As artificial intelligence(AI)technology has continued to develop,its efficient data processing and pattern recognition capabilities have significantly improved the precision and speed of decision-making processes,and...As artificial intelligence(AI)technology has continued to develop,its efficient data processing and pattern recognition capabilities have significantly improved the precision and speed of decision-making processes,and it has been widely applied across various fields.In the field of astronomy,AI techniques have demonstrated unique advantages,particularly in the identification of pulsars and their candidates.AI is able to address the challenges of pulsar celestial body identification and classification because of its accuracy and efficiency.This paper systematically surveys commonly used AI models for pulsar candidate identification,analyzing and discussing the typical applications of machine learning,artificial neural networks,convolutional neural networks,and generative adversarial networks in candidate identification.Furthermore,it explores how th.e introduction of AI techniques not only enhances the efficiency and accuracy of pulsar identification but also provides new perspectives and tools for pulsar survey data processing,thus playing a significant role in advancing pulsar research and the field of astronomy.展开更多
Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in...Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in cucumber have been identified.Here,the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments,with naturally occurring high temperatures over two years.Seventeen of the 88 accessions were identified as highly heat-tolerant.Using a genome-wide association study,five loci(gHII3.1,gHII3.2,gHII3.3,gHII4.1 and gHII6.1)on three chromosomes associated with heat tolerance were detected.Pairwise linkage disequilibrium correlation,sequence polymorphisms,and qRT-PCR analyses at these loci,identified five candidate genes predicted to be casual for heat stress response in cucumber.CsaV3_3G04883,CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs,and were significantly up-regulated by heat stress in the heat-tolerant genotypes.CsaV3_3G031890 was also induced by heat stress,but in the heatsensitive genotypes,and sequence polymorphism was only found in the promoter region.Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms.Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge.It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.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
Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.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
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 pe...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 root mean square error(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.展开更多
Large grain is a favorable trait for appearance quality and a large sink potential in wheat breeding.The stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from ...Large grain is a favorable trait for appearance quality and a large sink potential in wheat breeding.The stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871(ZM871)and its sister line Zhongmai 895(ZM895).Here,a BC_(1)F_6 residual heterozygous line was selected from the cross of a ZM871/ZM895//ZM871 population,and six heterozygous recombinant plants were identified in the BC_(1)F_(7)population from self-pollination of the heterozygous line.QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2(25.3-27.5 Mb)by phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants.Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses.Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS.The gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed,and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population of 166 cultivars using this marker.These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat.展开更多
Productive tiller number(PTN)is a pivotal trait that significantly influences wheat grain yield.To date,there have been limited reports on the cloning of genes that regulate PTN in wheat.The quantitative trait locus(Q...Productive tiller number(PTN)is a pivotal trait that significantly influences wheat grain yield.To date,there have been limited reports on the cloning of genes that regulate PTN in wheat.The quantitative trait locus(QTL)QPtn.sau-4B,associated with PTN,was previously mapped between the markers KASP-1 and KASP-3 on the chromosome 4B.Here,utilizing 12 newly developed markers and phenotypic data of PTN from recombinants identified within this interval,QPtn.sau-4B was further fine-mapped to a 2.58 Mb interval on wheat chromosome arm 4BS.Within this interval,we identified 14 genes with high-confidence and 32 genes with low-confidence.A 0.17 Mb deletion fragment contained TraesCS4B03G0092600 and TraesCS4B03G0093100,which were assigned as candidate genes for QPtn.sau-4B.Additionally,QPtn.sau-4B had potential to enhance both PTN and grain yield in wheat.Cloning this locus would support the development of wheat cultivars with increased grain yield.展开更多
