The response of N₂O emissions to nitrogen (N) addition is usually positive, but its response to phosphorus (P) addition varies, and the underlying mechanisms for the changes in N₂O emissions remain unclear.  We conducted field studies to examine the response of N₂O emissions to N and P addition over two years in three typical alpine grasslands, alpine meadow (AM), alpine steppe (AS), and alpine cultivated grassland (CG) on the Qinghai-Tibet Plateau (QTP).  Our results showed consistent increases in N₂O emissions under N addition alone or with P addition, and insignificant change in N₂O emissions under P addition alone in all three grasslands.  N addition increased N₂O emissions directly in AM, by lowering soil pH in AS, and by lowering abundance of denitrification genes in CG.  N and P co-addition increased N₂O emissions in AM and AS but only showed an interactive effect in AM.  P addition enhanced the increase in N₂O emissions caused by N addition mainly by promoting plant growth in AM.  Overall, our results illustrate that short-term P addition cannot alleviate the stimulation of N₂O emissions by N deposition in alpine grassland ecosystems, and may even further stimulate N₂O emissions.

Senecavirus A (SVA) has a positive-sense, single-stranded RNA genome. Its 5´ untranslated region harbors an internal ribosome entry site (IRES), comprising 10 larger or smaller stem-loop structures (including a pseudoknot) that have been demonstrated to be well conserved. However, it is still unclear whether each stem-loop subdomain, such as a single stem or loop, is also highly conserved. To clarify this issue in the present study, a set of 29 SVA cDNA clones were constructed by site-directed mutagenesis (SDM) on the IRES. The SDM-modified scenarios included: (1) stem-formed complementary sequences exchanging with each other; (2) loop transversion; (3) loop transition; and (4) point mutations. All cDNA clones were separately transfected into cells for rescuing viable viruses, whereas only four SVAs of interest could be recovered, and were genetically stable during 20 passages. One progeny grew significantly slower than the other three did. The dual-luciferase reporter assay showed that none of the SDM-modified IRESes significantly inhibited the IRES activity. Our previous study indicated that a single motif from any of the ten stem structures, if completely mutated, would cause the failure of virus recovery. Interestingly, our present study revealed three stem structures, whose individual complementary sequences could exchange with each other to rescue sequence-modifying SVAs. Moreover, one apical loop was demonstrated to have the ability to tolerate its own full-length transition, also having no impact on the recovery of sequence-modifying SVA. The present study suggested that not every stem-loop structure was strictly conserved in its conformation, while the full-length IRES itself was well conserved. This provides a new research direction on interaction between the IRES and many factors.

Straw mulching is a widespread practice for reducing the soil carbon loss caused by erosion.  However, the effects of straw mulching on dissolved organic matter (DOM) runoff loss from black soil are not well studied.  How straw mulching affects the composition and loss of runoff DOM by changing soil aggregates remains largely unclear.  Here, a straw mulching treatment was compared to a no mulching treatment (as a control) on sloping farmland with black soil erosion in Northeast China.  We divided the soil into large macroaggregates (>2 mm), small macroaggregates (0.25–2 mm), and microaggregates (<0.25 mm).  After five rain events, the effects of straw mulching on the concentration (characterized by dissolved organic carbon (DOC)) and composition (analyzed by fluorescence spectroscopy) of runoff and soil aggregate DOM were studied.  The results showed that straw mulching reduced the runoff amount by 54.7%.  Therefore, although straw mulching increased the average DOC concentration in runoff, it reduced the total runoff DOM loss by 48.3%.  The composition of runoff DOM is similar to that of soil, as both contain humic-like acid and protein-like components.  With straw mulching treatment, the protein-like components in small macroaggregates accumulated and the protein-like components in runoff declined with rain events.  Fluorescence spectroscopy technology may help in understanding the hydrological paths of rain events by capturing the dynamic changes of runoff and soil DOM characteristics.  A variation partitioning analysis (VPA) indicated that the DOM concentration and composition of microaggregates explained 68.2% of the change in runoff DOM from no mulching plots, while the change in runoff DOM from straw mulching plots was dominated by small macroaggregates at a rate of 55.1%.  Taken together, our results demonstrated that straw mulching reduces the fragmentation of small macroaggregates and the loss of microaggregates, thus effecting DOM compositions in soil and reducing the DOM loss in runoff.  These results provide a theoretical basis for reducing carbon loss in sloping farmland.

