Researchers from the Institute of Genetics and Developmental Biology(IGDB)of the Chinese Academy of Sciences,with collaborators,identified two sorghum genes(SbSLT1 and SbSLT2)that block Striga-a parasitic plant,also k...Researchers from the Institute of Genetics and Developmental Biology(IGDB)of the Chinese Academy of Sciences,with collaborators,identified two sorghum genes(SbSLT1 and SbSLT2)that block Striga-a parasitic plant,also known as“witchweed,”that causes$1.5 billion annual losses in Africa by draining crop nutrients.Published in Cell(February 12,2025),the study shows that these genes regulate strigolactones(SLs).展开更多
Objective To predict the autophagy-related pathogenesis and key diagnostic genes of diabetic kidney disease(DKD)through bioinformatics analysis,and to identify related Chinese medicines.Methods Data from sequencing mi...Objective To predict the autophagy-related pathogenesis and key diagnostic genes of diabetic kidney disease(DKD)through bioinformatics analysis,and to identify related Chinese medicines.Methods Data from sequencing microarrays GSE30528,GSE30529,and GSE1009 in the Gene Expression Omnibus(GEO)were employed.Differentially expressed genes(DEGs)with adjusted P<0.05 from GSE30528 and GSE30529 were identified.Combining these DEGs with the human autophagy gene database,Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses,and protein-protein interaction(PPI)network analysis were conducted on the obtained DKD autophagy-related genes.Subsequently,the least absolute shrinkage and selection operator(LASSO)regression and support vector machinerecursive feature elimination(SVM-RFE)algorithms were adopted to select autophagy-related genes.The diagnostic capability of these genes was assessed through analysis with the external validation set from microarray GSE1009,and relevant Chinese medicines were inversely predicted using the SymMap database.Results A total of 2014 DEGs were selected from GSE30528 and GSE30529,leading to the identification of 37 DKD autophagy-related genes.GO analysis indicated 681 biological mechanisms,including autophagy regulation and plasma membrane microdomain activity.KEGG enrichment analysis identified 112 related signaling pathways.PPI network analysis showed a marked enrichment of autophagy-related genes in DKD.Through LASSO regression and SVM-RFE,four core diagnostic genes for autophagy in DKD were identified:protein phosphatase 1 regulatory subunit 15A(PPP1R15A),hypoxia inducible factor 1 alpha subunit(HIF1α),deleted in liver cancer 1(DLC1),and ceroid lipofuscinosis neuronal 3(CLN3).The external validation set demonstrated high diagnostic efficiency for these genes.Finally,146 kinds of potential Chinese medicines were predicted using the SymMap database,with heatclearing and detoxifying medicine and blood-activating and stasis-eliminating medicine accounting for the largest proportion(25/146 and 13/146,respectively).Conclusion This study analyzed and validated bioinformatics sequencing databases to elucidate the potential molecular mechanisms of DKD autophagy and predicted key diagnostic genes,potential therapeutic targets,and related Chinese medicines,laying a solid foundation for clinical research and application.展开更多
Reductive soil disinfestation(RSD)is commonly employed for soil remediation in greenhouse cultivation.However,its influence on antibiotic resistance genes(ARGs)in soil remains uncertain.This study investigated the dyn...Reductive soil disinfestation(RSD)is commonly employed for soil remediation in greenhouse cultivation.However,its influence on antibiotic resistance genes(ARGs)in soil remains uncertain.This study investigated the dynamic changes in soil communities,potential bacterial pathogens,and ARG profiles under various organicmaterial treatments during RSD,including distillers’grains,potato peel,peanut vine,and peanut vine combined with charcoal.Results revealed that applying diverse organic materials in RSD significantly altered bacterial community composition and diminished the relative abundance of potential bacterial pathogens(P<0.05).The relative abundance of high-risk ARGs decreased by 10.7%-30.6%after RSD treatments,the main decreased ARG subtypeswere AAC(3)_Via,dfrA1,ErmB,lnuB,aadA.Actinobacteria was the primary host of ARGs and was suppressed by RSD.Soil physicochemical properties,such as total nitrogen,soil pH,total carbon,were crucial factors affecting ARG profiles.Our findings demonstrated that RSD treatment inhibited pathogenic bacteria and could be an option for reducing high-risk ARG proliferation in soil.展开更多
The effects of disinfectants and plasmid-based antibiotic resistance genes(ARGs)on the growth of microorganisms and the plasmid-mediated transfer of ARGs in the water and biofilm of the drinkingwater distribution syst...The effects of disinfectants and plasmid-based antibiotic resistance genes(ARGs)on the growth of microorganisms and the plasmid-mediated transfer of ARGs in the water and biofilm of the drinkingwater distribution system under simulated conditionswere explored.The heterotrophic plate count of the water in reactors with 0.1 mg/L NaClO and NH_(2)Cl was higher than in the control groups.Therewas no similar phenomenon in biofilm.In thewater of reactors containing NaClO,the aphA and bla geneswere lower than in the antibiotic resistant bacteria group,while both genes were higher in the water of reactors with NH_(2)Cl than in the control group.Chloramine may promote the transfer of ARGs in the water phase.Both genes in the biofilm of the reactors containing chlorine were lower than the control group.Correlation analysis between ARGs and water quality parameters revealed that the copy numbers of the aphA gene were significantly positively correlated with the copy numbers of the bla gene in water and significantly negatively correlated in biofilm(p<0.05).The results of the sequencing assay showed that bacteria in the biofilm,in the presence of disinfectant,were primarily Gram-negative.1.0 mg/L chlorine decreased the diversity of the community in the biofilm.The relative abundance of some bacteria that may undergo transfer increased in the biofilm of the reactor containing 0.1 mg/L chlorine.展开更多
Because of the recent widespread usage of antibiotics,the acquisition and dissemination of antibiotic-resistance genes(ARGs)were prevalent in the majority of habitats.Generally,the biological wastewater treatment proc...Because of the recent widespread usage of antibiotics,the acquisition and dissemination of antibiotic-resistance genes(ARGs)were prevalent in the majority of habitats.Generally,the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria(ARB)disinfection and ARGs degradation and even promote the proliferation of ARGs.Problematically,ARB and ARGs in effluent pose potential risks if they are not further treated.Photocatalytic oxidation is considered a promising disinfection technology,where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid(DNA)for ARB elimination and subsequent degradation of ARGs.This reviewaims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant(AR)from wastewater in recent years.We discuss the sources and transfer of ARGs in wastewater.The overall removal efficiencies of ultraviolet radiation(UV)/chlorination,UV/ozone,UV/H_(2)O_(2),and UV/sulfate-radical based system for ARB and ARGs,as well as the experimental parameters and removal mechanisms,are systematically discussed.The contribution of photocatalytic materials based on TiO_(2) and g-C_(3)N_(4) to the inactivation of ARB and degradation of ARGs is highlighted,producingmany free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer(HGT)in wastewater.Finally,based on the reviewed studies,future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.展开更多
Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase alle...Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase allele mining using six updated FNP marker systems,the functional haplotypes at Pit,Pib,and Pi63 strictly diverged into the X-populations and were defined as X-R loci,while those at Pi54,Pi37,and Pi36 into the G-populations as G-R loci.The genic diversity at the three X-R loci(16 alleles)was twofold higher than that at the three G-R loci(8 alleles),and the allelic diversity in the Southern region(21 alleles)was nearly double that in the Northeastern region(11 alleles).Both observations reflect a significant difference in genetic diversity between X-and G-populations,and indicate that the effective R-genes mainly originated from X-subspecies.Based on the allelic structures characterized by a set of 10 parameters,8 and 16 alleles were respectively recognized as favorable and promising ones for the regional breeding programs.The genotypic structures of the two regional populations were almost different,indicating that the diverged alleles have been further assembled into two series of regional genotypes through long-term breeding programs,despite the presence of one-third of region-common alleles.The genotypic diversity in the Southern region(55 genotypes)was nearly twice as high as that in the Northeastern region(28),which perfectly reflects the aforementioned differences in both genic and allelic diversities.After analyzing the genotypic structures using a set of 13 parameters,4 and 23 genotypes,respectively,can be recommended as the favorable and promising ones for the regional breeding programs.The case study serves as a concrete sample of how to identify the favorable and promising alleles and genotypes,and beneficial parents based their comprehensive population structures for gene-designed breeding.展开更多
Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herb...Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herbaceous plants,with notable applications in species such as Arabidopsis(Yin et al.,2024),soybean(Zhang et al.,2024),rice(Zhang et al.,2020),and Chinese cabbage(Li et al.,2021).However,its application in fruit trees is limited.This is primarily due to their long growth cycles and lack of rapid,efficient,and stable transgenic systems,which severely hinders foundational research involving plant genetic transformation(Mei et al.,2024).Furthermore,for subtropical fruit trees,the presence of recalcitrant seeds adds an extra layer of difficulty to genetic transformation(Umarani et al.,2015),as most methods rely on seed germination as a basis for transformation.展开更多
Background:Tetralogy of Fallot(TOF),the predominant cyanotic congenital heart defect,arisesfrom multifactorial gene-envirorment interactions disrup ting cardiac developmental networks.This studyinvestiga ted TOF-speci...Background:Tetralogy of Fallot(TOF),the predominant cyanotic congenital heart defect,arisesfrom multifactorial gene-envirorment interactions disrup ting cardiac developmental networks.This studyinvestiga ted TOF-specific transcriptional alterations and identified high-confidence candidate genes.Methods:Based on GSE36761 transcriptome data,a weighted gene co-exp ression network analysis(WGCNA)andprotein-protein interaction(PPI)network were conducted to identify TOF-related sub-netrwork and Hub genes.The potentialbiological functions among these genes were revealed by enrichment analysis.Genetic,epigeneticand transcriptional alteration in the Fub genes were analyzed with leveraged public resources:a methylationdataset(CSE62629)and two single-cell datasets(EGAS00001003996 and GSE126128),Results:Eight Hub geneswere identified using the WGCNA network and PPl network,and functional errichment analysis revealedthatGJA1,RUNX2,FTK7,PRICKLE1,and SPRP1 were involved in the morphogenesis of an epithelium,anddysregulation of the signaling were also found in the other two TOF datasets,Furthermore,the study foundthat the promoters of GJA1,RUNX2,FTK7,and PRICKLE1 genes were hypermethylated and that GJA1 andSFRP1 are highly expressed in mouse second heart field cells and neural crest cells,and the la tter is expressedin human embry onic outflow tract cells.Since RUNX2 was not expressed in human and mouse embryonichearts,GJA1,FTK7,PRICKLE1,and SPRP1 were ultimately identified as TOF candidate genes.Conclusion:Based on the WGCNA network and various bioinformatics analysis approaches,we screened 4 TOF candidatepathogenic genes,and found that the signaling pathways related to the morphogenesis of an epithelium maybe involved in the pathogenesis of TOF.展开更多
Wheat(Triticum aestivum L.)is an important staple food crop in the world and supplies about 20%of human caloric and protein consumption(Giraldo et al.,2019;Xiao et al.,2022).Wheat production accounts for~30%of global ...Wheat(Triticum aestivum L.)is an important staple food crop in the world and supplies about 20%of human caloric and protein consumption(Giraldo et al.,2019;Xiao et al.,2022).Wheat production accounts for~30%of global cereal crops(Li et al.,2019).With the global population increasing and the frequency of natural disasters rising,enhancing wheat yield is crucial to meet food demand.Spike traits such as increased grain number per spike are key determinants of wheat yield.Pre-harvest sprouting(PHS)is a significant natural disaster that severely impacts grain yield and end-use quality of wheat(Tai et al.,2021,2024).展开更多
Peanut(Arachis hypogaea L.)bacterial wilt(BW)is a devastating soil-borne disease caused by Ralstonia solanacearum(RS)that poses a significant threat to peanut yield and quality.Nucleotide-binding leucine-rich repeat(N...Peanut(Arachis hypogaea L.)bacterial wilt(BW)is a devastating soil-borne disease caused by Ralstonia solanacearum(RS)that poses a significant threat to peanut yield and quality.Nucleotide-binding leucine-rich repeat(NBS-LRR)proteins are a class of plant-specific immune receptors that recognize pathogen-secreted effector molecules and activate immune responses to resist pathogen infections.However,the precise functions of AhCN genes(where CN is a class of nucleotide-binding site,leucine-rich repeat receptor(NLR)genes that lack LRR structural domains)in peanut plants are not fully understood.In this study,a total of 150 AhCN genes were identified and classified into nine subfamilies based on a systematic phylogenetic analysis.The AhCN genes showed highly conserved structural features,and the promoter cis-elements indicated involvement in plant hormone signaling and defense responses.After inoculation with RS,the highly resistant peanut variety‘H108’significantly outperformed the susceptible variety‘H107’based on physiological indicators such as plant height,main stem diameter,and fresh weight,likely due to the inhibition of bacterial proliferation and diffusion in the stem vascular bundle.AhCN34 was found to be significantly upregulated in‘H108’compared to‘H107’during plant infection and in response to treatments with each of three plant hormones.Importantly,AhCN34 overexpression in peanut leaves enhanced their resistance to BW.These findings demonstrate the great potential of AhCN34 for applications in peanut resistance breeding.Our identification and characterization of the AhCN genes provide insights into the mechanisms underlying BW resistance in peanut and can inform future research into genetic methods of improving BW resistance in peanut.展开更多
The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes(ARGs)for blocking their environmental dissemination.The distribution of ARGs in chromosomes,plasmids,and ...The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes(ARGs)for blocking their environmental dissemination.The distribution of ARGs in chromosomes,plasmids,and phages for understanding their respective contributions to the development of antimicrobial resistance in aerobic biofilm consortium under increasing stresses of oxytetracycline,streptomycin,and tigecyclinewere revealed based on metagenomics analysis.Results showed that the plasmids harbored 49.2%-83.9%of resistomes,which was higher(p<0.001)than chromosomes(2.0%-35.6%),and no ARGs were detected in phage contigs under the strict alignment standard of over 80%identity used in this study.Plasmids and chromosomes tended to encode different types of ARGs,whose abundances all increased with the hike of antibiotic concentrations,and the variety of ARGs encoded by plasmids(14 types and 64 subtypes)was higher than that(11 types and 27 subtypes)of chromosomes.The dosing of the three antibiotics facilitated the transposition and recombination of ARGs on plasmids,mediated by transposable and integrable transfer elements,which increased the co-occurrence of associated and unassociated ARGs.The results quantitatively proved that plasmids dominate the proliferation of ARGs in aerobic biofilm driven by antibiotic selection,which should be a key target for blocking ARG dissemination.展开更多
