Cotton(Gossypium hirsutum L.)is one of the most important global crops that supports the textile industry and pro-vides a living for millions of farmers.The constantly increasing demand needs a significant rise in cot...Cotton(Gossypium hirsutum L.)is one of the most important global crops that supports the textile industry and pro-vides a living for millions of farmers.The constantly increasing demand needs a significant rise in cotton production.Genome editing technology,specifically with clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)tools,has opened new possibilities for trait development in cotton.It allows pre-cise and efficient manipulation within the cotton genome when compared with other genetic engineering tools.Current developments in CRISPR/Cas technology,including prime editing,base editing,and multiplexing editing,have expanded the scope of traits in cotton breeding that can be targeted.CRISPR/Cas genome editing has been employed to generate effectively CRISPRized cotton plants with enhanced agronomic traits,including fiber yield and quality,oil improvement,stress resistance,and enhanced nutrition.Here we summarized the various target genes within the cotton genome which have been successfully altered with CRISPR/Cas tools.However,some challenges remain,cotton is tetraploid genome having redundant gene sets and homologs making challenges for genome edit-ing.To ensure specificity and avoiding off-target effects,we need to optimize various parameters such as target site,guide RNA design,and choosing right Cas variants.We outline the future prospects of CRISPR/Cas in cotton breeding,suggesting areas for further research and innovation.A combination of speed breeding and CRISPR/Cas might be useful for fastening trait development in cotton.The potentials to create customized cotton cultivars with enhanced traits to meet the higher demands for the agriculture and textile industry.展开更多
Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cyt...Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.展开更多
Integrative physical mapping is the centerpieceof and essential for advanced genomics research.Upland cotton(Gossypium hirsutum L.)geneticstandard line TM-1 is used as the referencegenotype to develop a whole-genome,B...Integrative physical mapping is the centerpieceof and essential for advanced genomics research.Upland cotton(Gossypium hirsutum L.)geneticstandard line TM-1 is used as the referencegenotype to develop a whole-genome,BAC/BIBAC-based integrated physical/genetic map ofthe cotton genome.From the TM-1 line we haveconstructed two BAC libraries with HindIII展开更多
Exotic Gossypium germplasm is a rich source of useful agronomic traits for improvement programs of cultivated cotton.Efficient use of genetic variation available in the wild relatives depends
Cotton is not only an important source of textilefibre and edible oil,but also a valuable source ofhigh-quality protein and fodder,because 45%～50% of the cotton seed powder is protein.However,the seeds of cultivated ...Cotton is not only an important source of textilefibre and edible oil,but also a valuable source ofhigh-quality protein and fodder,because 45%～50% of the cotton seed powder is protein.However,the seeds of cultivated cotton usuallycontain a special polyphenol compound calledgossypol,which is poisonous and hinders theutilization of the seeds.Therefore breeding展开更多
This paper presents an integrated approach towards solving the problem of "Gene Prediction".The "Gene Prediction" problem solving undergoes well defined stages starting with a DNA
The genus Gossypium is one of the largest havingnearly 50 species of which two are tetraploidcultivars and two are diploid cultivars with 2n =52 and 26 chromosome respectively and the restare wild to semi-wild at both...The genus Gossypium is one of the largest havingnearly 50 species of which two are tetraploidcultivars and two are diploid cultivars with 2n =52 and 26 chromosome respectively and the restare wild to semi-wild at both these ploidy levels.The tetraploids(AD)are supposed to containthe Asiatic cotton(A)and American diploid(D)species genomes.展开更多
Gossypium mustelinum [(AD)4] is one of five tetraploid species in Gossypium.Three pairs of nucleolar organizer regions(NOR) in(AD)4 were detected by FISH with 45S rDNA as a probe,they also were observed with genomic D...Gossypium mustelinum [(AD)4] is one of five tetraploid species in Gossypium.Three pairs of nucleolar organizer regions(NOR) in(AD)4 were detected by FISH with 45S rDNA as a probe,they also were observed with genomic DNA(gDNA) from Gossypium D genome species as probes.Of展开更多
A software and algorithm which based on random sequence model uses osmotic stress responding cis elements from existing information sources of biology was designed. It can infer the genic downstream function of Arabid...A software and algorithm which based on random sequence model uses osmotic stress responding cis elements from existing information sources of biology was designed. It can infer the genic downstream function of Arabidopsis thaliana through analyzing its promoter region, and can offer effective aided analysis to mine osmotic stress responding genes in Arabidopsis thatiana genome. The practical application proves that this software can aid to analyze vast genic data and offer important data evidence.展开更多