Presently, integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy.  Here, we set the genomic and transcriptomic data as the training population data, using BSLMM, TWAS, and eQTL mapping to prescreen features according to | ^β_b|>0, top 1% of phenotypic variation explained (PVE), expression-associated single nucleotide polymorphisms (eSNPs), and egenes (false discovery rate (FDR)<0.01), where these loci were set as extra fixed effects (named GBLUP-Fix) and random effects (GFBLUP) to improve the prediction accuracy in the validation population, respectively.  The results suggested that both GBLUP-Fix and GFBLUP models could improve the accuracy of longissimus dorsi muscle (LDM), water holding capacity (WHC), shear force (SF), and pH in Huaxi cattle on average from 2.14 to 8.69%, especially the improvement of GFBLUP-TWAS over GBLUP was 13.66% for SF.  These methods also captured more genetic variance than GBLUP.  Our study confirmed that multi-omics-assisted large-effects loci prescreening could improve the accuracy of genomic prediction.

Streptococcus suis serotype 2 (S. suis 2) is a zoonotic pathogen that clinically causes severe swine and human infections (such as meningitis, endocarditis, and septicemia).  In order to cause widespread diseases in different organs, S. suis 2 must colonize the host, break the blood barrier, and cause exaggerated inflammation.  In the last few years, most studies have focused on a single virulence factor and its influences on the host.  Membrane vesicles (MVs) can be actively secreted into the extracellular environment contributing to bacteria-host interactions.  Gram-negative bacteria-derived outer membrane vesicles (OMVs) were recently shown to activate host Caspase-11-mediated non-canonical inflammasome pathway via deliverance of OMV-bound lipopolysaccharide (LPS), causing host cell pyroptosis.  However, little is known about the effect of the MVs from S. suis 2 (Gram-positive bacteria without LPS) on cell pyroptosis.  Thus, we investigated the molecular mechanism by which S. suis 2 MVs participate in endothelial cell pyroptosis.  In this study, we used proteomics, electron scanning microscopy, fluorescence microscope, Western blotting, and bioassays, to investigate the MVs secreted by S. suis 2.  First, we demonstrated that S. suis 2 secreted MVs with an average diameter of 72.04 nm, and 200 proteins in MVs were identified.  Then, we showed that MVs were transported to cells via mainly dynamin-dependent endocytosis.  The S. suis 2 MVs activated NLRP3/Caspase-1/GSDMD canonical inflammasome signaling pathway, resulting in cell pyroptosis, but it did not activate the Caspase-4/-5 pathway.  More importantly, endothelial cells produce large amounts of reactive oxygen species (ROS) and lost their mitochondrial membrane potential under induction by S. suis 2 MVs.  The results in this study suggest for the first time that MVs from S. suis 2 were internalized by endothelial cells via mainly dynamin-dependent endocytosis and might promote NLRP3/Caspase-1/GSDMD pathway by mitochondrial damage, which produced mtDNA and ROS  under induction, leading to the pyroptosis of endothelial cells.

Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution.  The Green Revolution gene Semidwarf 1 (SD1), which modulates gibberellic acid (GA) biosynthesis, plays a principal role in determining rice plant height.  Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production.  The plant height mediated by SD1 also favors grain yield under certain conditions.  However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production.  In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions.  In response to dryland environments, rice requires a reduction in plant height to cope with water deficits.  Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation.  Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem.  Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields.  In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height.  During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height.  Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production.  All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.

‘Corollas and spines’ is an important trait for fresh market cucumber.  In a unique cucumber line, ‘6457’, the super ovary is much larger and corolla opening is delayed by 4–5 days, thus the resulting fruit has a flower that remains on the tip, which has a high commodity value.  In this study, to better understand the molecular basis of corolla opening, mRNA and miRNA transcriptome analyses were performed during corolla development of the super and normal ovaries.  A total of 234 differentially expressed miRNAs (DEMs) and 291 differentially expressed target genes (DE-target genes) were identified from four developmental stages, and the greatest number of DEMs was found at the yellow bud stage.  Thirty of the DE-target genes were regulated by more than five DEMs, among which, CsHD-Zip was regulated by 28 DEMs, followed by DD2X (18).  In addition, the expression patterns of miRNA_104, miRNA_157, miRNA_349, miRNA_242, and miRNA_98 were similar during corolla development, and they shared the same target gene, CsCuRX.  Moreover, several critical candidate DEMs and DE-target genes were characterized and profiled by a qRT-PCR experiment.  Three of the miRNAs, miRNA_157-CsCuRX, miRNA_411-CsGH3.6, and miRNA_161/297/257-CsHD-Zip, might be responsible for corolla opening in the cucumber super ovary.  This integrated study on the transcriptional and post-transcriptional profiles can provide insights into the molecular regulatory mechanism underlying corolla opening in the cucumber.

