IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix.

Genome-wide association study (GWAS), exploring the historical and evolutionary recombinations at the population level, is a major method adopted to identify quantitative trait loci (QTL) for complex traits. However, to summarize GWAS results, gene structure, and linkage disequilibrium (LD) in a single view, multiple tools are required. It is tedious to generate these three results and manually put them together; moreover, it may eventually lead to inaccuracies.

Expression Analyses of Soybean VOZ Transcription Factors and the Role of in Drought and Salt Stress Tolerance.

Vascular plant one-zinc-finger (VOZ) transcription factor, a plant specific one-zinc-finger-type transcriptional activator, is involved in regulating numerous biological processes such as floral induction and development, defense against pathogens, and response to multiple types of abiotic stress. Six VOZ transcription factor-encoding genes () have been reported to exist in the soybean () genome. In spite of this, little information is currently available regarding In this study, were cloned and characterized.

Immune response to acute heat stress in the intestine of the red swamp crayfish, Procambarus clarkii.

High temperature is an important environmental factor that affects the survival and immunity of aquatic animals. The intestine of crustaceans is their first line of defense, and the physiological homeostasis of this organ can be influenced by high temperature stress. The red swamp crayfish Procambarus clarkii is an important commercial aquaculture species in China, but little is known about its intestinal immune response to acute heat stress.

The Soybean Transcription Factor Gene Confers Drought and Salt Resistances in Transgenic Plants.

Abiotic stresses, such as drought and salt, are major environmental stresses, affecting plant growth and crop productivity. Plant bZIP transcription factors (bZIPs) confer stress resistances in harsh environments and play important roles in each phase of plant growth processes. In this research, 15 soybean bZIP family members were identified from drought-induced de novo transcriptomic sequences of soybean, which were unevenly distributed across 12 soybean chromosomes.

The effect of nitrite and sulfide on the antioxidant capacity and microbial composition of the intestines of red swamp crayfish, Procambarus clarkii.

Nitrite and sulfide are harmful pollutants in water ecosystems that negatively influence the survival and growth of crayfish. It is currently known that the intestine of crustaceans acts as a significant immune organ, serving as the front line of defense against diseases. In this study, we investigated how the oxidative damage parameters, antioxidant status and microbial composition of the intestine of Procambarus clarkii were influenced under acute nitrite (60 mg/L) and sulfide (18 mg/L) stress for 72 h.

Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat ().

Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed.

qPCR and loop mediated isothermal amplification for rapid detection of .

Loose smut of wheat caused by the basidiomycete fungus , a seed-borne disease, is difficult to control because of the expanse of wheat planting area and difficulty in pathogen detection. In this study, real-time fluorescence quantitative PCR (qPCR) and loop-mediated isothermal amplification (LAMP) assays are used to rapidly amplify the DNA of . Five pairs of primers for qPCR and two series primers for LAMP were designed.

Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress.

Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear.

Comparative transcriptome analysis revealing the potential mechanism of seed germination stimulated by exogenous gibberellin in Fraxinus hupehensis.

Background: Fraxinus hupehensis is an endangered tree species that is endemic to in China; the species has very high commercial value because of its intricate shape and potential to improve and protect the environment. Its seeds show very low germination rates in natural conditions. Preliminary experiments indicated that gibberellin (GA) effectively stimulated the seed germination of F.

Community dynamics of free-living and particle-attached bacteria following a reservoir Microcystis bloom.

The composition of microbial communities can vary at the microspatial scale between free-living (FL) and particle-attached (PA) niches. However, it remains unclear how FL and PA bacterial communities respond to cyanobacterial blooms across water depths. Here, we examined the community dynamics of the FL (0.

Design, synthesis and biological activity of hydroxybenzoic acid ester conjugates of phenazine-1-carboxylic acid.

We prepared 16 novel hydroxybenzoic acid ester conjugates of phenazine-1-carboxylic acid (PCA) and investigated their biological activity. Most of the synthesized conjugates displayed some level of fungicidal activities in vitro against five phytopathogenic fungi. Nine conjugates 5b, 5c, 5d, 5e, 5h, 5i, 5m, 5n and 5o (EC between 3.

Molecular characterization and expression analysis of Asian swamp eel (Monopterus albus) CXC chemokine receptor (CXCR) 1a, CXCR1b, CXCR2, CXCR3a, CXCR3b, and CXCR4 after bacteria and poly I:C challenge.

The CXC chemokine receptors (CXCRs) play critical roles in innate and adaptive immune systems. In this study, six Asian swamp eel (Monopterus albus) CXCRs (MaCXCR1-4) were identified and their molecular characterization and expression patterns were analyzed. The open reading frames (ORFs) of MaCXCR1a, MaCXCR1b, MaCXCR2, MaCXCR3a, MaCXCR3b, and MaCXCR4 were 1074 bp (base pairs), 1080 bp, 1125 bp, 1146 bp, 1083 bp, and 1140 bp, and encoded proteins of 357 aa (amino acids), 359 aa, 374 aa, 381 aa, 360 aa, and 379 aa, respectively.

Complete sequence of a novel alphaendornavirus from the phytopathogenic fungus Arthrocladiella mougeotii.

A novel double-stranded RNA (dsRNA) virus, which was provisionally named Arthrocladiella mougeotii endornavirus (AmEV), was isolated from Arthrocladiella mougeotii, the phytopathogenic fungus infecting Lycium chinense in Beijing, China. The genome of AmEV is 11,683 nucleotides in length with a 5' and 3' non-coding region of 16 and 50 nt, respectively, as well as a single 11,617-nt long open reading frame potentially encoding a putative protein of 3,871 amino acids with conserved Helicase and RNA-dependent RNA polymerase (RdRp) domains. Phylogenetic analysis based on the the amino acid sequence of the RdRp showed that AmEV is most closely related to Erysiphe cichoracearum endornavirus (EcEV).