Accurate prediction of wind energy plays a vital role in maintaining grid stability and supporting the broader shift toward renewable energy systems.Nevertheless,the inherently variable nature of wind and the intricac...Accurate prediction of wind energy plays a vital role in maintaining grid stability and supporting the broader shift toward renewable energy systems.Nevertheless,the inherently variable nature of wind and the intricacy of high-dimensional datasets pose major obstacles to reliable forecasting.To address these difficulties,this study presents an innovative hybrid method for short-term wind power prediction by combining a Long Short-Term Memory(LSTM)network with a Single Candidate Optimizer(SCO)algorithm.In contrast to conventional techniques that rely on random parameter initialization,the proposed LSTM-SCO framework leverages the distinctive capability of SCO to work with a single candidate solution,thereby substantially reducing the computational overhead compared to traditional population-based metaheuristics.The performance of the model was benchmarked against various classical and deep learning models across datasets from three geographically diverse sites,using multiple evaluation metrics.Experimental findings demonstrate that the SCO-optimized model enhances prediction accuracy by up to 12.5%over standard LSTM implementations.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
Maternal health during pregnancy has a direct impact on the risk and severity of neurodevelopmental disorders(NDDs)in the offspring,especially in the case of drug exposure.However,little progress has been made to asse...Maternal health during pregnancy has a direct impact on the risk and severity of neurodevelopmental disorders(NDDs)in the offspring,especially in the case of drug exposure.However,little progress has been made to assess the risk of drug exposure during pregnancy due to ethical constraints and drug use factors.We collected and manually curated sub-pathways and pathways(sub-/pathways)and drug information to propose an analytical framework for predicting drug candidates.This framework linked sub-/pathway activity and drug response scores derived from gene transcription data and was applied to human fetal brain development and six NDDs.Further,specific and pleiotropic sub-/pathways/drugs were identified using entropy,and sex bias was analyzed in conjunction with logistic regression and random forest models.We identified 19 disorder-associated and 256 regionally pleiotropic and specific candidate drugs that targeted risk sub-/pathways in NDDs,showing temporal or spatial changes across fetal development.Moreover,5443 differential drug-sub-/pathways exhibited sex-biased differences after filling in the gender labels.A user-friendly NDDP visualization website(https://ndd-lab.shinyapps.io/NDDP)was developed to allow researchers and clinicians to access and retrieve data easily.Our framework overcame data gaps and identified numerous pleiotropic and specific candidates across six disorders and fetal developmental trajectories.This could significantly contribute to drug discovery during pregnancy and can be applied to a wide range of traits.展开更多
BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-...BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-chain non-coding RNA discovered in recent years,and previous studies have found that lncRNA CASC9 participates in the occurrence and development of HCC,but its clinical value remains unclear.AIM To determine the expression of lncRNA CASC9 in HCC and its diagnostic and prognostic value.METHODS Data on CASC9 expression in patients with HCC were collected from the Cancer Genome Atlas(TCGA)database to analyze the relationship between CASC9 and patient survival.A total of 80 HCC patients treated in The First Affiliated Hospital of Guangxi Medical University from May 2012 to January 2014 were enrolled in the patient group,and 50 healthy subjects were enrolled in the control group during the same period.CASC9 expression in the two groups was determined using quantitative real-time polymerase chain reaction,and its diagnostic and prognostic value was analyzed based on the CASC9 data and pathological data in these HCC patients.The relationship between CASC9 and patient survival was assessed during the 5-year follow-up period.RESULTS Analysis of data from TCGA database revealed that control samples showed significantly lower CASC9 expression than carcinoma tissue samples(P<0.001);the low CASC9 expression group had a higher survival rate than the high CASC9 expression group(P=0.011),and the patient group showed significantly increased expression of serum CASC9,with the area under the curve(AUC)of 0.933.CASC9 expression was related to tumor size,combined hepatitis,tumor,node,metastasis(TNM)staging,lymph node metastasis,differentiation and alpha fetoprotein,and the high CASC9 expression group showed lower 1-year,3-year and 5-year survival rates than the low CASC9 expression group(all aP<0.05).Multivariate Cox regression analysis revealed that TNM staging,lymph node metastasis,differentiation,alpha fetoprotein and CASC9 were independent factors affecting the prognosis of patients.Stage I+II patients with lymph node metastasis,low differentiation,and alpha fetoprotein>200 ng/mL had a poor 5-year survival rate.CONCLUSION High CASC9 expression is beneficial in the prognosis of HCC patients.CASC9 is expected to be a potential diagnostic and prognostic indicator of HCC.展开更多
Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 0242...Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 02428 and YZX,two cultivars differing in vigor during early seedling growth,was used for QTL analysis.Nine traits associated with ESV were examined using a high-density map.Of 16 additive loci identified,three were detected in two generations and thus considered stable.Four epistatic interactions were detected,one of which was repeated in two generations.Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL.These results were combined with results from our previous QTL analysis of the germination index.The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed.These two lines showed rapid germination and strong ESV.A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents.The QTL are targets for ESV breeding and the candidate genes await functional validation.This study provides a theoretical basis and a genetic resource for the breeding of directseeded rice.展开更多
Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS syst...Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.展开更多
Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related t...Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.展开更多
Drought is one of the primary abiotic stress factors affecting the yield,growth,and development of soybeans.In extreme cases,drought can reduce yield by more than 50%.The seedling stage is an important determinant of ...Drought is one of the primary abiotic stress factors affecting the yield,growth,and development of soybeans.In extreme cases,drought can reduce yield by more than 50%.The seedling stage is an important determinant of soybean growth:the number and vigor of seedlings will affect growth and yield at harvest.Therefore,it is important to study the drought resistance of soybean seedlings.In this study,a recombinant inbred line(RIL)population comprising 234 F_(6:10)lines(derived from Zhonghuang35×Jindou 21)and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these conditions.Using a genetic map constructed by single nucleotide polymorphism(SNPs)markers,18 quantitative trait loci(QTL)on 7 soybean chromosomes were identified in two environments.This included 9 QTL clusters identified in the RIL population.Fifty-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis(GWAS)in the panel of accessions,including 69 significant SNPs(-log_(10)(P)≥3.97).A combination of the two populations revealed that two SNPs(-log_(10)(P)≥3.0)fell within two of the QTL(qPH7-4 and qPH7-6)confidence intervals.We not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents,involving Glyma.07 g093000,Glyma.07 g093200,Glyma.07 g094100 and Glyma.07 g094200.One previously unreported new gene related to drought stress,Glyma.07 g094200,was found by regional association analysis.The significant SNP CHR7-17619(G/T)was within an exon of the Glyma.07 g094200 gene.In the RIL population,the DSP value of the"T"allele of CHR7-17619 was significantly(P<0.05)larger than the"G"allele in different environments.The results of our study lay the groundwork for cloning and molecular marker-assisted selection of droughtresistance genes in soybeans at the seedling stage.展开更多
Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathoge...Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F7recombinant inbred line(RIL) population lacking the Yr18 gene, a near-isogenic line(NIL) population was developed to map the resistance gene. An allstage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exomecapture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge,the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.展开更多
There is a consensus in the aerospace field that the development of reusable liquid rockets can effectively reduce the launch expense.The pursuit of a long service life and reutilization highly depends on the bearing ...There is a consensus in the aerospace field that the development of reusable liquid rockets can effectively reduce the launch expense.The pursuit of a long service life and reutilization highly depends on the bearing components.However,the rolling element bearings(REBs)used in the existing rocket turbopumps present obvious and increasing limitations due to their mechanical contacting mode.For REBs,high rotational speed and long service life are two performance indexes that mutually restrict each other.To go beyond the DN value(the product of the bearing bore and rotational speed)limit of REBs,the major space powers have conducted substantial explorations on the use of new types of bearings to replace the REB.This review discusses,first,the crucial role of bearings in rocket turbopumps and the related structural improvements of REBs.Then,with the prospect of application to the next generation of reusable liquid rocket turbopumps,the bearing candidates investigated by major space powers are summarized comprehensively.These promising alternatives to REBs include fluid-film,foil,and magnetic bearings,together with the novel superconducting compound bearings recently proposed by our team.Our more than ten years of relevant research on fluid-film and magnetic bearings are also introduced.This review is meaningful for the development of long-life and highly reliable bearings to be used in future reusable rocket turbopumps.展开更多