OVATE family proteins (OFPs) are plant-specific proteins with a conserved OVATE domain that regulate plant growth and development.  Although OFPs have been studied in several species, their biological functions remain largely unknown in cucumber (Cucumis sativus L.).  This study identified 19 CsOFPs distributed on seven chromosomes in cucumber.  Most CsOFP genes were expressed in reproductive organs, but with different expression patterns.  Ectopic expression of CsOFP12-16c in Arabidopsis resulted in shorter and blunt siliques.  The overall results indicated that CsOFP12-16c regulates silique development in Arabidopsis and may have a similar function in cucumber.

Interactions of lignocellulosic components during fiber analysis were investigated using the highly adopted compositional analysis procedure from the National Renewable Energy Laboratory (NREL), USA.  Synthetic feedstock samples were used to study the effects of lignin/protein, cellulose/protein, and xylan/protein interaction on carbohydrate analysis.  Disregarding structural influence in the synthetic samples, lignin and protein components were the most significant (P<0.05) factors on cellulose analysis.  Measured xylan was consistent and unaffected by content variation throughout the synthetic analysis.  Validation of the observed relationships from synthetic feedstocks was fulfilled using real lignocellulosic feedstocks: corn stover, poplar, and alfalfa, in which similar results have been obtained, excluding cellulose analysis of poplar under higher protein content and xylan analysis of alfalfa under higher protein content.  The results elucidated that according to their protein and lignin contents of different lignocellulosic materials, accuracy of the NREL method on cellulose and xylan analyses could be improved by applying a stronger extraction step to replace water/ethanol extraction.

To make recycling utilization of organic materials produced in various agricultural systems, five kinds of organic materials were applied in a field test, including crop straw (CS), biogas residue (BR), mushroom residue (MR), wine residue (WR), pig manure (PM), with a mineral fertilizer (CF) and a no-fertilizer (CK) treatment as a control. Our objectives were: i) to quantify the effects of organic materials on soil C and N accumulation; ii) to evaluate the effects of organic materials on soil aggregate stability, along with the total organic carbon (TOC), and N in different aggregate fractions; and iii) to assess the relationships among the organic material components, soil C and N, and C, N in aggregate fractions. The trial was conducted in Wuqiao County, Hebei Province, China. The organic materials were incorporated at an equal rate of C, and combined with a mineral fertilizer in amounts of 150 kg N ha-1, 26 kg P ha-1 and 124 kg K ha-1 respectively during each crop season of a wheat-maize rotation system. The inputted C quantity of each organic material treatment was equivalent to the total amount of C contained in the crop straw harvested in CS treatement in the previous season. TOC, N, water-stable aggregates, and aggregate-associated TOC and N were investigated. The results showed that organic material incorporation increased soil aggregation and stabilization. On average, the soil macroaggregate proportion increased by 14%, the microaggregate proportion increased by 3%, and mean-weight diameter (MWD) increased by 20%. TOC content followed the order of PM>WR>MR>BR>CS>CK>CF; N content followed the order WR>PM>MR>BR>CS>CF>CK. No significant correlation was found between TOC, N, and the quality of organic material. Soil silt and clay particles contained the largest part of TOC, whereas the small macroaggregate fraction was the most sensitive to organic materials. Our results indicate that PM and WR exerted better effects on soil C and N accumulation, followed by MR and BR, suggesting that organic materials from ex situ farmland could promote soil quality more as compared to straw returned in situ.

The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology, contractility, cell proliferation, differentiation, interactions, migration, and death. The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes. The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages. Hi-C was used to build a chromatin architectures during four representative stages. ChIP-seq was conducted to identify enhancers in these four stages, which are occupied by histone H3K27ac and H3K4me3 peaks. Results show that large-scale genome architecture changes are mostly unidirectional, and coupled by complex on/off dynamic patterns of gene expression. Specifically, we observed 258.30 Mb of the genome undergoing A/B compartment switching. Notable alterations (316.57 Mb) of interaction frequencies within TADs were observed. Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development. Some muscle-related gene promoters that interacted with active enhancers during development, and some myopathy/aging-associated genes that were activated in aging muscle were founded. These results provide key insights into skeletal muscle development in vivo, and offer a valuable resource that allows in-depth functional characterization of candidate genes.

