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
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: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
Rice cooking and eating qualities(CEQ)are mainly determined by cooked rice textural parameters and starch physicochemical properties.However,the genetic bases of grain texture and starch properties in rice have not be...Rice cooking and eating qualities(CEQ)are mainly determined by cooked rice textural parameters and starch physicochemical properties.However,the genetic bases of grain texture and starch properties in rice have not been fully understood.We conducted a genome-wide association study for apparent amylose content(AAC),starch pasting viscosities,and cooked rice textural parameters using 279 indica rice accessions from the 3000 Rice Genome Project.We identified 26 QTLs in the whole population and detected single nucleotide polymorphisms(SNPs)with the lowest P-value at the Waxy(Wx)locus for all traits except pasting temperature and cohesiveness.Additionally,we detected significant SNPs at the SUBSTANDARD STARCH GRAIN6(SSG6)locus for AAC,setback(SB),hardness,adhesiveness,chewiness(CHEW),gumminess(GUM),and resilience.We subsequently divided the population using a SNP adjacent to the Waxy locus,and identified 23 QTLs and 12 QTLs in two sub-panels,WxT and WxA,respectively.In these sub-panels,SSG6 was also identified to be associated with pasting parameters,including peak viscosity,hot paste viscosity,cold paste viscosity,and consistency viscosity.Furthermore,a candidate gene encoding monosaccharide transporter 5(OsMST5)was identified to be associated with AAC,breakdown,SB,CHEW,and GUM.In total,39 QTLs were co-localized with known genes or previously reported QTLs.These identified genes and QTLs provide valuable information for genetic manipulation to improve rice CEQ.展开更多
Nitrogen(N)fertilizer application is essential for crop-plant growth and development.Identifying genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused ...Nitrogen(N)fertilizer application is essential for crop-plant growth and development.Identifying genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by overfertilization.We subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling stage.Genotyping the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate.These SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type plant.We developed two functional markers for Hap 1,the favorable allele of TaBOX.展开更多
Objective N6-methyladenosine(m^(6)A)is a common epigenetic modification in eukaryotes.In this study,we explore the potential impact of m^(6)A-associated single nucleotide polymorphisms(m^(6)A-SNPs)on heart failure(HF)...Objective N6-methyladenosine(m^(6)A)is a common epigenetic modification in eukaryotes.In this study,we explore the potential impact of m^(6)A-associated single nucleotide polymorphisms(m^(6)A-SNPs)on heart failure(HF).Methods Data from genome-wide association studies(GWAS)investigating HF in humans and from m^(6)A-SNPs datasets were used to identify HF-associated m^(6)A-SNPs.Their functions were explored using expression quantitative trait locus(eQTL),gene expression,and gene enrichment analyses.Mediation protein quantitative trait locus(pQTL)-Mendelian randomization(MR)was used to investigate the potential mechanism between critical protein levels and risk factors for HF.Results We screened 44 HF-associated m^(6)A-SNPs,including 10 m^(6)A-SNPs that showed eQTL signals and differential expressions in HF.The SNP rs1801270 in CDKN1A showed the strongest association with HF(P=7.75×10^(−6)).Additionally,MR verified the genetic association between the CDKN1A protein and HF,as well as the mediating effect of blood pressure(BP)in this pathway.Higher circulating level of CDKN1A was associated with a lower risk of HF(odds ratio[OR]=0.82,95%confidence interval[CI]:0.69 to 0.99).The proportions of hypertension,systolic BP,and diastolic BP were 48.10%,28.94%,and 18.02%,respectively.Associations of PDIA6(P=1.30×10^(−2))and SMAD3(P=4.80×10^(−2))with HF were also detected.Conclusion Multiple HF-related m^(6)A-SNPs were identified in this study.Genetic associations of CDKN1A and other proteins with HF and its risk factors were demonstrated,providing new ideas for further exploration of the molecular mechanisms of HF.展开更多
