rapa, Brassica oleracea, and AtHsps. Gene structure and conservative motif analysis of these 35 Hsps indicated that the Hsps were relatively conservative in each group. Strong collinearity was also detected between the genomes of Brassica rapa, Brassica oleracea and B. napus, along with identifying syntenic gene pairs of Hsps among the three genomes. In addition, whole genome duplication was discovered as the main reason for the generation of BnHsp gene family. The analysis of cis-acting elements indicated that BnHsp90 might be involved in a variety of abiotic and biotic stress responses. Analysis of the expression pattern indicated that BnHsp90 participates in the responses of B. napus to salt stress and the infection of S. sclerotiorum. Fourteen and nine BnHsp90s were validated to be involved in the defense responses of B. napus against salt stress and S. sclerotiorum, respectively. Our results provide new insights for the roles of BnHsp90s in the responses of B. napus to salt stress and S. sclerotiorum.

Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications.

Gene co-expression network (GCN) becomes an increasingly important tool in omics data analysis. A great challenge for GCN construction is that the sample size is far lower than the number of genes. Traditional methods rely on considerable samples. Moreover, association signals are likely weak, nonlinear and stochastic, which are difficult to be identified among thousands of candidates. In this paper, the gray correlation coefficient (GCC) is introduced, and a novel method to construct gene differential co-expression networks (GDCNs) is proposed. Based on the GDCNs, three measures are proposed to explore informative genes. The proposed method can make full use of the information provided by a handful of samples and overcome the shortages of GCNs, which can evaluate the changes of co-expression relationships that are possibly triggered by treatments. Based on RNA-seq data of Brassica napus, GDCNs under multiple experimental conditions are constructed and investigated. It is found that the GCC-based method is very robust to data processing. The GDCNs facilitate the inference of gene functions and the identification of informative genes that are responsible for stress responsiveness. The GDCN-based approaches integrate the 'guilt by association' and the 'guilt by rewiring' rules, which provide alternative tools for omics data analysis.

Identification of WRKY transcription factors responding to abiotic stresses in Brassica napus L.

MAIN CONCLUSION: A total of 278 BnWRKYs were identified and analyzed. Ectopic expression of BnWRKY149 and BnWRKY217 suggests that they function in the ABA signaling pathway. WRKY transcription factors play an important role in plant development, however, their function in Brassica napus L. abiotic stress response is still unclear. In this study, a total of 278 BnWRKY transcription factors were identified from the B. napus genome data, and they were subsequently distributed in three main groups. The protein motifs and classification of BnWRKY transcription factors were analyzed, and the locations of their corresponding encoding genes were mapped on the chromosomes of B. napus. Transcriptome analysis of rapeseed seedlings exposed to drought, salt, heat, cold and abscisic acid treatment revealed that 99 BnWRKYs responded to at least one of these stresses. The expression profiles of 12 BnWRKYs were examined with qPCR and the result coincided with RNA-seq analysis. Two genes of interest, BnWRKY149 and BnWRKY217 (homologs of AtWRKY40), were overexpressed in Arabidopsis, and the corresponding proteins were located to the nucleus. Transgene plants of BnWRKY149 and BnWRKY217 were less sensitive to ABA than Arabidopsis Col-0 plants, suggesting they might play important roles in the responses of rapeseed to abiotic stress.

Identification of tumour immune microenvironment-related alternative splicing events for the prognostication of pancreatic adenocarcinoma.

PURPOSE: Pancreatic adenocarcinoma (PAAD) is characterized by low antitumour immune cell infiltration in an immunosuppressive microenvironment. This study aimed to systematically explore the impact on prognostic alternative splicing events (ASs) of tumour immune microenvironment (TIME) in PAAD. METHODS: The ESTIMATE algorithm was implemented to compute the stromal/immune-related scores of each PAAD patient, followed by Kaplan-Meier (KM) survival analysis of patients with different scores grouped by X-tile software. TIME-related differentially expressed ASs (DEASs) were determined and evaluated through functional annotation analysis. In addition, Cox analyses were implemented to construct a TIME-related signature and an AS clinical nomogram. Moreover, comprehensive analyses, including gene set enrichment analysis (GSEA), immune infiltration, immune checkpoint gene expression, and tumour mutation were performed between the two risk groups to understand the potential mechanisms. Finally, Cytoscape was implemented to illuminate the AS-splicing factor (SF) regulatory network. RESULTS: A total of 437 TIME-related DEASs significantly related to PAAD tumorigenesis and the formation of the TIME were identified. Additionally, a robust TIME-related prognostic signature based on seven DEASs was generated, and an AS clinical nomogram combining the signature and four clinical predictors also exhibited prominent discrimination by ROC (0.762 ~ 0.804) and calibration curves. More importantly, the fractions of CD8 T cells, regulatory T cells and activated memory CD4 T cells were lower, and the expression of four immune checkpoints-PD-L1, CD47, CD276, and PVR-was obviously higher in high-risk patients. Finally, functional analysis and tumour mutations revealed that aberrant immune signatures and activated carcinogenic pathways in high-risk patients may be the cause of the poor prognosis. CONCLUSION: We extracted a list of DEASs associated with the TIME through the ESTIMATE algorithm and constructed a prognostic signature on the basis of seven DEASs to predict the prognosis of PAAD patients, which may guide advanced decision-making for personalized precision intervention.