The advantages of genome selection (GS) in animal and plant breeding are self-evident. Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects accurately. Machine learning models have demonstrated remarkable potential in addressing these challenges. In this study, we introduced the concept of mixed kernel functions to explore the performance of support vector machine regression (SVR) in GS. Six single kernel functions (SVR_L, SVR_C, SVR_G, SVR_P, SVR_S, SVR_L) and four mixed kernel functions (SVR_GS, SVR_GP, SVR_LS, SVR_LP) were used to predict genome breeding values. The prediction accuracy, mean squared error (MSE) and mean absolute error (MAE) were used as evaluation indicators to compare with two traditional parametric models (GBLUP, BayesB) and two popular machine learning models (RF, KcRR). The results indicate that in most cases, the performance of the mixed kernel function model significantly outperforms that of GBLUP, BayesB and single kernel function. For instance, for T1 in the pig dataset, the predictive accuracy of SVR_GS is improved by 10% compared to GBLUP, and by approximately 4.4 and 18.6% compared to SVR_G and SVR_S respectively. For E1 in the wheat dataset, SVR_GS achieves 13.3% higher prediction accuracy than GBLUP. Among single kernel functions, the Laplacian and Gaussian kernel functions yield similar results, with the Gaussian kernel function performing better. The mixed kernel function notably reduces the MSE and MAE when compared to all single kernel functions. Furthermore, regarding runtime, SVR_GS and SVR_GP mixed kernel functions run approximately three times faster than GBLUP in the pig dataset, with only a slight increase in runtime compared to the single kernel function model. In summary, the mixed kernel function model of SVR demonstrates speed and accuracy competitiveness, and the model such as SVR_GS has important application potential for GS.

Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments. The data on daily weight, feed intake and feed behaviors in pigs are collected in test period by automated feeding stations, which facilitate to evaluate the resilience traits. In this study, we adopted the mean square error roots (RMSE) of ordinary least squares (OLS) and the negative residuals of quantile regression (QR) to generate four different novel resilience traits using daily records of feed intake and feed duration between 90 and 180 days of age in a population of commercial Duroc pigs. The genome-wide association studies (GWAS) based on single- and two- trait mixed models were carried out on 550 pigs using 48,603 single nucleotide polymorphisms (SNPs) to identify genomic regions associated with resilience traits in growing pigs. We further focused on the GWAS signals to conduct gene annotation, colocalization with multi-tissue eQTL summary statistics of PigGTEx project and identification of enhancers and promoters using the publicly available data. The genomic heritabilities of four novel resilience traits ranged from 0.09 to 0.41. The pairwise genetic and phenotypic correlations ranged from 0.16 to 0.95 and from 0.05 to 0.36, respectively. Twenty-seven SNPs were identified to be significantly associated with these resilience traits. They were distributed on nine chromosomes (SSC1, SSC2, SSC6, SSC7, SSC8, SSC12, SSC14, SSC16, and SSC17). After annotation, 39 QTLs and 49 candidate genes were identified. Several of these are functionally relevant candidate genes including OTUD4, TIFA and CARD14, which are involved in the host immune response, disease susceptibility and signal transduction. Eight unique SNPs were found to be causal in both GWAS and eQTL analyses across 15 tissues. Notably, one SNP (rs80794541) was associated with eQTLs identified concurrently across seven tissues/cell types, including the macrophage cell type. Furthermore, four significant SNPs (rs81467127, rs81356029, rs80794541, and rs81305085) were linked to the function of the primed enhancer, active element, and poised promoter in five pig tissues. Using the porcine fibroblast HiC dataset, SNP (rs81356029) on SSC2 regulates the CARNS1 and SSH3, while SNP (rs80794541) on SSC7 regulates the H2AC6. In this study, we generated four novel resilience traits and identified SNPs significantly associated with these resilience traits in a Duroc pig population. GWAS signals were associated with candidate genes involving in the immune traits, and were linked to the crucial regulatory elements as well. Our findings will contribute to elucidating the genetic mechanism that can enhance genome-enabled breeding and inform further research on resilience in domestic pigs.

Malate dehydrogenase (MDH) is a widely expressed enzyme that plays a key role in plant growth, development, and the stress response.  However, information on MDH genes in the soybean genome is limited. Seventeen members of the soybean MDH family were identified by genome-wide analysis, and the presence of conserved protein motifs was analyzed.  The genes were divided into five clusters according to their phylogenetic relationships.  The intracellular localizations of six GmMDHs were determined by confocal microscopy on Arabidopsis mesophyll protoplasts.  Transcripts of GmMDHs were significantly increased by abiotic stress (drought, salt, and alkalinity) and hormone treatments, as shown by analysis of cis-regulatory elements and quantitative real-time polymerase chain reaction (qRT-PCR).  GmMDHs displayed unique expression patterns in diverse soybean tissues.  It is noteworthy that under salt stress, the expression levels of a chloroplast isoform (GmMDH2) were unusually high, presumably indicating a critical role in soybean responses to salinity.  Expression of GmMDH2 in Escherichia coli showed that the recombinant enzyme had NADP-dependent MDH activity. The redox states of the nicotinamide adenine dinucleotide phosphate (NADPH) pool and antioxidant activities were shown to be modulated by GmMDH2 gene overexpression, which in turn reduced reactive oxygen species (ROS) formation in transgenic soybean, significantly enhancing the salt stress resistance.  Gene-based association analysis showed that variations in GmMDH2 were strongly linked to seedling salt tolerance.  A polymorphism possibly associated with salt tolerance was discovered in the promoter region of GmMDH2.  These findings not only improve our understanding of the stress response mechanism by identifying and characterizing the MDH gene family throughout the soybean genome but it also identified a potential candidate gene for the future enchancement of salt tolerance in the soybean.

