Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability ...Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.展开更多
"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic s..."Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.展开更多
In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation meth...In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation method and characterized by XRD,Raman and XPS techniques. Appropriate amount of CO2 in the reactant gases enhanced the formation of surface tetrahedral Na2WO4 species and promoted the migration of O in MOx,Na,W from the catalyst bulk to surface,which were favorable for oxidative coupling of methane. When the molar ratio of CH4/O2/CO2 was 3/1/2,enriched surface tetrahedral Na2WO4 species and high surface concentration of O in MOx,Na,W were detected,and then high CH4 conversion of 33.1% and high C2H4 selectivity of 56.2% were obtained. With further increase of CO2 in the reagent gases,the content of active surface tetrahedral Na2WO4 species and surface concentration of O in MOx,Na,W decreased,while that of inactive species(Mn WO4 and Mn2O3) increased dramatically,leading to low CH4 conversion and low C2H4 selectivity. It could be speculated that Na2WO4 crystal was transformed into Mn WO4 crystal with excessive CO2 added under the reaction conditions. Pretreatment of Na2WO4/Mn/Si O2 catalyst by moderate amount of CO2 before OCM also promoted the formation of Na2WO4 species.展开更多
Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a hi...Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a high-quality genome assembly of Gossypium barbadense acc.Tanguis,a landrace that is closely related to formation of extra-long-staple(ELS)cultivated cotton.An SV-based pan-genome(Pan-SV)was then constructed using a total of 182593 non-redundant SVs,including 2236 inversions,97398 insertions,and 82959 deletions from 11 assembled genomes of allopolyploid cotton.The utility of this Pan-sV was then demonstrated through population structure analysis and genome-wide association studies(GWASs).Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an Sv-based GWAs,certain SVs responsible for speciation,domestication,and improvement in tetraploid cottons were identified.Importantly,some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS.In particular,a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G.barbadense.Collectively,this study provides new insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop spe-cies and highlights the importance of sVs during the speciation,domestication,and improvement of culti-vated crop species.展开更多
Advanced three-dimensional structure variations of chromatin in large genome fragments,such as conversion of A/B compartment,topologically associated domains(TADs)and chromatin loops are related closely to occurrence ...Advanced three-dimensional structure variations of chromatin in large genome fragments,such as conversion of A/B compartment,topologically associated domains(TADs)and chromatin loops are related closely to occurrence of malignant tumors.However,the structural characteristics of lung cancer still remain uncovered.In this study,we used high-throughput chromosome(Hi-C)conformation capture technology to detect the advanced structural variations in chromatin of two nonsmoking lung adenocarcinoma(LUAD)tumor and paired normal tissues.The results indicate that significant chromatin variations are detected in tumor tissues compared with normal tissues.At compartment scale,the main conversion type of compartment is A→B in tumor tissues,which are concentrated mainly on chromosome 3(Chr3)(33.6%).A total of 216 tumor-specific TADs are identified in tumor tissues,which are distributed mainly in Chr1(19),Chr2(15)and Chr3(17).Forty-one distinct enhancer-promoter loops are observed in tumor tissue,which are associated closely to tumor-related pathways including mitogen-activated protein kinase(MAPK),Phosphatidylinositol-3-kinase-Protein kinase B(PI3K-AKT),Ras,Wnt and Ras1.The most important observation in this study is that we identify five important genes(SYT16,NCEH1,NXPE3,MB21D2,and DZIP1L),which are detected in both A→B compartment,TADs and chromatin loops in tumor samples,and four of these genes(NCEH1,NXPE3,MB21D2,and DZIP1L)locate on q arm of Chr3.Further gene expression and invasion experiment analysis show that NCEH1,MB21D2 and SYT16 are involved in the tumor development.Thus,we provide a comprehensive overview of advanced structures in LUAD for the first time and provide a basis for further research on the genetic variation of this tumor.展开更多
Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their rela...Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched.In this study,an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)technology with two synthetic chromosomes,namely synV and synX.The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries.Our findings showed that complex SVs,including a pericentric inversion and a trans-chromosome translocation between synV and synX,resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin.Also,genetic targets were mapped,which resulted in a higher astaxanthin yield,thus demonstrating the SVs’ability to reorganize genetic information along the chromosomes.The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena.Collectively,this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.展开更多
Genomic structural variations (SVs), particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contributio...Genomic structural variations (SVs), particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation (Alkan et al., 2011; Bickhart and Liu, 2014). With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps (Li et al., 2011). Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies (Baker, 2012; Wang et al., 2012;展开更多
As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of ...As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.展开更多
It is well known that large genomic variations can greatly impact the phenotype of an organism.Structural Variants(SVs)encompass any genomic variation larger than 30 base pairs,and include changes caused by deletions,...It is well known that large genomic variations can greatly impact the phenotype of an organism.Structural Variants(SVs)encompass any genomic variation larger than 30 base pairs,and include changes caused by deletions,inversions,duplications,transversions,and other genome modifications.Due to their size and complex nature,until recently,it has been difficult to truly capture these variations.Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes.In tomato,advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes,and tomato relatives.These studies have identified SVs related to fruit size and flavor,as well as plant disease response,resistance/susceptibility,and the ability of plants to detect pathogens(immunity).In this review,we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity.We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes,the current evidence for the role of SVs in biotic and abiotic stress responses,and the outlook for genetic modification of SVs to advance plant breeding objectives.展开更多
This study aims to identify potential influential literature and potential influential topics in the field of information science(IS).Using citation structural variation approach,provided by CiteSpace,we discerned the...This study aims to identify potential influential literature and potential influential topics in the field of information science(IS).Using citation structural variation approach,provided by CiteSpace,we discerned the potential influential theses in IS.Then,we proposed an analyzing framework based on"citation network-citation structural variation-citation cluster,"which is used to discern the potential influential topics in IS.Using the structural variation approach,we analyzed the contents and features of potential influential theses.The potential influential topics,discerned by the"citation network-citation structural variation-citation cluster"framework,corroborated the existing knowledge base to some extent and seemed to be divergent and intermingled.Such potential impact literature and potential impact research topics are of certain reference value for future frontier research.展开更多
Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nev...Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.展开更多
The proximal-based decomposition method was originally proposed by Chen and Teboulle (Math. Programming, 1994, 64:81-101 for solving corrvex minimization problems. This paper extends it to solving monotone variation...The proximal-based decomposition method was originally proposed by Chen and Teboulle (Math. Programming, 1994, 64:81-101 for solving corrvex minimization problems. This paper extends it to solving monotone variational inequalities associated with separable structures with the improvements that the restrictive assumptions on the involved parameters are much relaxed, and thus makes it practical to solve the subproblems easily. Without additional assumptions, global convergence of the new method is proved under the same mild assumptions on the problem's data as the original method.展开更多
A novelty method,frontal polymerization(FP),was employed to directly produce a series of polyacrylamide (PAM),poly(N-isopropylacrylamide)(PNIPAM) and acrylamide-N-isopropylacrylamide copolymer macroporous monoliths. F...A novelty method,frontal polymerization(FP),was employed to directly produce a series of polyacrylamide (PAM),poly(N-isopropylacrylamide)(PNIPAM) and acrylamide-N-isopropylacrylamide copolymer macroporous monoliths. Field emission scanning electronic microscope and mercury intrusion method were adopted to measure some parameters of these monoliths,such as frame,pore size distribution as well as porosity.Effects of types of monomer,thicker and surfactant on porous structure of monoliths were studied.A variet...展开更多
