Directed breeding of horticultural crops is essential for increasing yield,nutritional content,and consumer-valued characteristics such as shape and color of the produce.However,limited genetic diversity restricts the...Directed breeding of horticultural crops is essential for increasing yield,nutritional content,and consumer-valued characteristics such as shape and color of the produce.However,limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches.Natural genetic changes in cisregulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression.Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner.The advent of CRISPR/Cas-mediated cis-regulatory region engineering(cis-engineering)provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement.Here,we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops.We describe strategies and limitations for its use in crop improvement,including de novo cis-regulatory element(CRE)discovery,precise genome editing,and transgene-free genome editing.In addition,we discuss the challenges and prospects regarding current technologies and achievements.CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.展开更多
Fleshy fruit shape is an important external quality trait influencing the usage of fruits and consumer preference.Thus,modification of fruit shape has become one of the major objectives for crop improvement.However,th...Fleshy fruit shape is an important external quality trait influencing the usage of fruits and consumer preference.Thus,modification of fruit shape has become one of the major objectives for crop improvement.However,the underlying mechanisms of fruit shape regulation are poorly understood.In this review we summarize recent progress in the genetic basis of fleshy fruit shape regulation using tomato,cucumber,and peach as examples.Comparative analyses suggest that the OFP-TRM(OVATE Family Protein-TONNEAU1 Recruiting Motif)and IQD(IQ67 domain)pathways are probably conserved in regulating fruit shape by primarily modulating cell division patterns across fleshy fruit species.Interestingly,cucumber homologs of FRUITFULL(FUL1),CRABS CLAW(CRC)and 1-aminocyclopropane-1-carboxylate synthase 2(ACS2)were found to regulate fruit elongation.We also outline the recent progress in fruit shape regulation mediated by OFP-TRM and IQD pathways in Arabidopsis and rice,and propose that the OFP-TRM pathway and IQD pathway coordinate regulate fruit shape through integration of phytohormones,including brassinosteroids,gibberellic acids,and auxin,and microtubule organization.In addition,functional redundancy and divergence of the members of each of the OFP,TRM,and IQD families are also shown.This review provides a general overview of current knowledge in fruit shape regulation and discusses the possible mechanisms that need to be addressed in future studies.展开更多
Within large-fruited germplasm,fruit size is influenced by flat and globe shapes.Whereas flat fruits are smaller and retain better marketability,globe fruits are larger and more prone to cuticle disorders.Commercial h...Within large-fruited germplasm,fruit size is influenced by flat and globe shapes.Whereas flat fruits are smaller and retain better marketability,globe fruits are larger and more prone to cuticle disorders.Commercial hybrids are often developed from crosses between flat and globe shaped parents because flat shape is thought to be dominant and fruit size intermediate.The objectives of this study were to determine the genetic basis of flat/globe fruit shape in large-fruited fresh-market tomato germplasm and to characterize its effects on several fruit traits.Twenty-three advanced single plant selections from the Fla.8000×Fla.8111B cross were selectively genotyped using a genome-wide SNP array,and inclusive composite interval mapping identified a single locus on the upper arm of chromosome 12 associated with shape,which we termed globe.A 238-plant F 2 population and 69 recombinant inbred lines for this region from the same parents delimited globe to approximately 392-kilobases.A germplasm survey representing materials from multiple breeding programs demonstrated that the locus explains the flat/globe shape broadly.A single base insertion in an exon of Solyc12g006860,a gene annotated as a brassinosteroid hydroxylase,segregated completely with shape in all populations tested.CRISPR/Cas9 knock out plants confirmed this gene as underlying the globe locus.In silico analysis of the mutant allele of GLOBE among 595 wild and domesticated accessions suggested that the allele arose very late in the domestication process.Fruit measurements in three genetic backgrounds evidenced that globe impacts fruit size and several fruit shape attributes,pedicel length/width,and susceptibility of fruit to weather check.The mutant allele of GLOBE appears mostly recessive for all traits except fruit size where it acts additively.展开更多
Rice bean(Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and so...Rice bean(Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop.Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers.In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides(17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT(14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean.However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice bean and other Vigna species.展开更多
A high-density inferred consensus map for 13homoeologous groups of cotton was constructedthrough the integration of three genetic maps(At,Dt and D)of homoeologous chromosomes.The consensus map included 2843 markers an...A high-density inferred consensus map for 13homoeologous groups of cotton was constructedthrough the integration of three genetic maps(At,Dt and D)of homoeologous chromosomes.The consensus map included 2843 markers andspanned about 2242 cM in 13 linkage groups.1777 mapped probes were sequenced andcompared to the Arabidopsis using the展开更多
Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold...Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold over the past 60 years,the continually growing global population necessitates further increases in soybean production.In the past,especially in the last decade,significant progress has been made in both functional genomics and molecular breeding.However,many more challenges should be overcome to meet the anticipated future demand.Here,we summarize past achievements in the areas of soybean omics,functional genomics,and molecular breeding.Furthermore,we analyze trends in these areas,including shortages and challenges,and propose new directions,potential approaches,and possible outputs toward 2035.Our views and perspectives provide insight into accelerating the development of elite soybean varieties to meet the increasing demands of soybean production.展开更多
