Wei Yang

Although remarkable progress has been made toward understanding carotenoid biosynthesis, the mechanisms that regulate the transcription of carotenogenic genes remain poorly understood. Lycopene β-cyclases (LCYb) are critical enzymes located at the branch point of the carotenoid biosynthetic pathway. Here, we used the promoter sequence of LCYb1 as bait in a yeast one-hybrid screen for promoter-binding proteins from sweet orange (Citrus sinensis). This screen identified a MADS transcription factor, CsMADS6, that was coordinately expressed with fruit development and coloration. Acting as a nucleus-localized transcriptional activator, CsMADS6 directly bound the promoter of LCYb1 and activated its expression. Overexpression of CsMADS6 in citrus calli increased carotenoid contents and induced the expression of LCYb1 and other carotenogenic genes, including phytoene synthase (PSY), phytoene desaturase (PDS), and carotenoid cleavage dioxygenase1 (CCD1). CsMADS6 up-regulated the expression of PSY, PDS, and CCD1 by directly binding to their promoters, which suggested the multitargeted regulation of carotenoid metabolism by CsMADS6. In addition, the ectopic expression of CsMADS6 in tomato (Solanum lycopersicum) affected carotenoid contents and the expression of carotenogenic genes. The sepals of CsMADS6-overexpressing tomato lines exhibited dramatic changes in carotenoid profiles, accompanied by changes in plastid ultrastructure. Global transcriptome analysis of transgenic sepals revealed that CsMADS6 regulates a series of pathways that promote increases in flux through the carotenoid pathway. Overall, these findings establish that CsMADS6 directly regulates LCYb1 and other carotenogenic genes to coordinately and positively modulate carotenoid metabolism in plants, which may provide strategies to improve the nutritional quality of crops.

Although the functions of carotenogenic genes are well documented, little is known about the mechanisms that regulate their expression, especially those genes involved in α - and β-branch carotenoid metabolism. In this study, an R2R3-MYB transcriptional factor (CrMYB68) that directly regulates the transformation of α- and β-branch carotenoids was identified using Green Ougan (MT), a stay-green mutant of Citrus reticulata cv Suavissima. A comprehensive analysis of developing and harvested fruits indicated that reduced expression of β-carotene hydroxylases 2 (CrBCH2) and 9-cis-epoxycarotenoid dioxygenase 5 (CrNCED5) was responsible for the delay in the transformation of α- and β-carotene and the biosynthesis of ABA. Additionally, the expression of these genes was negatively correlated with the expression of CrMYB68 in MT. Further, electrophoretic mobility shift assays (EMSAs) and dual luciferase assays indicated that CrMYB68 can directly and negatively regulate CrBCH2 and CrNCED5. Moreover, transient overexpression experiments using leaves of Nicotiana benthamiana indicated that CrMYB68 can also negatively regulate NbBCH2 and NbNCED5. To overcome the difficulty of transgenic validation, we quantified the concentrations of carotenoids and ABA, and gene expression in a revertant of MT. The results of these experiments provide more evidence that CrMYB68 is an important regulator of carotenoid metabolism.

The timing of the developmental transition to flowering is critical to reproductive success in plants. Here, we show that Arabidopsis thaliana homologs of human Lysine-Specific Demethylase1 (LSD1; a histone H3-Lys 4 demethylase) reduce the levels of histone H3-Lys 4 methylation in chromatin of the floral repressor FLOWERING LOCUS C (FLC) and the sporophytically silenced floral repressor FWA. Two of the homologs, LSD1-LIKE1 (LDL1) and LSD1-LIKE2 (LDL2), act in partial redundancy with FLOWERING LOCUS D (FLD; an additional homolog of LSD1) to repress FLC expression. However, LDL1 and LDL2 appear to act independently of FLD in the silencing of FWA, indicating that there is target gene specialization within this histone demethylase family. Loss of function of LDL1 and LDL2 affects DNA methylation on FWA, whereas FLC repression does not appear to involve DNA methylation; thus, members of the LDL family can participate in a range of silencing mechanisms.

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

Soil structure and the soil pore system are important for many soil environmental processes. However, little is known about the influence of intra-aggregate microstructure on aggregate stability. The objective of this study was to evaluate the effect of soil pore characteristics on wet aggregate stability and aggregate tensile strength (TS) using synchrotron-based X-ray micro-computed tomography (SR-μCT) under wetting and drying cycles. Undisturbed topsoils (200 cm3) derived from shale (S) and Quaternary red clay (Q) were submitted to three wetting and drying treatments under controlled laboratory conditions. 3–5 mm aggregates were collected from different treatments and scanned at 3.7 μm voxel-resolution for the reconstruction of 3D micro tomography images. The wet aggregate stability and TS were measured after each treatment. The relationships among pore characteristics, wet aggregate stability, and TS were analyzed using partial least squares regression (PLSR). The results indicated that porosity (P), percentage of pores >100 μm (Pd>100), and fraction of elongated pores (FEP) all significantly increased with an increasing number of wetting and drying cycles, while the opposite trends were observed for the total number of pores (TNP), the percentage of pores with a diameter of 75–100, 30–75, and <30 μm. Decrease in wet aggregate stability and TS of both soils was mainly due to higher P, a more extensive and complex pore network, which caused increased air pressure, increased rate of water entry, and high probability of crack propagation and interaction. The TNP, Pd75–100, P, and Pd>100, were identified as the primary factors controlling the wet aggregate stability and TS according to PLSR. The pore characteristics and soil clay content accounted for as much as 99% of the variation in wet aggregate stability and TS. This study provides insights for improved understanding of the change in topsoil microstructure; however, the effect of pore characteristics on the aggregate breakdown mechanism requires further investigation.

Histone demethylation regulates chromatin structure and gene expression, and is catalyzed by various histone demethylases. Trimethylation of histone H3 at lysine 4 (H3K4) is coupled to active gene expression; trimethyl H3K4 is demethylated by Jumonj C (JmjC) domain-containing demethylases in mammals. Here we report that a plant-specific JmjC domain-containing protein known as PKDM7B (At4g20400) demethylates trimethyl H3K4. PKDM7B mediates H3K4 demethylation in a key floral promoter, FLOWERING LOCUS T (FT), and an FT homolog, TWIN SISTER OF FT (TSF), and represses their expression to inhibit the floral transition in Arabidopsis. Our findings suggest that there are at least two distinct sub-families of JmjC domain-containing demethylases that demethylate the active trimethyl H3K4 mark in eukaryotic genes, and reveal a plant-specific JmjC domain enzyme capable of H3K4 demethylation.

Abstract Flavonols and hydroxycinnamic acids are important phenylpropanoid metabolites in plants. In this study, we isolated and characterized a citrus R2R3-MYB transcription factor CsMYBF1 , encoding a protein belonging to the flavonol-specific MYB subgroup. Ectopic expression of CsMYBF1 in tomato led to an up-regulation of a series of genes involved in primary metabolism and the phenylpropanoid pathway, and induced a strong accumulation of hydroxycinnamic acid compounds but not the flavonols. The RNAi suppression of CsMYBF1 in citrus callus caused a down-regulation of many phenylpropanoid pathway genes and reduced the contents of hydroxycinnamic acids and flavonols. Transactivation assays indicated that CsMYBF1 activated several promoters of phenylpropanoid pathway genes in tomato and citrus. Interestingly, CsMYBF1 could activate the CHS gene promoter in citrus, but not in tomato. Further examinations revealed that the MYBPLANT cis-elements were essential for CsMYBF1 in activating phenylpropanoid pathway genes. In summary, our data indicated that CsMYBF1 possessed the function in controlling the flavonol and hydroxycinnamic acid biosynthesis, and the regulatory differences in the target metabolite accumulation between two species may be due to the differential activation of CHS promoters by CsMYBF1. Therefore, CsMYBF1 constitutes an important gene source for the engineering of specific phenylpropanoid components.

Exposure to short-term cold stress influences disease resistance by mechanisms that remain poorly characterized. The molecular basis of cold-activated immunity was therefore investigated in Arabidopsis thaliana inoculated with the bacterial pathogen Pst DC3000, using a transcriptomic analysis. Exposure to cold stress for 10 hr was sufficient to activate immunity, as well as H2 O2 accumulation and callose deposition. Transcriptome changes induced by the 10-hr cold treatment were similar to those caused by pathogen infection, including increased expression of the salicylic acid (SA) pathway marker genes, PR2 and PR5, and genes playing positive roles in defence against (hemi)-biotrophs. In contrast, transcripts encoding jasmonic acid (JA) pathway markers such as PR4 and MYC2 and transcripts with positive roles in defence against necrotrophs were less abundant following the 10-hr cold treatment. Cold-activated immunity was dependent on SA, being partially dependent on NPR1 and ICS1/SID2. In addition, transcripts encoding SA biosynthesis enzymes such as ICS2, PAL1, PAL2, and PAL4 (but not ICS1/SID2) and MES9 were more abundant, whereas GH3.5/WES1 and SOT12 transcripts that encode components involved in SA modification were less abundant following cold stress treatment. These findings show that cold stress cross-activates innate immune responses via a SA-dependent pathway.

The root nodule symbiosis with its global impact on nitrogen fertilization of soils is characterized by an intracellular colonization of legume roots by rhizobia. Although the symbionts are initially taken up by morphologically adapted root hairs, rhizobia persistently progress within a membrane-confined infection thread through several root cortical and later nodular cell layers. Throughout this transcellular passaging, rhizobia have to repeatedly pass host plasma membranes and cell walls. Here, we investigated this essential process and describe the concerted action of one of the symbiosis-specific pectin methyl esterases (SyPME1) and the nodulation pectate lyase (NPL) at the infection thread and transcellular passage sites. Their coordinated function mediates spatially confined pectin alterations in the cell-cell interface that result in the establishment of an apoplastic compartment where bacteria are temporarily released into and taken up from the subjacent cell. This process allows successful intracellular progression of infection threads through the entire root cortical tissue.

RNA molecules such as small-interfering RNAs (siRNAs) and antisense RNAs (asRNAs) trigger chromatin silencing of target loci. In the model plant Arabidopsis, RNA–triggered chromatin silencing involves repressive histone modifications such as histone deacetylation, histone H3 lysine-9 methylation, and H3 lysine-27 monomethylation. Here, we report that two Arabidopsis homologs of the human histone-binding proteins Retinoblastoma-Associated Protein 46/48 (RbAp46/48), known as MSI4 (or FVE) and MSI5, function in partial redundancy in chromatin silencing of various loci targeted by siRNAs or asRNAs. We show that MSI5 acts in partial redundancy with FVE to silence FLOWERING LOCUS C (FLC), which is a crucial floral repressor subject to asRNA–mediated silencing, FLC homologs, and other loci including transposable and repetitive elements which are targets of siRNA–directed DNA Methylation (RdDM). Both FVE and MSI5 associate with HISTONE DEACETYLASE 6 (HDA6) to form complexes and directly interact with the target loci, leading to histone deacetylation and transcriptional silencing. In addition, these two genes function in de novo CHH (H = A, T, or C) methylation and maintenance of symmetric cytosine methylation (mainly CHG methylation) at endogenous RdDM target loci, and they are also required for establishment of cytosine methylation in the previously unmethylated sequences directed by the RdDM pathway. This reveals an important functional divergence of the plant RbAp46/48 relatives from animal counterparts.

Stable macro- or micro-aggregates are important for preventing soil degradation. The interactions among soil aggregates and stabilizing agents—like clay, soil organic matter (SOM), Fe, and Al oxides—are complex and have not been fully understood. Eight ultisol samples were collected from the surface (0–10 cm) and subsurface layers (10–20 cm). The macro-aggregate stability was determined by wet sieving, and the micro-aggregate distribution was determined via particle size distribution analysis; however, no chemical dispersant (sodium hydroxide) was applied. Using the PLSR models, the main soil properties that affect macro-aggregate and micro-aggregate stability were estimated. All soils were strongly acidic (pH 4.28–5.56) with low SOM content (< 20 g kg− 1). The dithionite-citrate-bicarbonate extractable Fed and Ald were the dominant forms in Fe and Al oxides, much greater than acid ammonium oxalate extractable Feo and Alo. For most soils, the percentage of > 5 mm aggregates was the highest, and the percentage of 2–1 mm aggregates was the lowest after wet sieving. Soil parent materials had a significant effect on the particle size distribution of the micro-aggregates. The stability of macro-aggregates and micro-aggregates from Quaternary red clay was stronger than that from Shale (p < 0.05). Regardless of the soil parent materials, the water stability of surface cropland soil macro-aggregates was significantly lower than that of the other land-use types, but the micro-aggregate stability exhibited no trend across different land use types. Ald was the most important binding agent of the macro-aggregates, and clay was the main binding agent of the micro-aggregates, followed by the Fed, Alo, CEC and SOM, while Feo was the weakest agent.

Hexoses are important metabolic signals that respond to abiotic and biotic stresses. Cold stress adversely affects plant growth and development, limiting productivity. The mechanism by which sugars regulate plant cold tolerance remains elusive.We examined the function of INVINH1, a cell wall invertase inhibitor, in tomato chilling tolerance. Cold stress suppressed the transcription of INVINH1 and increased that of cell wall invertase genes, Lin6 and Lin8 in tomato seedlings. Silencing INVINH1 expression in tomato increased cell wall invertase activity and enhanced chilling tolerance. Conversely, transgenic tomatoes over-expressing INVINH1 showed reduced cell wall invertase activity and were more sensitive to cold stress. Chilling stress increased glucose and fructose levels, and the hexoses content increased or decreased by silencing or overexpression INVINH1. Glucose applied in vitro masked the differences in chilling tolerance of tomato caused by the different expressions of INVINH1. The repression of INVINH1 or glucose applied in vitro regulated the expression of C-repeat binding factors (CBFs) genes. Transcript levels of NCED1, which encodes 9-cisepoxycarotenoid dioxygenase (NCED), a key enzyme in the biosynthesis of abscisic acid, were suppressed by INVINH1 after exposure to chilling stress. Meanwhile, application of ABA protected plant from chilling damage caused by the different expression of INVINH1.In tomato, INVINH1 plays an important role in chilling tolerance by adjusting the content of glucose and expression of CBFs.

Abstract Auxin plays central roles in rhizobial infection and nodule development in legumes. However, the sources of auxin during nodulation are unknown. In this study, we analyzed the YUCCA (YUC) gene family of soybean and identified GmYUC2a as an important regulator of auxin biosynthesis that modulates nodulation. Following rhizobial infection, GmYUC2a exhibited increased expression in various nodule tissues. Overexpression of GmYUC2a (35S::GmYUC2a) increased auxin production in soybean, resulting in severe growth defects in root hairs and root development. Upon rhizobial infection, 35S::GmYUC2a hairy roots displayed altered patterns of root hair deformation and nodule formation. Root hair deformation occurred mainly on primary roots, and nodules formed exclusively on primary roots of 35S::GmYUC2a plants. Moreover, transgenic 35S::GmYUC2a composite plants showed delayed nodule development and a reduced number of nodules. Our results suggest that GmYUC2a plays an important role in regulating both root growth and nodulation by modulating auxin balance in soybean.

Abstract Although abscisic acid (ABA) is a vital regulator of fruit ripening and several transcription factors have been reported to regulate ABA biosynthesis, reports of the effect of ABA on citrus ripening and the regulation of its biosynthesis by a multiple-transcription-factor complex are scarce. In the present study, a systematic metabolic, cytological, and transcriptome analysis of an ABA-deficient mutant (MT) of Citrus reticulata cv. Suavissima confirmed the positive effect of ABA on the citrus ripening process. The analysis of transcriptome profiles indicated that CrNAC036 played an important role in the ABA deficiency of the mutant, most likely due to an effect on the expression of 9-cis-epoxycarotenoid dioxygenase 5 (CrNCED5). Electrophoretic mobility shift assays and dual luciferase assays demonstrated that CrNAC036 can directly bind and negatively regulate CrNCED5 expression. Furthermore, yeast two-hybrid, bimolecular fluorescence complementation, and dual luciferase assays demonstrated that CrNAC036 interacted with CrMYB68, also down-regulating the expression of CrNCED5. Taken together, our results suggest that CrNAC036 and CrMYB68 synergistically inhibit ABA biosynthesis in citrus fruit by regulating the expression of CrNCED5.

ABSTRACT Soil detachment in concentrated flow is due to the dislodging of soil particles from the soil matrix by surface runoff. Both aggregate stability and shear strength of the topsoil reflect the erosion resistance of soil to concentrated runoff, and are important input parameters in predicting soil detachment models. This study was conducted to develop a formula to predict soil detachment rate in concentrated flow by using the aggregate stability index ( As ), root density ( R d ) and saturated soil strength ( σ s ) in the subtropical Ultisols region of China. The detachment rates of undisturbed topsoil samples collected from eight cultivated soil plots were measured in a 3.8 m long, 0.2 m wide hydraulic flume under five different flow shear stresses ( τ = 4.54, 9.38, 15.01, 17.49 and 22.54 Pa). The results indicated that the stability index ( As ) was well related with soil detachment rate, particularly for results obtained with high flow shear stress (22.54 Pa), and the stability index ( As ) has a good linear relationship with concentrated flow erodibility factors ( K c ). There was a positive linear relationship between saturated soil strength ( σ s ) and critical flow shear stress ( τ c ) for different soils. A significant negative exponential relationship between erodibility factors ( K c ) and root density ( R d ) was detected. This study yielded two prediction equations that allowed comparison of their efficiency in assessing soil detachment rate in concentrated flow. The equation including the root density ( R d ) may have a better correlation coefficient ( R 2 = 0.95). It was concluded that the formula based on the stability index ( As ), saturated soil strength ( σ s ) and root density ( R d ) has the potential to improve methodology for assessing soil detachment rate in concentrated flow for the subtropical Chinese Ultisols. Copyright © 2012 John Wiley &amp; Sons, Ltd.