Rice bakanae disease (RBD) is a devastating plant disease caused by Fusarium fujikuroi. This study aimed to evaluate the potential of cyclobutrifluram, a novel succinate dehydrogenase inhibitor (SDHI), to control RBD, and determine the risk and mechanism of resistance to cyclobutrifluram in F. fujikuroi. In vitro experiments showed that cyclobutrifluram significantly inhibited mycelial growth and spore germination, and altered the morphology of mycelia and conidia. Treatment with cyclobutrifluram significantly decreased mycotoxin production and increased cell membrane permeability in F. fujikuroi. The baseline sensitivity of 72 F. fujikuroi isolates to cyclobutrifluram was determined using mycelial growth and spore germination inhibition assays, which revealed EC₅₀ values of 0.0114 – 0.1304 μg mL^-1 and 0.0012 – 0.016 μg mL^-1, with mean EC₅₀ values of 0.0410 ± 0.0470 μg mL^-1 and 0.0038 ± 0.0015 μg mL^-1, respectively. Pot experiments demonstrated that the protective effect of cyclobutrifluram against F. fujikuroi was more significant than that of phenamacril and azoxystrobin, indicating that cyclobutrifluram is a promising antifungal agent for the control of RBD. Six cyclobutrifluram-resistant mutants of F. fujikuroi were obtained via fungicide adaptation. Moreover, these mutants exhibited weaker fitness than their parental isolate and positive cross-resistance with other SDHI fungicides, including pydiflumetofen and penflufen; however, no cross-resistance was detected with other classes of fungicides, including phenamacril, fludioxonil, prochloraz, or azoxystrobin. These results indicated that the resistance risk of F. fujikuroi to cyclobutrifluram might be moderate. Sequencing analysis revealed that mutations, including H248D in FfSdhB, A83V in FfSdhC₂, and S106F and E166K in FfSdhD, contributed to resistance, which was confirmed by molecular docking and homologous replacement experiments. The results suggest a high potential for cyclobutrifluram to control RBD and a moderate resistance risk of F. fujikuroi to cyclobutrifluram, which are meaningful findings for the scientific application of cyclobutrifluram.

Leaves and glumes act as lateral organs and have essential effects on photosynthesis and seed morphology, thus affecting yield.  However, the molecular mechanisms controlling their polarity development in rice is still worth further analysis.  Here, we isolated a polarity defect of lateral organs 1 (pdl1) mutant in rice, which exhibits twisted/filamentous-shaped leaves and cracked/filamentous-shaped lemmas caused by defects in polarity development.  PDL1 encodes a SUPPRESSOR OF GENE SILENCING 3 protein localized in the cytoplasm granules.  PDL1 is expressed in the shoot apical meristem, inflorescence meristem, floral meristem, and lateral organs including leaf and floral organs.  PDL1 is involved in the synthesis of tasiR-ARF, which may subsequently modulate the expression of OsARFs.  Meanwhile, the expression of abaxial miR165/166 and the adaxial identity genes OSHBs was increased and decreased significantly, respectively.  The results of this study clarified the molecular mechanism that the PDL1-mediated tasiR-ARF synthesis regulates the lateral organ polarity development in rice.

