Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathoge...Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F7recombinant inbred line(RIL) population lacking the Yr18 gene, a near-isogenic line(NIL) population was developed to map the resistance gene. An allstage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exomecapture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge,the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.展开更多
Seeds might deteriorate,and lose the ability to germinate when stored under high temperature and high humidity.Brassica napus is one of the most important oil crops in China.However,B.napus seeds were generally stored...Seeds might deteriorate,and lose the ability to germinate when stored under high temperature and high humidity.Brassica napus is one of the most important oil crops in China.However,B.napus seeds were generally stored through summer season with high ambient temperature,which lead to seed viability loss.In order to understand the mechanism of seed response to heat stress and improve seed heat tolerance,B.napus seeds were treated with high temperature(40℃)and ultra-high temperature(60℃)for 4 h.The germination of heatstressed seeds were obviously slower,the germination index and vigor index decreased with temperature increase from 40 to 60℃,and the 40℃ pretreatment could improve the seed tolerance to 60℃ heat stress.Transcriptomics results showed that 442 differentially expressed genes(DEGs)were identified in seeds after heat stress.Gene ontology and KEGG pathway enrichment analysis revealed that some of the genes were involved in posttranslational modification,protein turnover,chaperones and carbohydrate transport,metabolic pathways and secondary metabolites biosynthesis pathway.Among these DEGs,sHSP and transcription factors genes were involved in heat stress tolerance.Thirty-two overlapping genes under different high temperature stress(40℃ and 60℃)were enriched in biological processes of response to oxidative stress and abiotic stimulus.The expression trends of 12 genes randomly selected from the RNA-seq data were almost consistent with the results of qRT-PCR.Our results revealed several potential candidate genes and pathways related to heat responsive by high temperature,which is beneficial for further improving the heat tolerance in B.napus seeds.展开更多
Stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is a devastating disease in wheat worldwide.Discovering and characterizing new resistance genes/QTL is crucial for wheat breeding programs.In this study,we ...Stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is a devastating disease in wheat worldwide.Discovering and characterizing new resistance genes/QTL is crucial for wheat breeding programs.In this study,we fine-mapped and characterized a stripe rust resistance gene,YRAYH,on chromosome arm 5BL in the Chinese wheat landrace Anyuehong(AYH).Evaluations of stripe rust response to prevalent Chinese Pst races in near-isogenic lines derived from a cross of Anyuehong and Taichung 29 showed that YrAYH conferred a high level of resistance at all growth stages.Fine mapping using a large segregating population of 9748 plants,narrowed the YRAYH locus to a 3.7 Mb interval on chromosome arm 5BL that included 61 annotated genes.Transcriptome analysis of two NIL pairs identified 64 upregulated differentially expressed genes(DEGs)in the resistant NILs(NILs-R).Annotations indicated that many of these genes have roles in plant disease resistance pathways.Through a combined approach of fine-mapping and transcriptome sequencing,we identified a serine/threonine-protein kinase SRPK as a candidate gene underlying YrAYH.A unique 25 bp insertion was identified in the NILs-R compared to the NILs-S and previously published wheat genomes.An InDel marker was developed and co-segregated with YrAYH.Agronomic trait evaluation of the NILs suggested that YrAYH not only reduces the impact of stripe rust but was also associated with a gene that increases plant height and spike length.展开更多
Plant growth promoting fungi are receiving increased attention as valuable beneficial microorganisms in crop cultivation due to their capacity to produce bioactive substances,promote plant growth and enhance immune de...Plant growth promoting fungi are receiving increased attention as valuable beneficial microorganisms in crop cultivation due to their capacity to produce bioactive substances,promote plant growth and enhance immune defense functions.In this study,a novel Trichoderma isolate,designated as TM2-4,was screened from healthy tomato rhizosphere soil and identified as Trichoderma afroharzianum.Culture filtrate of the isolate TM2-4 displayed obvious bioactive substance production and an evident effect in promoting tomato seed germination,with hypocotyl length,radical length and vigor index increased by 28.7,19.4 and 62.1%,respectively,after a 100-fold dilution treatment.To assess the promotion effect and related mechanism of isolate TM2-4,the plant biological indexes