Sucrose transporters(SUTs)play a crucial role in carbon allocation from the source leaf to the sink end,and the function of SUTs varies among family members.However,the genome-wide identifcation of the SUT superfamily...Sucrose transporters(SUTs)play a crucial role in carbon allocation from the source leaf to the sink end,and the function of SUTs varies among family members.However,the genome-wide identifcation of the SUT superfamily in Camellia oleifera is lacking,and their biological function remains elusive.In this study,four SUT genes-designated Co SUT1-4-were identifed in C.oleifera through a genome-wide analysis and classifed into three subfamilies.We used a combination of cis-acting elements analysis,mRNA quantifcation,histochemical analysis,and heterologous transformation to evaluate the expression profiles and functions of these SUTs.A key finding is that CoSUT4,localized on the plasma membrane,is highly expressed in mature leaves and the early stage of seed development in C.oleifera.In vitro culture of C.oleifera seed revealed the responsiveness of CoSUT4 to various exogenous hormones such as ABA and GA.CoSUT4 was able to restore the growth of the yeast strain SUSY7/ura3(a sucrose transport-defcient mutant)on sucrose-containing media and specifcally contributed to sucrose translocation and tissue growth in CoSUT4-overexpressed apple calli.In situ hybridization identifed chalazal nucellus and transfer cells as the action sites of CoSUT4 at the maternal-flial interface mediating sucrose transportation in oil tea seeds.CoSUT4 overexpression in Arabidopsis thaliana atsuc4 mutant restored the growth and seed yield defciencies of the mutant,leading to an increase in flled seeds and oil content.Additionally,CoSUT4 overexpression enhanced the drought and salt stress tolerance by augmenting sugar content.Overall,these fndings provide valuable insights into the function of SUTs and present promising candidates for the genetic enhancement of seed production in C.oleifera.展开更多
Background Cotton is a significant crop for fiber production;however,seed shape-related traits have been less investigated in comparison to fiber quality.Comprehending the genetic foundation of traits associated with ...Background Cotton is a significant crop for fiber production;however,seed shape-related traits have been less investigated in comparison to fiber quality.Comprehending the genetic foundation of traits associated with seed shape is crucial for improving the seed and fiber quality in cotton.Results A total of 238 cotton accessions were evaluated in four different environments over a period of two years.Traits including thousand grain weight(TGW),aspect ratio(AR),seed length,seed width,diameter,and roundness demonstrated high heritability and significant genetic variation,as indicated by phenotypic analysis.The association analysis involved 145 simple sequence repeats(SSR)markers and identified 50 loci significantly associated with six traits related to seed shape.The markers MON_DPL0504aa and BNL2535ba were identified as influencing multiple traits,including aspect ratio and thousand grain weight.Notably,markers such as HAU2588a and MUSS422aa had considerable influence on seed diameter and roundness.The identified markers represented an average phenotypic variance between 3.92%for seed length and 16.54%for TGW.Conclusions The research finds key loci for seed shape-related traits in cotton,providing significant potential for marker-assisted breeding.These findings establish a framework for breeding initiatives focused on enhancing seed quality,hence advancing the cotton production.展开更多
Rice grain yield is primarily determined by three key agronomic traits:panicle number,grain number per panicle,and grain weight(GW).However,the inherent tradeoffs among these yield components remain a persistent chall...Rice grain yield is primarily determined by three key agronomic traits:panicle number,grain number per panicle,and grain weight(GW).However,the inherent tradeoffs among these yield components remain a persistent challenge in rice breeding programs.Notably,compared with GW,brown rice weight(BRW)provides a more direct metric associated with actual grain yield potential.In this study,we conducted a two-year replicated genome-wide association study to elucidate the genetic architecture of BRW and identify new loci regulating GW.Among seven consistently detected loci across experimental replicates,four were not co-localized with previously reported genes associated with BRW or GW traits.BRW1.1,one of the four newly identified loci,was found to encode a novel RNA-binding protein.Functional characterization revealed that BRW1.1 acts as a negative regulator of BRW,potentially through modulating mRNA translation processes.Intriguingly,through integrated analysis of mutant phenotypes and haplotype variations,we demonstrated that BRW1.1 mediates the physiological tradeoff between GW and panicle number.This study not only delineates the genetic determinants of BRW but also identifies BRW1.1 as a promising molecular target for breaking the yield component tradeoff in precision rice breeding.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
The nuclear factor Y(NF-Y)is a class of heterotrimeric transcription factors comprising three subunits:NF-YA,NF-YB,and NF-YC.These transcription factors participate in many plant bioprocesses,including the regulation ...The nuclear factor Y(NF-Y)is a class of heterotrimeric transcription factors comprising three subunits:NF-YA,NF-YB,and NF-YC.These transcription factors participate in many plant bioprocesses,including the regulation of flowering time.Although the NF-Y gene family has been systematically studied in many species,little is known about its role in the non-heading Chinese cabbage(NHCC)[Brassica campestris(syn.Brassica rapa)ssp.chinensis].In this study,we identified 57 NF-Y members in the genome of NHCC using BLASTP,including 20 BcNF-YAs,24BcNF-YBs,and 13 BcNF-YCs.These genes are randomly distributed on the 10 chromosomes of NHCC.The results of yeast two-hybrid experiments indicated that among some members of the three subunits of BcNF-Ys,the members of the NF-YA and NF-YC subunits interact with each other,a third of the members of the NF-YB and NF-YC subunits interact with each other,while no interaction was observed between the members of the NF-YA and NF-YB subunits.Subcellular localization experiments in tobacco showed that Bc NF-YA2 and BcNF-YA8 were expressed in the nucleus;BcNF-YB18 and BcNF-YB23 were located in the cell membrane and cytoplasm;and BcNF-YC6 and BcNF-YC7 were expressed in the nucleus,cytoplasm,and cell membrane.We analyzed the cis-acting elements in the promoter of BcNF-Y genes and found that the ABA response element is the most distributed hormone response element,which is regulated by ABA signals triggered by environmental stimuli.Accordingly,we treated three-week-old NHCC leaves with 100μmol L^(-1) ABA and analyzed the expression profile of BcNF-Ys through RNA-seq.The results showed that except for six undetected BcNF-Ys,the remaining 51 BcNF-Ys showed varying degrees of response to ABA signals.Among these,BcNF-YA8 was positively regulated by ABA signals,with the highest upregulation amplitude.Subsequently,the function of BcNF-YA8 was extensively studied,which demonstrated that its expression promotes plant flowering.This result enriches our understanding of the potential molecular mechanism by which ABA positively regulates NHCC flowering.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