Pentatricopeptide repeat (PPR) proteins play crucial roles in the post-transcriptional regulation of gene expression, specifically RNA editing and RNA splicing, in plant organelles. Despite longstanding research on chloroplast biogenesis and development, the roles of most PPR genes in this process in rice (Oryza sativa) remain unclear. In this study, we identified a novel P-type PPR protein, YELLOW-GREEN LEAF AND SEEDLING LETHAL (YGS), that is targeted to rice chloroplasts.  YGS is preferentially expressed in leaves.  The ygs mutants were obtained by knocking out YGS gene using CRISPR/Cas9-mediated genome editing; these mutants exhibited yellow-green leaves and a seedling-lethal phenotype.  Consistent with these phenotypes, the ygs mutants had lower levels of pigment contents and an abnormal chloroplast ultrastructure compared to the wild type.  Moreover, the expression levels of genes related to chloroplast development and chlorophyll biosynthesis were significantly altered in the ygs mutants.   In addition, loss of function of YGS impaired RNA editing of rpl2 and intron splicing of ycf3-1 in the plastid genome. Finally, YGS interacted with the chloroplast signal recognition particle protein OscpSRP54b in yeast two-hybrid and bimolecular fluorescence complementation assays.  These findings suggest that YGS is involved in RNA editing and RNA splicing in chloroplasts, thereby playing a crucial role in chloroplast development in rice.

The strawberry crimp nematode (Aphelenchoides fragariae) is a serious pathogen of ornamental crops and an important quarantine object in approximately 50 countries and regions including China. One nematode population within the genus Aphelenchoides was discovered from diseased leaves of fuchsia plants (Fuchsia × hybrid Voss.) in Chengdu city, Sichuan province of China. Morphological and morphometric data were obtained using light microscopy and scanning electron microscopy. After detailed examination, the species was identified as A. fragariae. Three rDNA sequences of this species, including partial rRNA small subunit, D2-D3 expansion domains of the rRNA large subunit and internal transcribed spacer, were amplified and sequenced. Bayesian trees inferred from these three rDNA sequences were constructed, revealing that this species is placed in a high support monophyletic clade with A. fragariae but clearly separated from all other Aphelenchoides species. Moreover, host-suitability tests showed that the Aphelenchoides population not only can harm and reproduce in F. hybrid, but also in Fragaria ananassa and Pteris vittata (two common hosts of A. fragariae). In conclusion, the study confirmed A. fragariae identity of the nematode from F. hybrid in Chengdu city based on morphology, molecular analysis and host-suitability tests. To our knowledge, this is the first molecular and morphological confirmation of A. fragariae in China, and F. hybrid was first discovered to be attacked by A. fragariae.

Glycosylphosphatidylinositol (GPI) anchoring is one of the common post-translational modifications in eukaryotic cells. In fungi, it exerts a wide range of biological functions by targeting proteins to the cell wall, but only few studies focus on the roles of GPI anchoring in plant pathogenic fungi. Here, we reveal a role of GPI anchoring in the maize fungal pathogen Cochlibolus heterostrophus. We found that GPI-anchored proteins were widely accumulated in hyphae, appressorium and infection hyphae of C. heterostrophus. Deletion of ChGPI7, which encodes a key enzyme involved in the biosynthesis of GPI anchors, resulted in significant reduction of vegetative growth and conidiation, as well as virulence due to impairment of appressorium formation and invasive growth. The ∆Chgpi7 mutants also showed severe defects in cell wall integrity, resulting in a significant reduction of stress resistance. Deletion of ChGPI7 and hydrofluoric acid (HF) pyridine treatment both led to removal of cell wall GPI-anchored proteins and exposure of chitin, the results suggested that GPI anchored proteins could protect chitin from host immune recognition. A total of 124 proteins were predicted to be GPI anchored proteins in C. heterostrophus, including a putative cell wall glycoprotein ChFEM1. Deletion of ChFEM1 also resulted in significant reduction in virulence and defects in infection structures, as well as cell wall integrity. We further found that cell wall localization and protein abundance of ChFEM1 were affected by ChGPI7. Our results showed that GPI anchoring regulates cell wall integrity and immune evasion for infection of C. heterostrophus.