and gene expression profiles of tomato plants treated with or without T.afroharzianum TM2-4 microbial agent were investigated by greenhouse pot experiment and RNA sequencing.The results demonstrated that T.afroharzianum TM2-4 significantly promoted tomato plant growth in terms of plant height,dry weight,number of leaves per plant and root activity,through efficient colonization in the rhizosphere and root system of the plants.Transcriptome analyses identified a total of 984 differentially expressed genes in T.afroharzianum microbial agent inoculated tomato roots,which were mainly engaged in the biological process of phytohormone homeostasis,antioxidant activity,as well as metabolic pathways including phenylpropanoid biosynthesis and glutathione metabolism.These findings provide useful information for understanding the mechanism of isolate TM2-4 for tomato plant growth promotion,which would facilitate further development of T.afroharzianum TM2-4 microbial agent for use in vegetable crop production.展开更多
Dimethyl phthalate(DMP), used as a plasticizer in industrial products, exists widely in air,water and soil.Staphylococcus aureus is a typical model organism representing Gram-positive bacteria.The molecular mechanisms...Dimethyl phthalate(DMP), used as a plasticizer in industrial products, exists widely in air,water and soil.Staphylococcus aureus is a typical model organism representing Gram-positive bacteria.The molecular mechanisms of DMP toxicology in S.aureus were researched by proteomic and transcriptomic analyses.The results showed that the cell wall, membrane and cell surface characteristics were damaged and the growth was inhibited in S.aureus by DMP.Oxidative stress was induced by DMP in S.aureus.The activities of succinic dehydrogenase(SDH) and ATPase were changed by DMP, which could impact energy metabolism.Based on proteomic and transcriptomic analyses, the oxidative phosphorylation pathway was enhanced and the glycolysis/gluconeogenesis and pentose phosphate pathways were inhibited in S.aureus exposed to DMP.The results of real-time reverse transcription quantitative PCR(RT-qPCR) further confirmed the results of the proteomic and transcriptomic analyses.Lactic acid, pyruvic acid and glucose were reduced by DMP in S.aureus, which suggested that DMP could inhibit energy metabolism.The results indicated that DMP damaged the cell wall and membrane, induced oxidative stress, and inhibited energy metabolism and activation in S.aureus.展开更多
Enhancer RNAs(eRNAs),a subclass of non-coding RNAs transcribed from enhancer regions,have emerged as critical regulators of gene expression;however,their functional roles in prostate cancer remain largely unexplored.I...Enhancer RNAs(eRNAs),a subclass of non-coding RNAs transcribed from enhancer regions,have emerged as critical regulators of gene expression;however,their functional roles in prostate cancer remain largely unexplored.In this study,we performed integrated chromatin accessibility and transcriptomic analyses using ATAC-seq and RNA-seq on twenty pairs of prostate cancer and matched benign tissues.By incorporating chromatin immunoprecipitation sequencing data,we identified a subset of differentially expressed eRNAs significantly associated with genes involved in prostate development and oncogenic signaling pathways.Among these,lactotransferrin-eRNA(LTFe)was markedly downregulated in prostate cancer tissues,with functional analyses revealing its tumor-suppressive role.Mechanistically,LTFe promotes the transcription of its target gene,lactotransferrin(LTF),by interacting with heterogeneous nuclear ribonucleoprotein F(HNRNPF)and facilitating enhancer-promoter chromatin interactions.Furthermore,we demonstrate that the LTFe-LTF axis facilitates ferroptosis by modulating iron transport.Notably,androgen receptor(AR)signaling disrupts LTFe-associated chromatin looping,leading to ferroptosis resistance.Therapeutically,co-administration of the AR inhibitor enzalutamide and the ferroptosis inducer RSL3 significantly suppressed tumor growth,offering a promising strategy for castrationresistant prostate cancer.Collectively,this study provides novel insights into the mechanistic role of eRNAs in prostate cancer,highlighting the LTFe-LTF axis as a critical epigenetic regulator and potential therapeutic target for improved treatment outcomes.展开更多
基金supported by the Major Program of National Agricultural Science and Technology of China (NK20220607)the National Natural Science Foundation of China (32272059 and31971883)the Science and Technology Department of Sichuan Province (2022ZDZX0014, 2021YFYZ0002, 2021YJ0297, and23NSFTD0045)。
文摘Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F7recombinant inbred line(RIL) population lacking the Yr18 gene, a near-isogenic line(NIL) population was developed to map the resistance gene. An allstage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exomecapture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge,the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.