Hypertrophic cardiomyopathy(HCM)is an autosomal dominant inherited cardiomyopathy characterized by left ventricular hypertrophy.It is one of the chief causes of sudden cardiac death in younger people and athletes.Mole...Hypertrophic cardiomyopathy(HCM)is an autosomal dominant inherited cardiomyopathy characterized by left ventricular hypertrophy.It is one of the chief causes of sudden cardiac death in younger people and athletes.Molecular-genetic studies have confirmed that the vast majority of HCM is caused by mutations in genes encoding sarcomere proteins.HCM has a relatively wide phenotypic heterogeneity,varying from asymptomatic to sudden cardiac death,because of the many different mutations and pathogenic genes underlying it.Many studies have explored the clinical symptoms and prognosis of HCM,emphasizing the importance of genotype in evaluating patient prognosis and guiding the clinical management of HCM.To elaborate the main pathogenic genes and phenotypic prognosis in HCM to promote a better understanding of this genetic disease.Retrospective analysis of literature to evaluate the association between underlying gene mutations and clinical phenotypes in HCM patients.As sequencing technology advances,the pathogenic gene mutation spectrum and phenotypic characteristics of HCM are gradually becoming clearer.HCM is a widespread inherited disease with a highly variable clinical phenotype.The precise mechanisms linking known pathogenic gene mutations and the clinical course of this heterogeneous condition remain elusive.展开更多
Microalgae-bacteria system is an emerging alternative for sustainable wastewater treatment.Exploring the structure and diversity of microbial community in microalgae-bacteria system under sulfadiazine stress can contr...Microalgae-bacteria system is an emerging alternative for sustainable wastewater treatment.Exploring the structure and diversity of microbial community in microalgae-bacteria system under sulfadiazine stress can contribute to the understanding of the sulfadiazine behavior in environments.Furthermore,as important carriers of antibiotic resistance genes(ARGs),microalgae can influence the profiles of ARGs either directly or indirectly through the secretion of metabolites.However,the effects of sulfadiazine on ARGs dissemination of microalgae-bacteria systems remain underreported.Herein,the impacts of sulfadiazine(1 mg/L)on the structural diversity and metabolic activity of microorganisms were examined in microalgae-bacteria systems.Results showed thatmicroalgae-bacteria system could remove NH_(4)^(+)-N better(about 72.3%)than activated sludge system,and hydrolysis was the first step in sulfadiazine degradation.A high level of intI1(5.7×10^(4) copies/mL)was detected in the initial media of the microalgae-bacteria system.Microalgae could hamper the rate of horizontal gene transfer activation.Compared with activated sludge system,the abundance of sul genes(sul1,sul2,sul3,and sulA)was significantly lowered after treating with microalgae-bacteria system.Additionally,the number of proteins and the sum of polysaccharides in the extracellular polymeric substances of the activated sludge system were lower than those of themicroalgae-bacteria system.Microalgae can altermicrobial communities.The genus Rozellomycota predominated all samples.Fungi with relatively high abundance increased in the microalgae-bacteria system,including Dipodascaceae,Rhodotorula,and Geotrichum.These results offer valuable insights into the application processes involving microalgae-bacteria system.展开更多
Sesame is a multi-purpose high-value oilseed crop,which can beused in the food,feed,and cosmetics applica-tions.The low yield of sesame is due to the lack of high-yielding and locally adapted varieties,which have the ...Sesame is a multi-purpose high-value oilseed crop,which can beused in the food,feed,and cosmetics applica-tions.The low yield of sesame is due to the lack of high-yielding and locally adapted varieties,which have the susceptibility to capsule shattering and biotic and abiotic stresses.The breeding gains in sesame are low and stagnant compared to other oilseed crops such as canola,groundnut and sunflower.Breeding for enhanced yieldrelated,oil quantity and quality,biotic and abiotic stresses tolerant varieties is vital to the adaptation of the climate change.Several genes and quantitative trait loci(QTLs)related to yield-related,oil quantity and quality,biotic and abiotic stresses tolerant have been identified through modern plant breeding tools in sesame.The depth understanding of the genetic basis,molecular mechanisms and regulatory genes involved in yield-related,oil quantity and quality,biotic and abiotic stresses tolerant in sesame is important for the improvement of sesame breeding programs.This article reviews and documents these achievements will provide fundamental data and references for practical applications of sesam research.展开更多
Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and...Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield components.In this study,a natural population of 201 maize inbred lines was used for genome-wide association analysis,which identified nine SNPs on chromosomes 2,5,8,9,and 10 that were significantly associated with ear leaf type structure.Further verification through qRT-PCR confirmed the association of five candidate genes with these SNPs,with the Zm00001d008651 gene showing significant differential expression in the compact and flat maize inbred lines.Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)databasessuggested that this gene is involved in the glycolysis process.An analysis of the basic properties of this gene revealed that it encodes a stable,basic protein consisting of 593 amino acids with some hydrophobic properties.The promoter region contains stress and hormone(abscisic acid(ABA))related elements.The mutant of this gene increased the first ear leaf angle(eLA)and leaf angle of the first leaf below the first ear(bLA)by 4.96 and 0.97°,respectively,compared with normal inbred lines.Overall,this research sheds light on the regulatory mechanism of ear and leaf structures that influence density tolerance and provides solid foundational work for the development of new varieties.展开更多
As an emerging environmental contaminant,antibiotic resistance genes(ARGs)in tap water have attracted great attention.Although studies have provided ARG profiles in tap water,research on their abundance levels,composi...As an emerging environmental contaminant,antibiotic resistance genes(ARGs)in tap water have attracted great attention.Although studies have provided ARG profiles in tap water,research on their abundance levels,composition characteristics,and potential threat is still insufficient.Here,9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area(GBA)in China.Additionally,75 sets of environmental sample data(9 types)were downloaded from the public database.Metagenomics was then performed to explore the differences in the abundance and composition of ARGs.221 ARG subtypes consisting of 17 types were detected in tap water.Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs,their composition varied.In tap water samples,the three most abundant classes of resistance genes were multidrug,fosfomycin and MLS(macrolide-lincosamidestreptogramin)ARGs,and their corresponding subtypes ompR,fosX and macB were also the most abundant ARG subtypes.Regarding the potential mobility,vanS had the highest abundance on plasmids and viruses,but the absence of key genes rendered resistance to vancomycin ineffective.Generally,the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline.Although the current potential threat to human health posed by ARGs in tap water is limited,with persistent transfer and accumulation,especially in pathogens,the potential danger to human health posed by ARGs should not be ignored.展开更多