The aim of the present study is to analyze the global research trend of radiation-responsive genes and identify the highly reproducible radiation-responsive genes. Bibliometric methods were applied to analyze the glob...The aim of the present study is to analyze the global research trend of radiation-responsive genes and identify the highly reproducible radiation-responsive genes. Bibliometric methods were applied to analyze the global research trend of radiation-responsive genes. We found 79 publications on radiation-responsive genes from 2000 to 2017. A total of 35 highly reproducible radiation-responsive genes were identified. Most genes are involved in response to DNA damage, cell proliferation, cell cycle regulation, and DNA repair.The p53 signal pathway was the top enriched pathway. The expression levels of 18 genes in human B lymphoblastoid cell line（AHH-1） cells were significantly up-regulated in a dose-dependent manner at 24 h after exposure to 0-5 Gy ^60 Coγ-ray irradiation. Our results indicate that developing a gene expression panel with the 35 high reproducibility radiation-responsive genes may be necessary for qualitative and quantitative assessment after exposure.展开更多
基金supported by the National Key R&D Program of China(2021YFC2203502 and 2022YFF0711502)the National Natural Science Foundation of China(NSFC)(12173077)+4 种基金the Tianshan Talent Project of Xinjiang Uygur Autonomous Region(2022TSYCCX0095 and 2023TSYCCX0112)the Scientific Instrument Developing Project of the Chinese Academy of Sciences(PTYQ2022YZZD01)China National Astronomical Data Center(NADC)the Operation,Maintenance and Upgrading Fund for Astronomical Telescopes and Facility Instruments,budgeted from the Ministry of Finance of China(MOF)and administrated by the Chinese Academy of Sciences(CAS)Natural Science Foundation of Xinjiang Uygur Autonomous Region(2022D01A360)。
文摘As artificial intelligence(AI)technology has continued to develop,its efficient data processing and pattern recognition capabilities have significantly improved the precision and speed of decision-making processes,and it has been widely applied across various fields.In the field of astronomy,AI techniques have demonstrated unique advantages,particularly in the identification of pulsars and their candidates.AI is able to address the challenges of pulsar celestial body identification and classification because of its accuracy and efficiency.This paper systematically surveys commonly used AI models for pulsar candidate identification,analyzing and discussing the typical applications of machine learning,artificial neural networks,convolutional neural networks,and generative adversarial networks in candidate identification.Furthermore,it explores how th.e introduction of AI techniques not only enhances the efficiency and accuracy of pulsar identification but also provides new perspectives and tools for pulsar survey data processing,thus playing a significant role in advancing pulsar research and the field of astronomy.
基金supported by Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(Grant No.G20220628003-03)Chongqing Municipal People's Government and Chinese Academy of Agricultural Sciences strategic cooperation project,Key-Area Research and Development Program of Guangdong Province(Grant No.2020B020220001)+3 种基金the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.CARS-23)Science and Technology Innovation Program of the Chinese Academy of Agricultural Science(Grant No.CAAS-ASTIP-IVFCAAS)Central public-interest Scientific Institution Basal Research Fund(Grant No.Y2017PT52)the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture,P.R.China。
文摘Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in cucumber have been identified.Here,the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments,with naturally occurring high temperatures over two years.Seventeen of the 88 accessions were identified as highly heat-tolerant.Using a genome-wide association study,five loci(gHII3.1,gHII3.2,gHII3.3,gHII4.1 and gHII6.1)on three chromosomes associated with heat tolerance were detected.Pairwise linkage disequilibrium correlation,sequence polymorphisms,and qRT-PCR analyses at these loci,identified five candidate genes predicted to be casual for heat stress response in cucumber.CsaV3_3G04883,CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs,and were significantly up-regulated by heat stress in the heat-tolerant genotypes.CsaV3_3G031890 was also induced by heat stress,but in the heatsensitive genotypes,and sequence polymorphism was only found in the promoter region.Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms.Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge.It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.
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 Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
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funded by the National Key Research and Development Program of China(2024YFF1000100 and 2021YFD1301102)the National Natural Science Foundations of China(32172702)the National Agricultural Science and Technology Innovation Program,Chinese Academy of Agricultural Sciences(ASTIP-IAS02).
文摘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 root mean square error(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.