Grapes,one of the oldest tree species globally,are rich in vitamins.However,environmental conditions such as low temperature and soil salinization significantly affect grape yield and quality.The glutamate receptor(GLR...Grapes,one of the oldest tree species globally,are rich in vitamins.However,environmental conditions such as low temperature and soil salinization significantly affect grape yield and quality.The glutamate receptor(GLR)family,comprising highly conserved ligand-gated ion channels,regulates plant growth and development in response to stress.In this study,11 members of the VvGLR gene family in grapes were identified using whole-genome sequence analysis.Bioinformatic methods were employed to analyze the basic physical and chemical properties,phylogenetic trees,conserved domains,motifs,expression patterns,and evolutionary relationships.Phylogenetic and collinear analyses revealed that the VvGLRs were divided into three subgroups,showing the high conservation of the grape GLR family.These members exhibited 2 glutamate receptor binding regions(GABAb and GluR)and 3-4 transmembrane regions(M1,M2,M3,and M4).Real-time quantitative PCR analysis demonstrated the sensitivity of all VvGLRs to low temperature and salt stress.Subsequent localization studies in Nicotiana tabacum verified that VvGLR3.1 and VvGLR3.2 proteins were located on the cell membrane and cell nucleus.Additionally,yeast transformation experiments confirmed the functionality of VvGLR3.1 and VvGLR3.2 in response to low temperature and salt stress.Thesefindings highlight the significant role of the GLR family,a highly conserved group of ion channels,in enhancing grape stress resistance.This study offers new insights into the grape GLR gene family,providing fundamental knowledge for further functional analysis and breeding of stress-resistant grapevines.展开更多
Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS a...Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.展开更多
Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese...Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations(GS1, 2010, ex-situ;GS2, 2019, ex-situ;GS3, 2019, in-situ;XB1, 2010, in-situ;and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs(in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.展开更多
Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant breeding.The number of available phenotypic and genomic data sets in which medium-s...Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant breeding.The number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly increasing.Combining these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects,but is hindered by data heterogeneity and lack of interoperability.In this study,we used genomic and phenotypic data sets,focusing on Central European winter wheat populations evaluated for heading date.We explored strategies for integrating these data and subsequently the resulting potential for GWAS.Establishing interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols,resulting in high quality integrated phenotypic data.In this context,genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series,which was low in our case.Contrary to expectations,fewer associations between markers and traits were found in the larger combined data than in the individual experimental series.However,the predictive power based on the marker-trait associations of the integrated data set was higher across data sets.Therefore,the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in GWAS.The results encourage further efforts to standardize and share data in the plant breeding community.展开更多
Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more e...Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.展开更多
Phosphorus(P)is essential for living plants,and P deficiency is one of the key factors limiting the yield in rapeseed production worldwide.As the most important organ for plants,root morphology traits(RMTs)play a key ...Phosphorus(P)is essential for living plants,and P deficiency is one of the key factors limiting the yield in rapeseed production worldwide.As the most important organ for plants,root morphology traits(RMTs)play a key role in P absorption.To investigate the genetic variability of RMT under low P availability,we dissected the genetic structure of RMTs by genome-wide association studies(GWAS),linkage mapping and candidate gene association studies(CGAS).A total of 52 suggestive loci were associated with RMTs under P stress conditions in 405 oilseed rape accessions.The purple acid phosphatase gene BnPAP17 was found to control the lateral root number(LRN)and root dry weight(RDW)under low P stress.The expression of BnPAP17 was increased in shoot tissue in P-efficient cultivars compared to root tissue and P-inefficient cultivars in response to low P stress.Moreover,the haplotype of BnPAP17^(Hap3)was detected for the selective breeding of P efficiency in oilseed rape.Over-expression of the BnPAP17^(Hap3)could promote the shoot and root growth with enhanced tolerance to low P stress and organic phosphorus(Po)utilization in oilseed rape.Collectively,these findings increase our understanding of the mechanisms underlying BnPAP17-mediated low P stress tolerance in oilseed rape.展开更多