Background:Rice grain morphology—including traits such as awn length,hull color,size,and shape—is of central importance to yield,quality,and domestication,yet comprehensive quantification at scale has remained chall...Background:Rice grain morphology—including traits such as awn length,hull color,size,and shape—is of central importance to yield,quality,and domestication,yet comprehensive quantification at scale has remained challenging.Apromising solution has been provided by the integration of high-throughput imaging with genomic analysis.Methods:A standardized 2D image-processing pipeline was established to extract four categories of traits—awn length,hull color,projected grain area,and shape descriptors via PCA of normalized contours—from high-resolution photographs of 229 Oryza sativa japonica landraces.Genome-wide association analyses were then performed using a mixed linearmodel to control for population structure and kinship.Results:Broad phenotypic diversity was evident in awn length,hull coloration,grain dimensions,and morphological shape,with the first principal component explaining the dominant axis of shape variation.Known awn regulators GAD1/OsRAE2(chr 8;P=4.75×10^(-17))and An-1(chr 4;P=1.91×10^(-6))were identified.The hull color gene Rd(chr 1;P=3.13×10^(-6))was detected.A novel locus on chr 12 at 8.75 Mb with Os12g0257600(P=1.41×10^(-8)),and the known grain size gene FLO2(chr 4;P=8.28×10^(-6))were associated with projected area.Shape PC1 was mapped to GLW7/OsSPL13(chr 7;P=3.86×10^(-10)),NAL2/OsWOX3A(chr 11;P=1.41×10^(-11)),and OsGIF1(chr 11;P=1.27×10^(-8)).Conclusions:This study demonstrates that image-based phenotyping combined with genome-wide association studies(GWAS)can efficiently reveal both established and novel genetic determinants of rice grain morphology.These findings provide actionable targets for marker-assisted selection and genome editing to tailor grain traits in rice breeding programs.展开更多
Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes h...Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen.Using phenotypic SCR resistance-related data collected over two years and three geographical environments,a genome-wide association study was carried out in this work,which eventually identified 91 loci that were substantially correlated with SCR susceptibility.These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes(B73_RefGen_v4).Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection,with 2,586 and 797 differentially expressed genes(DEGs)ultimately being identified in the resistant Qi319and susceptible 8112 inbred lines following P.polysora infection,respectively,including 306 genes common to both lines.Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes.One of these genes is ZmHCT9,which encodes the protein hydroxycinnamoyl transferase 9.This gene was up-regulated in susceptible inbred lines and linked to greater P.polysora resistance as confirmed through cucumber mosaic virus(CMV)-based virus induced-gene silencing(VIGS)system-mediated gene silencing.These data provide important insights into the genetic basis of the maize SCR response.They will be useful for for future research on potential genes related to SCR resistance in maize.展开更多
Late embryogenesis abundant (LEA) proteins generally accumulate in seeds during the later stages of maturation.Here we studied the LEA genes in two wild peanut species (Arachis duranensis and Arachis ipaensis) in an e...Late embryogenesis abundant (LEA) proteins generally accumulate in seeds during the later stages of maturation.Here we studied the LEA genes in two wild peanut species (Arachis duranensis and Arachis ipaensis) in an effort to create a genetic resource for peanut crop improvement.we identified 65 AdLEA and 69 AiLEA genes representing all 8 LEA subfamilies,which were unevenly distributed across 10 peanut chromosomes.The majority of LEA proteins were found to be highly hydrophilic.MEME analysis indicated that LEA gene motifs were conserved within groups,but not between groups.The LEA genes contained a diverse array of stress-and phytohormoneresponsive cis-acting elements,with the AdLEA2-20 and AiLEA2-20 genes containing the greatest number of elements.Both AdLEA2-20 and AiLEA2-20 were upregulated in response to cold temperatures,drought,salinity,and abscisic acid exposure,although the dynamics were tissue-dependent.This study lays the foundation for future studies on the LEA gene family and abiotic stress in peanut,and our results will be invaluable for the genetic improvement of peanut by characterizing the genetic resources of wild peanut species.展开更多
Background Compared to many other vertebrates,chickens have a high reproductive efficiency in terms of egg production.The classic traits for evaluating egg-laying performance include age at first egg,egg number,clutch...Background Compared to many other vertebrates,chickens have a high reproductive efficiency in terms of egg production.The classic traits for evaluating egg-laying performance include age at first egg,egg number,clutch size,laying rate,etc.These egg-laying traits were not specifically designed to characterize egg production efficiency and stability.By considering the stage-specific variations in the egg production curve,this study aims to investigate the genetic mechanisms that directly influence the efficiency of egg production at each stage of the laying cycle.Results Using whole-genome sequencing data,we perform comprehensive genome-wide association study for 39 traits that focus on egg production efficiency and stability in the Gushi chicken.We showed that the haplotype-based approach is more effective for genetic mapping and capturing polygenic architecture.By combining the signals of Singleton Density Score(SDS),which is a population-genetic statistic designed to detect recent selection by leveraging the distribution of singletons,and association analyses,multiple egg-laying traits related to egg production efficiency were found to have experienced polygenic selection.Consistently,functional analysis of associated genes demonstrates that egg production efficiency benefits from multiple physiological functions.Furthermore,our results identified the CNNM2 gene,known for its role in magnesium homeostasis,plays a dual role in egg production variance,promoting variability during the up-stage while reducing it during the sustained-stage to optimize egg production efficiency.Conclusions Collectively,our multiple genome analyses reveal a complex genetic mechanism underlying more efficient and stable egg production,and establish chicken genetics as a model for studying reproductive efficiency across species.展开更多
Background:Dysregulation of enhancer transcription occurs in multiple cancers.Enhancer RNAs(eRNAs)are transcribed products from enhancers that play critical roles in transcriptional control.Characterizing the genetic ...Background:Dysregulation of enhancer transcription occurs in multiple cancers.Enhancer RNAs(eRNAs)are transcribed products from enhancers that play critical roles in transcriptional control.Characterizing the genetic basis of eRNA expression may elucidate the molecular mechanisms underlying cancers.Methods:Initially,a comprehensive analysis of eRNA quantitative trait loci(eRNAQTLs)was performed in The Cancer Genome Atlas(TCGA),and functional features were characterized using multi-omics data.To establish the first eRNAQTL profiles for colorectal cancer(CRC)in China,epigenomic data were used to define active enhancers,which were subsequently integrated with transcription and genotyping data from 154 paired CRC samples.Finally,largescale case-control studies(34,585 cases and 69,544 controls)were conducted along with multipronged experiments to investigate the potential mechanisms by which candidate eRNAQTLs affect CRC risk.Results:A total of 300,112 eRNAQTLs were identified across 30 different cancer types,which exert their influence on eRNA transcription by modulating chromatin status,binding affinity to transcription factors and RNA-binding proteins.These eRNAQTLs were found to be significantly enriched in cancer risk loci,explaining a substantial proportion of cancer heritability.Additionally,tumor-specific eRNAQTLs exhibited high responsiveness to the development of cancer.Moreover,the target genes of these eRNAs were associated with dysregulated signaling pathways and immune cell infiltration in cancer,highlighting their potential as therapeutic targets.Furthermore,multiple ethnic population studies have confirmed that an eRNAQTL rs3094296-T variant decreases the risk of CRC in populations from China(OR=0.91,95%CI 0.88–0.95,P=2.92×10^(-7))and Europe(OR=0.92,95%CI 0.88–0.95,P=4.61×10^(-6)).Mechanistically,rs3094296 had an allele-specific effect on the transcription of the eRNA ENSR00000155786,which functioned as a transcriptional activator promoting the expression of its target gene SENP7.These two genes synergistically suppressed tumor cell proliferation.Our curated list of variants,genes,and drugs has been made available in CancereRNAQTL(http://canernaqtl.whu.edu.cn/#/)to serve as an informative resource for advancing this field.Conclusion:Our findings underscore the significance of eRNAQTLs in transcriptional regulation and disease heritability,pinpointing the potential of eRNA-based therapeutic strategies in cancers.展开更多