基金funded by the National Natural Science Foundation of China(31961143007)the Key Research and Development Program of Xinjiang Uygur Autonomous Region,China(2023B02006)+1 种基金the Core Research Budget of the Non-profit Governmental Research Institutions,Institute of Crop Sciences,Chinese Academy of Agricultural Sciences(S2021ZD04 and S2022ZD04)the Natural Science Foundation of Hebei Province,China(C2021205013)。
文摘Large grain is a favorable trait for appearance quality and a large sink potential in wheat breeding.The stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871(ZM871)and its sister line Zhongmai 895(ZM895).Here,a BC_(1)F_6 residual heterozygous line was selected from the cross of a ZM871/ZM895//ZM871 population,and six heterozygous recombinant plants were identified in the BC_(1)F_(7)population from self-pollination of the heterozygous line.QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2(25.3-27.5 Mb)by phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants.Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses.Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS.The gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed,and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population of 166 cultivars using this marker.These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat.
基金supported by National Key Research and Development Program of China(2023YFD1201900)National Nat-ural Science Foundation of China(32472078,31971937)+2 种基金Natural Science Foundation of Sichuan Province(2024NSFSC0312)Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province(myzdsys24-01)the Key Laboratory of Exploitation and Study of Distinctive Plants in Education Department of Sichuan Province(TSZW2023ZB-10).
文摘Productive tiller number(PTN)is a pivotal trait that significantly influences wheat grain yield.To date,there have been limited reports on the cloning of genes that regulate PTN in wheat.The quantitative trait locus(QTL)QPtn.sau-4B,associated with PTN,was previously mapped between the markers KASP-1 and KASP-3 on the chromosome 4B.Here,utilizing 12 newly developed markers and phenotypic data of PTN from recombinants identified within this interval,QPtn.sau-4B was further fine-mapped to a 2.58 Mb interval on wheat chromosome arm 4BS.Within this interval,we identified 14 genes with high-confidence and 32 genes with low-confidence.A 0.17 Mb deletion fragment contained TraesCS4B03G0092600 and TraesCS4B03G0093100,which were assigned as candidate genes for QPtn.sau-4B.Additionally,QPtn.sau-4B had potential to enhance both PTN and grain yield in wheat.Cloning this locus would support the development of wheat cultivars with increased grain yield.
文摘Accurate prediction of wind energy plays a vital role in maintaining grid stability and supporting the broader shift toward renewable energy systems.Nevertheless,the inherently variable nature of wind and the intricacy of high-dimensional datasets pose major obstacles to reliable forecasting.To address these difficulties,this study presents an innovative hybrid method for short-term wind power prediction by combining a Long Short-Term Memory(LSTM)network with a Single Candidate Optimizer(SCO)algorithm.In contrast to conventional techniques that rely on random parameter initialization,the proposed LSTM-SCO framework leverages the distinctive capability of SCO to work with a single candidate solution,thereby substantially reducing the computational overhead compared to traditional population-based metaheuristics.The performance of the model was benchmarked against various classical and deep learning models across datasets from three geographically diverse sites,using multiple evaluation metrics.Experimental findings demonstrate that the SCO-optimized model enhances prediction accuracy by up to 12.5%over standard LSTM implementations.
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 Natural Science Foundation of China[81701350 and 31671252]the Health Technology Plan of Zhejiang Province[2023RC205].
文摘Maternal health during pregnancy has a direct impact on the risk and severity of neurodevelopmental disorders(NDDs)in the offspring,especially in the case of drug exposure.However,little progress has been made to assess the risk of drug exposure during pregnancy due to ethical constraints and drug use factors.We collected and manually curated sub-pathways and pathways(sub-/pathways)and drug information to propose an analytical framework for predicting drug candidates.This framework linked sub-/pathway activity and drug response scores derived from gene transcription data and was applied to human fetal brain development and six NDDs.Further,specific and pleiotropic sub-/pathways/drugs were identified using entropy,and sex bias was analyzed in conjunction with logistic regression and random forest models.We identified 19 disorder-associated and 256 regionally pleiotropic and specific candidate drugs that targeted risk sub-/pathways in NDDs,showing temporal or spatial changes across fetal development.Moreover,5443 differential drug-sub-/pathways exhibited sex-biased differences after filling in the gender labels.A user-friendly NDDP visualization website(https://ndd-lab.shinyapps.io/NDDP)was developed to allow researchers and clinicians to access and retrieve data easily.Our framework overcame data gaps and identified numerous pleiotropic and specific candidates across six disorders and fetal developmental trajectories.This could significantly contribute to drug discovery during pregnancy and can be applied to a wide range of traits.