Objective:Employing bioinformatics methodologies to identify core genes intricately associated with the pathogenesis and progression of gastric cancer,and to evaluate their clinical significance.Method:Gene expression...Objective:Employing bioinformatics methodologies to identify core genes intricately associated with the pathogenesis and progression of gastric cancer,and to evaluate their clinical significance.Method:Gene expression datasets GSE19826 and GSE13911 were acquired from the Gene Expression Omnibus(GEO).Differential gene expression analysis was conducted using GEO2R.Common differentially expressed genes(DEGs)were discerned via Venn diagram analysis on a bioinformatics platform.Functional enrichment analyses,including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG),were performed on these overlapping DEGs.A protein-protein interaction(PPI)network was constructed with the STRING database,and central hub genes were identified using Cytoscape software.The expression profiles,prognostic value,and immune infiltration correlations of these key genes were further examined utilizing the GEPIA,Kaplan-Meier plotter,Human Protein Atlas(HPA),and TIMER databases.Results:Analysis revealed 120 commonly differentially expressed genes.These genes were significantly enriched in biological pathways concerning muscle cell cytoskeleton regulation,nutrient absorption,and extracellular matrix receptor interactions.PPI network analysis highlighted 10 core genes,including COL1A1,COL1A2,BGN,THBS2,COL5A2,and TIMP1.These genes exhibited marked upregulation in GC tissues.Statistical evaluation confirmed a significant link between their elevated expression and unfavorable patient outcomes(P<0.01).Furthermore,immune infiltration assessment indicated a positive correlation between the expression of these genes and macrophage infiltration within the tumor microenvironment,implying their involvement in modulating the immune response in GC,which could affect tumor behavior and clinical progression.Conclusion:The six genes identified may function as diagnostic biomarkers and represent promising therapeutic targets for gastric cancer.展开更多
Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet ful...Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet fully understood.Therefore,determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands.The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development.Specifically,to mine a greater number of candidate genes related to grape seed traits,this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study(GWAS)to mine candidate genes.In the two-year analysis using principal component analysis(PCA),we extracted five principal components with a cumulative contribution rate of 96.586%.The cumulative contribution rate for component 1 reached 87.352%.Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits.The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits.These SNP loci were distributed on 18 chromosomes,except for chromosome 4,with most SNP loci distributed on chromosome 18.Based on the physical location of single nucleotide polymorphism(SNP)markers significantly associated with seed-related traits in the grape reference genome,candidate genes are screened within the range of linkage disequilibrium(LD)attenuation distance,both upstream and downstream of the significant SNP loci.These candidate genes were mainly transcription factor-related genes(VvMADS4 and VvMADS5),ubiquitin ligase-related genes(E3 ubiquitin ligase BIG BROTHER),serine/threonine protein kinase-related genes,and carbohydrate metabolism-related genes(Sucrose Synthase 2)and simultaneously controlled multiple(at least two or more)seed traits.These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation.In this work,we identified new gene loci related to grape seed traits.Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.展开更多
Rice seed germination marks the start of cultivation and influences subsequent seedling growth,and is affected by hormones and environmental factors.Ubiquitination plays a critical role in this process by regulating h...Rice seed germination marks the start of cultivation and influences subsequent seedling growth,and is affected by hormones and environmental factors.Ubiquitination plays a critical role in this process by regulating hormonal homeostasis.In the ubiquitination cascade,ubiquitin-conjugating enzymes(UBCs)function as ubiquitin carriers to determine linkage specificity of ubiquitin chains.In rice(Oryza sativa),39 UBC genes are identified,but only one gene OsUBC12 has been functionally studied to promote seed germination under low-temperatures in japonica rice.To elucidate the role of UBCs in seed germination,we generated CRISPR-Cas9 mutants for 23 UBC genes and overexpressed 20 members in rice.Among them,seven UBC genes(OsUBC4/6/7/12/25/27/48)were found to regulate seed germination,with OsUBC27 and OsUBC48 acting through the ABA pathway.Exogenous ABA inhibitors restored the germination rate of osubc27^(CR).RT-qPCR analysis revealed that the ABA synthesis genes OsNCED1-5 were significantly upregulated in the mutants.Further differential ubiquitination proteomics in knockout mutants and wild-type plants showed that OsUBC27 regulates ABA homeostasis by modulating ubiquitination of the ABA-degrading protein OsABA8ox1,thereby balancing seed dormancy and germination.Sequence analysis identified distinct haplotypes of the seven OsUBCs that showed differential distribution between japonica and indica subspecies.Our study provides valuable molecular targets for developing rice varieties resistant to seed vivipary.展开更多
Helicobacter pylori infection represents a widespread chronic condition with varying prevalence influenced by race, ethnicity, and geography. The severity of H. pylori-associated diseases is determined by an array of ...Helicobacter pylori infection represents a widespread chronic condition with varying prevalence influenced by race, ethnicity, and geography. The severity of H. pylori-associated diseases is determined by an array of virulence factors. Although extensive studies have been conducted globally, data on the distribution of Helicobacter pylori virulence genes in Libya remain limited, constraining insights into the pathogenicity of local strains and hindering the development of targeted interventions. This study aimed to evaluate the prevalence of H. pylori infection, characterize essential virulence genes [vacA variants (s1/s2, m1/m2), cagA, and iceA1], and examine their association with gastroduodenal diseases among Libyan patients. Gastric biopsies from 144 participants were analyzed using polymerase chain reaction (PCR) assays, and risk factor data were collected via questionnaires. H. pylori was detected in 63.2% of samples by PCR. The vacA gene was present in 84.6% of cases, cagA in 58.2%, and iceA1 in 29.7%. Among vacA variants, s1 allele was most common (53.2%), followed by m1 (42.9%), m2 (37.7%), and s2 (13%) alleles. Significant associations were identified between specific virulence genes and the development of gastroduodenal diseases, highlighting their role in pathogenicity. This investigation is one of Libya’s first comprehensive assessments of H. pylori virulence factors, addressing a critical epidemiological gap. The high prevalence of virulence genes suggests their potential as disease biomarkers. These findings contribute to a deeper understanding of H. pylori pathogenicity within the Libyan population and establish a basis for future clinical interventions and public health strategies to manage and prevent H. pylori-associated diseases in Libya and comparable regions.展开更多
文摘Researchers from the Institute of Genetics and Developmental Biology(IGDB)of the Chinese Academy of Sciences,with collaborators,identified two sorghum genes(SbSLT1 and SbSLT2)that block Striga-a parasitic plant,also known as“witchweed,”that causes$1.5 billion annual losses in Africa by draining crop nutrients.Published in Cell(February 12,2025),the study shows that these genes regulate strigolactones(SLs).
基金National Natural Science Foundation of China(82170747),and Shanghai Key Laboratory of Traditional Chinese Clinical Medicine(20DZ2272200).