Sea cucumber Apostichopus japonicus is a crucial aquatic species known for its nutritional value.However,the genetic basis and regulatory mechanisms underlying its nutritional quality remain underexplored.This study i...Sea cucumber Apostichopus japonicus is a crucial aquatic species known for its nutritional value.However,the genetic basis and regulatory mechanisms underlying its nutritional quality remain underexplored.This study investigates the nutritional quality of A.japonicus from different geographical regions and identifies genetic markers associated with these traits through a genome-wide association study(GWAS).We observed significant regional variations in the nutritional content of A.japonicus.Samples collected from Nanhuangcheng Island displayed the highest levels of saponins,whereas those from Laizhou exhibited the highest concentrations of glycosaminoglycans.Lingshan Island samples were the richest in amino acids,while samples from Rizhao contained the highest levels of polyunsaturated fatty acids.Through GWAS,265 candidate genes and related single nucleotide polymorphisms(SNPs)were identified as being significantly associated with essential nutritional traits,including genes like ubiquitin domain-containing protein 1(UBTD1),inactive pancreatic lipase-related protein 1,protein arginine N-methyltransferase 5(PRMT5)and GDP-fucose protein O-fucosyltransferase 1(POFUT1).This study advanced our knowledge of the genetic mechanisms underlying the nutritional quality of A.japonicus.The genetic markers identified herein o ffer crucial insights for breeding initiatives aimed at optimizing the nutritional profile of sea cucumbers.展开更多
Starch is the most important component in endosperm of sorghum grain.Usually,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,st...Starch is the most important component in endosperm of sorghum grain.Usually,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,structure,and quality of sorghum grains and in marketing applications.In the present study,a panel of 634 sorghum(Sorghum bicolor(L.)Moench)accessions were evaluated for starch,AM,and AP contents of grain,which included a mini core collection of 242 accessions from the International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)in India,and 252 landraces and 140 cultivars from China.The average starch content was 67.64%and the average AM and AP contents were 20.19 and 79.81%,respectively.We developed a total of 260000 high-confidence single nucleotide polymorphism(SNP)markers in the panel of 634 accessions of S.bicolor using specific locus amplified fragment sequencing(SLAF-seq).We performed genome-wide association studies(GWAS)of starch,AM,and AM/AP of grain and SNP markers based on a mixed linear model(MLM).In total,70 significant association signals were detected for starch,AM,and AM/AP ratio of grain with P<4.452×10^-7,of which 10 SNPs were identified with significant starch,51 SNPs were associated with AM,and nine SNPs were associated with the AM/AP ratio.The Gene Ontology(GO)analysis identified 12 candidate genes at five QTLs associated with starch metabolism within the 200-kb intervals,located on chromosomes 1,5,6,and 9.Of these genes,Sobic.006G036500.1 encodes peptidyl-prolyl cis-trans-isomerase CYP38 responsible for hexose monophosphate shunt(HMS)and Sobic.009G071800 encodes 6-phospho-fructokinase(PFK),which is involved in the embden-meyerhof pathway(EMP).Kompetitive allele specific PCR(KASP)markers were developed to validate the GWAS results.The C allele is correlated with a high starch content,while the T allele is linked with a low level of starch content,and provides reliable haplotypes for MAS in sorghum quality improvement.展开更多
It is a long-standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Eur...It is a long-standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Europeans and Han Chinese look different. Facial traits were analyzed based on high-dense 3D facial images; numerous biometric spaces were examined for divergent facial features between European and Han Chinese, ranging from inter-landmark distances to dense shape geometrics, Genome-wide associ- ation studies （GWAS） were conducted on a discovery panel of Uyghurs, Six significant loci were iden- tified, four of which, rs1868752, rs118078182, rs60159418 at or near UBASH3B, COL23A1, PCDH7 and rs17868256 were replicated in independent cohorts of Uyghurs or Southern Han Chinese. A prospective model was also developed to predict 3D faces based on top GWAS signals and tested in hypothetic forensic scenarios.展开更多
The clinical outcome of hepatitis B virus(HBV) infection depends on the success or failure of the immune responses to HBV,and varies widely among individuals,ranging from asymptomatic self-limited infection,inactive c...The clinical outcome of hepatitis B virus(HBV) infection depends on the success or failure of the immune responses to HBV,and varies widely among individuals,ranging from asymptomatic self-limited infection,inactive carrier state,chronic hepatitis,cirrhosis,hepatocellular carcinoma,to liver failure,depending on the success or failure of immune response to HBV.Genome-wide association studies(GWAS) identified key genetic factors influencing the pathogenesis of HBV-related traits.In this review,we discuss GWAS for persistence of HBV infection,antibody response to hepatitis B vaccine,and HBV-related advanced liver diseases.HBV persistence is associated with multiple genes with diverse roles in immune mechanisms.The strongest associations are found within the classical human leukocyte antigen(HLA) genes,highlighting the central role of antigen presentation in the immune response to HBV.Associated variants affect both epitope binding specificities and expression levels of HLA molecules.Several other susceptibility genes regulate the magnitude of adaptive immune responses,determining immunity vs tolerance.HBV persistence and nonresponse to vaccine share the same risk variants,implying overlapping genetic bases.On the other hand,the risk variants for HBV-related advanced liver diseases are largely different,suggesting different host-virus dynamics in acute vs chronic HBV infections.The findings of these GWAS are likely to pave the way for developing more effective preventive and therapeutic interventions by personalizing the management of HBV infection.展开更多
Objective: In the past few decades, more than 500 reports have been published on the relationship between single nucleotide polymorphisms(SNPs) on candidate genes and gastric cancer(GC) risk. Previous findings have be...Objective: In the past few decades, more than 500 reports have been published on the relationship between single nucleotide polymorphisms(SNPs) on candidate genes and gastric cancer(GC) risk. Previous findings have been disputed and are controversial. Therefore, we performed this article to summarize and assess the credibility and strength of genetic polymorphisms on the risk of GC.Methods: We used Web of Science, PubMed, and Medline to identify meta-analyses published before July 30 th, 2018 that assessed associations between variants on candidate genes and the risk of GC. Cumulative epidemiological evidence of statistical associations was assessed combining Venice criteria and a false-positive report probability(FPRP) test.Results: Sixty-one variants demonstrated a significant association with GC risk, whereas 29 demonstrated no association. Nine variants on nine genes were rated as presenting strong cumulative epidemiological evidence for a nominally significant association with GC risk, including APE1(rs1760944), DNMT1(rs16999593), ERCC5(rs751402), GSTT1(null/presence), MDM2(rs2278744), PPARG(rs1801282), TLR4(rs4986790), IL-17 F(rs763780), and CASP8(rs3834129). Eleven SNPs were rated as moderate, and 33 SNPs were rated as weak. We also used the FPRP test to identify 13 noteworthy SNPs in five genome-wide association studies.Conclusions: Sixty-one variants are significantly associated with GC risk, and 29 variants are not associated with GC risk;however, five variants on five genes presented strong evidence for an association upgraded from moderate. Further study of these variants may be needed in the future. Our study also provides referenced information for the genetic predisposition to GC.展开更多