Plant defence mechanisms are suppressed in the absence of pathogen attack to prevent wasted energy and growth inhibition. However, how defence responses are repressed is not well understood. Histone deacetylase 6 (HDA6) is a negative regulator of gene expression, and its role in pathogen defence response in plants is not known. In this study, a novel allele of hda6 (designated as shi5) with spontaneous defence response was isolated from a forward genetics screening in Arabidopsis. The shi5 mutant exhibited increased resistance to hemibiotrophic bacterial pathogen Pst DC3000, constitutively activated expression of pathogen-responsive genes including PR1, PR2, etc. and increased histone acetylation levels at the promoters of most tested genes that were upregulated in shi5. In both wild type and shi5 plants, the expression and histone acetylation of these genes were upregulated by pathogen infection. HDA6 was found to bind to the promoters of these genes under both normal growth conditions and pathogen infection. Our research suggests that HDA6 is a general repressor of pathogen defence response and plays important roles in inhibiting and modulating the expression of pathogen-responsive genes in Arabidopsis.

Organic acids are a major index of fresh fruit marketing properties. However, the genetic effects on the organic acid level in postharvest citrus fruit still remain unknown. Here, we used the fruits of about 40 lines in a hybrid population (high-acid “HB Pumelo” × low-acid “Fairchild”) to analyze the organic acid metabolism of postharvest citrus fruit. A transgressive content of titratable acid (TA) was observed, which was attributed to citrate accumulation. High- and low-acid fruits (No. 130, 168 and No. 080, 181, respectively) were chosen for further study. Gene expression analysis on citrate metabolism showed that the high accumulation of citrate could be attributed to the low activity of γ-aminobutyric acid (GABA) shunt, and was partially due to the block of tricarboxylic acid (TCA) cycle by low mitochondrial aconitase (m-ACO) expression. TA level was significantly negatively correlated with weight loss in fruits during postharvest storage, implying a close relationship between organic acid and water metabolism.

Soil aggregate stability is an important aspect of soil function and health. Fertilization could potentially alter soil properties and thereby affect aggregate stability. To determine which fertilizer is useful for improving soil fertility and stabilizing soil aggregates and thereby reducing soil erodibility, we examined three types of fertilizer, and measured how soil organic carbon, carbohydrates, and related soil properties influenced aggregate stability in eroded Ultisols. Treatments included control (CK), mineral fertilizer nitrogen (N), phosphorus (P), potassium (K) (NPK), fertilizer NPK plus straw (NPKS), and farmyard manure (FYM). Aggregate stability was tested according to Le Bissonnais method, involving three disruptive tests: fast wetting (FW), slow wetting (SW), and mechanical breakdown (WS). Total organic carbon, particulate organic carbon, mineral-associated carbon, and cold-water-soluble carbohydrate, hot-water-soluble carbohydrate, and dilute acid hydrolysable carbohydrate were measured, as well as soil intrinsic properties (including pH, bulk density, iron and aluminum oxides). The 12-year fertilization had a larger effect on aggregate stability and related soil properties in a 0–15 cm soil layer, whereas no effect was evident at a soil depth of 15–40 cm. MWD (mean weight diameter) under the three tests decreased with increasing soil depth. Fertilization, especially farmyard manure evidently improved MWDFW and MWDWS at a depth of 0–15 cm. Slaking was the main mechanism of aggregate breakdown in Ultisols studied, followed by mechanical breakdown. Correlation analysis showed that MWDFW and MWDWS at a depth of 0–15 cm increased with the increase of particulate organic carbon, total organic carbon, hot-water-soluble carbohydrate and pH. Furthermore, their interaction with amorphous iron oxides enhanced aggregate stability against slaking or, with amorphous aluminum oxides, modified aggregate stability against mechanical breakdown. Consequently, particulate organic carbon was the dominant cementing agent for aggregation in Ultisols studied, and its combination with pH, amorphous aluminum oxides, amorphous iron oxides, and free aluminum oxides play a synergetic role in stabilizing soil aggregate. Accordingly, farmyard manure or fertilizer NPK plus straw improved soil fertility and the ability to resist slaking.

Ammonium transporters (AMTs) are responsible for ammonium absorption and utilization in plants. As a high-nitrogen-demand crop and a legume, soybean can also obtain ammonium from symbiotic root nodules in which nitrogen-fixing rhizobia convert atmospheric nitrogen (N2) into ammonium. Although increasing evidence implicates vital roles of ammonium transport in soybean, no systematic analyses of AMTs in soybean (named GmAMTs) or functional analyses of GmAMTs are available. In this study, we aimed to identify all GmAMT family genes and gain a better understanding of the characteristics of GmAMT genes in soybean. Here, due to the improved genome assembly and annotation of soybean, we tried to generate a phylogenetic tree of 16 GmAMTs based on new information. Consistent with reported data, GmAMT family members can be divided into two subfamilies of GmAMT1 (6 genes) and GmAMT2 (10 genes). Interestingly, unlike Arabidopsis, which has only one AMT2, soybean has substantially increased the number of GmAMT2s, suggesting enhanced demand for ammonium transport. These genes were distributed on nine chromosomes, of which GmAMT1.3, GmAMT1.4, and GmAMT1.5 were three tandem repeat genes. The gene structures and conserved protein motifs of the GmAMT1 and GmAMT2 subfamilies were different. All the GmAMTs were membrane proteins with varying numbers of transmembrane domains ranging from 4 to 11. Promoter analysis found that these GmAMT genes have phytohormone-, circadian control-, and organ expression-related cis-elements in their promoters, and notably, there were nodulation-specific and nitrogen-responsive elements in the promoters of the GmAMT1 and GmAMT2 genes. Further expression data showed that these GmAMT family genes exhibited different spatiotemporal expression patterns across tissues and organs. In addition, GmAMT1.1, GmAMT1.2, GmAMT2.2, and GmAMT2.3 were responsive to nitrogen treatment, while GmAMT1.2, GmAMT1.3, GmAMT1.4, GmAMT1.5, GmAMT1.6, GmAMT2.1, GmAMT2.2, GmAMT2.3, GmAMT3.1, and GmAMT4.6 showed circadian rhythms in transcription. RT-qPCR validated the expression patterns of GmAMTs in response to different forms of nitrogen and exogenous ABA treatments. Gene expression analysis also confirmed that GmAMTs are regulated by key nodulation gene GmNINa, indicating a role of GmAMTs in symbiosis. Together, these data indicate that GmAMTs may differentially and/or redundantly regulate ammonium transport during plant development and in response to environmental factors. These findings provide a basis for future research on the functions of GmAMTs and the mechanisms through which GmAMTs regulate ammonium metabolism and nodulation in soybean.

G1 + HBP is a male sterile cybrid line with nuclear genome from Hirado Buntan pummelo (C. grandis Osbeck) (HBP) and mitochondrial genome from "Guoqing No.1" (G1, Satsuma mandarin), which provides a good opportunity to study male sterility and nuclear-cytoplasmic cross talk in citrus. High-throughput sRNA and degradome sequencing were applied to identify miRNAs and their targets in G1 + HBP and its fertile type HBP during reproductive development.A total of 184 known miRNAs, 22 novel miRNAs and 86 target genes were identified. Some of the targets are transcription factors involved in floral development, such as auxin response factors (ARFs), SQUAMOSA promoter binding protein box (SBP-box), MYB, basic region-leucine zipper (bZIP), APETALA2 (AP2) and transport inhibitor response 1 (TIR1). Eight target genes were confirmed to be sliced by corresponding miRNAs using 5' RACE technology. Based on the sequencing abundance, 42 differentially expressed miRNAs between sterile line G1 + HBP and fertile line HBP were identified. Differential expression of miRNAs and their target genes between two lines was validated by quantitative RT-PCR, and reciprocal expression patterns between some miRNAs and their targets were demonstrated. The regulatory mechanism of miR167a was investigated by yeast one-hybrid and dual-luciferase assays that one dehydrate responsive element binding (DREB) transcription factor binds to miR167a promoter and transcriptionally repress miR167 expression.Our study reveals the altered expression of miRNAs and their target genes in a male sterile line of pummelo and highlights that miRNA regulatory network may be involved in floral bud development and cytoplasmic male sterility in citrus.

The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber industry. Moreover olfactory proteins are crucial components to function in related processes, but the B. horsfieldi genome is not readily available for olfactory proteins analysis. In the present study, developmental transcriptomes of larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing to establish a genetic background that may help understand olfactory genes. Approximately 199 million clean reads were obtained and assembled into 171,664 transcripts, which were classified into 23,380, 26,511, 22,393, 30,270, and 87, 732 unigenes for larvae, pupae, females, males, and combined datasets, respectively. The unigenes were annotated against NCBI’s non-redundant nucleotide and protein sequences, Swiss-Prot, Gene Ontology (GO), Pfam, Clusters of Eukaryotic Orthologous Groups (KOG), and KEGG Orthology (KO) databases. A total of 43,197 unigenes were annotated into 55 sub-categories under the three main GO categories; 25,237 unigenes were classified into 26 functional KOG categories, and 25,814 unigenes were classified into five functional KEGG Pathway categories. RSEM software identified 2,983, 3,097, 870, 2,437, 5,161, and 2,882 genes that were differentially expressed between larvae and males, larvae and pupae, larvae and females, males and females, males and pupae, and females and pupae, respectively. Among them, genes encoding seven candidate odorant binding proteins (OBPs) and three chemosensory proteins (CSPs) were identified. RT-PCR and RT-qPCR analyses showed that BhorOBP3, BhorCSP2, and BhorOBPC1/C3/C4 were highly expressed in the antenna of males, indicating these genes may may play key roles in foraging and host-orientation in B. horsfieldi. Our results provide valuable molecular information about the olfactory system in B. horsfieldi and will help guide future functional studies on olfactory genes.

The R2R3-MYB transcription factor (TF) family regulates metabolism of phenylpropanoids in various plant lineages. Species-expanded or specific MYB TFs may regulate species-specific metabolite biosynthesis including phenylpropanoid-derived bioactive products. Camellia sinensis produces an abundance of specialized metabolites, which makes it an excellent model for digging into the genetic regulation of plant-specific metabolite biosynthesis. The most abundant health-promoting metabolites in tea are galloylated catechins, and the most bioactive of the galloylated catechins, epigallocatechin gallate (EGCG), is specifically relative abundant in C. sinensis. However, the transcriptional regulation of galloylated catechin biosynthesis remains elusive. This study mined the R2R3-MYB TFs associated with galloylated catechin biosynthesis in C. sinensis. A total of 118 R2R3-MYB proteins, classified into 38 subgroups, were identified. R2R3-MYB subgroups specific to or expanded in C. sinensis were hypothesized to be essential to evolutionary diversification of tea-specialized metabolites. Notably, nine of these R2R3-MYB genes were expressed preferentially in apical buds (ABs) and young leaves, exactly where galloylated catechins accumulate. Three putative R2R3-MYB genes displayed strong correlation with key galloylated catechin biosynthesis genes, suggesting a role in regulating biosynthesis of epicatechin gallate (ECG) and EGCG. Overall, this study paves the way to reveal the transcriptional regulation of galloylated catechins in C. sinensis.

As a common adverse environmental factor, heat stress (HS) not only drastically changes the plant transcriptome at the transcription level but also increases alternative splicing (AS), especially intron retention (IR) events. However, the exact mechanisms are not yet well understood. Here, we reported that NTC-related protein 1 (NTR1), which acts as an accessory component for spliceosome disassembly, is necessary for this process. The mutants of NTR1, both the T-DNA insertion and the point mutation identified through ethyl methanesulfonate (EMS) mutagenesis screening, are vulnerable to HS, indicating that NTR1 is essential for plant HS tolerance. At the molecular level, genes of response to heat and response to temperature stimulus are highly enriched among those of heat-induced but less-expressed ntr1 mutants. Moreover, a large portion of HS response (HSR) genes such as heat shock transcription factors (HSFs) and heat shock proteins (HSPs) are less induced by heat treatment, and more AS events, especially IR events, were found in heat-treated ntr1 mutants. Furthermore, HS suppressed the expression of NTR1 and NTR1-associated complex components. Thus, it is very likely that upon HS, the plant reduces the expression of the NTR1-associated complex to fulfill the fast demands for transcription of HSR genes such as HSFs and HSPs, which in turn results in the accumulation of improperly spliced especially IR products and eventually causes harm to plants.

Results are accumulating that ACE2 (angiotensin I-converting enzyme 2) might act as a protective protein for cardiovascular diseases; however, only a few studies in human populations have been carried out. This prompted us to perform a case-control study to investigate the relationship of ACE2 polymorphisms with CHD (coronary heart disease) and MI (myocardial infarction). Three single nucleotide polymorphisms in the ACE2 gene (1075A/G, 8790A/G and 16854G/C) were genotyped by PCR-RFLP (restriction-fragment-length polymorphism) in 811 patients with CHD (of which 508 were patients with MI) and 905 normal controls in a Chinese population. The polymorphisms were in linkage disequilibrium (r(2)=0.854-0.973). Analyses were conducted by gender, because the ACE2 gene is on the X chromosome. In females, an association was detected with MI for 1075A/G (P=0.026; odds ratio=1.98) and 16854G/C (P=0.028; odds ratio=1.97) in recessive models after adjusting for covariates. In male subjects, two haplotypes (AAG and GGC) were common in frequency. In male subjects not consuming alcohol, the haplotype GGC was associated with a 1.76-fold risk of CHD [95% CI (confidence interval), 1.15-2.69; P=0.007] and a 1.77-fold risk of MI (95% CI, 1.12-2.81; P=0.015) with environmental factors adjusted, when compared with the most common haplotype AAG. In conclusion, the results of the present study indicate that common genetic variants in the ACE2 gene might impact on MI in females, and may possibly interact with alcohol consumption to affect the risk of CHD and MI in Chinese males.

Polyamines involve in gene regulation by interacting with and modulating the functions of various anionic macromolecules such as DNA, RNA and proteins. In this study, we identified an important function of the polyamine transporter LHR1 (LOWER EXPRESSION OF HEAT RESPONSIVE GENE1) in heat-inducible gene expression in Arabidopsis thaliana. The lhr1 mutant was isolated through a forward genetic screening for altered expression of the luciferase reporter gene driven by the promoter from the heat-inducible gene AtHSP18.2. The lhr1 mutant showed reduced induction of the luciferase gene in response to heat stress and was more sensitive to high temperature than the wild type. Map-based cloning identified that the LHR1 gene encodes the polyamine transporter PUT3 (POLYAMINE UPTAKE TRANSPORTER 3) localized in the plasma membrane. The LHR1/PUT3 is required for the uptake of extracellular polyamines and plays an important role in stabilizing the mRNAs of several crucial heat stress responsive genes under high temperature. Genome-wide gene expression analysis using RNA-seq identified an array of differentially expressed genes, among which the transcript levels of some of the heat shock protein genes significantly reduced in response to prolonged heat stress in the lhr1 mutant. Our findings revealed an important heat stress response and tolerance mechanism involving polyamine influx which modulates mRNA stability of heat-inducible genes under heat stress conditions.

Spinach is a useful source of dietary vitamins and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identification of single nucleotide polymorphism (SNP) markers for mineral element concentrations is necessary to support spinach molecular breeding. The purpose of this study was to conduct a genome-wide association study (GWAS) and to identify SNP markers associated with mineral elements in the USDA-GRIN spinach germplasm collection. A total of 14 mineral elements: boron (B), calcium (Ca), cobalt (Co), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), molybdenum (Mo), sodium (Na), nickel (Ni), phosphorus (P), sulfur (S), and zinc (Zn) were evaluated in 292 spinach accessions originally collected from 29 countries. Significant genetic variations were found among the tested genotypes as evidenced by the 2 to 42 times difference in mineral concentrations. A total of 2402 SNPs identified from genotyping by sequencing (GBS) approach were used for genetic diversity and GWAS. Six statistical methods were used for association analysis. Forty-five SNP markers were identified to be strongly associated with the concentrations of 13 mineral elements. Only two weakly associated SNP markers were associated with K concentration. Co-localized SNPs for different elemental concentrations were discovered in this research. Three SNP markers, AYZV02017731_40, AYZV02094133_57, and AYZV02281036_185 were identified to be associated with concentrations of four mineral components, Co, Mn, S, and Zn. There is a high validating correlation coefficient with r > 0.7 among concentrations of the four elements. Thirty-one spinach accessions, which rank in the top three highest concentrations in each of the 14 mineral elements, were identified as potential parents for spinach breeding programs in the future. The 45 SNP markers strongly associated with the concentrations of the 13 mineral elements: B, Ca, Co, Cu, Fe, Mg, Mn, Mo, Na, Ni, P, S, and Zn could be used in breeding programs to improve the nutritional quality of spinach through marker-assisted selection (MAS). The 31 spinach accessions with high concentrations of one to several mineral elements can be used as potential parents for spinach breeding programs.