文摘Objective To predict the autophagy-related pathogenesis and key diagnostic genes of diabetic kidney disease(DKD)through bioinformatics analysis,and to identify related Chinese medicines.Methods Data from sequencing microarrays GSE30528,GSE30529,and GSE1009 in the Gene Expression Omnibus(GEO)were employed.Differentially expressed genes(DEGs)with adjusted P<0.05 from GSE30528 and GSE30529 were identified.Combining these DEGs with the human autophagy gene database,Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses,and protein-protein interaction(PPI)network analysis were conducted on the obtained DKD autophagy-related genes.Subsequently,the least absolute shrinkage and selection operator(LASSO)regression and support vector machinerecursive feature elimination(SVM-RFE)algorithms were adopted to select autophagy-related genes.The diagnostic capability of these genes was assessed through analysis with the external validation set from microarray GSE1009,and relevant Chinese medicines were inversely predicted using the SymMap database.Results A total of 2014 DEGs were selected from GSE30528 and GSE30529,leading to the identification of 37 DKD autophagy-related genes.GO analysis indicated 681 biological mechanisms,including autophagy regulation and plasma membrane microdomain activity.KEGG enrichment analysis identified 112 related signaling pathways.PPI network analysis showed a marked enrichment of autophagy-related genes in DKD.Through LASSO regression and SVM-RFE,four core diagnostic genes for autophagy in DKD were identified:protein phosphatase 1 regulatory subunit 15A(PPP1R15A),hypoxia inducible factor 1 alpha subunit(HIF1α),deleted in liver cancer 1(DLC1),and ceroid lipofuscinosis neuronal 3(CLN3).The external validation set demonstrated high diagnostic efficiency for these genes.Finally,146 kinds of potential Chinese medicines were predicted using the SymMap database,with heatclearing and detoxifying medicine and blood-activating and stasis-eliminating medicine accounting for the largest proportion(25/146 and 13/146,respectively).Conclusion This study analyzed and validated bioinformatics sequencing databases to elucidate the potential molecular mechanisms of DKD autophagy and predicted key diagnostic genes,potential therapeutic targets,and related Chinese medicines,laying a solid foundation for clinical research and application.
基金supported by the Key Research and Development Program of Shandong Province,China(No 2021CXGC010803)Pan’an County Chinese Medicine Industry Project(No.PZYF202103).
文摘Reductive soil disinfestation(RSD)is commonly employed for soil remediation in greenhouse cultivation.However,its influence on antibiotic resistance genes(ARGs)in soil remains uncertain.This study investigated the dynamic changes in soil communities,potential bacterial pathogens,and ARG profiles under various organicmaterial treatments during RSD,including distillers’grains,potato peel,peanut vine,and peanut vine combined with charcoal.Results revealed that applying diverse organic materials in RSD significantly altered bacterial community composition and diminished the relative abundance of potential bacterial pathogens(P<0.05).The relative abundance of high-risk ARGs decreased by 10.7%-30.6%after RSD treatments,the main decreased ARG subtypeswere AAC(3)_Via,dfrA1,ErmB,lnuB,aadA.Actinobacteria was the primary host of ARGs and was suppressed by RSD.Soil physicochemical properties,such as total nitrogen,soil pH,total carbon,were crucial factors affecting ARG profiles.Our findings demonstrated that RSD treatment inhibited pathogenic bacteria and could be an option for reducing high-risk ARG proliferation in soil.
基金supported by the Natural Science Foundation of China(No.52070145,51778453).
文摘The effects of disinfectants and plasmid-based antibiotic resistance genes(ARGs)on the growth of microorganisms and the plasmid-mediated transfer of ARGs in the water and biofilm of the drinkingwater distribution system under simulated conditionswere explored.The heterotrophic plate count of the water in reactors with 0.1 mg/L NaClO and NH_(2)Cl was higher than in the control groups.Therewas no similar phenomenon in biofilm.In thewater of reactors containing NaClO,the aphA and bla geneswere lower than in the antibiotic resistant bacteria group,while both genes were higher in the water of reactors with NH_(2)Cl than in the control group.Chloramine may promote the transfer of ARGs in the water phase.Both genes in the biofilm of the reactors containing chlorine were lower than the control group.Correlation analysis between ARGs and water quality parameters revealed that the copy numbers of the aphA gene were significantly positively correlated with the copy numbers of the bla gene in water and significantly negatively correlated in biofilm(p<0.05).The results of the sequencing assay showed that bacteria in the biofilm,in the presence of disinfectant,were primarily Gram-negative.1.0 mg/L chlorine decreased the diversity of the community in the biofilm.The relative abundance of some bacteria that may undergo transfer increased in the biofilm of the reactor containing 0.1 mg/L chlorine.
基金supported by the National Natural Science Foundation of China (Nos.52100182 and 52300204)the the Science and Technology Innovation Program of Hunan Province (No.2023RC3122).
文摘Because of the recent widespread usage of antibiotics,the acquisition and dissemination of antibiotic-resistance genes(ARGs)were prevalent in the majority of habitats.Generally,the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria(ARB)disinfection and ARGs degradation and even promote the proliferation of ARGs.Problematically,ARB and ARGs in effluent pose potential risks if they are not further treated.Photocatalytic oxidation is considered a promising disinfection technology,where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid(DNA)for ARB elimination and subsequent degradation of ARGs.This reviewaims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant(AR)from wastewater in recent years.We discuss the sources and transfer of ARGs in wastewater.The overall removal efficiencies of ultraviolet radiation(UV)/chlorination,UV/ozone,UV/H_(2)O_(2),and UV/sulfate-radical based system for ARB and ARGs,as well as the experimental parameters and removal mechanisms,are systematically discussed.The contribution of photocatalytic materials based on TiO_(2) and g-C_(3)N_(4) to the inactivation of ARB and degradation of ARGs is highlighted,producingmany free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer(HGT)in wastewater.Finally,based on the reviewed studies,future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.
基金funded by grants from the National Key R&D Project(2023YFD1400201-02,2023YFD1400203-02)the National Natural Science Foundation of China(31870137)+1 种基金the National Transgenic Research Project(2015ZX08001-002)the Key R&D Project of Guangdong Province(2022B0202060005).
文摘Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase allele mining using six updated FNP marker systems,the functional haplotypes at Pit,Pib,and Pi63 strictly diverged into the X-populations and were defined as X-R loci,while those at Pi54,Pi37,and Pi36 into the G-populations as G-R loci.The genic diversity at the three X-R loci(16 alleles)was twofold higher than that at the three G-R loci(8 alleles),and the allelic diversity in the Southern region(21 alleles)was nearly double that in the Northeastern region(11 alleles).Both observations reflect a significant difference in genetic diversity between X-and G-populations,and indicate that the effective R-genes mainly originated from X-subspecies.Based on the allelic structures characterized by a set of 10 parameters,8 and 16 alleles were respectively recognized as favorable and promising ones for the regional breeding programs.The genotypic structures of the two regional populations were almost different,indicating that the diverged alleles have been further assembled into two series of regional genotypes through long-term breeding programs,despite the presence of one-third of region-common alleles.The genotypic diversity in the Southern region(55 genotypes)was nearly twice as high as that in the Northeastern region(28),which perfectly reflects the aforementioned differences in both genic and allelic diversities.After analyzing the genotypic structures using a set of 13 parameters,4 and 23 genotypes,respectively,can be recommended as the favorable and promising ones for the regional breeding programs.The case study serves as a concrete sample of how to identify the favorable and promising alleles and genotypes,and beneficial parents based their comprehensive population structures for gene-designed breeding.