Vitamin E,consisting of tocopherols and tocotrienols,serves as a lipid-soluble antioxidant in sweet corn kernels,providing nutrients to both plants and humans.Though the key genes involved in the vitamin E biosynthesi...Vitamin E,consisting of tocopherols and tocotrienols,serves as a lipid-soluble antioxidant in sweet corn kernels,providing nutrients to both plants and humans.Though the key genes involved in the vitamin E biosynthesis pathway have been identified in plants,the genetic architecture of vitamin E content in sweet corn kernels remains largely unclear.In the present study,an association panel of 204 inbred lines of sweet corn was constructed.Seven compounds of vitamin E were quantified in sweet corn kernels at 28 days after pollination.A total of 119 loci for vitamin E were identified using a genome-wide association study based on genotyping by sequencing,and a genetic network of vitamin E was constructed.Candidate genes identified were involved mainly in RNA regulation and protein metabolism.The known gene ZmVTE4,encodingγ-tocopherol methyltransferase,was significantly associated with four traits(α-tocopherol,α-tocotrienol,theα/γ-tocopherol ratio,and theα/γ-tocotrienol ratio).The effects of two causative markers on ZmVTE4 were validated by haplotype analysis.Finally,two elite cultivars(Yuetian 9 and Yuetian 22)with a 4.5-fold increase in the sum ofα-andγ-tocopherols were developed by marker-assisted selection,demonstrating the successful biofortification of sweet corn.Three genes(DAHPS,ADT2,and cmu2)involved in chorismate and tyrosine synthesis were significantly associated with theα/γ-tocotrienol ratio.These results shed light on the genetic architecture of vitamin E and may accelerate the nutritional improvement of sweet corn.展开更多
Sheath blight(SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease....Sheath blight(SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci(QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study(GWAS) of SB resistance using 299 varieties from the rice diversity panel 1(RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism(SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica(TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.展开更多
Fusarium ear rot(FER)is a destructive maize fungal disease worldwide.In this study,three tropical maize populations consisting of 874 inbred lines were used to perform genomewide association study(GWAS)and genomic pre...Fusarium ear rot(FER)is a destructive maize fungal disease worldwide.In this study,three tropical maize populations consisting of 874 inbred lines were used to perform genomewide association study(GWAS)and genomic prediction(GP)analyses of FER resistance.Broad phenotypic variation and high heritability for FER were observed,although it was highly influenced by large genotype-by-environment interactions.In the 874 inbred lines,GWAS with general linear model(GLM)identified 3034 single-nucleotide polymorphisms(SNPs)significantly associated with FER resistance at the P-value threshold of 1×10^(-5),the average phenotypic variation explained(PVE)by these associations was 3%with a range from 2.33%to 6.92%,and 49 of these associations had PVE values greater than 5%.The GWAS analysis with mixed linear model(MLM)identified 19 significantly associated SNPs at the P-value threshold of 1×10^(-4),the average PVE of these associations was 1.60%with a range from 1.39%to 2.04%.Within each of the three populations,the number of significantly associated SNPs identified by GLM and MLM ranged from 25 to 41,and from 5 to 22,respectively.Overlapping SNP associations across populations were rare.A few stable genomic regions conferring FER resistance were identified,which located in bins 3.04/05,7.02/04,9.00/01,9.04,9.06/07,and 10.03/04.The genomic regions in bins 9.00/01 and 9.04 are new.GP produced moderate accuracies with genome-wide markers,and relatively high accuracies with SNP associations detected from GWAS.Moderate prediction accuracies were observed when the training and validation sets were closely related.These results implied that FER resistance in maize is controlled by minor QTL with small effects,and highly influenced by the genetic background of the populations studied.Genomic selection(GS)by incorporating SNP associations detected from GWAS is a promising tool for improving FER resistance in maize.展开更多
Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present stu...Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present study, large phenotypic variation was observed in 760 accessions from the 3 K Rice Genomes Project for both appearance quality and cooked rice elongation. Most component traits of appearance quality and cooked rice elongation showed significant pairwise correlations, but a low correlation was found between appearance quality and cooked rice elongation. A genome-wide association study identified 74 QTL distributed on all 12 chromosomes for grain length, grain width, length to width ratio, degree of endosperm with chalkiness, rice elongation difference, and elongation index. Thirteen regions containing QTL stably expressed in multiple environments and/or exerting pleiotropic effects on multiple traits were detected. By gene-based association analysis and haplotype analysis, 46 candidate genes, including five cloned genes, and 49 favorable alleles were identified for these 13 QTL. The effect of the candidate gene Wx on rice elongation difference was validated by a transgenic strategy. These results shed light on the genetic bases of appearance quality and cooked rice elongation and provide gene resources for improving rice quality by molecular breeding.展开更多
基金supported by the National Natural Science Foundation of China(32071798)5·5 Engineering Research&Innovation Team Project of Beijing Forestry University,China(BLRC2023B08)。
文摘Sucrose transporters(SUTs)play a crucial role in carbon allocation from the source leaf to the sink end,and the function of SUTs varies among family members.However,the genome-wide identifcation of the SUT superfamily in Camellia oleifera is lacking,and their biological function remains elusive.In this study,four SUT genes-designated Co SUT1-4-were identifed in C.oleifera through a genome-wide analysis and classifed into three subfamilies.We used a combination of cis-acting elements analysis,mRNA quantifcation,histochemical analysis,and heterologous transformation to evaluate the expression profiles and functions of these SUTs.A key finding is that CoSUT4,localized on the plasma membrane,is highly expressed in mature leaves and the early stage of seed development in C.oleifera.In vitro culture of C.oleifera seed revealed the responsiveness of CoSUT4 to various exogenous hormones such as ABA and GA.CoSUT4 was able to restore the growth of the yeast strain SUSY7/ura3(a sucrose transport-defcient mutant)on sucrose-containing media and specifcally contributed to sucrose translocation and tissue growth in CoSUT4-overexpressed apple calli.In situ hybridization identifed chalazal nucellus and transfer cells as the action sites of CoSUT4 at the maternal-flial interface mediating sucrose transportation in oil tea seeds.CoSUT4 overexpression in Arabidopsis thaliana atsuc4 mutant restored the growth and seed yield defciencies of the mutant,leading to an increase in flled seeds and oil content.Additionally,CoSUT4 overexpression enhanced the drought and salt stress tolerance by augmenting sugar content.Overall,these fndings provide valuable insights into the function of SUTs and present promising candidates for the genetic enhancement of seed production in C.oleifera.