文摘BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-chain non-coding RNA discovered in recent years,and previous studies have found that lncRNA CASC9 participates in the occurrence and development of HCC,but its clinical value remains unclear.AIM To determine the expression of lncRNA CASC9 in HCC and its diagnostic and prognostic value.METHODS Data on CASC9 expression in patients with HCC were collected from the Cancer Genome Atlas(TCGA)database to analyze the relationship between CASC9 and patient survival.A total of 80 HCC patients treated in The First Affiliated Hospital of Guangxi Medical University from May 2012 to January 2014 were enrolled in the patient group,and 50 healthy subjects were enrolled in the control group during the same period.CASC9 expression in the two groups was determined using quantitative real-time polymerase chain reaction,and its diagnostic and prognostic value was analyzed based on the CASC9 data and pathological data in these HCC patients.The relationship between CASC9 and patient survival was assessed during the 5-year follow-up period.RESULTS Analysis of data from TCGA database revealed that control samples showed significantly lower CASC9 expression than carcinoma tissue samples(P<0.001);the low CASC9 expression group had a higher survival rate than the high CASC9 expression group(P=0.011),and the patient group showed significantly increased expression of serum CASC9,with the area under the curve(AUC)of 0.933.CASC9 expression was related to tumor size,combined hepatitis,tumor,node,metastasis(TNM)staging,lymph node metastasis,differentiation and alpha fetoprotein,and the high CASC9 expression group showed lower 1-year,3-year and 5-year survival rates than the low CASC9 expression group(all aP<0.05).Multivariate Cox regression analysis revealed that TNM staging,lymph node metastasis,differentiation,alpha fetoprotein and CASC9 were independent factors affecting the prognosis of patients.Stage I+II patients with lymph node metastasis,low differentiation,and alpha fetoprotein>200 ng/mL had a poor 5-year survival rate.CONCLUSION High CASC9 expression is beneficial in the prognosis of HCC patients.CASC9 is expected to be a potential diagnostic and prognostic indicator of HCC.
基金This research was supported by the Breeding New Varieties of Rice Suitable for Light and Simple Cultivation and Mechanized Production Project(2017YFD0100104)the Research and Development Plan for Key Areas in Guangdong Province(2018B020206002)+1 种基金the China Agriculture Research System(CARS-01-17)Special thanks are due to the South China Agricultural University Doctoral Innovative Talents(Domestic Training)Cultivation Program(CX2019N044)。
文摘Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 02428 and YZX,two cultivars differing in vigor during early seedling growth,was used for QTL analysis.Nine traits associated with ESV were examined using a high-density map.Of 16 additive loci identified,three were detected in two generations and thus considered stable.Four epistatic interactions were detected,one of which was repeated in two generations.Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL.These results were combined with results from our previous QTL analysis of the germination index.The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed.These two lines showed rapid germination and strong ESV.A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents.The QTL are targets for ESV breeding and the candidate genes await functional validation.This study provides a theoretical basis and a genetic resource for the breeding of directseeded rice.
文摘Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.
基金Project supported partly by the Rockefeller Foundation thesis dis-sertation training grant and the National Hi-Tech Research and De-velopment Program (863) of China
文摘Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.