Although significant progress has been made in the development of novel targeted drugs for the treatment of acute myeloid leukemia(AML)in recent years,chemotherapy still remains the mainstay of treatment and the overa...Although significant progress has been made in the development of novel targeted drugs for the treatment of acute myeloid leukemia(AML)in recent years,chemotherapy still remains the mainstay of treatment and the overall survival is poor in most patients.Here,we demonstrated the antileukemia activity of a novel small molecular compound NL101,which is formed through the modification on bendamustine with a suberanilohydroxamic acid(SAHA)radical.NL101 suppresses the proliferation of myeloid malignancy cells and primary AML cells.It induces DNA damage and caspase 3-mediated apoptosis.A genome-wide clustered regularly interspaced short palindromic repeats(CRISPR)library screen revealed that phosphatase and tensin homologous(PTEN)gene is critical for the regulation of cell survival upon NL101 treatment.The knockout or inhibition of PTEN significantly reduced NL101-induced apoptosis in AML and myelodysplastic syndrome(MDS)cells,accompanied by the activation of protein kinase B(AKT)signaling pathway.The inhibition of mammalian target of rapamycin(mTOR)by rapamycin enhanced the sensitivity of AML cells to NL101-induced cell death.These findings uncover PTEN protein expression as a major determinant of chemosensitivity to NL101 and provide a novel strategy to treat AML with the combination of NL101 and rapamycin.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.
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 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financially supported by the National Natural Science Foundation of China(Grant No.U20A2032)the Agro ST Project(Grant No.NK2022050102)the Hainan Provincial Natural Science Foundation,China(Grant No.323MS066)。
文摘Rice cooking and eating qualities(CEQ)are mainly determined by cooked rice textural parameters and starch physicochemical properties.However,the genetic bases of grain texture and starch properties in rice have not been fully understood.We conducted a genome-wide association study for apparent amylose content(AAC),starch pasting viscosities,and cooked rice textural parameters using 279 indica rice accessions from the 3000 Rice Genome Project.We identified 26 QTLs in the whole population and detected single nucleotide polymorphisms(SNPs)with the lowest P-value at the Waxy(Wx)locus for all traits except pasting temperature and cohesiveness.Additionally,we detected significant SNPs at the SUBSTANDARD STARCH GRAIN6(SSG6)locus for AAC,setback(SB),hardness,adhesiveness,chewiness(CHEW),gumminess(GUM),and resilience.We subsequently divided the population using a SNP adjacent to the Waxy locus,and identified 23 QTLs and 12 QTLs in two sub-panels,WxT and WxA,respectively.In these sub-panels,SSG6 was also identified to be associated with pasting parameters,including peak viscosity,hot paste viscosity,cold paste viscosity,and consistency viscosity.Furthermore,a candidate gene encoding monosaccharide transporter 5(OsMST5)was identified to be associated with AAC,breakdown,SB,CHEW,and GUM.In total,39 QTLs were co-localized with known genes or previously reported QTLs.These identified genes and QTLs provide valuable information for genetic manipulation to improve rice CEQ.
基金This work was supported by the National Key Research and Development Program of China(2022YFD1200201)Henan Provincial Science and Technology Research and Development Plan Joint Fund(222301420025)the Agricultural Science and Technology Innovation Program(ASTIP)of CAAS.
文摘Nitrogen(N)fertilizer application is essential for crop-plant growth and development.Identifying genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by overfertilization.We subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling stage.Genotyping the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate.These SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type plant.We developed two functional markers for Hap 1,the favorable allele of TaBOX.
基金supported by the National Natural Science Foundation of China[82070473,82170480,82030102]Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences[2021-I2M-1-010].