基金This work was supported by the Natural Science Foundation of China(31601341)The National Key Program Research and Development of China(2016YFD0100202).
文摘Seeds might deteriorate,and lose the ability to germinate when stored under high temperature and high humidity.Brassica napus is one of the most important oil crops in China.However,B.napus seeds were generally stored through summer season with high ambient temperature,which lead to seed viability loss.In order to understand the mechanism of seed response to heat stress and improve seed heat tolerance,B.napus seeds were treated with high temperature(40℃)and ultra-high temperature(60℃)for 4 h.The germination of heatstressed seeds were obviously slower,the germination index and vigor index decreased with temperature increase from 40 to 60℃,and the 40℃ pretreatment could improve the seed tolerance to 60℃ heat stress.Transcriptomics results showed that 442 differentially expressed genes(DEGs)were identified in seeds after heat stress.Gene ontology and KEGG pathway enrichment analysis revealed that some of the genes were involved in posttranslational modification,protein turnover,chaperones and carbohydrate transport,metabolic pathways and secondary metabolites biosynthesis pathway.Among these DEGs,sHSP and transcription factors genes were involved in heat stress tolerance.Thirty-two overlapping genes under different high temperature stress(40℃ and 60℃)were enriched in biological processes of response to oxidative stress and abiotic stimulus.The expression trends of 12 genes randomly selected from the RNA-seq data were almost consistent with the results of qRT-PCR.Our results revealed several potential candidate genes and pathways related to heat responsive by high temperature,which is beneficial for further improving the heat tolerance in B.napus seeds.
基金supported by grants from the Major Program of National Agricultural Science and Technology of China(NK20220607)the National Natural Science Foundation of China(32272059 and 31971883)the Science and Technology Department of Sichuan Province(2021YFYZ0002,2022ZDZX0014,and 2023NSFSC1995)。
文摘Stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is a devastating disease in wheat worldwide.Discovering and characterizing new resistance genes/QTL is crucial for wheat breeding programs.In this study,we fine-mapped and characterized a stripe rust resistance gene,YRAYH,on chromosome arm 5BL in the Chinese wheat landrace Anyuehong(AYH).Evaluations of stripe rust response to prevalent Chinese Pst races in near-isogenic lines derived from a cross of Anyuehong and Taichung 29 showed that YrAYH conferred a high level of resistance at all growth stages.Fine mapping using a large segregating population of 9748 plants,narrowed the YRAYH locus to a 3.7 Mb interval on chromosome arm 5BL that included 61 annotated genes.Transcriptome analysis of two NIL pairs identified 64 upregulated differentially expressed genes(DEGs)in the resistant NILs(NILs-R).Annotations indicated that many of these genes have roles in plant disease resistance pathways.Through a combined approach of fine-mapping and transcriptome sequencing,we identified a serine/threonine-protein kinase SRPK as a candidate gene underlying YrAYH.A unique 25 bp insertion was identified in the NILs-R compared to the NILs-S and previously published wheat genomes.An InDel marker was developed and co-segregated with YrAYH.Agronomic trait evaluation of the NILs suggested that YrAYH not only reduces the impact of stripe rust but was also associated with a gene that increases plant height and spike length.
基金the Youth Research Fund of Beijing Academy of Agriculture and Forestry Sciences,China(QNJJ201814)the National Key R&D Program of China(2017YFD0201102)the Beijing Key Laboratory of Green Control of Fruit Tree Diseases and Pests in the North China(BZ0432)。
文摘Plant growth promoting fungi are receiving increased attention as valuable beneficial microorganisms in crop cultivation due to their capacity to produce bioactive substances,promote plant growth and enhance immune defense functions.In this study,a novel Trichoderma isolate,designated as TM2-4,was screened from healthy tomato rhizosphere soil and identified as Trichoderma afroharzianum.Culture filtrate of the isolate TM2-4 displayed obvious bioactive substance production and an evident effect in promoting tomato seed germination,with hypocotyl length,radical length and vigor index increased by 28.7,19.4 and 62.1%,respectively,after a 100-fold dilution treatment.To assess the promotion effect and related mechanism of isolate TM2-4,the plant biological indexes and gene expression profiles of tomato plants treated with or without T.afroharzianum TM2-4 microbial agent were investigated by greenhouse pot experiment and RNA sequencing.The results demonstrated that T.afroharzianum TM2-4 significantly promoted tomato plant growth in terms of plant height,dry weight,number of leaves per plant and root activity,through efficient colonization in the rhizosphere and root system of the plants.Transcriptome analyses identified a total of 984 differentially expressed genes in T.afroharzianum microbial agent inoculated tomato roots,which were mainly engaged in the biological process of phytohormone homeostasis,antioxidant activity,as well as metabolic pathways including phenylpropanoid biosynthesis and glutathione metabolism.These findings provide useful information for understanding the mechanism of isolate TM2-4 for tomato plant growth promotion,which would facilitate further development of T.afroharzianum TM2-4 microbial agent for use in vegetable crop production.