In this special issue,we plan to publish articles covering the following topics:Timely review(s);Research articles;Brief communications;and Step-by-step protocol(s)for methodology development in genome editing,in eith...In this special issue,we plan to publish articles covering the following topics:Timely review(s);Research articles;Brief communications;and Step-by-step protocol(s)for methodology development in genome editing,in either plant or mammalian cells;Genotype-independent transformation of crop species;Exploring the potential mechanisms underlying the differences in transformation.展开更多
Cotton is an important cash crop in the world,and it plays an irreplaceable role in China's national economy.Cultivated upland cotton(Gossypium hirsutum L.) represents 95% of the world's cotton production,but ...Cotton is an important cash crop in the world,and it plays an irreplaceable role in China's national economy.Cultivated upland cotton(Gossypium hirsutum L.) represents 95% of the world's cotton production,but it has a complex allotetraploid genome that contains at least 30000 genes in 2500展开更多
Upland cotton has the highest yield,and accounts for >95% of world cotton production.Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural,functional,and evoluti...Upland cotton has the highest yield,and accounts for >95% of world cotton production.Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural,functional,and evolutionary studies of the species.Here,we employed GeneTrek and展开更多
Recombinant inbred lines(RILs) serve as powerful tools for genetic mapping.RILs are obtained by crossing two inbred lines followed by repeated selfing or sib-mating to create a set of new
Plant regeneration is the first step to cotton biotechnology.We screened over 100 genotypes and found two genotypes,YZ-1 and Y668,which are very easy to regenerate.It takes about 5 to 6
Cotton is viewed as the most important cash crop in the world,and sustains the agricultural economies of many nations by providing a sustainable fiber product for the textile industry.Due to
As it is known a complete coverage of cotton(Gossypium hirsutum L.) genome with hypoaneuploids is not still realized.Therefore the detection of new types of aneuploids especially in different cytogenetic collections i...As it is known a complete coverage of cotton(Gossypium hirsutum L.) genome with hypoaneuploids is not still realized.Therefore the detection of new types of aneuploids especially in different cytogenetic collections is very useful.In Uzbekistan,long-term investigations towards development展开更多
Introduction:Genome sequence plays an important role in both basic and applied studies.Gossypium raimondii,the putative contributor of the D subgenome of upland cotton(G.hirsutum,highlights the need to improve the gen...Introduction:Genome sequence plays an important role in both basic and applied studies.Gossypium raimondii,the putative contributor of the D subgenome of upland cotton(G.hirsutum,highlights the need to improve the genome quality rapidly and efficiently.Methods:We performed Hi-C sequencing of G.raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds.We also compared the reassembled genome sequenee with the previously published G raimondii genomes for gene and genome sequence collinearity.Result:A total of 9842%of scaffold sequences were clustered successfully,among which 99.72%of the clustered sequences were ordered and 99.92%of the ordered sequences were oriented with high-quality.Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than the previous one(Nat Genet 44:98-1103,2012).Conclusion:This improvement in G raimondii genome not only provides a better reference to increase study efficiency but also offers a new way to assemble cotton genomes.Furthermore,Hi-C data of G.raimondii may be used for 3D structure research or regulating analysis.展开更多
With the publication of "Toward Sequencing Cotton(Gossypium) Genomes" [Chen et al.Plant Physiology,2007,145:1303-1310] a clear consensus emerged from the cotton genomics
Gossypium hirsutum,the most widely planted cotton species,its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species.To better understand the genetic component of co...Gossypium hirsutum,the most widely planted cotton species,its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species.To better understand the genetic component of cotton,Huang et al.recently sequenced and assembled the first A1-genome G.herbaceum,and updated the A2-genome G.arboreum and(AD)1-genome G.hirsutum.On the basis of the three reference genomes,they resolved existing controversial concepts and provided novel evolutionary insights surrounding the A-genome.展开更多
Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this in...Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this investigation,we performed a comprehensive analysis encompassing genome sequencing,genomic analysis,and phenotypic characterization of L.reuteri Q35,an exceptionally proficient producer of reuterin.The whole genome sequencing results showed that the complete genome sequence spans 2145158 bp with a GC content of 38.9%and encompasses 2121 genes.Initial identification of antibiotic-resistant genes,virulence factors,and toxin-coding genes in the genome substantiated the strain’s low-risk status.Subsequent tests for antibiotic resistance,acute oral toxicology,and hemolysis further confirmed its elevated safety level.The genome of L.reuteri Q35 was found to contain genes associated with adhesion and stress tolerance.Following exposure to artificial gastric juice and bile salt,the strain exhibited a higher survival rate and demonstrated a strong scavenging ability for hydroxyl free radicals in antioxidant capacity tests.These findings suggested that L.reuteri Q35 possesses unique probiotic properties.Additionally,the genome of strain Q35 harbors three truncated oxaloyl-CoA decarboxylase genes(oxc1,oxc2 and oxc3),overexpression of which resulted in a significant increase in ammonium oxalate degradation from 29.5%to 48.8%.These findings highlight that L.reuteri Q35 exhibits both favorable safety characteristics alongside beneficial properties,making it a promising candidate for treating metabolic disorders such as hyperoxaluria.展开更多
文摘Cotton(Gossypium hirsutum L.)is one of the most important global crops that supports the textile industry and pro-vides a living for millions of farmers.The constantly increasing demand needs a significant rise in cotton production.Genome editing technology,specifically with clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)tools,has opened new possibilities for trait development in cotton.It allows pre-cise and efficient manipulation within the cotton genome when compared with other genetic engineering tools.Current developments in CRISPR/Cas technology,including prime editing,base editing,and multiplexing editing,have expanded the scope of traits in cotton breeding that can be targeted.CRISPR/Cas genome editing has been employed to generate effectively CRISPRized cotton plants with enhanced agronomic traits,including fiber yield and quality,oil improvement,stress resistance,and enhanced nutrition.Here we summarized the various target genes within the cotton genome which have been successfully altered with CRISPR/Cas tools.However,some challenges remain,cotton is tetraploid genome having redundant gene sets and homologs making challenges for genome edit-ing.To ensure specificity and avoiding off-target effects,we need to optimize various parameters such as target site,guide RNA design,and choosing right Cas variants.We outline the future prospects of CRISPR/Cas in cotton breeding,suggesting areas for further research and innovation.A combination of speed breeding and CRISPR/Cas might be useful for fastening trait development in cotton.The potentials to create customized cotton cultivars with enhanced traits to meet the higher demands for the agriculture and textile industry.
基金National Natural Science Foundation of China(31530053)
文摘Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.
文摘Integrative physical mapping is the centerpieceof and essential for advanced genomics research.Upland cotton(Gossypium hirsutum L.)geneticstandard line TM-1 is used as the referencegenotype to develop a whole-genome,BAC/BIBAC-based integrated physical/genetic map ofthe cotton genome.From the TM-1 line we haveconstructed two BAC libraries with HindIII
文摘Exotic Gossypium germplasm is a rich source of useful agronomic traits for improvement programs of cultivated cotton.Efficient use of genetic variation available in the wild relatives depends
文摘Cotton is not only an important source of textilefibre and edible oil,but also a valuable source ofhigh-quality protein and fodder,because 45%～50% of the cotton seed powder is protein.However,the seeds of cultivated cotton usuallycontain a special polyphenol compound calledgossypol,which is poisonous and hinders theutilization of the seeds.Therefore breeding
文摘This paper presents an integrated approach towards solving the problem of "Gene Prediction".The "Gene Prediction" problem solving undergoes well defined stages starting with a DNA
文摘The genus Gossypium is one of the largest havingnearly 50 species of which two are tetraploidcultivars and two are diploid cultivars with 2n =52 and 26 chromosome respectively and the restare wild to semi-wild at both these ploidy levels.The tetraploids(AD)are supposed to containthe Asiatic cotton(A)and American diploid(D)species genomes.
文摘Gossypium mustelinum [(AD)4] is one of five tetraploid species in Gossypium.Three pairs of nucleolar organizer regions(NOR) in(AD)4 were detected by FISH with 45S rDNA as a probe,they also were observed with genomic DNA(gDNA) from Gossypium D genome species as probes.Of
文摘A software and algorithm which based on random sequence model uses osmotic stress responding cis elements from existing information sources of biology was designed. It can infer the genic downstream function of Arabidopsis thaliana through analyzing its promoter region, and can offer effective aided analysis to mine osmotic stress responding genes in Arabidopsis thatiana genome. The practical application proves that this software can aid to analyze vast genic data and offer important data evidence.