Asian citrus psyllid (ACP) is a significant pest of citrus crops that can transmit citrus Huanglongbing (HLB) by feeding on the phloem sap of citrus plants, which poses a significant threat to citrus production. Volatile signal chemicals with plant communication functions can effectively enhance the resistance of recipient plants to herbivorous insects with minimal impacts on plant growth. While (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT), (E,E)-4,8,12-trimethyl-1,3,7,11-tridecene (TMTT), (E)-β-caryophyllene, and dimethyl disulfide (DMDS), are known as signaling molecules in guava-sweet orange communication, whether these four chemical signals can enhance the resistance of Citrus sinensis to feeding by ACP adults with no apparent costs in terms of plant growth remains unclear. Therefore, this study measured the effect of non-damaging induction by DMNT, TMTT, (E)-β-caryophyllene, and DMDS on the ability of C. sinensis to resist feeding by ACP, as well as their impacts on the defensive phytochemicals, defensive enzymes, functional nutrients, Photosystem II's utilization and allocation of light energy, photosynthetic pigments, growth conditions, and leaf stomatal aperture in C. sinensis. The results indicate that non-damaging induction by these four chemicals can enhance the activity of the defensive enzyme polyphenol oxidase (PPO) and increase the contents of total phenols, tannins, and terpenoid defensive phytochemicals within C. sinensis, thereby enhancing the resistance of C. sinensis to ACP feeding. Specifically, DMNT and DMDS exhibit more significant effects in inducing resistance compared to TMTT and (E)-β-caryophyllene. The characteristics of chlorophyll fluorescence parameters and changes in photosynthetic pigments in C. sinensis during different post-exposure induction periods revealed these chemicals can maintain the stability of the photosynthetic system in C. sinensis and regulate its capacity to capture, transmit, and distribute light energy, which significantly enhances the non-photochemical quenching ability (Y(NPQ)) of C. sinensis. In addition, detailed measurements of the water content, specific leaf mass (LMA), functional nutrients (soluble protein, soluble sugar, and amino acids), and stomatal parameters in C. sinensis leaves further indicated that the non-destructive induction by these chemicals can optimize the levels of functional nutrients in C. sinensis, primarily manifesting as the upregulation of soluble sugars, proline, or soluble proteins, and reduction of stomatal area and aperture, which maintains a stable leaf water content and LMA, thereby enhancing resistance to ACP while sustaining the healthy growth of C. sinensis. These results fully substantiate that the non-damaging induction by the signal chemicals DMNT, TMTT, (E)-β-caryophyllene, and DMDS can enhance the resistance of C. sinensis to ACP feeding while maintaining the balance between pest resistance and growth. This balance prevents any catastrophic effects on the growth of C. sinensis, so these agents can potentially be integrated with other pest management strategies for the collective protection of crops. This study provides theoretical support and assistance for the development of signal chemical inducers for the prevention and management of ACP in agricultural systems.

To ensure the reliability of learned information, most insects require multiple intervals of experience before storing the information as Long-term memory (LTM), and this requirement has been validated in insects from the behavioral to the molecular level. Recent studies have shown that some insects can form LTM after a single experience, although the mechanisms underlying one-trial LTM formation are not well understood. Therefore, understanding the mechanisms underlying rapid learning and subsequent preference formation in insects is crucial. Here we show that the agricultural pest Bactrocera dorsalis can rapidly form LTM, which is dependent on protein synthesis, and that the formation of LTM requires high energy support at the cost of reduced survival. Furthermore, based on a liquid chromatography-mass spectrometry (LC-MS) metabolomics approach, we found that LTM-related processes are sequentially coupled to two processes for energy generation, the TCA cycle and oxidative phosphorylation. This was further confirmed by blocking these energy generation processes. Our results provide a theoretical basis for the development of behavioral modulators in oriental fruit flies that target energy generation intermediate metabolites, as well as a new perspective on the rapid formation of LTM in insects.

Lysophosphatidic acid acyltransferases (LPATs) are enzymes widely expressed in various plant species, contributing to growth, development, and stress responses.  Currently, little information regarding the LPAT gene family is available in soybeans.  In this study, genome-wide analyses identified 15 soybean LPATs, which were then evaluated for the conserved protein motifs.  These genes were grouped into three clusters based on their phylogenetic relationships.  Confocal microscopy was used to visualize the localization of six GmLPATs within Arabidopsis mesophyll protoplasts.  cis-Acting regulatory element analyses and qRT-PCR experiments revealed that these GmLPATs were upregulated in response to hormone stimulation or exposure to abiotic stressors, including drought, alkaline conditions, and salt stress.  The expression patterns of these GmLPATs varied across different soybean tissue types.  One member of the solLPAT1 subtype (GmLPAT11) was found to be upregulated in response to a range of treatments, highlighting its role in soybean salt stress responses. GmLPAT11 expression in Escherichia coli confirmed the LPAT activity of this recombinant enzyme, and overexpressing this LPAT reduced reactive oxygen species production in transgenic soybean plants, enhancing their salt stress tolerance.  Gene association analyses indicated that GmLPAT11 variants are closely associated with seedling salt tolerance, and a polymorphism in the GmLPAT11 CDS region was potentially associated with salt tolerance.  These results provide new insight into the nature of the LPAT gene family in soybeans while also suggesting promising candidate genes for future research efforts aimed at enhancing the overall salt tolerance of soybean crops. 