基金supported by the National Natural Science Foundation of China (Nos.31870493 and 31670375)the Basic Research Fees of Universities in Heilongjiang Province, China (No.135409103)。
文摘Dimethyl phthalate(DMP), used as a plasticizer in industrial products, exists widely in air,water and soil.Staphylococcus aureus is a typical model organism representing Gram-positive bacteria.The molecular mechanisms of DMP toxicology in S.aureus were researched by proteomic and transcriptomic analyses.The results showed that the cell wall, membrane and cell surface characteristics were damaged and the growth was inhibited in S.aureus by DMP.Oxidative stress was induced by DMP in S.aureus.The activities of succinic dehydrogenase(SDH) and ATPase were changed by DMP, which could impact energy metabolism.Based on proteomic and transcriptomic analyses, the oxidative phosphorylation pathway was enhanced and the glycolysis/gluconeogenesis and pentose phosphate pathways were inhibited in S.aureus exposed to DMP.The results of real-time reverse transcription quantitative PCR(RT-qPCR) further confirmed the results of the proteomic and transcriptomic analyses.Lactic acid, pyruvic acid and glucose were reduced by DMP in S.aureus, which suggested that DMP could inhibit energy metabolism.The results indicated that DMP damaged the cell wall and membrane, induced oxidative stress, and inhibited energy metabolism and activation in S.aureus.
基金supported by the National Natural Science Foundation of China(Nos.82373333,82173068)to Z.Wang,and Nos.82073082,82311530050 to G.-H.Wei+2 种基金the Hubei Natural Science Foundation Innovation Development Joint Fund Key Project(2024AFD420 to Z.Wang)the National Key Research and Development Program of China(2022YFC2703600 to G.-H.Wei)Z.X.Wang was supported by the National Natural Science Foundation of China(82203416)。
文摘Enhancer RNAs(eRNAs),a subclass of non-coding RNAs transcribed from enhancer regions,have emerged as critical regulators of gene expression;however,their functional roles in prostate cancer remain largely unexplored.In this study,we performed integrated chromatin accessibility and transcriptomic analyses using ATAC-seq and RNA-seq on twenty pairs of prostate cancer and matched benign tissues.By incorporating chromatin immunoprecipitation sequencing data,we identified a subset of differentially expressed eRNAs significantly associated with genes involved in prostate development and oncogenic signaling pathways.Among these,lactotransferrin-eRNA(LTFe)was markedly downregulated in prostate cancer tissues,with functional analyses revealing its tumor-suppressive role.Mechanistically,LTFe promotes the transcription of its target gene,lactotransferrin(LTF),by interacting with heterogeneous nuclear ribonucleoprotein F(HNRNPF)and facilitating enhancer-promoter chromatin interactions.Furthermore,we demonstrate that the LTFe-LTF axis facilitates ferroptosis by modulating iron transport.Notably,androgen receptor(AR)signaling disrupts LTFe-associated chromatin looping,leading to ferroptosis resistance.Therapeutically,co-administration of the AR inhibitor enzalutamide and the ferroptosis inducer RSL3 significantly suppressed tumor growth,offering a promising strategy for castrationresistant prostate cancer.Collectively,this study provides novel insights into the mechanistic role of eRNAs in prostate cancer,highlighting the LTFe-LTF axis as a critical epigenetic regulator and potential therapeutic target for improved treatment outcomes.