文摘In this special issue,we plan to publish articles covering the following topics:Timely review(s);Research articles;Brief communications;and Step-by-step protocol(s)for methodology development in genome editing,in either plant or mammalian cells;Genotype-independent transformation of crop species;Exploring the potential mechanisms underlying the differences in transformation.
文摘Cotton is an important cash crop in the world,and it plays an irreplaceable role in China's national economy.Cultivated upland cotton(Gossypium hirsutum L.) represents 95% of the world's cotton production,but it has a complex allotetraploid genome that contains at least 30000 genes in 2500
文摘Upland cotton has the highest yield,and accounts for >95% of world cotton production.Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural,functional,and evolutionary studies of the species.Here,we employed GeneTrek and
文摘Recombinant inbred lines(RILs) serve as powerful tools for genetic mapping.RILs are obtained by crossing two inbred lines followed by repeated selfing or sib-mating to create a set of new
文摘Plant regeneration is the first step to cotton biotechnology.We screened over 100 genotypes and found two genotypes,YZ-1 and Y668,which are very easy to regenerate.It takes about 5 to 6
文摘Cotton is viewed as the most important cash crop in the world,and sustains the agricultural economies of many nations by providing a sustainable fiber product for the textile industry.Due to
文摘As it is known a complete coverage of cotton(Gossypium hirsutum L.) genome with hypoaneuploids is not still realized.Therefore the detection of new types of aneuploids especially in different cytogenetic collections is very useful.In Uzbekistan,long-term investigations towards development
文摘Introduction:Genome sequence plays an important role in both basic and applied studies.Gossypium raimondii,the putative contributor of the D subgenome of upland cotton(G.hirsutum,highlights the need to improve the genome quality rapidly and efficiently.Methods:We performed Hi-C sequencing of G.raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds.We also compared the reassembled genome sequenee with the previously published G raimondii genomes for gene and genome sequence collinearity.Result:A total of 9842%of scaffold sequences were clustered successfully,among which 99.72%of the clustered sequences were ordered and 99.92%of the ordered sequences were oriented with high-quality.Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than the previous one(Nat Genet 44:98-1103,2012).Conclusion:This improvement in G raimondii genome not only provides a better reference to increase study efficiency but also offers a new way to assemble cotton genomes.Furthermore,Hi-C data of G.raimondii may be used for 3D structure research or regulating analysis.
文摘With the publication of "Toward Sequencing Cotton(Gossypium) Genomes" [Chen et al.Plant Physiology,2007,145:1303-1310] a clear consensus emerged from the cotton genomics
文摘Gossypium hirsutum,the most widely planted cotton species,its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species.To better understand the genetic component of cotton,Huang et al.recently sequenced and assembled the first A1-genome G.herbaceum,and updated the A2-genome G.arboreum and(AD)1-genome G.hirsutum.On the basis of the three reference genomes,they resolved existing controversial concepts and provided novel evolutionary insights surrounding the A-genome.
文摘Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this investigation,we performed a comprehensive analysis encompassing genome sequencing,genomic analysis,and phenotypic characterization of L.reuteri Q35,an exceptionally proficient producer of reuterin.The whole genome sequencing results showed that the complete genome sequence spans 2145158 bp with a GC content of 38.9%and encompasses 2121 genes.Initial identification of antibiotic-resistant genes,virulence factors,and toxin-coding genes in the genome substantiated the strain’s low-risk status.Subsequent tests for antibiotic resistance,acute oral toxicology,and hemolysis further confirmed its elevated safety level.The genome of L.reuteri Q35 was found to contain genes associated with adhesion and stress tolerance.Following exposure to artificial gastric juice and bile salt,the strain exhibited a higher survival rate and demonstrated a strong scavenging ability for hydroxyl free radicals in antioxidant capacity tests.These findings suggested that L.reuteri Q35 possesses unique probiotic properties.Additionally,the genome of strain Q35 harbors three truncated oxaloyl-CoA decarboxylase genes(oxc1,oxc2 and oxc3),overexpression of which resulted in a significant increase in ammonium oxalate degradation from 29.5%to 48.8%.These findings highlight that L.reuteri Q35 exhibits both favorable safety characteristics alongside beneficial properties,making it a promising candidate for treating metabolic disorders such as hyperoxaluria.