基金supported by the Fund for BTNYGG(NYHXGG,2023AA102)the National Natural Science Foundation of China(32260510)+3 种基金the Key Project for Science,Technology Development of Shihezi city,Xinjiang Production and Construction Crops(2022NY01)Shihezi University high-level talent research project(RCZK202337)Science and Technology Major Project of the Department of Science and Technology of Xinjiang Uygur Autonomous region(2022A03004-1)the Key Programs for Science and Technology Development in Agricultural Field of Xinjiang Production and Construction Corps。
文摘Background Cotton is a significant crop for fiber production;however,seed shape-related traits have been less investigated in comparison to fiber quality.Comprehending the genetic foundation of traits associated with seed shape is crucial for improving the seed and fiber quality in cotton.Results A total of 238 cotton accessions were evaluated in four different environments over a period of two years.Traits including thousand grain weight(TGW),aspect ratio(AR),seed length,seed width,diameter,and roundness demonstrated high heritability and significant genetic variation,as indicated by phenotypic analysis.The association analysis involved 145 simple sequence repeats(SSR)markers and identified 50 loci significantly associated with six traits related to seed shape.The markers MON_DPL0504aa and BNL2535ba were identified as influencing multiple traits,including aspect ratio and thousand grain weight.Notably,markers such as HAU2588a and MUSS422aa had considerable influence on seed diameter and roundness.The identified markers represented an average phenotypic variance between 3.92%for seed length and 16.54%for TGW.Conclusions The research finds key loci for seed shape-related traits in cotton,providing significant potential for marker-assisted breeding.These findings establish a framework for breeding initiatives focused on enhancing seed quality,hence advancing the cotton production.
基金supported by the National Natural Science Foundation of China(Grant Nos.32000377,32172037,and 32472211)the Biological Breeding-National Science and Technology Major Project,China(Grant No.2023ZD04068)+2 种基金the Fundamental Research Funds for the Central Universities,China(Grant No.KJQN202103)the open funds of the State Key Laboratory of Crop Genetics&Germplasm Enhancement and Utilization,China(Grant No.ZW202401)the Cyrus Tang Innovation Center for Crop Seed Industry,China.
文摘Rice grain yield is primarily determined by three key agronomic traits:panicle number,grain number per panicle,and grain weight(GW).However,the inherent tradeoffs among these yield components remain a persistent challenge in rice breeding programs.Notably,compared with GW,brown rice weight(BRW)provides a more direct metric associated with actual grain yield potential.In this study,we conducted a two-year replicated genome-wide association study to elucidate the genetic architecture of BRW and identify new loci regulating GW.Among seven consistently detected loci across experimental replicates,four were not co-localized with previously reported genes associated with BRW or GW traits.BRW1.1,one of the four newly identified loci,was found to encode a novel RNA-binding protein.Functional characterization revealed that BRW1.1 acts as a negative regulator of BRW,potentially through modulating mRNA translation processes.Intriguingly,through integrated analysis of mutant phenotypes and haplotype variations,we demonstrated that BRW1.1 mediates the physiological tradeoff between GW and panicle number.This study not only delineates the genetic determinants of BRW but also identifies BRW1.1 as a promising molecular target for breaking the yield component tradeoff in precision rice breeding.
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 National Natural Science Foundation of China(Grant No.31872106)the National Vegetable Industry Technology System(Grant No.CARS-23-A-16)+1 种基金the Jiangsu Seed Industry Revitalization Project(Grant No.JBGS(2021)015)the Priority Academic Program Development of Jiangsu Higher Education Institutions。
文摘The nuclear factor Y(NF-Y)is a class of heterotrimeric transcription factors comprising three subunits:NF-YA,NF-YB,and NF-YC.These transcription factors participate in many plant bioprocesses,including the regulation of flowering time.Although the NF-Y gene family has been systematically studied in many species,little is known about its role in the non-heading Chinese cabbage(NHCC)[Brassica campestris(syn.Brassica rapa)ssp.chinensis].In this study,we identified 57 NF-Y members in the genome of NHCC using BLASTP,including 20 BcNF-YAs,24BcNF-YBs,and 13 BcNF-YCs.These genes are randomly distributed on the 10 chromosomes of NHCC.The results of yeast two-hybrid experiments indicated that among some members of the three subunits of BcNF-Ys,the members of the NF-YA and NF-YC subunits interact with each other,a third of the members of the NF-YB and NF-YC subunits interact with each other,while no interaction was observed between the members of the NF-YA and NF-YB subunits.Subcellular localization experiments in tobacco showed that Bc NF-YA2 and BcNF-YA8 were expressed in the nucleus;BcNF-YB18 and BcNF-YB23 were located in the cell membrane and cytoplasm;and BcNF-YC6 and BcNF-YC7 were expressed in the nucleus,cytoplasm,and cell membrane.We analyzed the cis-acting elements in the promoter of BcNF-Y genes and found that the ABA response element is the most distributed hormone response element,which is regulated by ABA signals triggered by environmental stimuli.Accordingly,we treated three-week-old NHCC leaves with 100μmol L^(-1) ABA and analyzed the expression profile of BcNF-Ys through RNA-seq.The results showed that except for six undetected BcNF-Ys,the remaining 51 BcNF-Ys showed varying degrees of response to ABA signals.Among these,BcNF-YA8 was positively regulated by ABA signals,with the highest upregulation amplitude.Subsequently,the function of BcNF-YA8 was extensively studied,which demonstrated that its expression promotes plant flowering.This result enriches our understanding of the potential molecular mechanism by which ABA positively regulates NHCC flowering.
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.
文摘Background:Rice grain morphology—including traits such as awn length,hull color,size,and shape—is of central importance to yield,quality,and domestication,yet comprehensive quantification at scale has remained challenging.Apromising solution has been provided by the integration of high-throughput imaging with genomic analysis.Methods:A standardized 2D image-processing pipeline was established to extract four categories of traits—awn length,hull color,projected grain area,and shape descriptors via PCA of normalized contours—from high-resolution photographs of 229 Oryza sativa japonica landraces.Genome-wide association analyses were then performed using a mixed linearmodel to control for population structure and kinship.Results:Broad phenotypic diversity was evident in awn length,hull coloration,grain dimensions,and morphological shape,with the first principal component explaining the dominant axis of shape variation.Known awn regulators GAD1/OsRAE2(chr 8;P=4.75×10^(-17))and An-1(chr 4;P=1.91×10^(-6))were identified.The hull color gene Rd(chr 1;P=3.13×10^(-6))was detected.A novel locus on chr 12 at 8.75 Mb with Os12g0257600(P=1.41×10^(-8)),and the known grain size gene FLO2(chr 4;P=8.28×10^(-6))were associated with projected area.Shape PC1 was mapped to GLW7/OsSPL13(chr 7;P=3.86×10^(-10)),NAL2/OsWOX3A(chr 11;P=1.41×10^(-11)),and OsGIF1(chr 11;P=1.27×10^(-8)).Conclusions:This study demonstrates that image-based phenotyping combined with genome-wide association studies(GWAS)can efficiently reveal both established and novel genetic determinants of rice grain morphology.These findings provide actionable targets for marker-assisted selection and genome editing to tailor grain traits in rice breeding programs.