Spinach (Spinacia oleracea L., 2n = 2x = 12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and minerals. The objective of this research was to conduct genetic diversity and population structure analysis of a collection of world-wide spinach genotypes using single nucleotide polymorphisms (SNPs) markers. Genotyping by sequencing (GBS) was used to discover SNPs in spinach genotypes. Three sets of spinach genotypes were used: 1) 268 USDA GRIN spinach germplasm accessions originally collected from 30 countries; 2) 45 commercial spinach F1 hybrids from three countries; and 3) 30 US Arkansas spinach cultivars/breeding lines. The results from this study indicated that there was genetic diversity among the 343 spinach genotypes tested. Furthermore, the genetic background in improved commercial F1 hybrids and in Arkansas cultivars/lines had a different structured populations from the USDA germplasm. In addition, the genetic diversity and population structures were associated with geographic origin and germplasm from the US Arkansas breeding program had a unique genetic background. These data could provide genetic diversity information and the molecular markers for selecting parents in spinach breeding programs.

Climate warming extends insect distribution areas, increases voltinism and makes pest prevention and control more difficult. The MaxEnt ecological niche modeling software was used to simulate Batocera lineolata distribution and predict potential range changes under climate change scenarios. Future B. lineolata distribution was modeled for three climate scenarios (RCP2.6, RCP4.5 and RCP8.5) to predict suitable regions in the 2050s and 2070s. A receiver operating characteristic curve was used to estimate model precision and a jackknife test was used to screen the dominant environmental variables. The results show that the area under the curve of the B. lineolata distribution model could reach an ‘Excellent’ standard. Under current climate conditions, the most suitable region for B. lineolata is 25.5–40.5°N, 102–120°E, distributed discontinuously from south to north and covering an area of 47.17 × 104 km2. For predicted future distribution, except for a decrease in moderately suitable regions under RCP2.6, RCP4.5 and RCP8.5 in the 2050s and RCP2.6 and RCP4.5 in the 2070s, other suitable regions are likely to extend; highly suitable regions would increase continuously. This research provides a theoretical basis to improve pest management strategies regarding B. lineolata to face the challenge of climate change.

The R2R3-MYB proteins comprise the largest class of MYB transcription factors, which play an essential role in regulating anthocyanin synthesis in various plant species. Ananas comosus var. bracteatus is an important colorful anthocyanins-rich garden plant. The spatio-temporal accumulation of anthocyanins in chimeric leaves, bracts, flowers, and peels makes it an important plant with a long ornamental period and highly improves its commercial value. We conducted a comprehensive bioinformatic analysis of the R2R3-MYB gene family based on genome data from A. comosus var. bracteatus. Phylogenetic analysis, gene structure and motif analysis, gene duplication, collinearity, and promoter analysis were used to analyze the characteristics of this gene family. In this work, a total of 99 R2R3-MYB genes were identified and classified into 33 subfamilies according to phylogenetic analysis, and most of them were localized in the nucleus. We found these genes were mapped to 25 chromosomes. Gene structure and protein motifs were conserved among AbR2R3-MYB genes, especially within the same subfamily. Collinearity analysis revealed four pairs of tandem duplicated genes and 32 segmental duplicates in AbR2R3-MYB genes, indicating that segmental duplication contributed to the amplification of the AbR2R3-MYB gene family. A total of 273 ABRE responsiveness, 66 TCA elements, 97 CGTCA motifs, and TGACG motifs were the main cis elements in the promoter region under response to ABA, SA, and MEJA. These results revealed the potential function of AbR2R3-MYB genes in response to hormone stress. Ten R2R3-MYBs were found to have high homology to MYB proteins reported to be involved in anthocyanin biosynthesis from other plants. RT-qPCR results revealed the 10 AbR2R3-MYB genes showed tissue-specific expression patterns, six of them expressed the highest in the flower, two genes in the bract, and two genes in the leaf. These results suggested that these genes may be the candidates that regulate anthocyanin biosynthesis of A. comosus var. bracteatus in the flower, leaf, and bract, respectively. In addition, the expressions of these 10 AbR2R3-MYB genes were differentially induced by ABA, MEJA, and SA, implying that these genes may play crucial roles in hormone-induced anthocyanin biosynthesis. Our study provided a comprehensive and systematic analysis of AbR2R3-MYB genes and identified the AbR2R3-MYB genes regulating the spatial-temporal anthocyanin biosynthesis in A. comosus var. bracteatus, which would be valuable for further study on the anthocyanin regulation mechanism of A. comosus var. bracteatus.

Chromosome 6p is one of the most commonly implicated regions in the genome-wide linkage scans of schizophrenia, whereas further association studies for markers in this region were inconsistent likely due to heterogeneity. This study aimed to identify more homogeneous subgroups of families for fine mapping on regions around markers D6S296 and D6S309 (both in 6p24.3) as well as D6S274 (in 6p22.3) by means of similarity in neurocognitive functioning. A total of 160 families of patients with schizophrenia comprising at least two affected siblings who had data for eight neurocognitive test variables of the continuous performance test (CPT) and the Wisconsin card sorting test (WCST) were subjected to cluster analysis with data visualization using the test scores of both affected siblings. Family clusters derived were then used separately in family-based association tests for 64 single nucleotide polymorphisms (SNPs) covering the region of 6p24.3 and 6p22.3. Three clusters were derived from the family-based clustering, with deficit cluster 1 representing deficit on the CPT, deficit cluster 2 representing deficit on both the CPT and the WCST, and a third cluster of nondeficit. After adjustment using false discovery rate for multiple testing, SNP rs13873 and haplotype rs1225934-rs13873 on BMP6-TXNDC5 genes were significantly associated with schizophrenia for the deficit cluster 1 but not for the deficit cluster 2 or nondeficit cluster. Our results provide further evidence that the BMP6-TXNDC5 locus on 6p24.3 may play a role in the selective impairments on sustained attention of schizophrenia.

Abstract During runoff on soil surface, aggregates travel, abrade, and produce finer and more transportable particles, resulting in a significant effect on sediment transport, water infiltration and soil erosion. This study was to assess the effects of stability, transport distance and two hydraulic parameters on aggregate abrasion using Ultisols in subtropical China. Aggregate stability was investigated for soils from two parent materials (Shale and Quaternary red clay) with different land uses using LB methods. They were studied with a series of aggregate abrasion experiments in a 3.8 m long flume with a fixed bed. Results indicated that slaking and mechanical breakdown were probably the main mechanisms of aggregate breakdown in these study soils. Two stages of aggregate abrasion process could be distinguished via the coefficient α in different transport distances. Aggregates were first rapidly abraded, became round, and was predominantly broken apart into smaller fragments, followed by weakly abrasion of smaller fragments and round aggregates, making them even light and less angular. A good multiple regression equation was obtained for estimating aggregate abrasion in overland flow with consideration of mechanical breakdown index RMI and transport distance x . From two selected Ultisols (SX3 and QX1) and under the combination of five slopes and five discharges, exponential relationships were found between aggregate abrasion and flow depth or friction factor. This research makes a good attempt at analyzing the aggregate abrasion in overland flow from simple laboratory experiments settings, and the results of the analysis could be valuable for the development of adequate soil erosion models.

Inflammation has been recognized as a key feature of both type 2 diabetes mellitus (T2DM) and atherosclerosis. However, the relationships between circulating levels of novel adipose tissue-derived inflammatory factors, including resistin, vaspin, and visfatin, and the severity of atherosclerosis have not been determined. Moreover, the associations between these inflammatory factors and obesity and insulin resistance in elderly patients remain to be clarified.A cross-sectional study of 256 elderly patients with T2DM admitted in our center was performed. Baseline circulating levels of resistin, vaspin and visfatin were measured with enzyme-linked immunosorbent assays. Ultrasonic evaluations of the carotid arteries of the patients were performed to reflect the severity of systemic atherosclerosis. Patients were classified as having mild, moderate, or severe atherosclerosis according to the results of carotid ultrasonic examination. Circulating levels of the inflammatory factors listed above also were correlated with body mass index (BMI) and homeostasis model assessment of insulin resistance (HOMA-IR).With more severe carotid atherosclerosis, circulating levels of resistin (mild: 2.01 ± 0.23; moderate: 2.89 ± 1.01; severe: 3.12 ± 1.12; p < 0.05) and visfatin (mild: 11.63 ± 7.48; moderate: 15.24 ± 2.19; severe: 17.54 ± 2.98; p < 0.05) gradually increased, while level of vaspin decreased (mild: 317 ± 23.12; moderate: 269 ± 32.12; severe: 229 ± 14.24; p < 0.05). Subsequent results of Pearson coefficient analyses indicated that all of the tested adipose tissue-derived inflammatory factors were positively correlated with the BMI and HOMA-IR of the patients (all p < 0.05), even after adjustment for hs-CRP.The adipose tissue-derived inflammatory factors resistin, vaspin and visfatin may be involved in the pathogenesis of atherosclerosis in elderly T2DM patients.

Abstract The Mu Us Sandy Land is located in the middle of the farming pastoral ecotone of northern China. The direction of the development of desertification has a direct impact on the economy and development of the northern region. Six remote sensing images acquired during 1990–2017 served as data sources. Using an ENVI 5.3 and ArcGIS 10.3 platform an analysis was conducted of the dynamic changes nearly 30 years in desertified land using a center of gravity moving model, annual change rate, a transfer matrix, and an aeolian desertification index; the factors driving desertification were discussed. The research shows that the time period can be divided into three stages of desertification: development (1990–2000), rapid reversal (2000–2010), and stable reversal (2010–2017). A total of 1680 km 2 of desertification were managed over the three stages. Spatially, the distribution of the center of desertification from west to east includes mild, moderate, severe, and extreme desertification, which is consistent with the spatial distribution trends of desertified land in the Mu Us Sandy Land. By the end of 2017, the degree of desertification of the Mu Us Sandy Land was in the central area &gt; northwest &gt; southwest &gt; east &gt; south. Nearly 30 years, the wind speed has decreased year by year at the rate of 0.1 m s −1 , which directly reduce the ability to winds to transport soil in the Mu Us Sandy Land and promoted the reversal of desertification. From 1990 to 2010, the climate tended to become warmer and drier. Environmental protection policies along with human intervention and control of desertification have played important roles in reversing desertification. From 2010 to 2020, under the general background of a warm-wet climatic tendency, rational use of sand resources and strengthening scientific control of desertification inducing factors are the keys to reversing desertification.

Hypertension is a common comorbidity that contributes to the development of various cardiovascular disorders in elderly patients. Moreover, hypertension has been associated with cognitive decline and dementia. Cognitive impairment leads to increased morbidity and mortality in elderly patients with hypertension. However, previous studies investigating the association between blood pressure (BP), BP variability (BPV), and antihypertensive drug use and the risk of cognitive impairment in elderly patients with hypertension have reported inconsistent findings. Given the global burden of hypertension, the aging population, and the low quality of life associated with cognitive impairment, a more comprehensive understanding of the association between hypertension and cognitive decline is needed. In this review, we summarized the current preclinical evidence and clinical research regarding the association of BP control, BPV, and antihypertensive drug use and cognitive function. We particularly focused on the differences among categories of antihypertensive drugs. We concluded that the correlation of BP and risk of cognitive function is non-linear and dependent on a patient's age. Intensive BP control is generally not recommended, particularly for the oldest-old. Increased BPV and characteristics of orthostatic hypotension in the elderly also increase the risk of cognitive decline. The current evidence does not support one category of antihypertensive drugs as superior to others for preventing dementia in elderly patients with hypertension.

Abstract Background Downy mildew, the most devastating disease of spinach ( Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [= P. farinosa f. sp. spinaciae ]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

The recent availability of a number of tea plant genomes has sparked substantial interest in using reverse genetics to explore gene function in tea (Camellia sinensis). However, a hurdle to this is the absence of an efficient transformation system, and virus-induced gene silencing (VIGS), a transient transformation system, could be an optimal choice for validating gene function in the tea plant. In this study, phytoene desaturase (PDS), a carotenoid biosynthesis gene, was used as a reporter to evaluate the VIGS system. The injection sites of the leaves (leaf back, petiole, and stem) for infiltration were tested, and the results showed that petiole injection had the most effective injection, without leading to necrotic lesions that cause the leaves to drop. Tea leaves were inoculated with Agrobacterium harboring a tobacco rattle virus plasmid (pTRV2) containing a CsPDS silencing fragment. The tea leaves exhibited chlorosis symptoms 7-14 days after inoculation, depending on the cultivar. In the chlorosis plants, the coat protein (CP) of tobacco rattle virus (TRV) was detected and coincided with the lower transcription of CsPDS and reduced chlorophyll content compared with the empty vector control, with 81.82% and 54.55% silencing efficiency of 'LTDC' and 'YSX', respectively. These results indicate that the VIGS system with petiole injection could quickly and effectively silence a gene in tea plants.

Background and objective Recent study supports the hypothesis that the abnormalities of vascular smooth muscle cell (VSMC) that alter the intrinsic contractile state of the cell can directly cause abnormal vascular tone and disorders of blood pressure regulation, including hypertension. This study aimed to explore the individual and interactive effects of five genes from the contractile pathway of VSMC (KCNMB1, RGS2, PRKG, ROCK2, and MYLK) on the risk of essential hypertension. Methods Potential functional polymorphisms of the five genes were analyzed in a large, representative Chinese Han sample of 4759 individuals, including 2411 hypertensive patients and 2348 age-matched and sex-matched healthy controls. Results Single locus analyses showed significant association of the alleles of RGS2-rs34717272 with hypertension (original P of χ2 test=0.005; P value of permutation=0.019). After the adjustment for covariates, the carriers of minor D allele of RGS2-rs34717272 had an increased hypertension risk (DD+ID vs. II; odds ratio=1.19; 95% confidence interval, 1.04–1.35; P value after the Bonferroni correction=0.009×5=0.045). We also found that the carriers of minor T allele of KCNMB1-rs11739136 had a significantly decreased risk for hypertension (TT+CT vs. CC; odds ratio=0.83; 95% confidence interval, 0.72–0.95; P value after the Bonferroni correction=0.008×5=0.040). Final interaction models were selected and evaluated by permutation test and/or cross-validation test. Both the multifactor-dimensionality reduction and classification and regression trees methods showed a high-order gene–gene interaction among KCNMB1, RGS2, PRKG, and MYLK genes (P value of permutation in multifactor-dimensionality reduction=0.012). Conclusion The overall results supported that the genetic variants in the contractile pathway of VSMC could contribute to hypertension risk independently or in an interactive manner.

We explored the influence of antidepressant therapy on blood pressure and quality of life in elderly patients with hypertension. Depression occurs at a higher rate in patients with hypertension than in the normal population. It has been reported that depressive symptoms lead to poorer hypertension control, resulting in the development of complications. We conducted a randomized, parallel group study. A total of 70 elderly patients with hypertension in the period of August 2008 to March 2011 were divided into two groups based on their antihypertensive therapy, a control group (amlodipine, 5 mg daily; n=35) and a therapy group (amlodipine, 5mg daily; citalopram, 20 mg daily; n=35). We compared 24 hour, daytime, and nighttime measurements of systolic and diastolic blood pressure, in addition to quality of life, assessed using the Hamilton rating scale for depression, and a 36 item Short Form quality of life questionnaire (SF-36). Both groups were followed for 3 months. At the end of 3 months, all blood pressure levels were significantly lower in the therapy group than in the control group. The other scores (with the exception of the physical function subcategory of the SF-36 quality of life scale) were significantly higher. Our study indicates that clinicians should be aware of depressive symptoms in elderly patients with hypertension, and should consider antidepressant therapy in these patients.

In citrus, genetic improvement via biotechnology is challenging due to insufficient understanding of molecular barriers that prevent regeneration by somatic embryogenesis (SE). Our previous study indicated that LEC genes were involved in SE in citrus, but their regulatory roles remain to be elucidated. Here, we cloned one of the LEC genes, CsFUS3, and show that it is preferentially expressed during SE and in the embryogenic callus (EC) derived from citrus varieties with strong embryogenic competence. The overexpression of CsFUS3 in recalcitrant citrus callus restored embryogenic competence. Complementation of the loss-of-function Arabidopsis fus3 mutant with the CsFUS3 gene restored normal late embryogenesis, which is consistent with the CsFUS3 and AtFUS3 proteins contributing to the same regulatory network in Arabidopsis. Transcriptome profiling revealed that the expression of particular TFs that promote SE was up-regulated in the citrus overexpression (OE) line. The 104 differentially expressed genes associated with hormone biosynthesis, catabolism, and signaling are particularly noteworthy. The dynamic change in the ratio of ABA to GA during SE in wild-type callus mirrored the expression pattern of CsFUS3. In contrast, in the OE line, the ratio of ABA to GA was higher and the capacity for SE was greater when the OE line was separately treated with ABA and GA biosynthesis inhibitors. Taken together, our results demonstrate that the overexpression of CsFUS3 appears to establish a cellular environment favorable to SE, at least in part by promoting a high ABA to GA ratio and by regulating the expression of TFs that promote SE.