To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical lo...To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical locations in Italy, were analyzed using three DNA fragments including the translation elongation factor(EF1α), the second largest subunit of t he RNA polymerase II(RPB2) and the largest subunit of the RNA polymerase II(RPB1). The results indicated relatively abundant genetic variability in the wild resources of P. ferulae. The analysis of molecular variance(AMOVA) showed that the vast majority of the genetic variation was found within geographical populations. Both the Chinese populations and the Italian populations of P. ferulae displayed a limited genetic differentiation. The degree of differentiation between the Chinese populations and the Italian populations was obviously higher than that between the populations from the same region, and moreover the genetic differentiation among all the tested populations was correlated to the geographical distance. T he phylogeny analyses confirmed that samples from China and Italy belonged to another genetic group separated from Pleurotus eryngii. They were closely related to each other but were clustered according to their geographical origins, which implied the Chinese populations were highly differentiated from the Italian populations because of distance isolation, and the two populations from different regions might be still in the process of allopatric divergence.展开更多
Marine biodiversity is changing in response to altered physical environment, subsequent ecological changes as well as anthropogenic disturbances. In this study, phytoplankton samples in situ collected in the Bering Se...Marine biodiversity is changing in response to altered physical environment, subsequent ecological changes as well as anthropogenic disturbances. In this study, phytoplankton samples in situ collected in the Bering Sea in July of 1999 and 2010 were analyzed to obtain phytoplankton community structure and spatial-temporal variation between the beginning and end of this decade, and the correlation of phytoplankton community dynamics and environmental factors was investigated. A total of 5 divisions, 58 genera and 153 species of phytoplankton belonging to 3 ecological groups were identified. The vast majority of phytoplankton consisted of diatoms accounting for 66.7% of the total species and 95.2% of the total abundance. Considering differentiation in spatial extent and phytoplankton sample types, there were subtle changes in species composition, large altering in abundance and significant variation in spatial distribution between two surveys. The abundance peak area was located at the Bering Strait while sub peak was found at the Bering Sea Basin. The boreal-temperate diatom was the dominant flora, which was subsequently replaced by eurythermal and frigid-water diatom. Phytoplankton community in the Bering Sea was not a simplex uniform community but composed of deep-ocean assemblage and neritic assemblage. The deep-ocean assemblage was located in the northwestern Pacific Ocean and Bering Sea Basin, dominated by boreal-temperate species(Neodenticula seminae, Thalassiothrix longissima, Amphiprora hyperborean, Chaetoceros atlanticus, Thalassiosira trifulta, etc.) and eurychoric species(Thalassionema nitzschioides, Ch. compressus, Rhizosolenia styliformis, etc.), and characterized by low abundance, even interspecies abundance allocations, diverse dominant species and high species diversity. The neritic assemblage was distributed on the continental shelf and slope of Bering Sea and was mainly composed of frigid-water species(Th.nordenski?ldii, Ch. furcellatus, Ch. socialis, Bacteriosira fragilis, etc.) and eurythermal and euryhaline species(L.danicus, Ch. curvisetus, Coscinodiscus curvatulus, etc.), and it was characterized by high abundance, uneven interspecies allocations, prominent dominant species and low species diversity. Spatial-temporal variation of species composition and abundance of phytoplankton in the Bering Sea was directly controlled by surface circulation,nutrient supply and ice edge.展开更多
Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genom...Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for breeding.Its pedigree showed genetic divergence from B73 and other lines in its pedigree.Comparison with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight disease.More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development.The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.展开更多
Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and s...Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.展开更多