基金National Key Research and Development Program of China(2016YFD0100201)Scientific Research Conditions Construction and Achievement Transformation Project of Gansu Academy of Agricultural Sciences(Modern Biological Breeding)(2019GAAS07)+1 种基金Science and Technology Major Project of Gansu Province(18ZD2NA008)Crop Germplasm Resources Protection(2017NWB036-5)。
文摘Drought is one of the primary abiotic stress factors affecting the yield,growth,and development of soybeans.In extreme cases,drought can reduce yield by more than 50%.The seedling stage is an important determinant of soybean growth:the number and vigor of seedlings will affect growth and yield at harvest.Therefore,it is important to study the drought resistance of soybean seedlings.In this study,a recombinant inbred line(RIL)population comprising 234 F_(6:10)lines(derived from Zhonghuang35×Jindou 21)and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these conditions.Using a genetic map constructed by single nucleotide polymorphism(SNPs)markers,18 quantitative trait loci(QTL)on 7 soybean chromosomes were identified in two environments.This included 9 QTL clusters identified in the RIL population.Fifty-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis(GWAS)in the panel of accessions,including 69 significant SNPs(-log_(10)(P)≥3.97).A combination of the two populations revealed that two SNPs(-log_(10)(P)≥3.0)fell within two of the QTL(qPH7-4 and qPH7-6)confidence intervals.We not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents,involving Glyma.07 g093000,Glyma.07 g093200,Glyma.07 g094100 and Glyma.07 g094200.One previously unreported new gene related to drought stress,Glyma.07 g094200,was found by regional association analysis.The significant SNP CHR7-17619(G/T)was within an exon of the Glyma.07 g094200 gene.In the RIL population,the DSP value of the"T"allele of CHR7-17619 was significantly(P<0.05)larger than the"G"allele in different environments.The results of our study lay the groundwork for cloning and molecular marker-assisted selection of droughtresistance genes in soybeans at the seedling stage.
基金supported by the Major Program of National Agricultural Science and Technology of China (NK20220607)the National Natural Science Foundation of China (32272059 and31971883)the Science and Technology Department of Sichuan Province (2022ZDZX0014, 2021YFYZ0002, 2021YJ0297, and23NSFTD0045)。
文摘Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F7recombinant inbred line(RIL) population lacking the Yr18 gene, a near-isogenic line(NIL) population was developed to map the resistance gene. An allstage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exomecapture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge,the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.
基金Supported by National Natural Science Foundation of China(Grant No.51805131)Postdoctoral Research Foundation of China(Grant No.2018M640580)Fundamental Research Funds for the Central Universities(CN)Fundamental Research Funds for the Central Universities of China(Grant No.JZ2018HGBZ0155).
文摘There is a consensus in the aerospace field that the development of reusable liquid rockets can effectively reduce the launch expense.The pursuit of a long service life and reutilization highly depends on the bearing components.However,the rolling element bearings(REBs)used in the existing rocket turbopumps present obvious and increasing limitations due to their mechanical contacting mode.For REBs,high rotational speed and long service life are two performance indexes that mutually restrict each other.To go beyond the DN value(the product of the bearing bore and rotational speed)limit of REBs,the major space powers have conducted substantial explorations on the use of new types of bearings to replace the REB.This review discusses,first,the crucial role of bearings in rocket turbopumps and the related structural improvements of REBs.Then,with the prospect of application to the next generation of reusable liquid rocket turbopumps,the bearing candidates investigated by major space powers are summarized comprehensively.These promising alternatives to REBs include fluid-film,foil,and magnetic bearings,together with the novel superconducting compound bearings recently proposed by our team.Our more than ten years of relevant research on fluid-film and magnetic bearings are also introduced.This review is meaningful for the development of long-life and highly reliable bearings to be used in future reusable rocket turbopumps.
基金financially supported by the National Natural Science Foundation of China[Nos.81172593,81573081]
文摘The aim of the present study is to analyze the global research trend of radiation-responsive genes and identify the highly reproducible radiation-responsive genes. Bibliometric methods were applied to analyze the global research trend of radiation-responsive genes. We found 79 publications on radiation-responsive genes from 2000 to 2017. A total of 35 highly reproducible radiation-responsive genes were identified. Most genes are involved in response to DNA damage, cell proliferation, cell cycle regulation, and DNA repair.The p53 signal pathway was the top enriched pathway. The expression levels of 18 genes in human B lymphoblastoid cell line（AHH-1） cells were significantly up-regulated in a dose-dependent manner at 24 h after exposure to 0-5 Gy ^60 Coγ-ray irradiation. Our results indicate that developing a gene expression panel with the 35 high reproducibility radiation-responsive genes may be necessary for qualitative and quantitative assessment after exposure.