Abstract Gene regulation is central for growth, development, and adaptation to environmental changes in all living organisms. Many genes are induced by environmental cues, and the expression of these inducible genes is often repressed under normal conditions. Here, we show that the SHINY2 (SHI2) gene is important for repressing salt-inducible genes and also plays a role in cold response. The shi2 mutant displayed hypersensitivity to cold, abscisic acid (ABA), and LiCl. Map-based cloning demonstrates that SHI2 encodes a DEAD- (Asp-Glu-Ala-Asp) box RNA helicase with similarity to a yeast splicing factor. Transcriptomic analysis of the shi2 mutant in response to cold revealed that the shi2 mutation decreased the number of cold-responsive genes and the magnitude of their response, and resulted in the mis-splicing of some cold-responsive genes. Under salt stress, however, the shi2 mutation increased the number of salt-responsive genes but had a negligible effect on mRNA splicing. Our results suggest that SHI2 is a component in a ready-for-transcription repressor complex important for gene repression under normal conditions, and for gene activation and transcription under stress conditions. In addition, SHI2 also serves as a splicing factor required for proper splicing of cold-responsive genes and affects 5' capping and polyadenylation site selection.

Despite a central role in angiosperm reproduction, few gametophyte-specific genes and promoters have been isolated, particularly for the inaccessible female gametophyte (embryo sac). Using the Ds-based enhancer-detector line ET253, we have cloned an egg apparatus-specific enhancer (EASE) from Arabidopsis (Arabidopsis thaliana). The genomic region flanking the Ds insertion site was further analyzed by examining its capability to control gusA and GFP reporter gene expression in the embryo sac in a transgenic context. Through analysis of a 5' and 3' deletion series in transgenic Arabidopsis, the sequence responsible for egg apparatus-specific expression was delineated to 77 bp. Our data showed that this enhancer is unique in the Arabidopsis genome, is conserved among different accessions, and shows an unusual pattern of sequence variation. This EASE works independently of position and orientation in Arabidopsis but is probably not associated with any nearby gene, suggesting either that it acts over a large distance or that a cryptic element was detected. Embryo-specific ablation in Arabidopsis was achieved by transactivation of a diphtheria toxin gene under the control of the EASE. The potential application of the EASE element and similar control elements as part of an open-source biotechnology toolkit for apomixis is discussed.

Cyrtotrachelus buqueti is an extremely harmful bamboo borer, and the larvae of this pest attack clumping bamboo shoots. Pheromone-binding proteins (PBPs) play an important role in identifying insect sex pheromones, but the C. buqueti genome is not readily available for PBP analysis. Developmental transcriptomes of eggs, larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing (RNA-Seq) in the present study to establish a sequence background of C. buqueti to help understand PBPs. Approximately 164.8 million clean reads were obtained and annotated into 108,854 transcripts. These were assembled into 24,338, 21,597, 24,798, 21,886, 24,642, and 83,115 unigenes for eggs, larvae, pupae, females, males, and the combined datasets, respectively. Unigenes were annotated against NCBI non-redundant protein sequences, NCBI non-redundant nucleotide sequences, Gene Ontology (GO), Protein family, Clusters of Orthologous Groups of Proteins/ Clusters of Eukaryotic Orthologous Groups (KOG), Swiss-Prot, and KEGG Orthology databases. A total of 17,213 unigenes were annotated into 55 sub-categories belonging to three main GO categories; 10,672 unigenes were classified into 26 functional categories by KOG classification, and 8,063 unigenes were classified into five functional KEGG categories. RSEM software for RNA sequencing showed that 4,816, 3,176, 3,661, 2,898, 4,316, 8,019, 7,273, 5,922, 5,844, and 4,570 genes were differentially expressed between larvae and males, larvae and eggs, larvae and pupae, larvae and females, males and females, males and eggs, males and pupae, females and eggs, females and pupae, and eggs and pupae, respectively. Of these, three were confirmed to be significantly differentially expressed between larvae, females, and males. Furthermore, PBP Cbuq7577_g1 was highly expressed in the antenna of males. A comprehensive sequence resource of a desirable quality was constructed from developmental transcriptomes of C. buqueti eggs, larvae, pupae, and adults. This work enriches the genomic data of C. buqueti, and facilitates our understanding of its metamorphosis, development, and response to environmental change. The identified candidate PBP Cbuq7577_g1 might play a crucial role in identifying sex pheromones, and could be used as a targeted gene to control C. buqueti numbers by disrupting sex pheromone communication.

Abstract Abiotic stresses greatly affect the immunity of plants. However, it is unknown whether pathogen infection affects abiotic stress tolerance of host plants. Here, the effect of defense response on cold and heat tolerance of host plants was investigated in Pst DC3000‐infected Arabidopsis plants, and it was found that the pathogen‐induced defense response could alleviate the injury caused by subsequent cold and heat stress (38°C). Transcriptomic sequencing plus RT‐qPCR analyses showed that some abiotic stress genes are up‐regulated in transcription by pathogen infection, including cold signaling components ICE1 , CBF1 , and CBF3 , and some heat signaling components HSFs and HSPs . Moreover, the pathogen‐induced alleviation of cold and heat injury was lost in NahG transgenic line (SA‐deficient), sid2‐2 and npr1‐1 mutant plants, and pathogen‐induced expression of cold and heat tolerance‐related genes such as CBFs and HSPs , respectively, was lost or compromised in these plants, indicating that salicylic acid signaling pathway is required for the alleviation of cold and heat injury by pathogen infection. In short, our current work showed that in fighting against pathogens, host plants also enhance their cold and heat tolerance via a salicylic acid‐dependent pathway.

Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves investigation. In order to explore the pigments behind the red section of the chimeric leaves, the green and red parts of chimeric leaves of Ananas comosus var. bracteatus were sampled and analyzed at phenotypic, cellular and molecular levels in this study.The CIELAB results indicated that the a* values and L* values samples had significant differences between two parts. Freehand sections showed that anthocyanin presented limited accumulation in the green leaf tissues but obviously accumulation in the epidermal cells of red tissues. Transcriptomic and metabolomic analyses were performed by RNA-seq and LC-ESI-MS/MS. Among the 508 identified metabolites, 10 kinds of anthocyanins were detected, with 6 significantly different between the two samples. The cyanidin-3,5-O-diglucoside content that accounts for nearly 95.6% in red samples was significantly higher than green samples. RNA-Seq analyses showed that 11 out of 40 anthocyanin-related genes were differentially expressed between the green and red samples. Transcriptome and metabolome correlations were determined by nine quadrant analyses, and 9 anthocyanin-related genes, including MYB5 and MYB82, were correlated with 7 anthocyanin-related metabolites in the third quadrant in which genes and metabolites showing consistent change. Particularly, the PCCs between these two MYB genes and cyanidin-3,5-O-diglucoside were above 0.95.Phenotypic colors are closely related to the tissue structures of different leaf parts of Ananas comosus var. bracteatus, and two MYB transcription factors might contribute to differences of anthocyanin accumulation in two parts of Ananas comosus var. bracteatus chimeric leaves. This study lay a foundation for further researches on functions of MYBs in Ananas comosus var. bracteatus and provides new insights to anthocyanin accumulation in different parts of chimeric leaves.

DEAD-box proteins are a large family of RNA helicases that play important roles in almost all cellular RNA processes in model plants. However, little is known about this family of proteins in crops such as soybean. Here, we identified 80 DEAD-box family genes in the Glycine max (soybean) genome. These DEAD-box genes were distributed on 19 chromosomes, and some genes were clustered together. The majority of DEAD-box family proteins were highly conserved in Arabidopsis and soybean, but Glyma.08G231300 and Glyma.14G115100 were specific to soybean. The promoters of these DEAD-box genes share cis-acting elements involved in plant responses to MeJA, salicylic acid (SA), low temperature and biotic as well as abiotic stresses; interestingly, half of the genes contain nodulation-related cis elements in their promoters. Microarray data analysis revealed that the DEAD-box genes were differentially expressed in the root and nodule. Notably, 31 genes were induced by rhizobia and/or were highly expressed in the nodule. Real-time quantitative PCR analysis validated the expression patterns of some DEAD-box genes, and among them, Glyma.08G231300 and Glyma.14G115100 were induced by rhizobia in root hair. Thus, we provide a comprehensive view of the DEAD-box family genes in soybean and highlight the crucial role of these genes in symbiotic nodulation.

This study evaluated the suitability, feasibility, safety, and outcomes of transport of the ECMO-dependent patient (EDP) by EDP transport team (EDPTT) in China. Eighty-two EDPs (forty-one cases on VV ECMO and forty-one cases on VA ECMO) received transport between June 2018 and June 2021 and were retrospectively analyzed. ECMO circulation was performed by the outlying hospital, mainly using percutaneous ECMO cannulation. The EDPTT consists of three intensive therapists, one of whom serves as a team leader, and one intensive care unit nurse. Of these, 81 (98.8%) patients were transferred by ambulance, no deaths occurred during transport, the EDP-related complications were 19% ( n = 16); bleeding at the cannula site ( n = 7, 8.5%) was the most prominent; equipment-related problems accounted for 14.6% of the problems requiring urgent intervention, with hand cranking being the most common (9.7%). The survival rate during transport was 100%, with 36 (43.9%) patients surviving to discharge. The ECMO weaning rate was 61% for VV ECMO and 63.7% for VA ECMO. The results demonstrated the suitability, feasibility, and safety of transporting EDP in a team led by an intensivist, with few complications and no deaths during transport. This may be the recommended staffing model for EDP transport in developing countries.

Abstract Objective To establish the exponential smoothing prediction model and SARIMA model to predict the number of inpatients in a third-class hospital in Zhejiang Province, and evaluate the prediction effect of the two models, and select the best number prediction model. Methods The data of hospital admissions from January 2019 to September 2022 were selected to establish the exponential smoothing prediction model and the SARIMA model respectively. Then compare the fitting parameters of different models: R 2 _adjusted, R 2 , Root Mean Square Error (RMSE)、Mean Absolute Percentage Error (MAPE)、Mean Absolute Error(MAE) and standardized BIC to select the best model. Finally, the established model was used to predict the number of hospital admissions from October to December 2022, and the prediction effect of the average relative error judgment model was compared. Results The best fitting exponential smoothing prediction model was Winters Addition model, whose R 2 _adjusted was 0.533, R 2 was 0.817, MAPE was 6.133, MAE was 447.341. The best SARIMA model is SARIMA(2,2,2)(0,1,1) 12 model, whose R 2 _adjusted is 0.449, R 2 is 0.199, MAPE is 8.240, MAE is 718.965. The Winters addition model and SARIMA(2,2,2)(0,1,1) 12 model were used to predict the number of hospital admissions in October-December 2022, respectively. The results showed that the average relative error was 0.038 and 0.015, respectively. The SARIMA(2,2,2)(0,1,1) 12 model had a good prediction effect. Conclusion Both models can better fit the number of admissions, and SARIMA model has better prediction effect.

Sensory neuron membrane proteins (SNMPs) play important roles in insect chemoreception and SNMP1s have been reported to be essential in detecting sex pheromones in Drosophila and some lepidopteran species. However, SNMPs for Cyrtotrachelus buqueti (Coleoptera: Curculionidae), a major insect pest of bamboo plantations, remain uncharacterized. In this study, a novel SNMP gene, CbuqSNMP1b, from C. buqueti was functionally characterized. The expression of CbuqSNMP1b was significantly higher in antennae than in other tissues of both sexes and the expression level was significantly male-biased. Additionally, CbuqSNMP1b showed significantly higher transcription levels in the adult stage and very low transcription levels in other stages, suggesting that CbuqSNMP1b is involved in the process of olfaction. Fluorescence binding assays indicated that CbuqSNMP1b displayed the strongest binding affinity to dibutyl phthalate (Ki = 9.03 μM) followed by benzothiazole (Ki = 11.59 μM) and phenol (Ki = 20.95 μM) among fourteen C. buqueti volatiles. Furthermore, molecular docking revealed key residues in CbuqSNMP1b that interact with dibutyl phthalate, benzothiazole, and phenol. In conclusion, these findings will lay a foundation to further understand the olfactory mechanisms of C. buqueti and promote the development of novel methods for controlling this pest.

For high-risk stageIImismatch repair deficient (dMMR) colon cancers, the benefit of adjuvant chemotherapy remains debatable. The principal aim of this study was to evaluate the prognostic value of high-risk factors and the effect of oxaliplatin-based adjuvant chemotherapy among dMMR stageIIcolon cancers.Patients with stage II dMMR colon cancers diagnosed between June 2011 and May 2018 were enrolled in the study. Clinicopathological characteristics, treatment, and follow-up data were retrospectively collected. The high-risk group was defined as having one of the following factors: pT4 disease, fewer than twelve lymph nodes harvested (< 12 LNs), poorly differentiated histology, perineural invasion (PNI), lymphatic vascular invasion (LVI), or elevated preoperative carcinoembryonic antigen (CEA). The low-risk group did not have any risk factors above. Factors associated with disease-free survival (DFS) were included in univariate and multivariate Cox analyses.We collected a total of 262 consecutive patients with stage II dMMR colon cancer. 179 patients (68.3%) have at least one high-risk factor. With a median follow-up of 50.1 months, the low-risk group was associated with a tended to have a better 3-year DFS than the high-risk group (96.4% vs 89.4%; P = 0.056). Both elevated preoperative CEA (HR 2.93; 95% CI 1.26-6.82; P = 0.013) and pT4 disease (HR 2.58; 95% CI 1.06-6.25; P = 0.037) were independent risk factors of recurrence. Then, the 3-year DFS was 92.6% for the surgery alone group and 88.1% for the adjuvant chemotherapy group (HR 1.64; 95% CI 0.67-4.02; P = 0.280). Furthermore, no survival benefit from oxaliplatin-based adjuvant chemotherapy was observed in the high-risk group and in the subgroups with pT4 disease or < 12 LNs.These data suggests that not all high-risk factors have a similar impact on stage II dMMR colon cancers. Elevated preoperative CEA and pT4 tumor stage are associated with increased recurrence risk. However, oxaliplatin-based adjuvant chemotherapy shows no survival benefits in stage II dMMR colon cancers, either with or without high-risk factors.

<sec><title>Objective</title> Outdoor jogging has been gaining popularity worldwide thanks to its various health, social and environmental benefits. Optimizing the design of urban built environment is an effective way to promote outdoor jogging activities for urban residents. To achieve this, it is necessary to clarify the association and interaction between urban built environment and outdoor jogging activities. However, the existing research mainly focuses on the independent effects of single factors on jogging activities, while neglecting the interactive effects between built environment factors and the spatio-temporal differences in their impacts. To this end, this research aims to analyze the association and interaction between urban built environment and jogging behavior, so as to provide a scientific basis for creating a human-friendly living environment. </sec><sec><title>Methods</title> Firstly, this research utilizes crowdsourced geographic information to measure outdoor jogging activities and urban built environments at a large scale. Specifically, jogging flow is calculated with jogging GPS trajectory data collected from the Edooon sport app. Eight built environment factors selected from the three dimensions of attractiveness, vibrancy and accessibility are calculated using multi-source spatial data, such as Baidu street view images, point of interest (POI) data and road data. Secondly, the Geographic Detector model is employed to investigate the associations and interactions between built environment factors and jogging behaviors. Thirdly, jogging flow is categorized into three types (morning peak, night peak and off-peak) at hourly scale, two types (weekdays and weekends) at daily scale, and four types (residential, commercial, industrial and recreational) based on land use type. Then, the variations in the aforesaid associations and interactions are explored and analyzed from the perspective of different time and different land use types with the Geographic Detector model. </sec><sec><title>Results</title> Empirical analysis is conducted with real jogging-related GPS trajectory data recorded by the sports app of 9,860 users in Chengdu City, China. Results show that population density, land use mix, and density of public transit station are core factors determining the spatial distribution of outdoor jogging. Across different time scales, the eight built environment factors, including green view index (GVI), normalized difference vegetation index (NDVI), park density, population density, land use mix, retail store density, road intersection density and bus stop density, have a significant impact on jogging activities. The explanatory power of different built environment factors varies significantly across different land use types. For example, the impact of park density on jogging is significantly greater in recreational land than in industrial or commercial land. Nevertheless, for industrial land, only three indicators, namely population density, land use mix, and accessibility, have significant impacts on outdoor jogging. Significantly, the explanatory power of interacted built environment factors for jogging flow is greater than that of single factors. This indicates that the differences in spatial distribution of jogging flow result from the combined effects of multiple built environment factors. The interaction between population density and land use mix explains the spatial variation of jogging activities to an extent of 50%. The interactive effects of some environmental factors on jogging may change over time and land use types. For instance, during morning peak period, outdoor jogging is more affected by the interaction of park density, GVI, and land use diversity in Chengdu. In contrast, outdoor jogging during the evening peak period is mainly affected by the interaction of population density, bus stop density, and land use diversity. The core interacting factors affecting the distribution of jogging flow in residential and commercial areas are population density and land use mix. In contrast, the core interacting factors in recreational and industrial areas are land use mix and park density. The interactive effects between population density/land use mix and other built environment factors may be synergistically enhanced, and the explanatory power of these core interaction factors varies over space and time. For example, after the interaction of two built environment factors, the explanatory power may increase by more than 10% in commercial land, 20% in industrial land, while only around 7% in residential land. These differential impacts will help planners formulate targeted design strategies for environmental intervention. </sec><sec><title>Conclusion</title> This research utilizes crowdsourced geographic information and a geographic detector model to establish multiple detection models, identifying the dominant built environment factors affecting outdoor jogging activities and quantitatively measuring the interactive effects of different built environment factors. Crowdsourced geographic information provides a new, extensive, and cost-effective means for measuring human activities and built environment characteristics. The interactive effects of multiple built environment factors on outdoor jogging activities are greater than those of single factors, exhibiting both dual-factor enhancement and nonlinear enhancement effects. Moreover, the interactive effects of built environment factors on outdoor jogging vary with time and land use types. This variability reflects the behavioral decisions of urban residents under the constraints of multiple scenarios, such as time (e.g., leisure time, commuting time), space (e.g., location), infrastructure (e.g., transportation infrastructure, sports facilities), and environment (e.g., visual environment, safety). A systematic analysis of the interactions between built environment and outdoor jogging may support health-oriented urban design. </sec>