基金supported by the National Key R&D Program of China(2022YFD1201802)the Shandong Key R&D Program,China(2022CXGC010607)+2 种基金the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-ZDRW202109)the Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-ASTIP2017-ICS)the Subproject of the Major Project of Science and Technology in Shanxi Province,China(202201140601025-1-02)。
文摘Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen.Using phenotypic SCR resistance-related data collected over two years and three geographical environments,a genome-wide association study was carried out in this work,which eventually identified 91 loci that were substantially correlated with SCR susceptibility.These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes(B73_RefGen_v4).Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection,with 2,586 and 797 differentially expressed genes(DEGs)ultimately being identified in the resistant Qi319and susceptible 8112 inbred lines following P.polysora infection,respectively,including 306 genes common to both lines.Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes.One of these genes is ZmHCT9,which encodes the protein hydroxycinnamoyl transferase 9.This gene was up-regulated in susceptible inbred lines and linked to greater P.polysora resistance as confirmed through cucumber mosaic virus(CMV)-based virus induced-gene silencing(VIGS)system-mediated gene silencing.These data provide important insights into the genetic basis of the maize SCR response.They will be useful for for future research on potential genes related to SCR resistance in maize.
基金supported by the Undergraduate Training Program for Innovation and Entrepreneurship (S202110580053,202410580011)the Zhaoqing University Project (190060,QN202329)Science and Technology Program of Zhaoqing (2023040308001)。
文摘Late embryogenesis abundant (LEA) proteins generally accumulate in seeds during the later stages of maturation.Here we studied the LEA genes in two wild peanut species (Arachis duranensis and Arachis ipaensis) in an effort to create a genetic resource for peanut crop improvement.we identified 65 AdLEA and 69 AiLEA genes representing all 8 LEA subfamilies,which were unevenly distributed across 10 peanut chromosomes.The majority of LEA proteins were found to be highly hydrophilic.MEME analysis indicated that LEA gene motifs were conserved within groups,but not between groups.The LEA genes contained a diverse array of stress-and phytohormoneresponsive cis-acting elements,with the AdLEA2-20 and AiLEA2-20 genes containing the greatest number of elements.Both AdLEA2-20 and AiLEA2-20 were upregulated in response to cold temperatures,drought,salinity,and abscisic acid exposure,although the dynamics were tissue-dependent.This study lays the foundation for future studies on the LEA gene family and abiotic stress in peanut,and our results will be invaluable for the genetic improvement of peanut by characterizing the genetic resources of wild peanut species.
基金supported by National Key Research and Development Program of China(2022YFF1000204 and 2021YFD1200803).
文摘Background Compared to many other vertebrates,chickens have a high reproductive efficiency in terms of egg production.The classic traits for evaluating egg-laying performance include age at first egg,egg number,clutch size,laying rate,etc.These egg-laying traits were not specifically designed to characterize egg production efficiency and stability.By considering the stage-specific variations in the egg production curve,this study aims to investigate the genetic mechanisms that directly influence the efficiency of egg production at each stage of the laying cycle.Results Using whole-genome sequencing data,we perform comprehensive genome-wide association study for 39 traits that focus on egg production efficiency and stability in the Gushi chicken.We showed that the haplotype-based approach is more effective for genetic mapping and capturing polygenic architecture.By combining the signals of Singleton Density Score(SDS),which is a population-genetic statistic designed to detect recent selection by leveraging the distribution of singletons,and association analyses,multiple egg-laying traits related to egg production efficiency were found to have experienced polygenic selection.Consistently,functional analysis of associated genes demonstrates that egg production efficiency benefits from multiple physiological functions.Furthermore,our results identified the CNNM2 gene,known for its role in magnesium homeostasis,plays a dual role in egg production variance,promoting variability during the up-stage while reducing it during the sustained-stage to optimize egg production efficiency.Conclusions Collectively,our multiple genome analyses reveal a complex genetic mechanism underlying more efficient and stable egg production,and establish chicken genetics as a model for studying reproductive efficiency across species.
基金supported by the National Science Fund for Excellent Young Scholars(NSFC-82322058)the Program of National Natural Science Foundation of China(NSFC-82103929,NSFC-82273713)+10 种基金the Young Elite Scientists Sponsorship Program by CAST(2022QNRC001)the National Science Fund for Distinguished Young Scholars of Hubei Province of China(2023AFA046)the Fundamental Research Funds for the Central Universities(WHU:2042022kf1205)Fundamental Research Funds for the Central Universities(WHU:2042022kf1031)for Ying Zhuthe Fundamental Research Funds for the Central Universities(2042022rc0026,2042023kf1005)for Xiao-Ping Miaothe Knowledge Innovation Program of Wuhan(whkxjsj011,2023020201010073)for Jian-Bo Tianthe Science and Technology Innovation Seed Fund of Zhongnan Hospital of Wuhan University(znpy2019060)for Yong-Chang Weithe Distinguished Young Scholars of China(NSFC-81925032)the Key Program of National Natural Science Foundation of China(NSFC-82130098)the Youth Program of National Natural Science Foundation of China(NSFC-82003547)the Program of Health Commission of Hubei Province(WJ2023M045)。
文摘Background:Dysregulation of enhancer transcription occurs in multiple cancers.Enhancer RNAs(eRNAs)are transcribed products from enhancers that play critical roles in transcriptional control.Characterizing the genetic basis of eRNA expression may elucidate the molecular mechanisms underlying cancers.Methods:Initially,a comprehensive analysis of eRNA quantitative trait loci(eRNAQTLs)was performed in The Cancer Genome Atlas(TCGA),and functional features were characterized using multi-omics data.To establish the first eRNAQTL profiles for colorectal cancer(CRC)in China,epigenomic data were used to define active enhancers,which were subsequently integrated with transcription and genotyping data from 154 paired CRC samples.Finally,largescale case-control studies(34,585 cases and 69,544 controls)were conducted along with multipronged experiments to investigate the potential mechanisms by which candidate eRNAQTLs affect CRC risk.Results:A total of 300,112 eRNAQTLs were identified across 30 different cancer types,which exert their influence on eRNA transcription by modulating chromatin status,binding affinity to transcription factors and RNA-binding proteins.These eRNAQTLs were found to be significantly enriched in cancer risk loci,explaining a substantial proportion of cancer heritability.Additionally,tumor-specific eRNAQTLs exhibited high responsiveness to the development of cancer.Moreover,the target genes of these eRNAs were associated with dysregulated signaling pathways and immune cell infiltration in cancer,highlighting their potential as therapeutic targets.Furthermore,multiple ethnic population studies have confirmed that an eRNAQTL rs3094296-T variant decreases the risk of CRC in populations from China(OR=0.91,95%CI 0.88–0.95,P=2.92×10^(-7))and Europe(OR=0.92,95%CI 0.88–0.95,P=4.61×10^(-6)).Mechanistically,rs3094296 had an allele-specific effect on the transcription of the eRNA ENSR00000155786,which functioned as a transcriptional activator promoting the expression of its target gene SENP7.These two genes synergistically suppressed tumor cell proliferation.Our curated list of variants,genes,and drugs has been made available in CancereRNAQTL(http://canernaqtl.whu.edu.cn/#/)to serve as an informative resource for advancing this field.Conclusion:Our findings underscore the significance of eRNAQTLs in transcriptional regulation and disease heritability,pinpointing the potential of eRNA-based therapeutic strategies in cancers.