Identification of Antioxidant and Anti-α-amylase Components in Lotus (Nelumbo nucifera, Gaertn.) Seed Epicarp.

Lotus seed epicarp, a byproduct of lotus seed production process, is usually discarded as a waste. In this study, antioxidant and anti-α-amylase activities of freeze-dried water and various methanol extracts of lotus seed epicarp were evaluated. The extract obtained by 80% methanol exhibited the strongest DPPH and ABTS radical scavenging activity and ferric reducing power, as well as the greatest inhibitory potential on α-amylase.

The complete genomic sequence of a novel botybirnavirus isolated from a phytopathogenic Bipolaris maydis.

Bipolaris maydis is the causal agent of corn southern leaf blight. Here, we report a novel double-stranded RNA (dsRNA) mycovirus designated Bipolaris maydis botybirnavirus 1 (BmBRV1) from B. maydis strain JZ11 in Jingzhou, Hubei province of China.

Synthesis and bioactivities of diamide derivatives containing a phenazine-1-carboxamide scaffold.

Taking natural product phenazine-1-carboxamide (PCN) as a lead compound, a series of novel phenazine-1-carboxylic acid diamide derivatives were designed and synthesised. Their structures were confirmed by H-NMR and HRMS. The bioassays showed that some of the target compounds exhibited promising fungicidal activities, and exhibited excellent and selective herbicidal activities.

A Salutary Role of Reactive Oxygen Species in Intercellular Tunnel-Mediated Communication.

The reactive oxygen species, generally labeled toxic due to high reactivity without target specificity, are gradually uncovered as signaling molecules involved in a myriad of biological processes. But one important feature of ROS roles in macromolecule movement has not caught attention until recent studies with technique advance and design elegance have shed lights on ROS signaling for intercellular and interorganelle communication. This review begins with the discussions of genetic and chemical studies on the regulation of symplastic dye movement through intercellular tunnels in plants (plasmodesmata), and focuses on the ROS regulatory mechanisms concerning macromolecule movement including small RNA-mediated gene silencing movement and protein shuttling between cells.

Functional characterization of interferon regulatory factor 5 and its role in the innate antiviral immune response.

In mammals, type I interferons (IFNs) are primarily regulated by transcription factors of the IFN regulatory (IRF) family. Interferon regulatory factor 5 (IRF-5) plays pivotal roles in antiviral and inflammatory responses. In the present study, we found that zebrafish (Danio rerio) IRF5 is a key player in the regulation of the expression of type I IFN and its antiviral immune response.

Cadmium remobilization from shoot to grain is related to pH of vascular bundle in rice.

The remobilization of cadmium (Cd) from shoots to grain is the key process to determine the Cd accumulation in grain. The apoplastic pH of plants is an important factor and signal in influencing on plant responding to environmental variation and inorganic elements uptake. It is proposed that pH of rice plants responds and influences on Cd remobilization from shoots to grain when rice is exposed to Cd stress.

Bulked Segregant RNA-seq Reveals Differential Expression and SNPs of Candidate Genes Associated with Waterlogging Tolerance in Maize.

Waterlogging has increasingly become one of the major constraints to maize productivity in some maize production zones because it causes serious yield loss. Bulked segregant RNA-seq (BSR-seq) has been widely applied to profile candidate genes and map associated Single Nucleotide Polymorphism (SNP) markers in many species. In this study, 10 waterlogging sensitive and eight tolerant inbred lines were selected from 60 maize inbred lines with waterlogging response determined and preselected by the International Maize and Wheat Improvement Center (CIMMYT) from over 400 tropical maize inbred lines.

The complete genomic sequence of a novel alphapartitivirus from Bipolaris maydis, the causal agent of corn southern leaf blight.

A novel double-stranded RNA (dsRNA) mycovirus, designated Bipolaris maydis partitivirus 1 (BmPV1), was isolated from the plant pathogenic fungus Bipolaris maydis. The BmPV1 genome has two dsRNA segments. The larger segment (1,930 bp) has a single open reading frame (ORF) with a conserved RNA-dependent RNA polymerase domain.

Full-length sequence and genome analysis of CHV1-CN280, a North China isolate of cryphonectria hypovirus 1.

CHV1-CN280 is a North China isolate of cryphonectria hypovirus 1 (CHV1), which has high horizontal transmission ability. The complete genomic sequence of CHV1-CN280 was determined and analyzed. Compared with other reported CHV1s, the genome of CHV1-CN280 shows some significantly different characteristics.

[Temporal and Spatial Distribution of Phosphorus in Paddy Fields Under Cyclic Irrigation of Drainage Water].

Considering the potential of cyclic irrigation to increase rainfall use efficiency and reduce agricultural non-point pollution, the experiment of phosphorus transport in paddy fields under cyclic irrigation of drainage water was conducted to address the problem of phosphorus loss pollution and the mismatch between rainfall temporal distribution and crop requirement in the south of China. Lotus pond water and fishpond water were used to irrigate paddy fields for monitoring concentrations of total phosphorus (TP), dissolved phosphorus (DP), and dissolved reactive phosphorus (DRP) in surface water and leachate, and soil profile total phosphorus and Olsen-P concentrations. The results showed that the concentrations of TP, DP and DRP in surface water and leachate decreased along the field under cyclic irrigation of drainage water, especially the phosphorus concentrations of leachate dropped more obviously.