Castanopsis chinensis (Spreng.) Hance is widespread in the subtropical forests of China. Castanopsis qiongbeiensis G.A. Fu and Castanopsis glabrifolia J. Q. Li &amp; Li Chen are limited to the coastal beaches of Wenchang county in the northeast of Hainan Island, and have similar morphological characteristics to C. chinensis. It is supposed that C. qiongbeiensis and C. glabrifolia are closely related to C. chinensis. In the present study, the genetic differentiation, gene flow, and genetic relationship of C. chinensis, C. qiongbeiensis, and C. glabrifolia were investigated by using 15 nuclear microsatellite markers; a total of 308 individuals from 17 populations were sampled in the three species. The allelic variation of nuclear microsatellites revealed moderate but significant genetic differentiation (FCT = 0.076) among C. chinensis, C. qiongbeiensis, and C. glabrifolia, and genetic differentiation between C. chinensis and C. glabrifolia was larger than that between C. chinensis and C. qiongbeiensis. Demographic simulations revealed unidirectional gene flow from C. chinensis to C. glabrifolia and C. qiongbeiensis, which highlight dispersal from mainland to island. The isolation effect of Qiongzhou Strait increased the genetic differentiation of species on both sides of the strait; however, the differentiation was diminished by gene flow that occurred during the historical period when Hainan Island was connected to mainland China. Our results supported the argument that C. glabrifolia should be considered an independent species and argued that C. qiongbeiensis should be regarded as an incipient species and independent conservation unit.

The pathophysiological process of schizophrenia is still unclear. The levels of interleukine-6 (IL-6) and its receptor, soluble IL-6R, have been reported to be elevated in the plasma and cerebrospinal fluid of schizophrenic patients. In this study, we tested the association of genetic variants of IL-6 and IL-6R with schizophrenia. Genotyping of three single nucleotide polymorphisms (SNP) for each IL-6 (IL-6-1, IL-6-2, and IL-6-3) and IL-6R (rs4845617=IL-6R1, rs4553185=IL-6R2, and rs4379670=IL-6R3) gene was performed in 100 patients with schizophrenia and 113 normal controls. The polymorphisms of IL-6R2 were genotyped using Tetra-primer ARMS PCR. IL-6R3 polymorphisms were genotyped using restriction fragment length polymorphism (RFLP) with Apo I enzyme as the restriction enzyme. All other polymorphisms were genotyped using the direct sequencing method. We found a di-nucleotide haplotype block and a tri-nucleotide haplotype block in the genes of IL-6 and IL-6R, respectively. All six SNPs and their haplotypes failed to show a significant association with schizophrenia. The IL-6-2 SNP showed a nominally significant association with the positive symptoms of schizophrenia (p=0.0472). We conclude that the genetic variants of IL-6 and IL-6R are not associated with schizophrenia. In order to verify this result, further study using a larger sample size and exploring the association between the genotype of IL-6-2 and plasma level of IL-6 is recommended.

Flowering at an appropriate time is crucial for seed maturity and reproductive success in all flowering plants. Soybean (Glycine max) is a typical short day plant, and both photoperiod and autonomous pathway genes exist in soybean genome. However, little is known about the functions of soybean autonomous pathway genes. In this article, we examined the functions of a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D (FLD), GmFLD in the flowering transition of A. thaliana. In soybean, GmFLD is highly expressed in expanded cotyledons of seedlings, roots, and young pods. However, the expression levels are low in leaves and shoot apexes. Expression of GmFLD in A. thaliana (Col) resulted in early flowering of the transgenic plants, and rescued the late flowering phenotype of the A. thaliana fld mutant. In GmFLD transgenic plants (Col or fld background), the FLC (FLOWERING LOCUS C) transcript levels decreased whereas the floral integrators, FT and SOC1, were up-regulated when compared with the corresponding non-transgenic genotypes. Furthermore, chromatin immuno-precipitation analysis showed that in the transgenic rescued lines (fld background), the levels of both tri-methylation of histone H3 Lys-4 and acetylation of H4 decreased significantly around the transcriptional start site of FLC. This is consistent with the function of GmFLD as a histone demethylase. Our results suggest that GmFLD is a functional ortholog of the Arabidopsis FLD and may play an important role in the regulation of chromatin state in soybean. The present data provides the first evidence for the evolutionary conservation of the components in the autonomous pathway in soybean.

ABSTRACT Sequencing the genomes of individual cancer cells provides the highest resolution of intratumoral heterogeneity. To enable high throughput single cell DNA-Seq across thousands of individual cells per sample, we developed a droplet-based, automated partitioning technology for whole genome sequencing. We applied this approach on a set of gastric cancer cell lines and a primary gastric tumor. In parallel, we conducted a separate single cell RNA-Seq analysis on these same cancers and used copy number to compare results. This joint study, covering thousands of single cell genomes and transcriptomes, revealed extensive cellular diversity based on distinct copy number changes, numerous subclonal populations and in the case of the primary tumor, subclonal gene expression signatures. We found genomic evidence of positive selection – where the percentage of replicating cells per clone is higher than expected – indicating ongoing tumor evolution. Our study demonstrates that joining single cell genomic DNA and transcriptomic features provides novel insights into cancer heterogeneity and biology. SIGNIFICANCE We conducted a massively parallel DNA sequencing analysis on a set of gastric cancer cell lines and a primary gastric tumor in combination with a joint single cell RNA-Seq analysis. This joint study, covering thousands of single cell genomes and transcriptomes, revealed extensive cellular diversity based on distinct copy number changes, numerous subclonal populations and in the case of the primary tumor, subclonal gene expression signatures. We found genomic evidence of positive selection where the percentage of replicating cells per clone is higher than expected indicating ongoing tumor evolution. Our study demonstrates that combining single cell genomic DNA and transcriptomic features provides novel insights into cancer heterogeneity and biology.

Stemphylium leaf spot, caused by Stemphylium botryosum f. sp.spinacia, is an important fungal disease of spinach (Spinacia oleracea L.).The aim of this study was to conduct association analysis to identify single nucleotide polymorphism (SNP) markers associated with Stemphylium leaf spot resistance in spinach.A total of 273 spinach genotypes, including 265 accessions from the USDA spinach germplasm collection and eight commercial cultivars, were used in this study.Phenotyping for Stemphylium leaf spot resistance was evaluated in greenhouse; genotyping was conducted using genotyping by sequencing (GBS) with 787 SNPs; and single marker regression, general linear model, and mixed linear model were used for association analysis of Stemphylium leaf spot.Spinach genotypes showed a skewed distribution for Stemphylium leaf spot resistance, with a range from 0.2% to 23.5% disease severity, suggesting that Stemphylium leaf spot resistance in spinach is a complex, quantitative trait.Association analysis indicated that eight SNP markers, AYZV02052595_115, AYZV02052595_122, AYZV02057770_10404, AYZV02129827_205, AYZV0-2152692_182, AYZV02180153_337, AYZV02225889_197, and AYZV02258563_213 were strongly associated with Stemphylium leaf spot resistance, with a Log of the Odds (LOD) of 2.5 or above.The SNP markers may provide a tool to select for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection (MAS).

Abstract Background Lysine succinylation, an important protein posttranslational modification (PTM), is widespread and conservative. The regulatory functions of succinylation in leaf color has been reported. The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts and albino white parts. However, the extent and function of lysine succinylation in chimeric leaves of Ananas comosus var. bracteatus has yet to be investigated. Results Compared to the green (Gr) parts, the global succinylation level was increased in the white (Wh) parts of chimeric leaves according to the Western blot and immunohistochemistry analysis. Furthermore, we quantitated the change in the succinylation profiles between the Wh and Gr parts of chimeric leaves using label-free LFQ intensity. In total, 855 succinylated sites in 335 proteins were identified, and 593 succinylated sites in 237 proteins were quantified. Compared to the Gr parts, 232 (61.1%) sites in 128 proteins were quantified as upregulated targets, and 148 (38.9%) sites in 70 proteins were quantified as downregulated targets in the Wh parts of chimeric leaves using a 1.5-fold threshold ( P &lt; 0.05). These proteins with altered succinylation level were mainly involved in crassulacean acid metabolism (CAM) photosynthesis, photorespiration, glycolysis, the citric acid cycle (CAC) and pyruvate metabolism. Conclusions Our results suggested that the changed succinylation level in proteins might function in the main energy metabolism pathways—photosynthesis and respiration. Succinylation might provide a significant effect in the growth of chimeric leaves and the relationship between the Wh and Gr parts of chimeric leaves. This study not only provided a basis for further characterization on the function of succinylated proteins in chimeric leaves of Ananas comosus var. bracteatus but also provided a new insight into molecular breeding for leaf color chimera.

Insulin resistance plays a role in the development of dementia and hypertension. We investigated a possible relationship between cognitive impairment and insulin resistance in elderly Chinese patients with primary hypertension.One hundred and thirty-two hypertensive elderly patients (>60 years) were enrolled in this study, and assigned into either the cognitive impairment group (n=61) or the normal cognitive group (n=71). Gender, age, education, body mass index (BMI), waist hip ratio (WHR), total cholesterol (TC), triglyceride (TG), C-reactive protein (CRP), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), creatinine (Cr), fasting plasma glucose (FPG), fasting insulin (FINS), homeostasis model of assessment for insulin resistance index (HOMA-IR), systolic blood pressure, diastolic blood pressure, smoking history, atherosclerosis and the proportion of uncontrolled hypertension were compared between the two groups. Multi-factorial logistic regression analysis was performed.No significant differences were found in gender, age, TC, CRP, HDL-C, LDL-C, Cr, BP, smoking history, atherosclerosis and the proportion of uncontrolled hypertension between the two groups. The cognitive impairment group had lower education levels, and higher BMI, WHR, TG, FPG, FINS, and HOMA-IR levels than the control group. Logistic regression analysis revealed the levels of education, BMI, WHR, and HOMA-IR as independent factors that predict cognitive impairment in patients.Our study demonstrates that poor education and increased BMI, WHR, and HOMA-IR are independent risk factors for cognitive impairment in elderly patients with hypertension. Insulin resistance plays an important role in the development of cognitive impairment in primary elderly hypertensive patients.

Many studies have shown the effects of mechanical properties on soil erosion. However, most have focused on the strength of bulk soil, with little attention paid to the strength of the aggregates. The objective of this study was to assess the effects of aggregate tensile strength and friability on aggregate breakdown under simulated rainfall. Different size aggregates of Ultisols, derived from Shale (S) and Quaternary red clay (Q), were exposed to simulated rainfall of 60 mm h−1. Fragment size distribution and splash loss were compared. The results showed that tensile strength decreased when aggregate size increased. For 1- to 2-mm aggregates, tensile strength of Q was greater than S, but the opposite was true for 10- to 20-mm aggregates. Estimates of friability from the coefficient of variation method were different with aggregate sizes tested and always gave larger numerical values than the volume dependence method. Aggregate breakdown was closely related to tensile strength because both depend on aggregate microstructure. Good correlations were observed between tensile strength and normalized mean weight diameters under different amounts of cumulative rainfall. As aggregate size increased, mean weight diameter of fragments increased, but normalized mean weight diameter and splash loss decreased. The tendency that aggregate splash decreased with increasing aggregate size was more obvious for the soil with low friability. For all size classes, the aggregates of soil with low friability produced more splash materials. It might be possible, with further experimentation, to develop empirically based criteria for stability of soil to erosion using tensile strength and friability.

Urapidil is putatively effective for patients with hypertension and acute heart failure, although randomized controlled trials thereon are lacking. We investigated the efficacy and safety of intravenous urapidil relative to that of nitroglycerin in older patients with hypertension and heart failure in a randomized controlled trial.Patients (>60 y) with hypertension and heart failure were randomly assigned to receive intravenous urapidil (n=89) or nitroglycerin (n=91) for 7 days. Hemodynamic parameters, cardiac function, and safety outcomes were compared.Patients in the urapidil group had significantly lower mean systolic blood pressure (110.1±6.5 mm Hg) than those given nitroglycerin (126.4±8.1 mm Hg, p=0.022), without changes in heart rate. Urapidil was associated with improved cardiac function as reflected by lower N terminal-pro B type natriuretic peptide after 7 days (3311.4±546.1 ng/mL vs. 4879.1±325.7 ng/mL, p=0.027) and improved left ventricular ejection fraction (62.2±3.4% vs. 51.0±2.4%, p=0.032). Patients given urapidil had fewer associated adverse events, specifically headache (p=0.025) and tachycardia (p=0.004). The one-month rehospitalization and all-cause mortality rates were similar.Intravenous administration of urapidil, compared with nitroglycerin, was associated with better control of blood pressure and preserved cardiac function, as well as fewer adverse events, for elderly patients with hypertension and acute heart failure.

Abstract Pheromone‐binding proteins ( PBP s) play important roles in the information exchange between insect sexes, specifically in the process of transporting fat‐soluble odour molecules from the external environment to olfactory receptors through the olfactory sensillum lymph. The PBP functions in this process may explain the sex pheromone identification mechanism used by insects, laying a theoretical foundation for the prevention and control of pests by interfering with olfactory recognition. In the present study, a PBP gene of Cyrtotrachelus buqueti ( G en B ank accession number: KU 845733) is cloned for prokaryotic expression. Using N ‐phenyl‐1‐naphthylamine as the fluorescent probe in a competitive binding assay, the ability of CbuqPBP 1 to bind 12 sex pheromone analogues and three volatiles of Neosinocalamus affinis shoots is examined. Of the 12 C. buqueti sex pheromone analogues, dibutyl phthalate gives the greatest displacement (inhibitory constant value of 11.1 μ m ), whereas the other sex pheromone components show much smaller displacements. Consistent with other PBP s, the three plant volatiles (linalool, benzaldehyde and indole) show only a limited displacement of CbuqPBP 1. However, the binding abilities of 1 : 1 ratios of each of the three plant volatiles with dibutyl phthalate show increases of 62.3%, 65.1% and 51.7% over the binding abilities of the three plant volatiles alone. CbuqPBP 1 has dual roles in the processes of sensing sex pheromones and plant volatiles.

Adipose tissue, an endocrine organ of the body, is involved in some obesity-related disease states such as insulin resistance, diabetes mellitus, and atherosclerosis. Vaspin is a novel adipocyte with insulin sensitizing effects. In this study, we planned to estimate serum vaspin concentrations as related to glycemic status and the presence of macrovascular complications among elderly patients with type-2 diabetes mellitus (T2DM). A total of 230 elderly patients with T2DM were evaluated. These patients were divided into two groups: patients without complications (T2DM group, n = 110), and patients with macrovascular complications (T2DM + MC group, n = 120). In addition, 60 healthy elderly subjects were enrolled and assigned into the control group (NC group). Relevant parameters were matched for age and gender ratio. Serum vaspin concentrations were measured by Enzyme-linked immunosorbent assay (ELISA). Anthropometric measurements, plasma glucose and HbA1C levels, insulin concentration, liver and kidney functions, and lipid profile were measured for each participant. Serum vaspin concentrations were significantly higher in the T2DM group than in the T2DM + MC group (F = 13.122, P < 0.01). These concentrations were also significantly higher among females, compared to males (T = 3.567, P < 0.05). Logistic regression analysis revealed that serum vaspin concentration, systolic blood pressure, HDL-C and T2DM duration were independent influencing factors for diabetic macrovascular complications. Serum vaspin may be considered as a potential marker to assess the status of elderly patients with T2DM and the risk of developing serious macrovascular complications. Further prospective studies are warranted. ChiCTR-OPC-14005698 , retrospectively registered on 20 Dec. 2014.