The basic leucine zipper(bZIP)is an important class of transcription factors in plants,playing a critical role in plant growth and development and responses to biotic and abiotic stress.Due to gene presence/absence va...The basic leucine zipper(bZIP)is an important class of transcription factors in plants,playing a critical role in plant growth and development and responses to biotic and abiotic stress.Due to gene presence/absence variations,it is limited to identify bZIP genes based on the reference genome.Therefore,we performed the bZIP gene family analysis in the rice pan-genome.By employing a rice pan-genome,ninety-four OsbZIPs(72 core genes and 22 variable genes)were identified and divided into 11 groups in a phylogenetic tree.Based upon Ka/Ks values in 33 accessions,OsbZIPs were subjected to different selection pressures during domestication.The analysis of the effects of structural variations(SVs)on gene expression,gene structure,and conserved domains showed that SVs could significantly alter the expression levels of certain OsbZIPs,leading to gene truncation and the emergence of numerous atypical genes.Thirty-four differentially expressed OsbZIPs were identified by analyzing RNA-seq data of the Xanthomonas oryzae pv.oryzae(Xoo)infection susceptible(IR24)and resistant(IRBB67)lines under high temperature,and by counting the number of differentially expressed OsbZIPs in different subgroups.These Osb-ZIPs were found to respond to Xoo infection at an early stage and may not be involved in the mechanism of Xa4 and Xa7 resistance to Xoo.The multiple variation patterns of OsbZIP genes provide new insights into the OsbZIP genes in rice.These results provide new resources and offer new directions for functional studies of OsbZIPs.展开更多
Despite one SINE retrotransposon insertion polymorphism(sRTIP)in the vertebrae development-associated(VRTN)gene was identified in pigs,the structural variations(SVs)in VRTN gene and its proximal flank regions were lar...Despite one SINE retrotransposon insertion polymorphism(sRTIP)in the vertebrae development-associated(VRTN)gene was identified in pigs,the structural variations(SVs)in VRTN gene and its proximal flank regions were largely unknown.VRTN genic and flanking sequences from 14 breeds were assembled or downloaded from whole genome shotgun contings(WGS)database,and aligned to identify the SVs with Clustalx,and retrotransposons in VRTN gene were annotated by RepeatMasker,the splicing patterns of VRTN gene were predicted by Genescan,and large SVs were evaluated by PCR.A total of 12 small SVs and three large SVs in intron of VRTN,derived from SINE insertion polymorphisms.were identifed,and two of them(VRTN-sRTIP2 and VRTN-sRTIP3)were not reported before.These VRTN-sRTIPs may affect the splicing patterns of VRTN.They displayed polymorphisms in most detected eight breeds.VRTN-sRTIP2 and VRTN-sRTIP3 showed Hardy-Weinberg equilibrium distributions in most populations except the Chinese local Erhualian pigs,while VRTN-sRTIP1 showed genetic equilbrium in Erhualian pigs.Three VRTN-sRTIPs were identified,and displayed polymorphisms in pigs,and two of them were not reported before.These SVs provide a useful molecular markers for genetic analysis in pigs,and offer new information to facilitate the understanding the SVs of VRTN gene and their putative roles in the variation of vertebral number.展开更多
基金supported by the National Key R&D Program of China(2021YFD1301101)National Swine Industry Technology System(CARS-35)Agricultural Science and Technology Innovation Program(ASTIP-IAS02)。
文摘Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.
基金supported by the National Natural Science Foundation of China(NSFC,31970564,32000397,32171982)the Fundamental Research Funds for the Central Universities(2662023PY004)。
文摘"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.
基金support from the Ministry of Science and Technology (Nos.2012BAC20B10)the National Natural Science Foundation of China (Nos. 21321061 and 20976109)
文摘In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation method and characterized by XRD,Raman and XPS techniques. Appropriate amount of CO2 in the reactant gases enhanced the formation of surface tetrahedral Na2WO4 species and promoted the migration of O in MOx,Na,W from the catalyst bulk to surface,which were favorable for oxidative coupling of methane. When the molar ratio of CH4/O2/CO2 was 3/1/2,enriched surface tetrahedral Na2WO4 species and high surface concentration of O in MOx,Na,W were detected,and then high CH4 conversion of 33.1% and high C2H4 selectivity of 56.2% were obtained. With further increase of CO2 in the reagent gases,the content of active surface tetrahedral Na2WO4 species and surface concentration of O in MOx,Na,W decreased,while that of inactive species(Mn WO4 and Mn2O3) increased dramatically,leading to low CH4 conversion and low C2H4 selectivity. It could be speculated that Na2WO4 crystal was transformed into Mn WO4 crystal with excessive CO2 added under the reaction conditions. Pretreatment of Na2WO4/Mn/Si O2 catalyst by moderate amount of CO2 before OCM also promoted the formation of Na2WO4 species.