基金funded by the Key-Area Research and Development Program of Guangdong Province(Grant No.2022B0202070002)the Guangxi Science and Technology Major Program(Grant No.GuikeAA23023007-2)+1 种基金the Guangdong Province Modern Agricultural Industry Technology System Innovation Team Construction Project(2024CXTD19)Guangdong Basic and Applied Basic Research Foundation(Grant No.2023A1515010303)。
文摘Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herbaceous plants,with notable applications in species such as Arabidopsis(Yin et al.,2024),soybean(Zhang et al.,2024),rice(Zhang et al.,2020),and Chinese cabbage(Li et al.,2021).However,its application in fruit trees is limited.This is primarily due to their long growth cycles and lack of rapid,efficient,and stable transgenic systems,which severely hinders foundational research involving plant genetic transformation(Mei et al.,2024).Furthermore,for subtropical fruit trees,the presence of recalcitrant seeds adds an extra layer of difficulty to genetic transformation(Umarani et al.,2015),as most methods rely on seed germination as a basis for transformation.
基金supported by the National Natural Science Found ation of China(No.8230045i for Zhen Wang,82302230 for jiawei Shi,82202194 for Jing Wang and 82171961 for Haiyan Cao).
文摘Background:Tetralogy of Fallot(TOF),the predominant cyanotic congenital heart defect,arisesfrom multifactorial gene-envirorment interactions disrup ting cardiac developmental networks.This studyinvestiga ted TOF-specific transcriptional alterations and identified high-confidence candidate genes.Methods:Based on GSE36761 transcriptome data,a weighted gene co-exp ression network analysis(WGCNA)andprotein-protein interaction(PPI)network were conducted to identify TOF-related sub-netrwork and Hub genes.The potentialbiological functions among these genes were revealed by enrichment analysis.Genetic,epigeneticand transcriptional alteration in the Fub genes were analyzed with leveraged public resources:a methylationdataset(CSE62629)and two single-cell datasets(EGAS00001003996 and GSE126128),Results:Eight Hub geneswere identified using the WGCNA network and PPl network,and functional errichment analysis revealedthatGJA1,RUNX2,FTK7,PRICKLE1,and SPRP1 were involved in the morphogenesis of an epithelium,anddysregulation of the signaling were also found in the other two TOF datasets,Furthermore,the study foundthat the promoters of GJA1,RUNX2,FTK7,and PRICKLE1 genes were hypermethylated and that GJA1 andSFRP1 are highly expressed in mouse second heart field cells and neural crest cells,and the la tter is expressedin human embry onic outflow tract cells.Since RUNX2 was not expressed in human and mouse embryonichearts,GJA1,FTK7,PRICKLE1,and SPRP1 were ultimately identified as TOF candidate genes.Conclusion:Based on the WGCNA network and various bioinformatics analysis approaches,we screened 4 TOF candidatepathogenic genes,and found that the signaling pathways related to the morphogenesis of an epithelium maybe involved in the pathogenesis of TOF.
基金supported by the National Key Research and Development Program of China(2023YFD1200403 and 2023YFF1000600)the Innovation Program of Chinese Academy of Agricultural Sciences。
文摘Wheat(Triticum aestivum L.)is an important staple food crop in the world and supplies about 20%of human caloric and protein consumption(Giraldo et al.,2019;Xiao et al.,2022).Wheat production accounts for~30%of global cereal crops(Li et al.,2019).With the global population increasing and the frequency of natural disasters rising,enhancing wheat yield is crucial to meet food demand.Spike traits such as increased grain number per spike are key determinants of wheat yield.Pre-harvest sprouting(PHS)is a significant natural disaster that severely impacts grain yield and end-use quality of wheat(Tai et al.,2021,2024).
基金supported by the grants from the National Natural Science Foundation of China(NSFC)-Henan United Fund(U22A20475 and U1704232)the Key Scientific and Technological Project of Henan Province,China(221111110500,161100111000,and HARS-22-05-G1)+2 种基金the Innovation Scientists and Technicians Troop Construction Projects of Henan Province,China(2018JR0001)the Henan Agricultural University High Level Talent Special Support Fund,China(30501418)the Key Scientific Research Project in Colleges and Universities of Henan Province,China(21A210018).
文摘Peanut(Arachis hypogaea L.)bacterial wilt(BW)is a devastating soil-borne disease caused by Ralstonia solanacearum(RS)that poses a significant threat to peanut yield and quality.Nucleotide-binding leucine-rich repeat(NBS-LRR)proteins are a class of plant-specific immune receptors that recognize pathogen-secreted effector molecules and activate immune responses to resist pathogen infections.However,the precise functions of AhCN genes(where CN is a class of nucleotide-binding site,leucine-rich repeat receptor(NLR)genes that lack LRR structural domains)in peanut plants are not fully understood.In this study,a total of 150 AhCN genes were identified and classified into nine subfamilies based on a systematic phylogenetic analysis.The AhCN genes showed highly conserved structural features,and the promoter cis-elements indicated involvement in plant hormone signaling and defense responses.After inoculation with RS,the highly resistant peanut variety‘H108’significantly outperformed the susceptible variety‘H107’based on physiological indicators such as plant height,main stem diameter,and fresh weight,likely due to the inhibition of bacterial proliferation and diffusion in the stem vascular bundle.AhCN34 was found to be significantly upregulated in‘H108’compared to‘H107’during plant infection and in response to treatments with each of three plant hormones.Importantly,AhCN34 overexpression in peanut leaves enhanced their resistance to BW.These findings demonstrate the great potential of AhCN34 for applications in peanut resistance breeding.Our identification and characterization of the AhCN genes provide insights into the mechanisms underlying BW resistance in peanut and can inform future research into genetic methods of improving BW resistance in peanut.
基金supported by the National Natural Science Foundation of China(Nos.52091545 and 51978645).
文摘The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes(ARGs)for blocking their environmental dissemination.The distribution of ARGs in chromosomes,plasmids,and phages for understanding their respective contributions to the development of antimicrobial resistance in aerobic biofilm consortium under increasing stresses of oxytetracycline,streptomycin,and tigecyclinewere revealed based on metagenomics analysis.Results showed that the plasmids harbored 49.2%-83.9%of resistomes,which was higher(p<0.001)than chromosomes(2.0%-35.6%),and no ARGs were detected in phage contigs under the strict alignment standard of over 80%identity used in this study.Plasmids and chromosomes tended to encode different types of ARGs,whose abundances all increased with the hike of antibiotic concentrations,and the variety of ARGs encoded by plasmids(14 types and 64 subtypes)was higher than that(11 types and 27 subtypes)of chromosomes.The dosing of the three antibiotics facilitated the transposition and recombination of ARGs on plasmids,mediated by transposable and integrable transfer elements,which increased the co-occurrence of associated and unassociated ARGs.The results quantitatively proved that plasmids dominate the proliferation of ARGs in aerobic biofilm driven by antibiotic selection,which should be a key target for blocking ARG dissemination.