Background Hirschsprung disease (HD) is a congenital intestinal anomaly resulting from a failure to form enteric ganglia in the lower bowel. Surgery is the main therapeutic strategy, although neural stem cell transplantation has recently shown promise. However, HD remains a challenging disorder to treat. Our aim was to identify drugs that could counteract the dysregulated pathways in HD and could thus be potential novel therapies. Methods We used microarray analysis to identify genes differentially expressed in ganglionic and aganglionic bowel samples from eight children with HD. The signature of differentially expressed genes was then used as a search query to explore the Connectivity Map (cMAP), a transcriptional expression database that catalogs gene signatures elicited by chemical perturbagens. Results We uncovered several dysregulated signaling pathways, and in particular regulation of neuron development, in HD. The cMAP search identified some compounds with the potential to counteract the effects of the dysregulated molecular signature in this disease. One of these, pepstatin A, was recently shown to rescue the migration defects observed in a mouse model of HD, providing strong support for our findings. Conclusions This study advances our understanding of the molecular changes in HD and identifies several potential pharmacological interventions. Further testing of the identified compounds is warranted.

The aim of this study was to investigate the association between common variants in the human tissue kallikrein 1 (KLK1) gene and susceptibility to essential hypertension in Chinese Han.A tagging single nucleotide polymorphism (tSNP) approach was used for a case-control study in 2411 patients with essential hypertension and 2348 controls. All DNA samples and clinical data were collected from the International Collaborative Study of Cardiovascular Disease in Asia (InterASIA).Based on the HapMap data of Han Chinese in Beijing (CHB) population, two non-synonymous polymorphisms, namely rs5517 (Glu162Lys) and rs5516 (Gln121Glu), were selected as tSNPs which could efficiently tag eight SNPs of the KLK1 gene with R larger than 90% for both haplotypes and single locus. Significant differences were found between groups for frequencies of rs5517 A allele (42.48% in cases versus 39.32% in controls, P=0.0019) and AA genotype [adjusted odds ratio (OR)=1.25 for AA versus AG/GG, P=0.0067]. The haplotype composed of the rs5517 A and rs5516 G allele significantly increased the risk of hypertension, with adjusted OR of 1.12 [95% confidence interval (CI), 1.04-1.28, P=0.0377] when compared with the common haplotype G-C. Diplotype analysis also showed a significant association between the diplotype of AG-AC and essential hypertension (OR=1.34, 95% CI, 1.07-1.68, P=0.0096).The present study suggested that rs5517 in the KLK1 gene was significantly associated with essential hypertension in a Chinese Han population.

Kininogens serve as the precursors of potent vasoactive kinin peptides and also function as cysteine proteinase inhibitors.Given its potential role in blood pressure homeostasis, a tagging single nucleotide polymorphism (SNP) based case-control study was conducted to explore the association between kininogen 1 gene common variants and essential hypertension in Chinese Han population. Four tagging SNPs were selected on the basis of the HapMap database and further genotyped in 2411 patients with essential hypertension and 2348 controls from the International Collaborative Study of Cardiovascular Disease in Asia (InterASIA in China).A significant gender-specific association between the kininogen 1 gene common variants and essential hypertension was observed. In male, but not female participants, rs2304456 CC genotype and rs4686799 TT genotype were significantly related to hypertension [odds ratio (OR) = 2.20, 95% confidence interval (CI): 1.24-3.90, P = 0.007 and OR = 1.31, 95% CI: 1.04-1.66, P = 0.025, respectively]. The haplotypes G-C-C-T and the A-A-T-T were significantly associated with essential hypertension in the male population with adjusted OR 1.43 (P < 0.001) and OR 1.24 (P = 0.001), respectively. The haplotype G-A-C-T was in significant association with essential hypertension (OR = 1.42, P = 0.003) as well as systolic blood pressure (P = 0.005) and diastolic blood pressure (P = 0.015).This is the first association study of the kininogen 1 gene with essential hypertension. Both single-locus and haplotype analyses indicated the kininogen 1 gene was associated with essential hypertension and blood pressure traits in the Chinese male population.

Sterol regulatory element binding proteins (SREBPs), as a family of membrane-bound transcription factors, control the metabolism of cholesterol and fatty acids. We conducted a case-control study to investigate whether the common variants of genes from the SREBP2 activating-related pathway, involving SREBP2, SCAP, INSIG1 and INSIG2 genes, were associated with coronary heart disease (CHD) of Chinese Han population individually or interactively. Three, four and two single nucleotide polymorphisms (SNPs) from the INSIG1, INSIG2 and SCAP genes were chosen as haplotype-tagging SNPs (htSNPs), respectively, and one nonsynonymous coding SNP was selected from SREBP2. All of the SNPs were genotyped in 853 CHD cases and 948 unrelated control subjects. The interactions among SNPs of the four genes were evaluated with multifactor-dimensionality reduction (MDR) and logistic regression models (LRM). The results from MDR indicated that there existed the SNP-SNP interactive effect of INSIG1 gene on CHD (best prediction accuracy=56.09%, p=0.002 on 1000 permutations). The results from LRM also identified the 2-locus interaction model (adjusted p< or =0.001 for interaction) as well as the 3-locus gene-gene interaction (adjusted p=0.026 for interaction). Single polymorphism analysis showed that the rs4822063 of SREBP2 was associated with LDL-C in the controls. The genotype CC carriers had higher LDL-C than the major allele G carriers (3.44+/-0.90 mmol/L versus 3.17+/-0.84 mmol/L, adjusted p=0.038). Our results suggested that the INSIG1 gene was associated with CHD; there might be potential interactive effect on CHD among genes from SREBP2 activating-related pathway; and the SREBP2 gene might be associated with plasma lipid level.

Soil erosion caused by water is a major form of soil degradation. Scientists suggest that this phenomenon can be predicted based on aggregate stability. However, most of these scientists have focused on the water stability of aggregates; only a few have devoted efforts to study the mechanical stability of aggregates. To investigate the relationship of aggregate breakdown with mechanical stability and the possibility of predicting soil erosion based on mechanical stability, we collected eight kinds of Ultisol aggregates (3–5 mm) from subtropical China and exposed these aggregates to simulated rainfall (60 mm h−1). Mean weight diameter (MWD) and splash loss after rainfall were analyzed and compared with aggregate water stability and mechanical stability. Aggregate water stability was determined by wet sieving methods; aggregate mechanical stability was tested by aggregate penetration resistance and tensile strength. Wet sieving method, tensile strength, and penetration resistance of dry aggregates exhibited a good relationship with aggregate MWD (R2 ≥ 0.838, 0.775, and 0.593, respectively) under rainfall and splash (R2 = 0.758, 0.865, and 0.563, respectively). In contrast, no relationship was found between penetration resistance of wet aggregates and MWD or splash. Thus, MWD of wet sieving method and tensile strength were the better indexes that could be used to estimate fragment size distribution and splash detachment. Tensile strength also correlated with clay contents (r = 0.793*), Fed (r = 0.735*), and Feo (r = 0.911**). With further studies, a simpler and faster method could be developed to estimate soil resistance to erosion based on tensile strength in this region.

Loquat (Eriobotrya japonica Lindl.), which originates from the cooler hill regions of southwestern China, is a typical subtropical evergreen tree. Loquat is one of the most important economic crops in China, but the available genomic information is very limited. Here, we present the first deep transcriptomic analysis of loquat. De novo assembly generated 116,723 contigs and 64,814 unigenes using Illumina sequencing technology. A total of 45,739 unigenes were annotated by Nr, GO, and COG datasets. In addition, we analyzed the gene expression profiles of loquat fruit under low temperature stress and 4017 differential expressed genes were identified. We found that the unigenes involved in the brassinosteroid biosynthesis and phosphatidylinositol signaling systems were upregulated, indicating that they have an important role in the resistance of plants to low temperature. Our results provide an invaluable resource for identification of specific genes and proteins involved in loquat development and response to low temperatures.

Multifactor heart failure is a common life-threatening event in elderly patients and often complicated by concomitant hypertension and diabetes mellitus (DM). The aim of this study was to evaluate whether α1-blocker, urapidil, provides additional therapeutic benefits compared to nitroglycerin (NG) in treatment of multifactor heart failure complicated by hypertension and DM in elderly patients.Seventy-two elderly consecutive patients were randomized into 2 groups that received treatment with urapidil or NG. All patients were monitored for blood pressure (BP) and heart rate and received tests for metabolic activity and cardiovascular function.Patients receiving urapidil had significantly lower systolic BP than their counterparts in NG group (P < 0.05). Moreover, patients in urapidil group showed lower N-terminal pro-B-type natriuretic peptide levels but higher ejection fraction (t = 2.206, P < 0.05), cardiac index (t = 3.13, P < 0.05) and left end-diastolic volume (t = -3.104, P < 0.05) compared to NG group. Although both urapidil and NG decreased fasting plasma glucose (FPG) levels, there was no significant difference of FPG levels between these 2 groups.Urapidil demonstrated better efficacy than NG on lowering and stabilizing systolic BP, attenuating cardiac afterload and improving cardiac function. Both NG and urapidil significantly reduced FPG levels in multifactor heart failure patients with DM. Urapidil is a therapeutic option for the multifactor heart failure patients complicated with hypertension and DM.

Salicylic acid (SA) plays an important role for plant immunity, especially resistance against biotrophic pathogens. SA quickly accumulates after pathogen attack to activate downstream immunity events and is normally associated with a tradeoff in plant growth. Therefore, the SA level in plants has to be strictly controlled when pathogens are absent, but how this occurs is not well understood. Previously we found that in Arabidopsis (Arabidopsis thaliana), HISTONE DEACETYLASE 6 (HDA6), a negative regulator of gene expression, plays an essential role in plant immunity since its mutation allele shining 5 (shi5) exhibits autoimmune phenotypes. Here we report that this role is mainly through suppression of SA biosynthesis: first, the autoimmune phenotypes and higher resistance to Pst DC3000 of shi5 mutants depended on SA; second, SA significantly accumulated in shi5 mutants; third, HDA6 repressed SA biosynthesis by directly controlling the expression of CALMODULIN BINDING PROTEIN 60g (CBP60g) and SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1). HDA6 bound to the chromatin of CBP60g and SARD1 promoter regions, and histone H3 acetylation was highly enriched within these regions. Furthermore, the transcriptome of shi5 mutants mimicked that of plants treated with exogenous SA or attacked by pathogens. All these data suggest that HDA6 is vital for plants in finely controlling the SA level to regulate plant immunity.