In the face of agricultural labor shortages, reducing labor and costs in rice production while meeting demand or increasing yield is crucial for sustainable agricultural development.  Utilizing crop straw boards and high-density seedling raising can reduce labor demand and enhance rice yield.  This study aimed to investigate the effects of seeding density and transplanting age on tillering patterns, panicle formation rates, and yield to determine optimal cultivation practices for maximizing rice yield.  Two-year field experiments were conducted in Sihong County, China, using the japonica rice variety Nanjing 5718.  Five seeding densities (150–350 g/tray) and four transplanting ages (10–25 days) were evaluated to assess their impact on tillering patterns, panicle formation rates, and yield.  Innovative crop straw boards were employed to enhance planting efficiency and reduce dependence on seedling-raising soil.  This approach also lessened tillage layer destruction, promoting sustainable practices.  The results indicated that increasing seeding density significantly altered tillering and panicle formation patterns, reducing the occurrence and panicle formation rates of lower-position tillers.  Although the occurrence of middle and high-position tillers increased, the overall number of panicles per hill decreased, especially at higher densities, negatively affecting yield.  Reducing transplanting age promoted the emergence and panicle formation of lower-position tillers, mitigating these negative effects.  Specifically, compared to traditional methods (150 g/tray, 20-day seedlings), the higher seeding density (300 g/tray) and shorter transplanting age (15-day seedlings) increased total panicle number by 3.79–4.73% and yield by 3.38–5.05%.  Combining higher seeding densities with reduced transplanting ages offers significant advantages over conventional practices by enhancing resource utilization, improving tillering efficiency.  These findings provide actionable recommendations for optimizing rice cultivation practices and contribute to sustainable agricultural development.

The rice stem borer, Chilo suppressalis (Walker) (Lepidoptera: Crambidae), is one of the most serious pests in rice-growing areas, and it has developed resistance to most insecticides currently used in the field. Cyproflanilide is a novel meta-diamide insecticide that has shown high activities to multiple pests. Evaluating the risk of resistance to cyproflanilide in C. suppressalis is necessary for its preventive resistance management. Here we established the baseline susceptibility of C. suppressalis to cyproflanilide by the rice-seedling dipping method and topical application, and the LC₅₀ and LD₅₀ values were 0.026 mg L^-1 and 0.122 ng/larva, respectively. The LC₅₀ values of cyproflanilide in 37 field populations ranged from 0.012 to 0.061 mg L^-1, and 25 field populations exhibited resistance to chlorantraniliprole with the highest LC₅₀ value of 3770.059 mg L^-1. In addition, a logistic distribution model analysis indicated that only 0.048 mg L^-1 of cyproflanilide was required to kill 90% field chlorantraniliprole-resistant populations of C. suppressalis, compared to 2087.764 mg L^-1 of chlorantraniliprole for a similar level of control. Resistance screening over 19 generations did not result in resistance to cyproflanilide (RR=3.1-fold). The realized heritability (h²) of resistance was estimated as 0.067 by using threshold trait analysis, suggesting a low risk of cyproflanilide resistance development in susceptible strains. The Cypro-SEL population (F₁₀) had no obvious fitness cost (relative fitness=0.96), and no significant changes in sensitivity to seven tested insecticides. These findings suggested that cyproflanilide is a promising insecticide for the management of chlorantraniliprole-resistant C. suppressalis. Moreover, this integrated risk assessment provides scientific application guidelines for the sustainable resistance management of cyproflanilide for controlling C. suppressalis.

In order to explore the molecular mechanisms underlying the contribution of autophagy to pepper’s heat tolerance, in previous study, we identified the zinc-finger protein B-BOX 9/CONSTANS-LIKE 13 (CaBBX9/CaCOL13) as an interaction partner of Autophagy regulated protein (ATG) CaATG8c, one of the core components in autophagy. However, the involvements of CaBBX9 in both autophagy and heat tolerance remain unclear. In this study, we further confirmed the interaction between CaBBX9 with CaATG8c, and defined the interaction regions of CaBBX9 are CONSTANS, CONSTANS-Like and TOC1 (CCT) domain and the fragment region. The expression of CaBBX9 can be induced by heat treatment. CaBBX9 is co-localized with CaATG8c in the nucleus and exhibits a transcriptional activity. When the expression of CaBBX9 is silenced, the heat-tolerance of pepper is enhanced, shown by the decrement of MDA content, H₂O₂, dead cells, and relative electrolyte leakage, and the increment of chlorophyll content and expression level of heat stress related genes. Overexpression of CaBBX9 in tomatoes displays the opposite effects. Taken together, our study demonstrates that CaBBX9 negatively regulates the heat-tolerance of peppers by exacerbating oxidative damage and inhibiting the expression of heat related genes. Our findings provide a new clue for guiding crop breeding for tolerance to adverse environment.