基金supported in part by the 2021 Research Program of Sanya Yazhou Bay Science and Technology City(SKJC-2021-02-001)the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang(2019R01002)the Fundamental Research Funds for the Central Universities(226-2022-00100 and 2022QZJH43).
文摘Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a high-quality genome assembly of Gossypium barbadense acc.Tanguis,a landrace that is closely related to formation of extra-long-staple(ELS)cultivated cotton.An SV-based pan-genome(Pan-SV)was then constructed using a total of 182593 non-redundant SVs,including 2236 inversions,97398 insertions,and 82959 deletions from 11 assembled genomes of allopolyploid cotton.The utility of this Pan-sV was then demonstrated through population structure analysis and genome-wide association studies(GWASs).Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an Sv-based GWAs,certain SVs responsible for speciation,domestication,and improvement in tetraploid cottons were identified.Importantly,some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS.In particular,a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G.barbadense.Collectively,this study provides new insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop spe-cies and highlights the importance of sVs during the speciation,domestication,and improvement of culti-vated crop species.
基金supported by National Guided Science and Technology Development Project of Sichuan Province(No:2020ZYD009)Clinical Research Incubation Project of West China Hospital of Sichuan University(No:2018HXFH012)+3 种基金Hospital-enterprise cooperation clinical research innovation project(Sichuan University West China Hospital-Shanghai Pharmaceutical)(No:2019HXCX04)Sichuan Science and Technology Program(No:2020ZYD007)Science and Technology Achievement Transformation Fund of Sichuan University West China Hospital(No:CGZH19013)we sincerely thanks to Biomarker Technologies Corporation(Beijing,China)for the analyses of bioinformation in this study.
文摘Advanced three-dimensional structure variations of chromatin in large genome fragments,such as conversion of A/B compartment,topologically associated domains(TADs)and chromatin loops are related closely to occurrence of malignant tumors.However,the structural characteristics of lung cancer still remain uncovered.In this study,we used high-throughput chromosome(Hi-C)conformation capture technology to detect the advanced structural variations in chromatin of two nonsmoking lung adenocarcinoma(LUAD)tumor and paired normal tissues.The results indicate that significant chromatin variations are detected in tumor tissues compared with normal tissues.At compartment scale,the main conversion type of compartment is A→B in tumor tissues,which are concentrated mainly on chromosome 3(Chr3)(33.6%).A total of 216 tumor-specific TADs are identified in tumor tissues,which are distributed mainly in Chr1(19),Chr2(15)and Chr3(17).Forty-one distinct enhancer-promoter loops are observed in tumor tissue,which are associated closely to tumor-related pathways including mitogen-activated protein kinase(MAPK),Phosphatidylinositol-3-kinase-Protein kinase B(PI3K-AKT),Ras,Wnt and Ras1.The most important observation in this study is that we identify five important genes(SYT16,NCEH1,NXPE3,MB21D2,and DZIP1L),which are detected in both A→B compartment,TADs and chromatin loops in tumor samples,and four of these genes(NCEH1,NXPE3,MB21D2,and DZIP1L)locate on q arm of Chr3.Further gene expression and invasion experiment analysis show that NCEH1,MB21D2 and SYT16 are involved in the tumor development.Thus,we provide a comprehensive overview of advanced structures in LUAD for the first time and provide a basis for further research on the genetic variation of this tumor.
基金This work was supported by the Ministry of Science and Technology,the National Key Research and Development Program of China(2021YFC2100800)the National Natural Science Foundation of China(31800719,31861143017,21621004).