HomeMolecular Plant-Microbe Interactions®Vol. 35, No. 10A High-Quality Genome of Rhizoctonia solani, a Devastating Fungal Pathogen with a Wide Host Range PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseA High-Quality Genome of Rhizoctonia solani, a Devastating Fungal Pathogen with a Wide Host RangeQun Yang, Lei Yang, Yin Wang, Yilyu Chen, Keming Hu, Wei Yang, Shimin Zuo, Jiandi Xu, Zhensheng Kang, Xueqiong Xiao, and Guotian LiQun YangState Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China, Lei YangState Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China, Yin WangState Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China, Yilyu ChenState Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China, Keming HuKey Laboratory of Plant Functional Genomics of The Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 25009, China, Wei YangState Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China, Shimin ZuoKey Laboratory of Plant Functional Genomics of The Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 25009, China, Jiandi XuInstitute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China, Zhensheng Kanghttp://orcid.org/0000-0001-5575-0122State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi China, Xueqiong XiaoState Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China, and Guotian Li†Corresponding author: G. Li; E-mail Address: li4@mail.hzau.edu.cnhttp://orcid.org/0000-0001-6780-7085State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, ChinaAffiliationsAuthors and Affiliations Qun Yang1 Lei Yang1 Yin Wang1 Yilyu Chen1 Keming Hu2 Wei Yang1 Shimin Zuo2 Jiandi Xu3 Zhensheng Kang4 Xueqiong Xiao1 Guotian Li1 † 1State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China 2Key Laboratory of Plant Functional Genomics of The Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 25009, China 3Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China 4State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi China Published Online:29 Sep 2022https://doi.org/10.1094/MPMI-06-22-0126-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementRice sheath blight caused by the filamentous fungus Rhizoctonia solani is a serious disease worldwide that leads to yield losses up to 45% and seriously threatens global food security (Nadarajah et al. 2017; Zhang et al. 2021). One of the distinct characteristics of R. solani is that it shows a wide host range and causes diseases on more than 200 plant species, including rice, maize, potato, pepper, cotton, and many ornamental plants (Sneh et al. 1998; Zhang et al. 2021). The infection process of R. solani initiates when sclerotia or mycelia attach to the host. Subsequently, specialized T-shaped structures called "infection cushions" form on the plant surface. Infection cushions secrete digestive enzymes that disrupt the plant cell walls, enabling colonization of the host tissue. Gradually, fungal hyphae invade and kill the plant cells, and the infected plant withers when seriously damaged (Abdoulaye et al. 2019). At the end of the disease cycle, R. solani produces sclerotia, which can survive in soil for many years (Long et al. 2019; Zhang et al. 2021). Owing to its wide host range, soil-borne, and saprotrophic nature, management measures to control R. solani including breeding strategies, crop rotation, and fungicides are ineffective (Abdoulaye et al. 2019), and diseases caused by R. solani have become increasingly serious all over the world (Li et al. 2021). Furthermore, the population genomics structure of R. solani strains is complex, consisting of 14 genetic groups, called anastomosis groups (AGs), named AG-1 to AG-13 and AG-BI (Zhang et al. 2021). There is also limited knowledge about the genetic structure within populations and the reproductive mode (Zheng et al. 2013). Here, therefore, we sequenced and assembled a high-quality genome of R. solani AG-1 IA strain HG81, using both Nanopore long reads and next-generation sequencing (NGS) short reads.Strain HG81 was isolated from diseased rice leaves with typical lesions of rice sheath blight in Huanggang, Hubei, China (Fig. 1). The morphology of pure cultured isolate on potato dextrose agar plates matched the description by Lal et al. (2020). We extracted fungal DNA, using the cetyltrimethylammonium bromide method, and amplified and sequenced the internally transcribed spacer (ITS) region (Zhao et al. 2022). BLAST comparisons show that the ITS sequence of strain HG81 is 99.9% similar to that of R. solani AG1-IA and 100% to that of R. solani Ms-2. High-quality genomic DNA of HG81 was extracted from fresh mycelia cultured in potato dextrose broth (Yang et al. 2022). Total DNA of HG81 was sequenced using Oxford Nanopore technology and NGS technology (Wang et al. 2021) on the PromethION platform and the MGISEQ-2000RS platform, respectively, at Nextomics Biosciences (Wuhan, China). A total of 2.9 Gb of Nanopore long reads and 4.1 Gb of NGS short reads were generated. We filtered the low-quality reads using the parameter '- q 20' to gain clean data, and the clean data were used for genome assembly, using NextDenovo (v2.5.0), and polished multiple rounds, using NextPolish (v1.3.1) (Hu et al. 2020). Finally, the 46.2-Mb genome of HG81 (N50 = 2.6 Mb, GC = 47.6%), consisting of 24 contigs, was assembled and was compared with genomes of other R. solani strains (Table 1). We anchored these contigs into 16 chromosomes using the RAGOO (v1.11) scaffolding approach (Alonge et al. 2019). Using RepeatMasker (v4.1.0) (Tarailo-Graovac and Chen 2009) and RepeatModeler (v2.0.1) (Flynn et al. 2020), a total of 9.7 Mb (23.4%) of repeat sequences were identified and masked. Using benchmarking universal single-copy orthologs (BUSCO) (v5.2.2) (Simão et al. 2015), we assessed the quality of final genome assembly using the fungi_odb10 lineage. The results showed that the HG81 genome covers 94.4% genes in the BUSCO database, including 709 complete and single-copy, seven complete and duplicated, and seven fragmented BUSCOs out of the total 758 records. Related parameters of the HG81 genome, including GC content, gene count, repeat density, and gene expression, were visualized using advanced circos in TBtools (v1.09876) (Chen et al. 2020, 2022) (Fig. 1).Fig. 1. Genomic analysis of Rhizoctonia solani HG81. A, The 16 chromosomes on a megabase scale. B, GC content. C, Gene count. D, Repeat density. E, Gene expression. The total RNA-seq reads in every analyzed window of 50 kb are from six samples. The innermost circle shows leaf inoculation assays on wheat cultivar Chinese Spring, maize cultivar Zhengdan 958, and rice cultivar Nanjing 66 with strain HG81. Symptoms were photographed 72, 72, and 120 h postinoculation on wheat, maize, and rice, respectively. Data in circles are displayed in nonoverlapping 50-kb intervals.Download as PowerPointTable 1. Summary of the Rhizoctonia solani genomeR. solani AG1-IACharacteristicsaHG81YN-7b1802/KBcXNdR. solani AG4 Rhs4caeSequencing technologyNanopore, MGISEQ-2000IlluminaIlluminaPacBio, IlluminaPacBio, IlluminaNumber of contigs246706,9082182Assembly length (bp)46,185,68438,916,67928,929,90941,104,06045,474,565Contig N50 (bp)2,611,525172,6997,1602,303,1181,560,204Maximum contig size (bp)4,485,786––––Minimum contig size (bp)98,089––––Average contig size (bp)1,924,403––––BUSCO completeness (%)94.4–––92.0Repeat rate (%)23.4––20.819.8GC content (%)47.641.747.047.648.0Predicted genes10,4989,71510,03712,34911,592CAZymes649–––109aBUSCO = benchmarking universal single-copy orthologs and CAZymes = carbohydrate-active enzymes.bLee et al. (2021).cNadarajah et al. (2017).dLi et al. (2021).eZhang et al. (2021).Table 1. Summary of the Rhizoctonia solani genomeView as image HTML To fully annotate the protein-coding genes in the genome of HG81, 3.5 Gb of RNA-seq data of six samples from the RSIADB database (Chen et al. 2016), a collective resource for R. solani AG1-IA transcriptomes, were used in the annotation process. Genome annotations were performed using Funannotate (v1.8.9) and 10,498 protein-coding genes were predicted. Using InterProScan (v5.52-86.0) (Quevillon et al. 2005), 7,940 genes have been annotated to the following databases: Pfam, Gene3D, PANTHER, SUPERFAMILY, Conserved Domain Database, and SMART (Simple Modular Architecture Research Tool) (Byrd and Raney 2012; Letunic et al. 2012; Lu et al. 2020; Mi et al. 2019; Punta et al. 2012; Yeats et al. 2008). Carbohydrate-active enzymes (CAZymes) play a key role in facilitating infection and gaining nutrition (Zhao et al. 2013). Using the dbCAN pipeline (Zhang et al. 2018), we annotated 639 CAZymes in the genome, including 135 auxiliary activities, 14 carbohydrate-binding modules, 285 glycoside hydrolases, 73 glycosyltransferases, 64 carbohydrate esterases, and 58 polysaccharide lyases (Wang 2022). Among them, 10 genes may have dual functions and were annotated into two categories of CAZymes. Compared with R. solani AG4 Rhs4ca (Zhang et al. 2021), more CAZymes were annotated in the genome of R. solani AG1-IA HG81.We compared the HG81 genome with recently published genomes of different strains, including R. solani AG1-IA YN-7, 1802/KB, and XN and R. solani AG4 Rhs4ca (Lee et al. 2021; Li et al. 2021; Nadarajah et al. 2017; Zhang et al. 2021) (Table 1). Comparison items include the number of contigs, assembly length, and N50 value. These results reveal that the quality of the HG81 genome has a notable improvement, especially in the number of contigs and the N50 value (Table 1). Using MUMmer (v4.0.0rc1) (Marcais et al. 2018), a total of 428,441 small genetic variations, including 377,201 single nucleotide polymorphisms (SNPs) and 51,240 small insertions and deletions (InDels), were detected between HG81 and R. solani AG1-IA XN. Further, using Lumpy-SV (v0.3.0) (Layer et al. 2014), we identified 10,882 structural variants (SVs) between HG81 and XN, including 9,130 BNDs (catch-all for a generic breakpoint), 1,413 deletions, 35 inversions, and 304 duplications.In summary, we report a high-quality genome of R. solani AG1-IA strain HG81, which causes rice sheath blight and other diseases. In total, we assembled 24 contigs and predicted 10,498 genes and annotated 639 CAZymes in the HG81 genome. We identified 377,201 SNPs and 51,240 InDels and 10,882 SVs between HG81 and the reference genome R. solani AG1-IA XN. The genome presented in this study provides a valuable basis for future research into the pathogenesis of R. solani and effective disease management.Data AvailabilityThe HG81 genome sequencing file is available at the National Center for Biotechnology Information under project accession number PRJNA841755. All the data generated in this study, including the comparative analysis files and the annotation file, have been deposited to the Figshare database.Author-Recommended Internet ResourcesFigshare: https://doi.org/10.6084/m9.figshare.19983728.v3Funannotate: https://github.com/nextgenusfs/funannotateNextDenovo: https://github.com/Nextomics/NextDenovoNextPolish: https://github.com/Nextomics/NextPolishPathogen Host Interactions database: http://www.phi-base.orgRSIADB, Rhizoctonia solani Genome data: http://genedenovoweb.ticp.net:81/rsia/index.php?m=index&f=indexThe author(s) declare no conflict of interest.Literature CitedAbdoulaye, A. H., Foda, M. F., and Kotta-Loizou, I. 2019. Viruses infecting the plant pathogenic fungus Rhizoctonia solani. Viruses 11:1113. https://doi.org/10.3390/v11121113 Crossref, ISI, Google ScholarAlonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B., and Schatz, M. C. 2019. RaGOO: Fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 20:224. https://doi.org/10.1186/s13059-019-1829-6 Crossref, Medline, ISI, Google ScholarByrd, A. K., and Raney, K. D. 2012. Superfamily 2 helicases. Front. Biosci. 17:2070-2088. https://doi.org/10.2741/4038 Crossref, ISI, Google ScholarChen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., and Xia, R. 2020. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 13:1194-1202. https://doi.org/10.1016/j.molp.2020.06.009 Crossref, Medline, ISI, Google ScholarChen, C., Wu, Y., and Xia, R. 2022. A painless way to customize Circos plot: From data preparation to visualization using TBtools. iMeta. 1:e35. https://doi.org/10.1002/imt2.35 Crossref, Google ScholarChen, L., Ai, P., Zhang, J., Deng, Q., Wang, S., Li, S., Zhu, J., Li, P., and Zheng, A. 2016. RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA. Database (Oxford) 2016:baw031. https://doi.org/10.1093/database/baw031 Crossref, Medline, ISI, Google ScholarFlynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., and Smit, A. F. 2020. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. U.S.A. 117:9451-9457. https://doi.org/10.1073/pnas.1921046117 Crossref, Medline, ISI, Google ScholarHu, J., Fan, J., Sun, Z., and Liu, S. 2020. NextPolish: A fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36:2253-2255. https://doi.org/10.1093/bioinformatics/btz891 Crossref, Medline, ISI, Google ScholarLal, M., Chaudhary, S., Kumar, M., Sharma, S., and Chakrabarti, S. K. 2020. First report of collar and stem rot caused by Rhizoctonia solani AG1-IA on Sesbania sesban in India. Plant Dis. 104:3251. https://doi.org/10.1094/PDIS-06-20-1342-PDN Google ScholarLayer, R. M., Chiang, C., Quinlan, A. R., and Hall, I. M. 2014. LUMPY: A probabilistic framework for structural variant discovery. Genome Biol. 15:R84. https://doi.org/10.1186/gb-2014-15-6-r84 Crossref, Medline, ISI, Google ScholarLee, D.-Y., Jeon, J., Kim, K.-T., Cheong, K., Song, H., Choi, G., Ko, J., Opiyo, S. O., Correll, J. C., Zuo, S., Madhav, S., Wang, G.-L., and Lee, Y.-H. 2021. Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. BMC Genomics 22:242. https://doi.org/10.1186/s12864-021-07549-7 Crossref, Medline, ISI, Google ScholarLetunic, I., Doerks, T., and Bork, P. 2012. SMART 7: Recent updates to the protein domain annotation resource. Nucleic Acids Res. 40:D302-D305. https://doi.org/10.1093/nar/gkr931 Crossref, Medline, ISI, Google ScholarLi, C., Guo, Z., Zhou, S., Han, Q., Zhang, M., Peng, Y., Hsiang, T., and Chen, X. 2021. Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi. Commun. Biol. 4:201. https://doi.org/10.1038/s42003-021-01724-y Crossref, Medline, ISI, Google ScholarLong, J. J., Luna, E. K., Jackson, M., Wheat, W., Jahn, C. E., and Leach, J. E. 2019. Interactions of free-living amoebae with the rice fungal pathogen, Rhizoctonia solani. BMC Res. Notes 12:746. https://doi.org/10.1186/s13104-019-4802-2 Crossref, Medline, ISI, Google ScholarLu, S., Wang, J., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Marchler, G. H., Song, J. S., Thanki, N., Yamashita, R. A., Yang, M., Zhang, D., Zheng, C., Lanczycki, C. J., and Marchler-Bauer, A. 2020. CDD/SPARCLE: The conserved domain database in 2020. Nucleic Acids Res. 48:D265-D268. https://doi.org/10.1093/nar/gkz991 Crossref, Medline, ISI, Google ScholarMarcais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., and Zimin, A. 2018. MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol. 14:e1005944. https://doi.org/10.1371/journal.pcbi.1005944 Crossref, Medline, ISI, Google ScholarMi, H., Muruganujan, A., Huang, X., Ebert, D., Mills, C., Guo, X., and Thomas, P. D. 2019. Protocol update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat. Protoc. 14:703-721. https://doi.org/10.1038/s41596-019-0128-8 Crossref, Medline, ISI, Google ScholarNadarajah, K., Mat Razali, N., Cheah, B. H., Sahruna, N. S., Ismail, I., Tathode, M., and Bankar, K. 2017. Draft genome sequence of Rhizoctonia solani Anastomosis Group 1 subgroup 1A strain 1802/KB isolated from rice. Genome Announc. 5:e01188-17. https://doi.org/10.1128/genomeA.01188-17 Crossref, Medline, Google ScholarPunta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E. L. L., Eddy, S. R., Bateman, A., and Finn, R. D. 2012. The Pfam protein families database. Nucleic Acids Res. 40:D290-D301. https://doi.org/10.1093/nar/gkr1065 Crossref, Medline, ISI, Google ScholarQuevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., and Lopez, R. 2005. InterProScan: Protein domains identifier. Nucleic Acids Res. 33:W116-W120. https://doi.org/10.1093/nar/gki442 Crossref, Medline, ISI, Google ScholarSimão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., and Zdobnov, E. M. 2015. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210-3212. https://doi.org/10.1093/bioinformatics/btv351 Crossref, Medline, ISI, Google ScholarSneh, B., Burpee, L., and Ogoshi, A. 1998. Identification of Rhizoctonia Species. APS Press, St. Paul, MN, U.S.A. Google ScholarTarailo-Graovac, M., and Chen, N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 25:4.10.1-4.10.14. https://doi.org/10.1002/0471250953.bi0410s25 Crossref, Google ScholarWang, H., Dong, Y., Liao, W., Zhang, X., Wang, Q., Li, G., Xu, J. R., and Liu, H. 2021. High-quality genome resource of Clonostachys rosea strain CanS41 by Oxford Nanopore long-read sequencing. Plant Dis. 105:2231-2234. https://doi.org/10.1094/PDIS-12-20-2615-A Link, ISI, Google ScholarWang, Y. 2022. Genome sequence of Magnaporthe oryzae strain EA18 virulent to multiple widely used rice varieties. Mol. Plant-Microbe Interact. 35:727-730. https://doi.org/10.1094/MPMI-01-22-0030-A Link, Google ScholarYang, L., Zhao, M., Sha, G., Sun, Q., Gong, Q., Yang, Q., Xie, K., Yuan, M., Mortimer, J. C., Xie, W., Wei, T., Kang, Z., and Li, G. 2022. The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains. Computational Struc. Biotechnol. J. 20:1012-1026. https://doi.org/10.1016/j.csbj.2022.01.030 Crossref, Medline, ISI, Google ScholarYeats, C., Lees, J., Reid, A., Kellam, P., Martin, N., Liu, X., and Orengo, C. 2008. Gene3D: Comprehensive structural and functional annotation of genomes. Nucleic Acids Res. 36:D414-D418. https://doi.org/10.1093/nar/gkm1019 Crossref, Medline, ISI, Google ScholarZhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P. K., Xu, Y., and Yin, Y. 2018. dbCAN2: A meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46:W95-W101. https://doi.org/10.1093/nar/gky418 Crossref, Medline, ISI, Google ScholarZhang, Z. K., Xia, X. Y., Du, Q., Xia, L., Ma, X. Y., Li, Q. Y., and Liu, W. D. 2021. Genome sequence of Rhizoctonia solani Anastomosis Group 4 strain Rhs4ca, a widespread pathomycete in field crops. Mol. Plant-Microbe Interact. 34:826-829. https://doi.org/10.1094/MPMI-12-20-0362-A Link, ISI, Google ScholarZhao, J., Sun, P., Sun, Q., Li, R., Qin, Z., Sha, G., Zhou, Y., Bi, R., Zhang, H., Zheng, L., Chen, X. L., Yang, L., Li, Q., and Li, G. 2022. The MoPah1 phosphatidate phosphatase is involved in lipid metabolism, development, and pathogenesis in Magnaporthe oryzae. Mol. Plant Pathol. 23:720-732. ISI, Google ScholarZhao, Z., Liu, H., Wang, C., and Xu, J.-R. 2013. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics 14:274. https://doi.org/10.1186/1471-2164-14-274 Crossref, Medline, ISI, Google ScholarZheng, A. P., Lin, R. M., Zhang, D. H., Qin, P. G., Xu, L. Z., Ai, P., Ding, L., Wang, Y. R., Chen, Y., Liu, Y., Sun, Z. G., Feng, H. T., Liang, X. X., Fu, R. T., Tang, C. Q., Li, Q., Zhang, J., Xie, Z. L., Deng, Q. M., Li, S. C., Wang, S. Q., Zhu, J., Wang, L. X., Liu, H. N., and Li, P. 2013. The evolution and pathogenic mechanisms of the rice sheath blight pathogen. Nat. Commun. 4:1424. https://doi.org/10.1038/ncomms2427 Crossref, Medline, ISI, Google ScholarQ. Yang and L. Yang contributed equally to this work.Funding: This work was supported by Fundamental Research Funds for the Central Universities (2662020ZKPY006) to G. Li and Innovation Promotion Program for Small and Medium-Sized Sci-Tech Enterprises (2021TSGC1223) to J. Xu. This study was also supported by Hubei Hongshan Laboratory.The author(s) declare no conflict of interest. Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.DetailsFiguresLiterature CitedRelated Vol. 35, No. 10 October 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Article History Issue Date: 8 Oct 2022Published: 29 Sep 2022Accepted: 12 Jul 2022 Pages: 954-958 InformationCopyright © 2022 The Author(s).This is an open access article distributed under the CC BY-NC-ND 4.0 International license.Funding Fundamental Research Funds for the Central UniversitiesGrant/Award Number: 2662020ZKPY006 Innovation Promotion Program for Small and Medium-Sized Sci-Tech EnterprisesGrant/Award Number: 2021TSGC1223 Hubei Hongshan Laboratory Keywordscarbohydrate-active enzymesNanoporeOryza sativaThanatephorus cucumeriswhole-genome sequencingThe author(s) declare no conflict of interest.PDF download

This paper reports on the EAG and behavioral responses of unmated females, unmated males, and mated females of Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae) to ten plant volatiles. Seven volatiles tested from the host species Viburnum awabuki K., Betula luminifera H. Winkl, Juglans regia L., and Populus tomentosa Carr. were β-myrcene, (Z)-3-hexen-1-ol, nonanal, dichloromethyl ether, salicyaldehyde, 3-methylbutyric acid, and trichloroethylene. Three volatiles tested from non-host conifers were (1S)-(−)-β-pinene, (1R)-( )-α-pinene, and (1S)-(−)-α-pinene. The EAG responses of unmated B. horsfieldi females to these ten volatiles were tested at five concentrations (0.0001, 0.001, 0.01, 0.1, and 0.2 µL/µL). For eight of the volatiles, the EAG responses did not change significantly after their concentration was increased to 0.1 µL/µL. However, the maximum EAG response to 3-methylbutyric acid was at 0.0001 µL/µL and it decreased at higher concentrations. The EAG response to salicyaldehyde increased throughout the range of concentrations. The EAG response of mated females to salicyaldehyde at 0.1 µL/µL was significantly stronger than for unmated females or unmated males. EAG data showed that (1S)-(−)-β-pinene at 0.2 µL/µL had a strong repellent affect on unmated female and unmated male B. horsfieldi adults (P < 0.01). At 0.2 µL/µL, (Z)-3-hexen-1-ol had an attractive effect on unmated females (P < 0.05) and salicyaldehyde had an attractive effect on mated female B. horsfieldi adults (P < 0.05) in a Y-tube olfactometer. There was no significant difference in the repellent or attractive effects of dichloromethyl ether, 3-methylbutyric acid, or (1R)-( )-α-pinene at five concentrations to unmated female or male B. horsfieldi adults.

The adsorption method of Tenax-TA absorbent with GC-MS was used to analyze diurnal rhythms of volatiles from undamaged holly plants, Viburnum awabuki Kock (Dipsacales: Adoxaceae) hol-ly infested by the white-striped longhorned beetle, Batocera lineolata Chevrolat (Coleoptera: Cerambycidae). Electroantennography and a Y-tube olfactometer were used to compare and ana-lyze electroantennogram and behavioral responses of unmated male and female adults to the volatiles from V. awabuki (both undamaged and infested plants). The results of the GC-MS anal-ysis showed that phytosterol and alkane are major volatiles for V. awabuki. The relative content of V. awabuki volatiles changed during the day. Electroantennogram and behavioral responses of unmated male and female adults to the volatiles from both undamaged and infested plants of V. awabuki were stronger between 08:00 and 10:00 and 16:00 and 18:00, which is consistent with early morning and evening feeding behaviors of adults in the field.