基金Supported by National Natural Science Foundation of China,No.81770379 and 81470521.
文摘Hypertrophic cardiomyopathy(HCM)is an autosomal dominant inherited cardiomyopathy characterized by left ventricular hypertrophy.It is one of the chief causes of sudden cardiac death in younger people and athletes.Molecular-genetic studies have confirmed that the vast majority of HCM is caused by mutations in genes encoding sarcomere proteins.HCM has a relatively wide phenotypic heterogeneity,varying from asymptomatic to sudden cardiac death,because of the many different mutations and pathogenic genes underlying it.Many studies have explored the clinical symptoms and prognosis of HCM,emphasizing the importance of genotype in evaluating patient prognosis and guiding the clinical management of HCM.To elaborate the main pathogenic genes and phenotypic prognosis in HCM to promote a better understanding of this genetic disease.Retrospective analysis of literature to evaluate the association between underlying gene mutations and clinical phenotypes in HCM patients.As sequencing technology advances,the pathogenic gene mutation spectrum and phenotypic characteristics of HCM are gradually becoming clearer.HCM is a widespread inherited disease with a highly variable clinical phenotype.The precise mechanisms linking known pathogenic gene mutations and the clinical course of this heterogeneous condition remain elusive.
基金supported by the Key Research Program of Wuhan(No.2022022202015015)the State Key Laboratory of Urban Water Resource and Environment(Harbin Institute of Technology)(No.2022TS13)+1 种基金the key projects of National Natural Science Foundation of China(No.2019YFC0408503)Shanghai Tongji Gao Tingyao Environmental Technology Development Foundation.
文摘Microalgae-bacteria system is an emerging alternative for sustainable wastewater treatment.Exploring the structure and diversity of microbial community in microalgae-bacteria system under sulfadiazine stress can contribute to the understanding of the sulfadiazine behavior in environments.Furthermore,as important carriers of antibiotic resistance genes(ARGs),microalgae can influence the profiles of ARGs either directly or indirectly through the secretion of metabolites.However,the effects of sulfadiazine on ARGs dissemination of microalgae-bacteria systems remain underreported.Herein,the impacts of sulfadiazine(1 mg/L)on the structural diversity and metabolic activity of microorganisms were examined in microalgae-bacteria systems.Results showed thatmicroalgae-bacteria system could remove NH_(4)^(+)-N better(about 72.3%)than activated sludge system,and hydrolysis was the first step in sulfadiazine degradation.A high level of intI1(5.7×10^(4) copies/mL)was detected in the initial media of the microalgae-bacteria system.Microalgae could hamper the rate of horizontal gene transfer activation.Compared with activated sludge system,the abundance of sul genes(sul1,sul2,sul3,and sulA)was significantly lowered after treating with microalgae-bacteria system.Additionally,the number of proteins and the sum of polysaccharides in the extracellular polymeric substances of the activated sludge system were lower than those of themicroalgae-bacteria system.Microalgae can altermicrobial communities.The genus Rozellomycota predominated all samples.Fungi with relatively high abundance increased in the microalgae-bacteria system,including Dipodascaceae,Rhodotorula,and Geotrichum.These results offer valuable insights into the application processes involving microalgae-bacteria system.
基金supported by the National Key Research and Devel-opment Program of China(2024YFD1600100)the Talented Young Scientist Program(TYSP)+5 种基金the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2024-OCRI)China Agriculture Research System(CARS-14)Hubei International Science and Technology Cooperation Project(2022EHB034,2024EHA055)Science and Technology Innovation Project of Hubei province(2024-620-000-001-031)Fundamental Research Funds for Central Non-profit Scientific Institution(1610172023003)the National Center for Crops Germplasm Re-sources(NCCGR-2024-016).
文摘Sesame is a multi-purpose high-value oilseed crop,which can beused in the food,feed,and cosmetics applica-tions.The low yield of sesame is due to the lack of high-yielding and locally adapted varieties,which have the susceptibility to capsule shattering and biotic and abiotic stresses.The breeding gains in sesame are low and stagnant compared to other oilseed crops such as canola,groundnut and sunflower.Breeding for enhanced yieldrelated,oil quantity and quality,biotic and abiotic stresses tolerant varieties is vital to the adaptation of the climate change.Several genes and quantitative trait loci(QTLs)related to yield-related,oil quantity and quality,biotic and abiotic stresses tolerant have been identified through modern plant breeding tools in sesame.The depth understanding of the genetic basis,molecular mechanisms and regulatory genes involved in yield-related,oil quantity and quality,biotic and abiotic stresses tolerant in sesame is important for the improvement of sesame breeding programs.This article reviews and documents these achievements will provide fundamental data and references for practical applications of sesam research.
基金supported by the Key Research and Development Project of Heilongjiang Province,China(2022ZX02B01)。
文摘Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield components.In this study,a natural population of 201 maize inbred lines was used for genome-wide association analysis,which identified nine SNPs on chromosomes 2,5,8,9,and 10 that were significantly associated with ear leaf type structure.Further verification through qRT-PCR confirmed the association of five candidate genes with these SNPs,with the Zm00001d008651 gene showing significant differential expression in the compact and flat maize inbred lines.Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)databasessuggested that this gene is involved in the glycolysis process.An analysis of the basic properties of this gene revealed that it encodes a stable,basic protein consisting of 593 amino acids with some hydrophobic properties.The promoter region contains stress and hormone(abscisic acid(ABA))related elements.The mutant of this gene increased the first ear leaf angle(eLA)and leaf angle of the first leaf below the first ear(bLA)by 4.96 and 0.97°,respectively,compared with normal inbred lines.Overall,this research sheds light on the regulatory mechanism of ear and leaf structures that influence density tolerance and provides solid foundational work for the development of new varieties.
基金supported by the National Key R&D Program of China(No.2022YFE0103200)the Hubei Provincial Natural Science Foundation of China(No.2021CFB016)the National Natural Science Foundation of China(No.52100217).
文摘As an emerging environmental contaminant,antibiotic resistance genes(ARGs)in tap water have attracted great attention.Although studies have provided ARG profiles in tap water,research on their abundance levels,composition characteristics,and potential threat is still insufficient.Here,9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area(GBA)in China.Additionally,75 sets of environmental sample data(9 types)were downloaded from the public database.Metagenomics was then performed to explore the differences in the abundance and composition of ARGs.221 ARG subtypes consisting of 17 types were detected in tap water.Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs,their composition varied.In tap water samples,the three most abundant classes of resistance genes were multidrug,fosfomycin and MLS(macrolide-lincosamidestreptogramin)ARGs,and their corresponding subtypes ompR,fosX and macB were also the most abundant ARG subtypes.Regarding the potential mobility,vanS had the highest abundance on plasmids and viruses,but the absence of key genes rendered resistance to vancomycin ineffective.Generally,the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline.Although the current potential threat to human health posed by ARGs in tap water is limited,with persistent transfer and accumulation,especially in pathogens,the potential danger to human health posed by ARGs should not be ignored.
