Wild progenitors are an excellent source for strengthening the genetic basis and accumulation of desirable variation lost because of directional selection and adaptation in modern cultivars.Here,we re-evaluate a landr...Wild progenitors are an excellent source for strengthening the genetic basis and accumulation of desirable variation lost because of directional selection and adaptation in modern cultivars.Here,we re-evaluate a landrace of Gossypium hirsutum,formerly known as Gossypium purpurascens.Our study seeks to understand the genomic structure,variation,and breeding potential of this landrace,providing potential insights into the biogeographic history and genomic changes likely associated with domestication.A core set of accessions,including current varieties,obsolete accessions,G.purpurascens,and other geographical landraces,are subjected to genotyping along with multilocation phenotyping.Population fixation statistics suggests a marked differentiation between G.purpurascens and three other groups,emphasizing the divergent genomic behavior of G.purpurascens.Phylogenetic analysis establishes the primitive nature of G.purpurascens,identifying it as a vital source of functional variation,the inclusion of which in the upland cotton(cultivated G.hirsutum)gene pool may broaden the genetic basis of modern cultivars.Genome-wide association results indicate multiple loci associated with domestication regions corresponding to flowering and fiber quality.Moreover,the conserved nature of G.purpurascens can also provide insights into the evolutionary process of G.hirsutum.展开更多
A secure operating system in the communication network can provide the stable working environment,which ensures that the user information is not stolen.The micro-kernel operating system in the communication network re...A secure operating system in the communication network can provide the stable working environment,which ensures that the user information is not stolen.The micro-kernel operating system in the communication network retains the core functions in the kernel,and unnecessary tasks are implemented by calling external processes.Due to the small amount of code,the micro-kernel architecture has high reliability and scalability.Taking the microkernel operating system in the communication network prototype VSOS as an example,we employ the objdump tool to disassemble the system source code and get the assembly layer code.On this basis,we apply the Isabelle/HOL,a formal verification tool,to model the system prototype.By referring to the mathematical model of finite automata and taking the process scheduling module as an example,the security verification based on the assembly language layer is developed.Based on the Hoare logic theory,each assembly statement of the module is verified in turn.The verification results show that the scheduling module of VSOS has good functional security,and also show the feasibility of the refinement framework.展开更多
In traditional digital twin communication system testing,we can apply test cases as completely as possible in order to ensure the correctness of the system implementation,and even then,there is no guarantee that the d...In traditional digital twin communication system testing,we can apply test cases as completely as possible in order to ensure the correctness of the system implementation,and even then,there is no guarantee that the digital twin communication system implementation is completely correct.Formal verification is currently recognized as a method to ensure the correctness of software system for communication in digital twins because it uses rigorous mathematical methods to verify the correctness of systems for communication in digital twins and can effectively help system designers determine whether the system is designed and implemented correctly.In this paper,we use the interactive theorem proving tool Isabelle/HOL to construct the formal model of the X86 architecture,and to model the related assembly instructions.The verification result shows that the system states obtained after the operations of relevant assembly instructions is consistent with the expected states,indicating that the system meets the design expectations.展开更多
Commercial varieties of upland cotton(Gossypium hirsutum)have undergone extensive breeding for agronomic traits,such as fiber quality,disease resistance,and yield.Cotton breeding programs have widely used Chinese upla...Commercial varieties of upland cotton(Gossypium hirsutum)have undergone extensive breeding for agronomic traits,such as fiber quality,disease resistance,and yield.Cotton breeding programs have widely used Chinese upland cotton source germplasm(CUCSG)with excellent agronomic traits.A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles.Here,we analyzed 10,522 high-quality singlenucleotide polymorphisms(SNP)with the CottonSNP63 K microarray in 137 cotton accessions(including 12 hybrids of upland cotton).These data were used to investigate the genetic diversity,population structure,and genomic characteristics of each population and the contribution of these loci to heterosis.Three subgroups were identified,in agreement with their knownpedigrees,geographical distributions,and times since introduction.For each group,we identified lineagespecific genomic divergence regions,which potentially harbor key alleles that determine the characteristics of each group,such as early maturity-related loci.Investigation of the distribution of heterozygous loci,among 12 commercial cotton hybrids,revealed a potential role for these regions in heterosis.Our study provides insight into the population structure of upland cotton germplasm.Furthermore,the overlap between lineagespecific regions and heterozygous loci,in the high-yield hybrids,suggests a role for these regions in cotton heterosis.展开更多
Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization.However,the global gene pattern variation during early fiber develo...Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization.However,the global gene pattern variation during early fiber development was unknown.In this study,through RNA-seq technology,we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton(G.hirsutum)and its diploid progenitors(G.arboreum and G.raimondii)at the fiber early development stage.In tetraploid cotton,genes showed expression level dominance(ELD)bias toward the A genome.This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor(D genome).Gene ontology(GO)enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession,and the ELD-D genes might be involved in transcription regulation and stress inducement.In addition,the number and proportion of completely A-and D-subfunctionalized gene were similar at different fiber development stages.However,for neofunctionalization,the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA.Eventually,we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process,further making the fiber property meet the human demands.Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages,providing new insights into the mechanism of cotton fiber evolution.展开更多
Optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most important fiber crop globally;however, ...Optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most important fiber crop globally;however, the genetic basis underlying plant height remains largely unexplored. In this study, we conducted a genome-wide association study to identify a major locus controlling plant height (PH1) in upland cotton. This locus encodes gibberellin 2-oxidase 1A (GhPH1) and features a 1133-bp structural variation (PAVPH1) located approximately 16 kb upstream. The presence or absence of PAVPH1 influences the expression of GhPH1, thereby affecting plant height. Further analysis revealed that a gibberellin-regulating transcription factor (GhGARF) recognizes and binds to a specific CATTTG motif in both the GhPH1 promoter and PAVPH1. This interaction downregulates GhPH1, indicating that PAVPH1 functions as a distant upstream silencer. Intriguingly, we found that DWARF53 (D53), a key repressor of the strigolactone (SL) signaling pathway, directly interacts with GhGARF to inhibit its binding to targets. Moreover, we identified a previously unrecognized gibberellin-SL crosstalk mechanism mediated by the GhD53-GhGARF-GhPH1/PAVPH1 module, which is crucial for regulating plant height in upland cotton. These findings shed light on the genetic basis and gene interaction network underlying plant height, providing valuable insights for the development of semi-dwarf cotton varieties through precise modulation of GhPH1 expression.展开更多
An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assem...An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes.Gypsy was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.展开更多
Watermelon fruit flesh displays various colors.Although genetic loci underlying these variations are identified,the molecular mechanism remains elusive.Here,we assembled a chromosome-scale reference genome of an elite...Watermelon fruit flesh displays various colors.Although genetic loci underlying these variations are identified,the molecular mechanism remains elusive.Here,we assembled a chromosome-scale reference genome of an elite watermelon and developed integrated genetic maps using single nucleotide polymorphism(SNP)and structural variation markers.Several key genetic varients for fruit shape and flesh color were identified.Two variants associated with flesh color were further studied,including one copy number variant(CNV,a triplicate of 1.2 kb DNA)in the promoter region of REDUCED CHLOROPLAST COVERAGE 2(ClREC2)and one SNP in Lycopeneβ-Cyclase(ClLCYB)coding region.These two variants together explained 99.7%of the flesh color variations in 314 watermelon accessions.The SNP in ClLCYB was the same as previously reported,disrupting ClLCYB function.The CNV could strongly enhance ClREC2 expression,consequently increasing the expression of carotenoid biosynthesis genes,the number of plastoglobules within chromoplasts,and carotenoid level in mature fruit flesh.Finally,we proposed a“two-switch”genetic model by integrating two major causative loci,which can explain the formation of the four main flesh colors in different watermelon accessions.These results provide new insights into the regulation of carotenoid biosynthesis and color formation in plants.展开更多
基金supported by funding from the National Key Technology R&D Program,the Ministry of Science and Technology(2016YFD0100203,2017FD0101601)the crop germplasm conservation program of the ministry of Agriculture(2015NWB039)。
文摘Wild progenitors are an excellent source for strengthening the genetic basis and accumulation of desirable variation lost because of directional selection and adaptation in modern cultivars.Here,we re-evaluate a landrace of Gossypium hirsutum,formerly known as Gossypium purpurascens.Our study seeks to understand the genomic structure,variation,and breeding potential of this landrace,providing potential insights into the biogeographic history and genomic changes likely associated with domestication.A core set of accessions,including current varieties,obsolete accessions,G.purpurascens,and other geographical landraces,are subjected to genotyping along with multilocation phenotyping.Population fixation statistics suggests a marked differentiation between G.purpurascens and three other groups,emphasizing the divergent genomic behavior of G.purpurascens.Phylogenetic analysis establishes the primitive nature of G.purpurascens,identifying it as a vital source of functional variation,the inclusion of which in the upland cotton(cultivated G.hirsutum)gene pool may broaden the genetic basis of modern cultivars.Genome-wide association results indicate multiple loci associated with domestication regions corresponding to flowering and fiber quality.Moreover,the conserved nature of G.purpurascens can also provide insights into the evolutionary process of G.hirsutum.