The Brassica napus fatty acid exporter FAX1-1 contributes to biological yield, seed oil content, and oil quality.

BACKGROUND: In the oilseed crop Brassica napus (rapeseed), various metabolic processes influence seed oil content, oil quality, and biological yield. However, the role of plastid membrane proteins in these traits has not been explored. RESULTS: Our genome-wide association study (GWAS) of 520 B. napus accessions identified the chloroplast membrane protein-localized FATTY ACID EXPORTER 1-1 (FAX1-1) as a candidate associated with biological yield. Seed transcript levels of BnaFAX1-1 were higher in a cultivar with high seed oil content relative to a low-oil cultivar. BnaFAX1-1 was localized to the plastid envelope. When expressed in Arabidopsis thaliana, BnaFAX1-1 enhanced biological yield (total plant dry matter), seed yield and seed oil content per plant. Likewise, in the field, B. napus BnaFAX1-1 overexpression lines (BnaFAX1-1-OE) displayed significantly enhanced biological yield, seed yield, and seed oil content compared with the wild type. BnaFAX1-1 overexpression also up-regulated gibberellic acid 4 (GA4) biosynthesis, which may contribute to biological yield improvement. Furthermore, oleic acid (C18:1) significantly increased in BnaFAX1-1 overexpression seeds. CONCLUSION: Our results indicated that the putative fatty acid exporter BnaFAX1-1 may simultaneously improve seed oil content, oil quality and biological yield in B. napus, providing new approaches for future molecular breeding.

Social-ecological system resilience of debris flow alluvial fans in the Awang basin, China.

Debris flow alluvial fans (DFAFs) are vulnerable, although they can be used as a natural resource. The relationships between different factors related to DFAF systems and between these factors and systems are important both for identifying the risks and opportunities presented by DFAFs and for tracking system status. In this regard, resilience may be used to characterize the status of a DFAF. This study aimed to explore the processes and mechanisms of interactions among the social, economic, and ecological factors related to DFAF with respect to resilience, and to discuss potential problems in a representative DFAF. Based on the site condition and characteristics of the Awang DFAF (China) in the period 1996-2017, we formed a comprehensive indicator evaluation framework by analyzing disturbance, function, and feedback. We also established a model for evaluating resilience by integrating the analytic hierarchy process (AHP) - an entropy evaluation method (EEM) and set pair analysis (SPA). The results showed that the system of the studied DFAF was dynamically stable. The domination of the ecological system was subsequently superseded by social and economic resilience. While disturbance had direct and immediate effects, coping ability was cumulative and characterized by hysteresis at a particular response time. Overall, resilience fluctuated within an acceptable range rather than linearly increasing or decreasing. This analysis illuminated the dynamic processes of DFAFs and contributed to the understanding and planning of system trade-offs and degraded-land utilization.

Screening of abiotic stress-responsive cotton genes using a cotton full-length cDNA overexpressing Arabidopsis library.

Cotton (Gossypium hirsutum L.) is a major crop and the main source of natural fiber worldwide. Because various abiotic and biotic stresses strongly influence cotton fiber yield and quality, improved stress resistance of this crop plant is urgently needed. In this study, we used Gateway technology to construct a normalized full-length cDNA overexpressing (FOX) library from upland cotton cultivar ZM12 under various stress conditions. The library was transformed into Arabidopsis to produce a cotton-FOX-Arabidopsis library. Screening of this library yielded 6,830 transgenic Arabidopsis lines, of which 757 were selected for sequencing to ultimately obtain 659 cotton ESTs. GO and KEGG analyses mapped most of the cotton ESTs to plant biological process, cellular component, and molecular function categories. Next, 156 potential stress-responsive cotton genes were identified from the cotton-FOX-Arabidopsis library under drought, salt, ABA, and other stress conditions. Four stress-related genes identified from the library, designated as GhCAS, GhAPX, GhSDH, and GhPOD, were cloned from cotton complementary DNA, and their expression patterns under stress were analyzed. Phenotypic experiments indicated that overexpression of these cotton genes in Arabidopsis affected the response to abiotic stress. The method developed in this study lays a foundation for high-throughput cloning and rapid identification of cotton functional genes.