文摘Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched.In this study,an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)technology with two synthetic chromosomes,namely synV and synX.The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries.Our findings showed that complex SVs,including a pericentric inversion and a trans-chromosome translocation between synV and synX,resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin.Also,genetic targets were mapped,which resulted in a higher astaxanthin yield,thus demonstrating the SVs’ability to reorganize genetic information along the chromosomes.The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena.Collectively,this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.
基金supported by the National High Technology Research and Development Program of China(863 Program)(No.2013AA102502)the National Natural Science Foundation of China(Nos.31372284 and 31402046)+1 种基金the Fund of Fok Ying-Tung Education Foundation(No.141117)the Fund for Distinguished Young Scientists of Sichuan Province(No. 2013JQ0013)
文摘Genomic structural variations (SVs), particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation (Alkan et al., 2011; Bickhart and Liu, 2014). With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps (Li et al., 2011). Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies (Baker, 2012; Wang et al., 2012;
基金supported by the National Natural Science Foundation of China (grant numbers 31961143021)the earmarked fund for Modern Agro-industry Technology Research System (grant numbers CARS-39-01)+1 种基金the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences (grant numbers ASTIP-IAS01) to YM and LJsupported by the Elite Youth Program in Chinese Academy of Agricultural Sciences
文摘As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.
基金Funding to RR was provided by the USDA Extension IPM Implementation Program(COL0-2017-04499,2021-70006-35439)the Colorado State University Agricultural Experiment Station(COL00410)Colorado State University startup funds.Funding to EJ was provided by Montana State Extension.
文摘It is well known that large genomic variations can greatly impact the phenotype of an organism.Structural Variants(SVs)encompass any genomic variation larger than 30 base pairs,and include changes caused by deletions,inversions,duplications,transversions,and other genome modifications.Due to their size and complex nature,until recently,it has been difficult to truly capture these variations.Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes.In tomato,advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes,and tomato relatives.These studies have identified SVs related to fruit size and flavor,as well as plant disease response,resistance/susceptibility,and the ability of plants to detect pathogens(immunity).In this review,we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity.We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes,the current evidence for the role of SVs in biotic and abiotic stress responses,and the outlook for genetic modification of SVs to advance plant breeding objectives.
基金supported by The National Social Science Fund of China(Grant No.20BTQ085)The Soft Science Project of Science and Technology Program of Guangdong Province(CN),2019B101001024
文摘This study aims to identify potential influential literature and potential influential topics in the field of information science(IS).Using citation structural variation approach,provided by CiteSpace,we discerned the potential influential theses in IS.Then,we proposed an analyzing framework based on"citation network-citation structural variation-citation cluster,"which is used to discern the potential influential topics in IS.Using the structural variation approach,we analyzed the contents and features of potential influential theses.The potential influential topics,discerned by the"citation network-citation structural variation-citation cluster"framework,corroborated the existing knowledge base to some extent and seemed to be divergent and intermingled.Such potential impact literature and potential impact research topics are of certain reference value for future frontier research.
基金This work has been supported by the National Key Research and Development Program of China(2021YFF1200105)National Natural Science Foundation of China(62172125,62371161).
文摘Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.
基金the National Natural Science Foundation of China(No.70671024)the Na-tional High-Tech Research and Development Program of China(863 Program)(No.2006AA11Z209)
文摘The proximal-based decomposition method was originally proposed by Chen and Teboulle (Math. Programming, 1994, 64:81-101 for solving corrvex minimization problems. This paper extends it to solving monotone variational inequalities associated with separable structures with the improvements that the restrictive assumptions on the involved parameters are much relaxed, and thus makes it practical to solve the subproblems easily. Without additional assumptions, global convergence of the new method is proved under the same mild assumptions on the problem's data as the original method.
基金supported by the National Natural Science Foundation of China(No50772013)
文摘A novelty method,frontal polymerization(FP),was employed to directly produce a series of polyacrylamide (PAM),poly(N-isopropylacrylamide)(PNIPAM) and acrylamide-N-isopropylacrylamide copolymer macroporous monoliths. Field emission scanning electronic microscope and mercury intrusion method were adopted to measure some parameters of these monoliths,such as frame,pore size distribution as well as porosity.Effects of types of monomer,thicker and surfactant on porous structure of monoliths were studied.A variet...