文摘Objective:Employing bioinformatics methodologies to identify core genes intricately associated with the pathogenesis and progression of gastric cancer,and to evaluate their clinical significance.Method:Gene expression datasets GSE19826 and GSE13911 were acquired from the Gene Expression Omnibus(GEO).Differential gene expression analysis was conducted using GEO2R.Common differentially expressed genes(DEGs)were discerned via Venn diagram analysis on a bioinformatics platform.Functional enrichment analyses,including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG),were performed on these overlapping DEGs.A protein-protein interaction(PPI)network was constructed with the STRING database,and central hub genes were identified using Cytoscape software.The expression profiles,prognostic value,and immune infiltration correlations of these key genes were further examined utilizing the GEPIA,Kaplan-Meier plotter,Human Protein Atlas(HPA),and TIMER databases.Results:Analysis revealed 120 commonly differentially expressed genes.These genes were significantly enriched in biological pathways concerning muscle cell cytoskeleton regulation,nutrient absorption,and extracellular matrix receptor interactions.PPI network analysis highlighted 10 core genes,including COL1A1,COL1A2,BGN,THBS2,COL5A2,and TIMP1.These genes exhibited marked upregulation in GC tissues.Statistical evaluation confirmed a significant link between their elevated expression and unfavorable patient outcomes(P<0.01).Furthermore,immune infiltration assessment indicated a positive correlation between the expression of these genes and macrophage infiltration within the tumor microenvironment,implying their involvement in modulating the immune response in GC,which could affect tumor behavior and clinical progression.Conclusion:The six genes identified may function as diagnostic biomarkers and represent promising therapeutic targets for gastric cancer.
基金supported by grants from the Basic Research Business Fees for Public Welfare in Xinjiang Autonomous Region(Mining candidate genes related to grape seed traits based on GWAS,KY2023028)the Xinjiang Uygur Autonomous Region Tianchi Talent-Young Doctor for Chuan Zhang(Revealing the domestication history of Xinjiang native grape varieties and genetic analysis of important agronomic traits)the Xinjiang Academy of Agricultural Sciences Youth Science and Technology Backbone Innovation Ability Training Project(xjnkq-2023006).
文摘Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet fully understood.Therefore,determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands.The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development.Specifically,to mine a greater number of candidate genes related to grape seed traits,this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study(GWAS)to mine candidate genes.In the two-year analysis using principal component analysis(PCA),we extracted five principal components with a cumulative contribution rate of 96.586%.The cumulative contribution rate for component 1 reached 87.352%.Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits.The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits.These SNP loci were distributed on 18 chromosomes,except for chromosome 4,with most SNP loci distributed on chromosome 18.Based on the physical location of single nucleotide polymorphism(SNP)markers significantly associated with seed-related traits in the grape reference genome,candidate genes are screened within the range of linkage disequilibrium(LD)attenuation distance,both upstream and downstream of the significant SNP loci.These candidate genes were mainly transcription factor-related genes(VvMADS4 and VvMADS5),ubiquitin ligase-related genes(E3 ubiquitin ligase BIG BROTHER),serine/threonine protein kinase-related genes,and carbohydrate metabolism-related genes(Sucrose Synthase 2)and simultaneously controlled multiple(at least two or more)seed traits.These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation.In this work,we identified new gene loci related to grape seed traits.Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.
基金supported by the Zhejiang Provincial Natural Science Foundation,China(ZCLMS25C1302)the Central Public-interest Scientific Institution Basal Research Fund(CPSIBRF-CNRRI-202408)the Agricultural Science and Technology Innovation Program(ASTIP)
文摘Rice seed germination marks the start of cultivation and influences subsequent seedling growth,and is affected by hormones and environmental factors.Ubiquitination plays a critical role in this process by regulating hormonal homeostasis.In the ubiquitination cascade,ubiquitin-conjugating enzymes(UBCs)function as ubiquitin carriers to determine linkage specificity of ubiquitin chains.In rice(Oryza sativa),39 UBC genes are identified,but only one gene OsUBC12 has been functionally studied to promote seed germination under low-temperatures in japonica rice.To elucidate the role of UBCs in seed germination,we generated CRISPR-Cas9 mutants for 23 UBC genes and overexpressed 20 members in rice.Among them,seven UBC genes(OsUBC4/6/7/12/25/27/48)were found to regulate seed germination,with OsUBC27 and OsUBC48 acting through the ABA pathway.Exogenous ABA inhibitors restored the germination rate of osubc27^(CR).RT-qPCR analysis revealed that the ABA synthesis genes OsNCED1-5 were significantly upregulated in the mutants.Further differential ubiquitination proteomics in knockout mutants and wild-type plants showed that OsUBC27 regulates ABA homeostasis by modulating ubiquitination of the ABA-degrading protein OsABA8ox1,thereby balancing seed dormancy and germination.Sequence analysis identified distinct haplotypes of the seven OsUBCs that showed differential distribution between japonica and indica subspecies.Our study provides valuable molecular targets for developing rice varieties resistant to seed vivipary.
文摘Helicobacter pylori infection represents a widespread chronic condition with varying prevalence influenced by race, ethnicity, and geography. The severity of H. pylori-associated diseases is determined by an array of virulence factors. Although extensive studies have been conducted globally, data on the distribution of Helicobacter pylori virulence genes in Libya remain limited, constraining insights into the pathogenicity of local strains and hindering the development of targeted interventions. This study aimed to evaluate the prevalence of H. pylori infection, characterize essential virulence genes [vacA variants (s1/s2, m1/m2), cagA, and iceA1], and examine their association with gastroduodenal diseases among Libyan patients. Gastric biopsies from 144 participants were analyzed using polymerase chain reaction (PCR) assays, and risk factor data were collected via questionnaires. H. pylori was detected in 63.2% of samples by PCR. The vacA gene was present in 84.6% of cases, cagA in 58.2%, and iceA1 in 29.7%. Among vacA variants, s1 allele was most common (53.2%), followed by m1 (42.9%), m2 (37.7%), and s2 (13%) alleles. Significant associations were identified between specific virulence genes and the development of gastroduodenal diseases, highlighting their role in pathogenicity. This investigation is one of Libya’s first comprehensive assessments of H. pylori virulence factors, addressing a critical epidemiological gap. The high prevalence of virulence genes suggests their potential as disease biomarkers. These findings contribute to a deeper understanding of H. pylori pathogenicity within the Libyan population and establish a basis for future clinical interventions and public health strategies to manage and prevent H. pylori-associated diseases in Libya and comparable regions.