BZU2/ZmMUTE controls symmetrical division of guard mother cell and specifies neighbor cell fate in maize.

Intercellular communication in adjacent cell layers determines cell fate and polarity, thus orchestrating tissue specification and differentiation. Here we use the maize stomatal apparatus as a model to investigate cell fate determination. Mutations in ZmBZU2 (bizui2, bzu2) confer a complete absence of subsidiary cells (SCs) and normal guard cells (GCs), leading to failure of formation of mature stomatal complexes. Nuclear polarization and actin accumulation at the interface between subsidiary mother cells (SMCs) and guard mother cells (GMCs), an essential pre-requisite for asymmetric cell division, did not occur in Zmbzu2 mutants. ZmBZU2 encodes a basic helix-loop-helix (bHLH) transcription factor, which is an ortholog of AtMUTE in Arabidopsis (BZU2/ZmMUTE). We found that a number of genes implicated in stomatal development are transcriptionally regulated by BZU2/ZmMUTE. In particular, BZU2/ZmMUTE directly binds to the promoters of PAN1 and PAN2, two early regulators of protodermal cell fate and SMC polarization, consistent with the low levels of transcription of these genes observed in bzu2-1 mutants. BZU2/ZmMUTE has the cell-to-cell mobility characteristic similar to that of BdMUTE in Brachypodium distachyon. Unexpectedly, BZU2/ZmMUTE is expressed in GMC from the asymmetric division stage to the GMC division stage, and especially in the SMC establishment stage. Taken together, these data imply that BZU2/ZmMUTE is required for early events in SMC polarization and differentiation as well as for the last symmetrical division of GMCs to produce the two GCs, and is a master determinant of the cell fate of its neighbors through cell-to-cell communication.

Exploring transcription factors reveals crucial members and regulatory networks involved in different abiotic stresses in Brassica napus L.

BACKGROUND: Brassica napus (B. napus) encompasses diverse transcription factors (TFs), but thorough identification and characterization of TF families, as well as their transcriptional responsiveness to multifarious stresses are still not clear. RESULTS: Totally 2167 TFs belonging to five families were genome-widely identified in B. napus, including 518 BnAP2/EREBPs, 252 BnbZIPs, 721 BnMYBs, 398 BnNACs and 278 BnWRKYs, which contained some novel members in comparison with existing results. Sub-genome distributions of BnAP2/EREBPs and BnMYBs indicated that the two families might have suffered from duplication and divergence during evolution. Synteny analysis revealed strong co-linearity between B. napus and its two ancestors, although chromosomal rearrangements have occurred and 85 TFs were lost. About 7.6% and 9.4% TFs of the five families in B. napus were novel genes and conserved genes, which both showed preference on the C sub-genome. RNA-Seq revealed that more than 80% TFs were abiotic stress inducible and 315 crucial differentially expressed genes (DEGs) were screened out. Network analysis revealed that the 315 DEGs are highly co-expressed. The homologous gene network in A. thaliana revealed that a considerable amount of TFs could trigger the differential expression of targeted genes, resulting in a complex clustered network with clusters of genes responsible for targeted stress responsiveness. CONCLUSIONS: We identified and characterized five TF families in B. napus. Some crucial members and regulatory networks involved in different abiotic stresses have been explored. The investigations deepen our understanding of TFs for stress tolerance in B. napus.

Multi-gene co-expression can improve comprehensive resistance to multiple abiotic stresses in Brassica napus L.

Rapeseed (Brassica napus L.) is an important oil crop worldwide. For current B. napus production, it is urgent to develop new varieties with higher seed productivity and increased stress tolerance for better adaptation to the abiotic stresses as a result of global climate change. Genetic engineering, to some extent, can overcome the limitations of genetic exchange in conventional breeding. Consequently, it considered as an effective method for improving modern crop breeding for B. napus. Since crop stress resistance is a polygenic complex trait, only by multi-gene synergistic effects can effectively achieve the comprehensive stress resistance of crops. Hence, in the present study, five stress resistance genes, NCED3, ABAR, CBF3, LOS5, and ICE1 were transferred into B. napus. Compared with wildtype (WT) plants, the multi-gene transformants K15 exhibited pronounced growth advantage under both normal growth and stress conditions. Additionally, K15 plants also showed significantly higher resistance response to multiple stresses at seed germination and seedling stages than WT plants. Furthermore, K15 plants had significantly higher leaf temperature and significantly lower stomatal aperture and water loss rate than WT plants, which indicated that the water-holding capacity of K15 plants was significantly superior to that of WT plants after stress treatment. In addition, K15 plants had significantly higher abscisic acid (ABA) content and significantly lower malondialdehyde (MDA) content than WT plants. In conclusion, the above results suggested that multi-gene co-expression could rapidly trigger plant stress resistance, reduce the stress injury on plants and synergistically improve the comprehensive resistance of B. napus.