文摘Objective N6-methyladenosine(m^(6)A)is a common epigenetic modification in eukaryotes.In this study,we explore the potential impact of m^(6)A-associated single nucleotide polymorphisms(m^(6)A-SNPs)on heart failure(HF).Methods Data from genome-wide association studies(GWAS)investigating HF in humans and from m^(6)A-SNPs datasets were used to identify HF-associated m^(6)A-SNPs.Their functions were explored using expression quantitative trait locus(eQTL),gene expression,and gene enrichment analyses.Mediation protein quantitative trait locus(pQTL)-Mendelian randomization(MR)was used to investigate the potential mechanism between critical protein levels and risk factors for HF.Results We screened 44 HF-associated m^(6)A-SNPs,including 10 m^(6)A-SNPs that showed eQTL signals and differential expressions in HF.The SNP rs1801270 in CDKN1A showed the strongest association with HF(P=7.75×10^(−6)).Additionally,MR verified the genetic association between the CDKN1A protein and HF,as well as the mediating effect of blood pressure(BP)in this pathway.Higher circulating level of CDKN1A was associated with a lower risk of HF(odds ratio[OR]=0.82,95%confidence interval[CI]:0.69 to 0.99).The proportions of hypertension,systolic BP,and diastolic BP were 48.10%,28.94%,and 18.02%,respectively.Associations of PDIA6(P=1.30×10^(−2))and SMAD3(P=4.80×10^(−2))with HF were also detected.Conclusion Multiple HF-related m^(6)A-SNPs were identified in this study.Genetic associations of CDKN1A and other proteins with HF and its risk factors were demonstrated,providing new ideas for further exploration of the molecular mechanisms of HF.
基金This research was funded by the Natural Science Foundation of Shandong Province of China(ZR2022MC144).
文摘Grapes,one of the oldest tree species globally,are rich in vitamins.However,environmental conditions such as low temperature and soil salinization significantly affect grape yield and quality.The glutamate receptor(GLR)family,comprising highly conserved ligand-gated ion channels,regulates plant growth and development in response to stress.In this study,11 members of the VvGLR gene family in grapes were identified using whole-genome sequence analysis.Bioinformatic methods were employed to analyze the basic physical and chemical properties,phylogenetic trees,conserved domains,motifs,expression patterns,and evolutionary relationships.Phylogenetic and collinear analyses revealed that the VvGLRs were divided into three subgroups,showing the high conservation of the grape GLR family.These members exhibited 2 glutamate receptor binding regions(GABAb and GluR)and 3-4 transmembrane regions(M1,M2,M3,and M4).Real-time quantitative PCR analysis demonstrated the sensitivity of all VvGLRs to low temperature and salt stress.Subsequent localization studies in Nicotiana tabacum verified that VvGLR3.1 and VvGLR3.2 proteins were located on the cell membrane and cell nucleus.Additionally,yeast transformation experiments confirmed the functionality of VvGLR3.1 and VvGLR3.2 in response to low temperature and salt stress.Thesefindings highlight the significant role of the GLR family,a highly conserved group of ion channels,in enhancing grape stress resistance.This study offers new insights into the grape GLR gene family,providing fundamental knowledge for further functional analysis and breeding of stress-resistant grapevines.
基金partially supported by the Science and Technology Innovation Program of Hunan Province,China(2023NK2001)the Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement,China(2022LZJJ08)+2 种基金the Special Funds for Construction of Innovative Provinces in Hunan Province,China(2021NK1011)the Natural Science Foundation of Hunan Province,China(2020JJ4039)the Key Research and Development Program of Hubei Province,China(2021BBA223)。
文摘Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.
基金supported by the Key Research Project of the Shennong Laboratory,Henan Province,China(SN012022-05)the National Natural Science Foundation of China(32272866)+1 种基金the Young Elite Scientists Sponsorship Program by CAST(2021QNRC001)the Starting Foundation for Outstanding Young Scientists of Henan Agricultural University,China(30500664&30501280)。
文摘Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations(GS1, 2010, ex-situ;GS2, 2019, ex-situ;GS3, 2019, in-situ;XB1, 2010, in-situ;and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs(in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.