基金funded by the National Basic Research Program of China (2014CB138305)the China Agriculture Research System (CARS24)
文摘To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical locations in Italy, were analyzed using three DNA fragments including the translation elongation factor(EF1α), the second largest subunit of t he RNA polymerase II(RPB2) and the largest subunit of the RNA polymerase II(RPB1). The results indicated relatively abundant genetic variability in the wild resources of P. ferulae. The analysis of molecular variance(AMOVA) showed that the vast majority of the genetic variation was found within geographical populations. Both the Chinese populations and the Italian populations of P. ferulae displayed a limited genetic differentiation. The degree of differentiation between the Chinese populations and the Italian populations was obviously higher than that between the populations from the same region, and moreover the genetic differentiation among all the tested populations was correlated to the geographical distance. T he phylogeny analyses confirmed that samples from China and Italy belonged to another genetic group separated from Pleurotus eryngii. They were closely related to each other but were clustered according to their geographical origins, which implied the Chinese populations were highly differentiated from the Italian populations because of distance isolation, and the two populations from different regions might be still in the process of allopatric divergence.
基金The National Natural Science Foundation of China under contract Nos 41306116 and 41506217the Basic Research of the National Department of Science and Technology under contract No.GASI-01-02-04the Polar Science Strategic Research Foundation of China under contract No.20140309
文摘Marine biodiversity is changing in response to altered physical environment, subsequent ecological changes as well as anthropogenic disturbances. In this study, phytoplankton samples in situ collected in the Bering Sea in July of 1999 and 2010 were analyzed to obtain phytoplankton community structure and spatial-temporal variation between the beginning and end of this decade, and the correlation of phytoplankton community dynamics and environmental factors was investigated. A total of 5 divisions, 58 genera and 153 species of phytoplankton belonging to 3 ecological groups were identified. The vast majority of phytoplankton consisted of diatoms accounting for 66.7% of the total species and 95.2% of the total abundance. Considering differentiation in spatial extent and phytoplankton sample types, there were subtle changes in species composition, large altering in abundance and significant variation in spatial distribution between two surveys. The abundance peak area was located at the Bering Strait while sub peak was found at the Bering Sea Basin. The boreal-temperate diatom was the dominant flora, which was subsequently replaced by eurythermal and frigid-water diatom. Phytoplankton community in the Bering Sea was not a simplex uniform community but composed of deep-ocean assemblage and neritic assemblage. The deep-ocean assemblage was located in the northwestern Pacific Ocean and Bering Sea Basin, dominated by boreal-temperate species(Neodenticula seminae, Thalassiothrix longissima, Amphiprora hyperborean, Chaetoceros atlanticus, Thalassiosira trifulta, etc.) and eurychoric species(Thalassionema nitzschioides, Ch. compressus, Rhizosolenia styliformis, etc.), and characterized by low abundance, even interspecies abundance allocations, diverse dominant species and high species diversity. The neritic assemblage was distributed on the continental shelf and slope of Bering Sea and was mainly composed of frigid-water species(Th.nordenski?ldii, Ch. furcellatus, Ch. socialis, Bacteriosira fragilis, etc.) and eurythermal and euryhaline species(L.danicus, Ch. curvisetus, Coscinodiscus curvatulus, etc.), and it was characterized by high abundance, uneven interspecies allocations, prominent dominant species and low species diversity. Spatial-temporal variation of species composition and abundance of phytoplankton in the Bering Sea was directly controlled by surface circulation,nutrient supply and ice edge.
基金the China Agriculture Research System(CARS-02-77)the Shaanxi Province Research and Development Project(2021LLRH-07)the Yangling Seed Industry Innovation Center Project(YLZY-YM-01).