基金Supported by the Key Research and Development Program of Shandong(Nos.2021LZGC029,2023LZGC019)the National Natural Science Foundation of China(No.42076093)+1 种基金the Special Funds for the Central Government to Guide Local Science and Technology Development(No.YDZX2023043)the Taishan Scholars Program(No.tsqn202306279)。
文摘Sea cucumber Apostichopus japonicus is a crucial aquatic species known for its nutritional value.However,the genetic basis and regulatory mechanisms underlying its nutritional quality remain underexplored.This study investigates the nutritional quality of A.japonicus from different geographical regions and identifies genetic markers associated with these traits through a genome-wide association study(GWAS).We observed significant regional variations in the nutritional content of A.japonicus.Samples collected from Nanhuangcheng Island displayed the highest levels of saponins,whereas those from Laizhou exhibited the highest concentrations of glycosaminoglycans.Lingshan Island samples were the richest in amino acids,while samples from Rizhao contained the highest levels of polyunsaturated fatty acids.Through GWAS,265 candidate genes and related single nucleotide polymorphisms(SNPs)were identified as being significantly associated with essential nutritional traits,including genes like ubiquitin domain-containing protein 1(UBTD1),inactive pancreatic lipase-related protein 1,protein arginine N-methyltransferase 5(PRMT5)and GDP-fucose protein O-fucosyltransferase 1(POFUT1).This study advanced our knowledge of the genetic mechanisms underlying the nutritional quality of A.japonicus.The genetic markers identified herein o ffer crucial insights for breeding initiatives aimed at optimizing the nutritional profile of sea cucumbers.
基金supported by the earmarked fund for China Agriculture Research System (CARS-06)
文摘Starch is the most important component in endosperm of sorghum grain.Usually,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,structure,and quality of sorghum grains and in marketing applications.In the present study,a panel of 634 sorghum(Sorghum bicolor(L.)Moench)accessions were evaluated for starch,AM,and AP contents of grain,which included a mini core collection of 242 accessions from the International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)in India,and 252 landraces and 140 cultivars from China.The average starch content was 67.64%and the average AM and AP contents were 20.19 and 79.81%,respectively.We developed a total of 260000 high-confidence single nucleotide polymorphism(SNP)markers in the panel of 634 accessions of S.bicolor using specific locus amplified fragment sequencing(SLAF-seq).We performed genome-wide association studies(GWAS)of starch,AM,and AM/AP of grain and SNP markers based on a mixed linear model(MLM).In total,70 significant association signals were detected for starch,AM,and AM/AP ratio of grain with P<4.452×10^-7,of which 10 SNPs were identified with significant starch,51 SNPs were associated with AM,and nine SNPs were associated with the AM/AP ratio.The Gene Ontology(GO)analysis identified 12 candidate genes at five QTLs associated with starch metabolism within the 200-kb intervals,located on chromosomes 1,5,6,and 9.Of these genes,Sobic.006G036500.1 encodes peptidyl-prolyl cis-trans-isomerase CYP38 responsible for hexose monophosphate shunt(HMS)and Sobic.009G071800 encodes 6-phospho-fructokinase(PFK),which is involved in the embden-meyerhof pathway(EMP).Kompetitive allele specific PCR(KASP)markers were developed to validate the GWAS results.The C allele is correlated with a high starch content,while the T allele is linked with a low level of starch content,and provides reliable haplotypes for MAS in sorghum quality improvement.
基金funded by the Max-Planck-Gesellschaft Partner Group Grant (KT)the National Natural Science Foundation of China (Nos.31371267,31322030,91331108 (KT)+10 种基金91731303,31771388,and 31711530221 (SX)91631307 (SW)31501011 (YL) and 31260263 (YG))supported by Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB13040100,SXXDB13041000,SW)the National Science Fund for Distinguished Young Scholars (31525014,SX)the Program of Shanghai Academic Research Leader (16XD1404700,to SX)the support of a National Thousand Young Talents Award and a Max Planck-CAS Paul Gerson Unna Independent Research Group Leadership Award (SW)the Science and Technology Commission of Shanghai Municipality (16JC1400504,SW14YF1406800,YL16YF1413900,HL)
文摘It is a long-standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Europeans and Han Chinese look different. Facial traits were analyzed based on high-dense 3D facial images; numerous biometric spaces were examined for divergent facial features between European and Han Chinese, ranging from inter-landmark distances to dense shape geometrics, Genome-wide associ- ation studies （GWAS） were conducted on a discovery panel of Uyghurs, Six significant loci were iden- tified, four of which, rs1868752, rs118078182, rs60159418 at or near UBASH3B, COL23A1, PCDH7 and rs17868256 were replicated in independent cohorts of Uyghurs or Southern Han Chinese. A prospective model was also developed to predict 3D faces based on top GWAS signals and tested in hypothetic forensic scenarios.
文摘The clinical outcome of hepatitis B virus(HBV) infection depends on the success or failure of the immune responses to HBV,and varies widely among individuals,ranging from asymptomatic self-limited infection,inactive carrier state,chronic hepatitis,cirrhosis,hepatocellular carcinoma,to liver failure,depending on the success or failure of immune response to HBV.Genome-wide association studies(GWAS) identified key genetic factors influencing the pathogenesis of HBV-related traits.In this review,we discuss GWAS for persistence of HBV infection,antibody response to hepatitis B vaccine,and HBV-related advanced liver diseases.HBV persistence is associated with multiple genes with diverse roles in immune mechanisms.The strongest associations are found within the classical human leukocyte antigen(HLA) genes,highlighting the central role of antigen presentation in the immune response to HBV.Associated variants affect both epitope binding specificities and expression levels of HLA molecules.Several other susceptibility genes regulate the magnitude of adaptive immune responses,determining immunity vs tolerance.HBV persistence and nonresponse to vaccine share the same risk variants,implying overlapping genetic bases.On the other hand,the risk variants for HBV-related advanced liver diseases are largely different,suggesting different host-virus dynamics in acute vs chronic HBV infections.The findings of these GWAS are likely to pave the way for developing more effective preventive and therapeutic interventions by personalizing the management of HBV infection.