Controllability Analysis of A Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families.

Based on structural controllability of complex networks and a constructed gene network with 9241 nodes for Arabidopsis thaliana, we classified nodes into five categories via their roles in control or node deletion, including indispensable, neutral, dispensable, driver and critical driver nodes. The indispensable nodes can increase the number of drivers after deletion, which are never drivers or critical drivers. About 10% nodes are indispensable. However, more than 60% nodes are neutral ones. More than 62% nodes are drivers, and indicates the gene network is very difficult to be fully controlled. Gene Ontology (GO) enrichment analysis reveals that different sets of nodes have preferred biological functions and processes.The indispensable nodes are significantly enriched as essential genes, drought responsive and abscisic acid (ABA) independent genes, transcriptional factors (TFs), core cell cycle genes, ABA and Gibberellin (GA) related genes. The critical drivers are enriched as receptor kinase-like genes, while shorted in WRKY TFs and functional genes that are enriched in the indispensable nodes. Robustness analysis based on node and edge additions, edge rewiring indicate the obtained conclusions are robust to network perturbations. Our investigations clarify control roles of some gene families and provide potential implications for identifying functional genes in other plant species, such as drought responsive genes and TFs.

Transcriptomic basis for drought-resistance in Brassica napus L.

Based on transcriptomic data from four experimental settings with drought-resistant and drought-sensitive cultivars under drought and well-watered conditions, statistical analysis revealed three categories encompassing 169 highly differentially expressed genes (DEGs) in response to drought in Brassica napus L., including 37 drought-resistant cultivar-related genes, 35 drought-sensitive cultivar-related genes and 97 cultivar non-specific ones. We provide evidence that the identified DEGs were fairly uniformly distributed on different chromosomes and their expression patterns are variety specific. Except commonly enriched in response to various stimuli or stresses, different categories of DEGs show specific enrichment in certain biological processes or pathways, which indicated the possibility of functional differences among the three categories. Network analysis revealed relationships among the 169 DEGs, annotated biological processes and pathways. The 169 DEGs can be classified into different functional categories via preferred pathways or biological processes. Some pathways might simultaneously involve a large number of shared DEGs, and these pathways are likely to cross-talk and have overlapping biological functions. Several members of the identified DEGs fit to drought stress signal transduction pathway in Arabidopsis thaliana. Finally, quantitative real-time PCR validations confirmed the reproducibility of the RNA-seq data. These investigations are profitable for the improvement of crop varieties through transgenic engineering.

Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development.

BACKGROUND: Pectin methylesterase (PME, EC 3.1.1.11) is a hydrolytic enzyme that utilizes pectin as substrates, and plays a significant role in regulating pectin reconstruction thereby regulating plant growth. Pectin is one of the important components of the plant cell wall, which forms the main structural material of cotton fiber. In this research, cotton genome information was used to identify PMEs. RESULTS: We identified 80 (GaPME01-GaPME80) PME genes from diploid G. arboreum (A genome), 78 (GrPME01-GrPME78) PME genes from G. raimondii (D genome), and 135 (GhPME001-GhPME135) PME genes from tetraploid cotton G. hirsutum (AD genome). We further analyzed their gene structure, conserved domain, gene expression, and systematic evolution to lay the foundation for deeper research on the function of PMEs. Phylogenetic data indicated that members from the same species demonstrated relatively high sequence identities and genetic similarities. Analysis of gene structures showed that most of the PMEs genes had 2-3 exons, with a few having a variable number of exons from 4 to 6. There are nearly no differences in the gene structure of PMEs among the three (two diploid and one tetraploid) cotton species. Selective pressure analysis showed that the Ka/Ks value for each of the three cotton species PME families was less than one. CONCLUSION: Conserved domain analysis showed that PMEs members had a relatively conserved C-terminal pectinesterase domain (PME) while the N-terminus was less conserved. Moreover, some of the family members contained a pectin methylesterase inhibitor (PMEI) domain. The Ka/Ks ratios suggested that the duplicated PMEs underwent purifying selection after the duplication events. This study provided an important basis for further research on the functions of cotton PMEs. Results from qRT-PCR indicated that the expression level of different PMEs at various fiber developmental stages was different. Moreover, some of the PMEs showed fiber predominant expression in secondary wall thickening indicating tissue-specific expression patterns.