基金This work was supported in part by the Natural Science Foundation of Jiangsu Province under grant No.BK20191475the fifth phase of“333 Project”scientific research funding project of Jiangsu Province in China under grant No.BRA2020306the Qing Lan Project of Jiangsu Province in China under grant No.2019.
文摘A secure operating system in the communication network can provide the stable working environment,which ensures that the user information is not stolen.The micro-kernel operating system in the communication network retains the core functions in the kernel,and unnecessary tasks are implemented by calling external processes.Due to the small amount of code,the micro-kernel architecture has high reliability and scalability.Taking the microkernel operating system in the communication network prototype VSOS as an example,we employ the objdump tool to disassemble the system source code and get the assembly layer code.On this basis,we apply the Isabelle/HOL,a formal verification tool,to model the system prototype.By referring to the mathematical model of finite automata and taking the process scheduling module as an example,the security verification based on the assembly language layer is developed.Based on the Hoare logic theory,each assembly statement of the module is verified in turn.The verification results show that the scheduling module of VSOS has good functional security,and also show the feasibility of the refinement framework.
基金supported in part by the Natural Science Foundation of Jiangsu Province in China under grant No.BK20191475the fifth phase of“333 Project”scientific research funding project of Jiangsu Province in China under grant No.BRA2020306the Qing Lan Project of Jiangsu Province in China under grant No.2019.
文摘In traditional digital twin communication system testing,we can apply test cases as completely as possible in order to ensure the correctness of the system implementation,and even then,there is no guarantee that the digital twin communication system implementation is completely correct.Formal verification is currently recognized as a method to ensure the correctness of software system for communication in digital twins because it uses rigorous mathematical methods to verify the correctness of systems for communication in digital twins and can effectively help system designers determine whether the system is designed and implemented correctly.In this paper,we use the interactive theorem proving tool Isabelle/HOL to construct the formal model of the X86 architecture,and to model the related assembly instructions.The verification result shows that the system states obtained after the operations of relevant assembly instructions is consistent with the expected states,indicating that the system meets the design expectations.
基金supported by grants from the National Key Research and Development Program of China (2017YFD0102000 and 2016YFD0100306)the National Natural Science Foundation of China (31301365)
文摘Commercial varieties of upland cotton(Gossypium hirsutum)have undergone extensive breeding for agronomic traits,such as fiber quality,disease resistance,and yield.Cotton breeding programs have widely used Chinese upland cotton source germplasm(CUCSG)with excellent agronomic traits.A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles.Here,we analyzed 10,522 high-quality singlenucleotide polymorphisms(SNP)with the CottonSNP63 K microarray in 137 cotton accessions(including 12 hybrids of upland cotton).These data were used to investigate the genetic diversity,population structure,and genomic characteristics of each population and the contribution of these loci to heterosis.Three subgroups were identified,in agreement with their knownpedigrees,geographical distributions,and times since introduction.For each group,we identified lineagespecific genomic divergence regions,which potentially harbor key alleles that determine the characteristics of each group,such as early maturity-related loci.Investigation of the distribution of heterozygous loci,among 12 commercial cotton hybrids,revealed a potential role for these regions in heterosis.Our study provides insight into the population structure of upland cotton germplasm.Furthermore,the overlap between lineagespecific regions and heterozygous loci,in the high-yield hybrids,suggests a role for these regions in cotton heterosis.
基金Funded by the National Key Research and Development Program of China(2016YFD0100203 and 2016YFD0100306)the Foundation and Frontier Research Grant of Henan Provincial Science and Technology Bureau(162300410171).