文摘Objective: In the past few decades, more than 500 reports have been published on the relationship between single nucleotide polymorphisms(SNPs) on candidate genes and gastric cancer(GC) risk. Previous findings have been disputed and are controversial. Therefore, we performed this article to summarize and assess the credibility and strength of genetic polymorphisms on the risk of GC.Methods: We used Web of Science, PubMed, and Medline to identify meta-analyses published before July 30 th, 2018 that assessed associations between variants on candidate genes and the risk of GC. Cumulative epidemiological evidence of statistical associations was assessed combining Venice criteria and a false-positive report probability(FPRP) test.Results: Sixty-one variants demonstrated a significant association with GC risk, whereas 29 demonstrated no association. Nine variants on nine genes were rated as presenting strong cumulative epidemiological evidence for a nominally significant association with GC risk, including APE1(rs1760944), DNMT1(rs16999593), ERCC5(rs751402), GSTT1(null/presence), MDM2(rs2278744), PPARG(rs1801282), TLR4(rs4986790), IL-17 F(rs763780), and CASP8(rs3834129). Eleven SNPs were rated as moderate, and 33 SNPs were rated as weak. We also used the FPRP test to identify 13 noteworthy SNPs in five genome-wide association studies.Conclusions: Sixty-one variants are significantly associated with GC risk, and 29 variants are not associated with GC risk;however, five variants on five genes presented strong evidence for an association upgraded from moderate. Further study of these variants may be needed in the future. Our study also provides referenced information for the genetic predisposition to GC.
基金the National Natural Science Foundation of China(31601309)Science and Technology Planning Project of Guangdong Province(2016B020233004,2015A020209063,2017B090907023)+2 种基金Science and Technology Planning Project of Guangzhou(201804020081)Agricultural Development and Rural Work Special Project-Modern Seed Industry Enhancement Project of Guangdong(201788)the Excellent PhD Program of Guangdong Academy of Agricultural Sciences(2017).
文摘Vitamin E,consisting of tocopherols and tocotrienols,serves as a lipid-soluble antioxidant in sweet corn kernels,providing nutrients to both plants and humans.Though the key genes involved in the vitamin E biosynthesis pathway have been identified in plants,the genetic architecture of vitamin E content in sweet corn kernels remains largely unclear.In the present study,an association panel of 204 inbred lines of sweet corn was constructed.Seven compounds of vitamin E were quantified in sweet corn kernels at 28 days after pollination.A total of 119 loci for vitamin E were identified using a genome-wide association study based on genotyping by sequencing,and a genetic network of vitamin E was constructed.Candidate genes identified were involved mainly in RNA regulation and protein metabolism.The known gene ZmVTE4,encodingγ-tocopherol methyltransferase,was significantly associated with four traits(α-tocopherol,α-tocotrienol,theα/γ-tocopherol ratio,and theα/γ-tocotrienol ratio).The effects of two causative markers on ZmVTE4 were validated by haplotype analysis.Finally,two elite cultivars(Yuetian 9 and Yuetian 22)with a 4.5-fold increase in the sum ofα-andγ-tocopherols were developed by marker-assisted selection,demonstrating the successful biofortification of sweet corn.Three genes(DAHPS,ADT2,and cmu2)involved in chorismate and tyrosine synthesis were significantly associated with theα/γ-tocotrienol ratio.These results shed light on the genetic architecture of vitamin E and may accelerate the nutritional improvement of sweet corn.
基金partially supported by the Open Funding from State Key Laboratory for Biology of Plant Diseases and Insect Pests(Grant No.SKLOF201403)by the Natural Science Foundation of China(Grant Nos.31571748 and 31701057)the Natural Science Foundation of Jiangsu Province,China(Grant Nos.BK20171293 and BK20141291)
文摘Sheath blight(SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci(QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study(GWAS) of SB resistance using 299 varieties from the rice diversity panel 1(RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism(SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica(TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.
基金The authors gratefully acknowledge the financial support from the MasAgro project funded by Mexico’s Secretary of Agriculture and Rural Development(SADER),the Genomic Open-source Breeding Informatics Initiative(GOBII)(grant number OPP1093167)supported by the Bill&Melinda Gates Foundation,and the CGIAR Research Program(CRP)on maize(MAIZE)MAIZE receives W1&W2 support from the Governments of Australia,Belgium,Canada,China,France,India,Japan,the Republic of Korea,Mexico,Netherlands,New Zealand,Norway,Sweden,Switzerland,the United Kingdom,USA,and the World Bank+2 种基金The authors also thank the National Natural Science Foundation of China(grant number 31801442)the CIMMYT–China Specialty Maize Research Center Project funded by the Shanghai Municipal Finance Bureauthe China Scholarship Council.
文摘Fusarium ear rot(FER)is a destructive maize fungal disease worldwide.In this study,three tropical maize populations consisting of 874 inbred lines were used to perform genomewide association study(GWAS)and genomic prediction(GP)analyses of FER resistance.Broad phenotypic variation and high heritability for FER were observed,although it was highly influenced by large genotype-by-environment interactions.In the 874 inbred lines,GWAS with general linear model(GLM)identified 3034 single-nucleotide polymorphisms(SNPs)significantly associated with FER resistance at the P-value threshold of 1×10^(-5),the average phenotypic variation explained(PVE)by these associations was 3%with a range from 2.33%to 6.92%,and 49 of these associations had PVE values greater than 5%.The GWAS analysis with mixed linear model(MLM)identified 19 significantly associated SNPs at the P-value threshold of 1×10^(-4),the average PVE of these associations was 1.60%with a range from 1.39%to 2.04%.Within each of the three populations,the number of significantly associated SNPs identified by GLM and MLM ranged from 25 to 41,and from 5 to 22,respectively.Overlapping SNP associations across populations were rare.A few stable genomic regions conferring FER resistance were identified,which located in bins 3.04/05,7.02/04,9.00/01,9.04,9.06/07,and 10.03/04.The genomic regions in bins 9.00/01 and 9.04 are new.GP produced moderate accuracies with genome-wide markers,and relatively high accuracies with SNP associations detected from GWAS.Moderate prediction accuracies were observed when the training and validation sets were closely related.These results implied that FER resistance in maize is controlled by minor QTL with small effects,and highly influenced by the genetic background of the populations studied.Genomic selection(GS)by incorporating SNP associations detected from GWAS is a promising tool for improving FER resistance in maize.
基金funded by the National Key Research and Development Program of China (2016YFD0100301)Project for Cultivating New Transgenic Varieties (2016ZX08009003-004)+2 种基金the Agricultural Science and Technology Innovation Program and the Cooperation and Innovation Mission (CAAS-ZDXT202001)Open Fund of Hubei Collaborative Innovation Center for Grain Industry (HCICGI2020-06)the National Natural Science Foundation of China (U19A2025 and 31870229)。
文摘Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present study, large phenotypic variation was observed in 760 accessions from the 3 K Rice Genomes Project for both appearance quality and cooked rice elongation. Most component traits of appearance quality and cooked rice elongation showed significant pairwise correlations, but a low correlation was found between appearance quality and cooked rice elongation. A genome-wide association study identified 74 QTL distributed on all 12 chromosomes for grain length, grain width, length to width ratio, degree of endosperm with chalkiness, rice elongation difference, and elongation index. Thirteen regions containing QTL stably expressed in multiple environments and/or exerting pleiotropic effects on multiple traits were detected. By gene-based association analysis and haplotype analysis, 46 candidate genes, including five cloned genes, and 49 favorable alleles were identified for these 13 QTL. The effect of the candidate gene Wx on rice elongation difference was validated by a transgenic strategy. These results shed light on the genetic bases of appearance quality and cooked rice elongation and provide gene resources for improving rice quality by molecular breeding.