文摘Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for breeding.Its pedigree showed genetic divergence from B73 and other lines in its pedigree.Comparison with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight disease.More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development.The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.
基金supported by Creative Research Team Project of the National Natural Science Foundation of China(32221005 to S.Zhao)grants from the National Natural Science Foundation of China(32202637 to Z.Zheng and 31972536 to X.Li)the earmarked fund for CARS-35,and China Postdoctoral Science Foundation(2020M682446 to Z.Zheng).
文摘Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.
基金The National Natural Science Foundation of China(31871964,31801738,and 32100352)the Major Science and Technology Projects in Anhui Province(202003a06020009)+2 种基金Earmarked Fund for China Agriculture Research System(CARS-01-40)the Special Funds for Supporting Innovation and Entrepreneurship for Returned Oversea-Students in Anhui Province(2020LCX035)Anhui Provincial Natural Science Foundation(Youth Project,2008085QC148).
文摘The basic leucine zipper(bZIP)is an important class of transcription factors in plants,playing a critical role in plant growth and development and responses to biotic and abiotic stress.Due to gene presence/absence variations,it is limited to identify bZIP genes based on the reference genome.Therefore,we performed the bZIP gene family analysis in the rice pan-genome.By employing a rice pan-genome,ninety-four OsbZIPs(72 core genes and 22 variable genes)were identified and divided into 11 groups in a phylogenetic tree.Based upon Ka/Ks values in 33 accessions,OsbZIPs were subjected to different selection pressures during domestication.The analysis of the effects of structural variations(SVs)on gene expression,gene structure,and conserved domains showed that SVs could significantly alter the expression levels of certain OsbZIPs,leading to gene truncation and the emergence of numerous atypical genes.Thirty-four differentially expressed OsbZIPs were identified by analyzing RNA-seq data of the Xanthomonas oryzae pv.oryzae(Xoo)infection susceptible(IR24)and resistant(IRBB67)lines under high temperature,and by counting the number of differentially expressed OsbZIPs in different subgroups.These Osb-ZIPs were found to respond to Xoo infection at an early stage and may not be involved in the mechanism of Xa4 and Xa7 resistance to Xoo.The multiple variation patterns of OsbZIP genes provide new insights into the OsbZIP genes in rice.These results provide new resources and offer new directions for functional studies of OsbZIPs.
基金Supported by the National Natural Science Foundation of China(31872977 and 31572364)the Jiangsu Agricultural Science and Technology Innovation Fund(CX(19)2016)the Priority Academic Program Development of Jiangsu Higher Education Institutions,China.
文摘Despite one SINE retrotransposon insertion polymorphism(sRTIP)in the vertebrae development-associated(VRTN)gene was identified in pigs,the structural variations(SVs)in VRTN gene and its proximal flank regions were largely unknown.VRTN genic and flanking sequences from 14 breeds were assembled or downloaded from whole genome shotgun contings(WGS)database,and aligned to identify the SVs with Clustalx,and retrotransposons in VRTN gene were annotated by RepeatMasker,the splicing patterns of VRTN gene were predicted by Genescan,and large SVs were evaluated by PCR.A total of 12 small SVs and three large SVs in intron of VRTN,derived from SINE insertion polymorphisms.were identifed,and two of them(VRTN-sRTIP2 and VRTN-sRTIP3)were not reported before.These VRTN-sRTIPs may affect the splicing patterns of VRTN.They displayed polymorphisms in most detected eight breeds.VRTN-sRTIP2 and VRTN-sRTIP3 showed Hardy-Weinberg equilibrium distributions in most populations except the Chinese local Erhualian pigs,while VRTN-sRTIP1 showed genetic equilbrium in Erhualian pigs.Three VRTN-sRTIPs were identified,and displayed polymorphisms in pigs,and two of them were not reported before.These SVs provide a useful molecular markers for genetic analysis in pigs,and offer new information to facilitate the understanding the SVs of VRTN gene and their putative roles in the variation of vertebral number.