基金funding within the Wheat BigData Project(German Federal Ministry of Food and Agriculture,FKZ2818408B18)。
文摘Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant breeding.The number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly increasing.Combining these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects,but is hindered by data heterogeneity and lack of interoperability.In this study,we used genomic and phenotypic data sets,focusing on Central European winter wheat populations evaluated for heading date.We explored strategies for integrating these data and subsequently the resulting potential for GWAS.Establishing interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols,resulting in high quality integrated phenotypic data.In this context,genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series,which was low in our case.Contrary to expectations,fewer associations between markers and traits were found in the larger combined data than in the individual experimental series.However,the predictive power based on the marker-trait associations of the integrated data set was higher across data sets.Therefore,the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in GWAS.The results encourage further efforts to standardize and share data in the plant breeding community.
基金funded by the CGIAR Research Program(CRP)on MAIZEthe USAID through the Accelerating Genetic Gains Supplemental Project(Amend.No.9 MTO 069033),and the One CGIAR Initiative on Accelerated Breeding+1 种基金funding from the governments of Australia,Belgium,Canada,China,France,India,Japan,the Republic of Korea,Mexico,the Netherlands,New Zealand,Norway,Sweden,Switzerland,the United Kingdom,the United States,and the World Banksupported by the China Scholarship Council。
文摘Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.
基金financially supported by the National Natural Science Foundation of China(32201868 and 32001575)。
文摘Phosphorus(P)is essential for living plants,and P deficiency is one of the key factors limiting the yield in rapeseed production worldwide.As the most important organ for plants,root morphology traits(RMTs)play a key role in P absorption.To investigate the genetic variability of RMT under low P availability,we dissected the genetic structure of RMTs by genome-wide association studies(GWAS),linkage mapping and candidate gene association studies(CGAS).A total of 52 suggestive loci were associated with RMTs under P stress conditions in 405 oilseed rape accessions.The purple acid phosphatase gene BnPAP17 was found to control the lateral root number(LRN)and root dry weight(RDW)under low P stress.The expression of BnPAP17 was increased in shoot tissue in P-efficient cultivars compared to root tissue and P-inefficient cultivars in response to low P stress.Moreover,the haplotype of BnPAP17^(Hap3)was detected for the selective breeding of P efficiency in oilseed rape.Over-expression of the BnPAP17^(Hap3)could promote the shoot and root growth with enhanced tolerance to low P stress and organic phosphorus(Po)utilization in oilseed rape.Collectively,these findings increase our understanding of the mechanisms underlying BnPAP17-mediated low P stress tolerance in oilseed rape.
基金supported by the Zhejiang Provincial Natural Science Foundation of China(No.LY21H080005)the National Natural Science Foundation of China(Nos.81572920 and 82100171).
文摘Although significant progress has been made in the development of novel targeted drugs for the treatment of acute myeloid leukemia(AML)in recent years,chemotherapy still remains the mainstay of treatment and the overall survival is poor in most patients.Here,we demonstrated the antileukemia activity of a novel small molecular compound NL101,which is formed through the modification on bendamustine with a suberanilohydroxamic acid(SAHA)radical.NL101 suppresses the proliferation of myeloid malignancy cells and primary AML cells.It induces DNA damage and caspase 3-mediated apoptosis.A genome-wide clustered regularly interspaced short palindromic repeats(CRISPR)library screen revealed that phosphatase and tensin homologous(PTEN)gene is critical for the regulation of cell survival upon NL101 treatment.The knockout or inhibition of PTEN significantly reduced NL101-induced apoptosis in AML and myelodysplastic syndrome(MDS)cells,accompanied by the activation of protein kinase B(AKT)signaling pathway.The inhibition of mammalian target of rapamycin(mTOR)by rapamycin enhanced the sensitivity of AML cells to NL101-induced cell death.These findings uncover PTEN protein expression as a major determinant of chemosensitivity to NL101 and provide a novel strategy to treat AML with the combination of NL101 and rapamycin.