文摘Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization.However,the global gene pattern variation during early fiber development was unknown.In this study,through RNA-seq technology,we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton(G.hirsutum)and its diploid progenitors(G.arboreum and G.raimondii)at the fiber early development stage.In tetraploid cotton,genes showed expression level dominance(ELD)bias toward the A genome.This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor(D genome).Gene ontology(GO)enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession,and the ELD-D genes might be involved in transcription regulation and stress inducement.In addition,the number and proportion of completely A-and D-subfunctionalized gene were similar at different fiber development stages.However,for neofunctionalization,the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA.Eventually,we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process,further making the fiber property meet the human demands.Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages,providing new insights into the mechanism of cotton fiber evolution.
基金funded by The National Key Research and Development Program of China(grant nos.2021YFF1000101 to S.H.and 2022YFD1200300 to X.D.)the National Natural Science Foundation of China(grant no.32122062 to S.H.)the Agricultural Science,Technology Innovation Program of the Chinese Academy of Agricultural Sciences and Henan Provincial Department of Science and Technology research project(grant no.232102111076).
文摘Optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most important fiber crop globally;however, the genetic basis underlying plant height remains largely unexplored. In this study, we conducted a genome-wide association study to identify a major locus controlling plant height (PH1) in upland cotton. This locus encodes gibberellin 2-oxidase 1A (GhPH1) and features a 1133-bp structural variation (PAVPH1) located approximately 16 kb upstream. The presence or absence of PAVPH1 influences the expression of GhPH1, thereby affecting plant height. Further analysis revealed that a gibberellin-regulating transcription factor (GhGARF) recognizes and binds to a specific CATTTG motif in both the GhPH1 promoter and PAVPH1. This interaction downregulates GhPH1, indicating that PAVPH1 functions as a distant upstream silencer. Intriguingly, we found that DWARF53 (D53), a key repressor of the strigolactone (SL) signaling pathway, directly interacts with GhGARF to inhibit its binding to targets. Moreover, we identified a previously unrecognized gibberellin-SL crosstalk mechanism mediated by the GhD53-GhGARF-GhPH1/PAVPH1 module, which is crucial for regulating plant height in upland cotton. These findings shed light on the genetic basis and gene interaction network underlying plant height, providing valuable insights for the development of semi-dwarf cotton varieties through precise modulation of GhPH1 expression.
基金supported by the International Cooperation Program of Henan Provincial Bureau of Foreign Experts Affairs Authority(2016GH18)the National Key R&D Program of China(2017YFD0101600,2016YFD0100203)+1 种基金the Foundation and Frontier Research Grant of Henan Provincial Science and Technology Bureau(162300410171)the Research Fund Project of Anyang Institute of Technology(YJJ2015013)
文摘An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes.Gypsy was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.
基金support from the National Key R&D Program of China(2016YFD0100204-26)the Agricultural Science and Technology Innovation Program of China(CAAS-ASTIP-2022-ZFRI)+1 种基金the Special Protection and Utilization of the Crop Germplasm Resources of Chinathe National R&D Infrastructure and Facility Development Program of China and the Scientific Institution Basal Research Fund of ZFRI,CAAS(No.ZGS202109).
文摘Watermelon fruit flesh displays various colors.Although genetic loci underlying these variations are identified,the molecular mechanism remains elusive.Here,we assembled a chromosome-scale reference genome of an elite watermelon and developed integrated genetic maps using single nucleotide polymorphism(SNP)and structural variation markers.Several key genetic varients for fruit shape and flesh color were identified.Two variants associated with flesh color were further studied,including one copy number variant(CNV,a triplicate of 1.2 kb DNA)in the promoter region of REDUCED CHLOROPLAST COVERAGE 2(ClREC2)and one SNP in Lycopeneβ-Cyclase(ClLCYB)coding region.These two variants together explained 99.7%of the flesh color variations in 314 watermelon accessions.The SNP in ClLCYB was the same as previously reported,disrupting ClLCYB function.The CNV could strongly enhance ClREC2 expression,consequently increasing the expression of carotenoid biosynthesis genes,the number of plastoglobules within chromoplasts,and carotenoid level in mature fruit flesh.Finally,we proposed a“two-switch”genetic model by integrating two major causative loci,which can explain the formation of the four main flesh colors in different watermelon accessions.These results provide new insights into the regulation of carotenoid biosynthesis and color formation in plants.