It is the first time for ChangE-3 lander landing on an extraterrestrial celestial body in China. Guidance, navigation and control system is one of the most important systems. Guidance, navigation, hazard avoidance and attitude control are demanded strictly for safe landing during powered descent. Adaptive powered explicit guidance, multibeam fault-tolerant navigation and partition quaternion control are proposed for ChangE-3 mission. The results in orbit show that these techniques are reasonable. The landing mission is successful and the performances of landing precision, attitude and velocity are better than the corresponding requirements. This paper presents requirement, composing and technique of ChangE-3 GNC system and results in orbit.

The bamboo snout beetle Cyrtotrachelus buqueti is a widely distributed wood-boring pest found in China, and its larvae cause significant economic losses because this beetle targets a wide range of host plants. A potential pest management measure of this beetle involves regulating olfactory chemoreceptors. In the process of olfactory recognition, pheromone-binding proteins (PBPs) play an important role. Homology modeling and molecular docking were conducted in this study for the interaction between CbuqPBP1 and dibutyl phthalate to better understand the relationship between PBP structures and their ligands. Site-directed mutagenesis and binding experiments were combined to identify the binding sites of CbuqPBP1 and to explore its ligand-binding mechanism. The 3D structural model of CbuqPBP1 has six a-helices. Five of these a-helices adopt an antiparallel arrangement to form an internal ligand-binding pocket. When docking dibutyl phthalate within the active site of CbuqPBP1, a CH- π interaction between the benzene ring of dibutyl phthalate and Phe69 was observed, and a weak hydrogen bond formed between the ester carbonyl oxygen and His53. Thus, Phe69 and His53 are predicted to be important residues of CbuqPBP1 involved in ligand recognition. Site-directed mutagenesis and fluorescence assays with a His53Ala CbuqPBP1 mutant showed no affinity toward ligands. Mutation of Phe69 only affected binding of CbuqPBP1 to cedar camphor. Thus, His53 (Between α2 and α3) of CbuqPBP1 appears to be a key binding site residue, and Phe69 (Located at α3) is a very important binding site for particular ligand interactions.

Reverse transcription quantitative real-time PCR (RT-qPCR) is a common way to study gene regulation at the transcriptional level due to its sensibility and specificity, but it needs appropriate reference genes to normalize data. Ananas comosus var. bracteatus, with white-green chimeric leaves, is an important pantropical ornamental plant. Up to date, no reference genes have been evaluated in Ananas comosus var. bracteatus. In this work, we used five common statistics tools (geNorm, NormFinder, BestKeeper, ΔCt method, RefFinder) to evaluate 10 candidate reference genes. The results showed that Unigene.16454 and Unigene.16459 were the optimal reference genes for different tissues, Unigene.16454 and zinc finger ran-binding domain-containing protein 2 (ZRANB2) for chimeric leaf at different developmental stages, isocitrate dehydrogenase [NADP] (IDH) and triacylglycerol lipase SDP1-like (SDP) for seedlings under different hormone treatments. The comprehensive results showed IDH, pentatricopeptide repeat-containing protein (PPRC), Unigene.16454, and caffeoyl-CoA O methyltransferase 5-like (CCOAOMT) are the top-ranked stable genes across all the samples. The stability of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was the least during all experiments. Furthermore, the reliability of recommended reference gene was validated by the detection of porphobilinogen deaminase (HEMC) expression levels in chimeric leaves. Overall, this study provides appropriate reference genes under three specific experimental conditions and will be useful for future research on spatial and temporal regulation of gene expression and multiple hormone regulation pathways in Ananas comosus var. bracteatus.

Pheromone-binding proteins (PBPs) play important roles in binding and transporting sex pheromones. However, the PBP genes identified in coleopteran insects and their information sensing mechanism are largely unknown. Cyrtotrachelus buqueti (Coleoptera: Curculionidae) is a major insect pest of bamboo plantations. In this study, a novel PBP gene, CbuqPBP2, from C. buqueti was functionally characterized. CbuqPBP2 was more abundantly expressed in the antennae of both sexes than other body parts, and its expression level was significantly male-biased. Fluorescence competitive binding assays showed that CbuqPBP2 exhibited the strongest binding affinity to dibutyl phthalate (Ki = 6.32 μM), followed by styrene (Ki = 11.37 μM), among twelve C. buqueti volatiles. CbuqPBP2, on the other hand, showed high binding affinity to linalool (Ki = 10.55), the main volatile of host plant Neosinocalamus affinis. Furthermore, molecular docking also demonstrated the strong binding ability of CbuqPBP2 to dibutyl phthalate, styrene, and linalool, with binding energy values of −5.7, −6.6, and −6.0 kcal/mol, respectively, and hydrophobic interactions were the prevailing forces. The knockdown of CbuqPBP2 expression via RNA interference significantly reduced the electroantennography (EAG) responses of male adults to dibutyl phthalate and styrene. In conclusion, these results will be conducive to understanding the olfactory mechanisms of C. buqueti and promoting the development of novel strategies for controlling this insect pest.

To investigate the farmland soil nitrogen input from atmospheric dry and wet deposition, a 1-year observation was conducted in the Yulin and Luochuan areas of North Shaanxi Province from June 2007 to May 2008. The total inorganic nitrogen (TIN) deposition in Yulin and Luochuan was 22.17 and 16.95 kg x hm(-2) x a(-1), among which, wet deposition accounted for 95.1% and 90.4%, while dry deposition accounted for 4.9% and 9.6%, respectively, illustrating that the nitrogen deposition in both Yulin and Luochuan was mainly come from wet deposition. In the TIN deposition, the amount of nitrate in Yulin and Luochuan was 12.22 and 9.24 kg x hm(-2) xa(-1), accounting for 55.1% and 54.5%, respectively. The amount of wet deposition and the percentage of nitrate in TIN deposition were higher in Yulin than in Luochuan, because of the differences in pollution level, weather condition, and underlying surface characteristics.

The destruction of soil aggregates upon transport by overland flow may produce a significant effect on sediment transport capacity and general intensity of erosion. The particle size distribution of destructed soil aggregates has a close relation to the surface runoff and permeability of soils. The objective of this study is to quantify the effects of transport distance and flow discharge of overland flow on the destruction of aggregates of Ultisols in a 3.8 m long flume with a fixed bed. A series of experiments were carried out at a slope of 17.6%, including six transport distances (9–108 m) and eight discharges (0.4–1.2 L/s). The results indicate that (1) the extent of the destruction of aggregates became weaker with the decrease in size over the same transport distances or at the same discharges; (2) the aggregates derived from Shale were rapidly abraded and had more serious destruction as compared to the aggregates from Quaternary red clay during the transport process, which was relevant to the stability difference of the two parent materials; (3) two stages of aggregate breakdown could be identified in terms of the coefficient α during transport, that is, the aggregates were rapidly abraded and became round and were predominantly broken down into smaller fragments at the first stage, while the smaller fragments and the round aggregates were weakly abraded with reduction in weight and their shape became regular; and (4) the extent of the destruction decreased with increasing discharge, which was due to the changes in the hydraulic properties (flow depth and friction factor) and in movement modes during the transport process. The analysis of the characteristics on aggregate destruction by overland flow can contribute to the development of soil erosion models.

Aims. This study was to evaluate the association of serum vaspin concentrations with body mass index (BMI) among elderly patients (>60 years old). Methods. A total of 227 elderly individuals included 76 healthy with normal glucose tolerance, which divided into normal weight control (BMI < 25, n = 38) and overweight or obese control (BMI ≥ 25, n = 38) subgroups, and 150 T2DM patients, which divided into normal weight diabetes (BMI < 25, n = 55), overweight diabetes (30 > BMI ≥ 25, n = 52), and obese diabetes (BMI ≥ 30, n = 43) subgroups. Relevant parameters were matched for age and gender ratio. Serum vaspin concentrations were measured by enzyme-linked immunosorbent assay. Results. Serum vaspin concentration was significantly higher in the T2DM than the healthy (451.9 ± 32.6 versus 284.2 ± 21.7, P < 0.01). In the diabetic patients, the vaspin concentration was significantly higher in the obese group than the normal weight group (498.2 ± 17.1 versus 382.1 ± 21.3, P < 0.05). In addition, the concentration of vaspin in normal weight T2DM was higher than in healthy control group with normal weight (382.1 ± 21.3 versus 192.5 ± 45.2, P < 0.05). Multiple regression analysis revealed that BMI was independent factors influencing the serum vaspin concentration in all participants. Conclusion. Vaspin may play an important compensatory role in obesity and insulin resistance in elderly people. The clinical trial registration number is ChiCTR-OPC-14005698.

Verticillium wilt, caused by Verticillium dahliae Kleb., is an important disease of spinach (Spinacia oleracea L.) and use of genetic resistance is the most economical method of controlling this disease.The objective of this research was to conduct molecular association analysis for Verticillium wilt resistance in spinach.A total of 95 USDA spinach accessions were evaluated for resistance to Verticillium wilt in this study.Phenotyping was conducted using a 0-4 scale of disease severity scores of Verticillium wilt and genotyping was performed using 2,878 SNPs which were postulated from genotyping by sequencing (GBS).STRUCTURE 2.3.4 and MEGA 6 were used for population structure and genetic diversity analysis.The single marker regression (SMR) from QGene, general linear mode (GLM) and mixed linear mode (MLM) from TEASSEL, and compressed mixed linear model (cMLM) and enriched compressed mixed linear model (EcMLM) from GAPIT were used for association analysis of Verticillium wilt resistance.Significant genetic variation of Verticillium wilt disease resistance was observed among the 95 spinach accessions with a wide range from 0.3 to 3.0 on a 0-4 scale.Two well-differentiated genetic populations and admixtures were postulated in the spinach panel.Five SNP markers, AYZV02052595_108, AYZV02112284_14543, AYZV02123399_146, AYZV02164612_331, and AYZV02170942_274 were identified to be associated with Verticillium wilt resistance with R-squared values from 9.3 to 18.2%.These markers may provide a tool utilized in molecular spinach breeding to select Verticillium wilt resistance through markerassisted selection.

It has long been known that the gaseous plant hormone ethylene plays a key role in nodulation in legumes. The perception of ethylene by a family of five membrane-localized receptors is necessary to trigger the ethylene signaling pathway, which regulates various biological responses in Arabidopsis. However, a systematic analysis of the ethylene receptors in leguminous plants and their roles in nodule development is lacking. In this study, we performed a characterization of ethylene receptor genes based on the latest Glycine max genome sequence and a public microarray database. Eleven ethylene receptor family genes were identified in soybean through homology searches, and they were divided into two subgroups. Exon-intron analysis showed that the gene structures are highly conserved within each group. Further analysis of their expression patterns showed that these ethylene receptor genes are differentially expressed in various soybean tissues and organs, including functional nodules. Notably, the ethylene receptor genes showed different responses to rhizobial infection and Nod factors, suggesting a possible role for ethylene receptors and ethylene signaling in rhizobia-host cell interactions and nodulation in soybean. Together, these data indicate the functional divergence of ethylene receptor genes in soybean, and that some of these receptors mediate nodulation, including rhizobial infection, nodule development, and nodule functionality. These findings provide a foundation for further elucidation of the molecular mechanism by which the ethylene signaling pathway regulates nodulation in soybean, as well as other legumes.

This study investigates how psychological contract influences employees' extra-role contribution, such as organizational identification and organizational citizenship behavior.Specifically, it proposes the mediating role of psychological capital in the abovementioned relationships.A total of 283 employees in China completed the questionnaires.Results indicate that psychological capital partially mediates the relationship between psychological contract breach and organizational identification, and fully mediates the relationship between psychological contract breach and organizational citizenship behavior.In addition, organizational identification mediates the relationship between psychological capital and organizational citizenship behavior.Implications for future research of the current study are discussed.

Summary To investigate the effect of long‐term storage on in vitro protein digestion of the retort‐pouched pork belly. The products were stored at 25 °C for 0, 30, 60 and 120 days and digested with pepsin and trypsin at each time point. SDS ‐ PAGE and LC ‐ MS ‐ MS were applied to separate and identify proteins and their digested products. In vitro protein digestibility decreased from 47.7% after 60‐day storage to 25.4% after 120‐day storage for the samples digested by pepsin, and from 63.9% to 45.7% for the samples digested by pepsin and trypsin at corresponding time points. LC ‐ MS ‐ MS demonstrated changes in peptide composition and abundance with storage time. Long‐term storage could deteriorate nutritive values of meat products by reducing digestible protein content.

Evidence for association with schizophrenia has been reported for NOTCH4, although results have been inconsistent. Previous studies have focused on polymorphisms in the 5′ promoter region and first exon of NOTCH4. Our aim was to test the association of the entire genomic region of NOTCH4 in 218 families with at least two siblings affected by schizophrenia in Taiwan. We genotyped seven single nucleotide polymorphisms (SNPs) of this gene, with average intermarker distances of 5.3 kb. Intermarker linkage disequilibrium (LD) was calculated using gold software, and single‐locus and haplotype association analyses were performed using transmit software. We found that the T allele of SNP rs2071285 ( P = 0.035) and the G allele of SNP rs204993 ( P = 0.0097) were significantly preferentially transmitted to the affected individuals in the single‐locus association analysis. The two SNPs were in high LD (D′ &gt; 0.8). Trend for overtransmission was shown for the T‐G haplotype of the two SNPs to affected individuals ( P = 0.053), with the A‐A haplotype significantly undertransmitted ( P = 0.034). The associated region distributed across the distal portion of the NOTCH4 gene and overlapped with the genomic region of the G‐protein signaling modulator 3 and pre‐B‐cell leukemia transcription factor 2. In summary, we found modest association evidence between schizophrenia and the distal genomic region of NOTCH4 in this Taiwanese family sample. Further replication for association with the distal genomic region of NOTCH4 is warranted.

To screen the composite components of the plant volatiles that effectively attract Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae) adults, GC-MS (Gas Chromatography – Mass Spectrometry) was used to analyze and identify the type and relative content of the volatiles of the host plants of B. horsfieldi adults: Viburnum awabuki K., Betula luminifera H. Winkl, Juglans regia L. and Populus tomentosa Carr. We measured the EAG (Electroantennogram) responses of the different antennal segments of unmated female and male B. horsfieldi adults to seven host plant volatiles (β-myrcene, (Z)-3-hexen-1-ol, nonanal, dichloromethyl ether, salicyaldehyde, 3-methyl-butanoic acid and trichloroethylene) and to their composite components. A Y-tube olfactometer was used to test the insects' behavioral responses. The results of GC-MS showed that the four host plants of B. horsfieldi had different chemical fingerprints. The EAG test results showed that the responses in the apical part of the unmated female and male B. horsfieldi antennae were stronger than those in the middle part and basal part (P < 0.01). For the seven volatiles, with five different concentrations (of 0.0001, 0.001, 0.01, 0.1 and 0.2 µL/µL), the unmated female B. horsfieldi had the strongest EAG responses to 3-methylbutyric acid of 0.0001 µL/µL and the unmated female and male B. horsfieldi had increasing EAG responses to salicyaldehyde after the concentration reached 0.1 µL/µL. Among the five composite components of plant volatiles, the one mixed according to a ratio of (Z)-3-hexen-1-ol: nonanal: trichloroethylene: β-myrcene (Z∶N∶T∶M) = 57∶15∶17∶11 caused the strongest EAG response, and that response was distinctly higher than for the other four composite components (P < 0.01). The behavioral response results tested by Y-tube olfactometer were in accordance with the EAG response results. The composite component mixed according to the ratio of Z∶N∶T∶M = 57∶15∶17∶11 had a stronger attractive effect for the unmated female and male B. horsfieldi adults.

During slope erosion, the travel and abrasion of aggregate during transport may produce finer and more transportable particles, causing a significant effect on the sediment transport capacity and erosion intensity. Little information is available on the effect of roughness on aggregate abrasion in overland flow. This study investigated the potential effects of slope gradient, flow discharge, and roughness on aggregate abrasion and hydraulic characteristics in overland flow. These factors were studied with a series of aggregate abrasion experiments in a 3.8 m long flume at four slope gradients (8.7%, 17.6%, 26.8%, 36.4%), five discharges (0.4 L s− 1, 0.6 L s− 1, 0.8 L s− 1, 1.0 L s− 1, 1.2 L s− 1), and five surfaces of artificial rough beds. The results indicated that the different roughness conditions (with contributions of 63.5%) had obvious effects on the abrasion of aggregate compared to the slope gradient and discharge. Regardless of the discharge and slope gradient, the abrasion degree of aggregate gradually increased as the roughness increased. The changes in the abrasion degree of the aggregate were not the same at the different combinations of discharge and slope for each artificial rough bed. Flow depth can well explain the extent of abrasion of the aggregate for the single fixed rough bed. However, the abrasion degree of the aggregate had no significant variation with increases in the flow depth from all the data of the five artificial rough beds. The ratio between the residual weight and initial weight of soil aggregates (Wr/Wi) decreased in a power function with increase in the friction factor and shear stress from all the data of the five artificial rough beds. The friction factor and shear stress should be appropriate indicators to reflect aggregate abrasion under various roughness conditions in overland flow. The information of the analysis of the abrasion of soil aggregate under different artificial rough beds can be useful for the development of soil process-based erosion models.