Teucrium chamaedrys,commonly known as wall germander,is a small woody shrub native to the Mediterranean region.Its name is derived from the Greek words meaning‘‘ground oak,’’as its tiny leaves resemble those of an...Teucrium chamaedrys,commonly known as wall germander,is a small woody shrub native to the Mediterranean region.Its name is derived from the Greek words meaning‘‘ground oak,’’as its tiny leaves resemble those of an oak tree.Teucrium species are prolific producers of diterpenes,endowing them with valuable properties widely utilized in traditional and modern medicine.Sequencing and assembly of the 3-Gbp tetraploid T.chamaedrys genome revealed 74 diterpene synthase genes,with a substantial number of these genes clustered at four synteny genomic loci,each harboring a copy of a large diterpene biosynthetic gene cluster.Comparative genomics revealed that this cluster is conserved in the closely related species Teucrium marum.Along with the presence of several cytochrome p450 sequences,this region is among the largest biosynthetic gene clusters identified.Teucrium is well known for accumulating clerodane-type diterpenoids,which are produced from a kolavenyl diphosphate precursor.To elucidate the complex biosynthetic pathways of these medicinal compounds,we identified and functionally characterized several kolavenyl diphosphate synthases from T.chamaedrys.The remarkable chemical diversity and tetraploid nature of T.chamaedrys make it a valuable model for studying genomic evolution and adaptation in plants.展开更多
Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplicati...Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.展开更多
Improved soybean cultivars have been adapted to grow at a wide range of latitudes,enabling expansion of cultivation worldwide.However,the genetic basis of this broad adaptation is still not clear.Here,we report the id...Improved soybean cultivars have been adapted to grow at a wide range of latitudes,enabling expansion of cultivation worldwide.However,the genetic basis of this broad adaptation is still not clear.Here,we report the identification of GmPRR3b as a major flowering time regulatory gene that has been selected during domestication and genetic improvement for geographic expansion.Through a genome-wide association study of a diverse soybean landrace panel consisting of 279 accessions,we identified 16 candidate quantitative loci associated with flowering time and maturity time.The strongest signal resides in the known flowering gene E2,verifying the effectiveness of our approach.We detected strong signals associated with both flowering and maturity time in a genomic region containing GmPRR3b.Haplotype analysis revealed that GmPRR3bH6 is the major form of GmPRR3b that has been utilized during recent breeding of modern cultivars.mRNA profiling analysis showed that GmPRR3bH6 displays rhythmic and photoperiod-dependent expression and is preferentially induced under long-day conditions.Overexpression of GmPRR3bH6 increased main stem node number and yield,while knockout of GmPRR3bH6 using CRISPR/Cas9 technology delayed growth and the floral transition.GmPRR3bH6 appears to act as a transcriptional repressor of multiple predicted circadian clock genes,including GmCCAIa,which directly upregulates J/GmELF3a to modulate flowering time.The causal SNP(Chr12:5520945)likely endows GmPRR3bH6 a moderate but appropriate level of activity,leading to early flowering and vigorous growth traits preferentially selected during broad adaptation of landraces and improvement of cultivars.展开更多
Peanut （Arachis hypogaea; 2n = 4x = 40） is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gai...Peanut （Arachis hypogaea; 2n = 4x = 40） is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facil- itate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide poiymorphisms （SNPs） were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic re- gions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone pos- itive selection. These observations provide key insights on the inclusion of new genetic diversity in culti- vated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.展开更多
Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the...Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean(Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces(G. max(L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.展开更多
Most plants are polyploid due to whole-genome duplications （WGD） and can thus have duplicated genes. Following a WGD, paralogs are often fractionated （lost） and few duplicate pairs remain. Little attention has bee...Most plants are polyploid due to whole-genome duplications （WGD） and can thus have duplicated genes. Following a WGD, paralogs are often fractionated （lost） and few duplicate pairs remain. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high- resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, DNA methylation likely contributed to the elimination of ge- netic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit partic- ular genomic features as they are often associated with proximal transposable elements （TEs） and are pref- erentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.展开更多
Plants are complex systems hierarchically organized and composed of various cell types.To understand the molecular underpinnings of complex plant systems,single-cell RNA sequencing(scRNA-seq)has emerged as a powerful ...Plants are complex systems hierarchically organized and composed of various cell types.To understand the molecular underpinnings of complex plant systems,single-cell RNA sequencing(scRNA-seq)has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity.Furthermore,scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology,which aims to modify plants genetically/epigenetically through genome editing,engineering,or re-writing based on rational design for increasing crop yield and quality,promoting the bioeconomy and enhancing environmental sustainability.In particular,data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects.To date,scRNA-seq has been demonstrated in a limited number of plant species,including model plants(e.g.,Arabidopsis thaliana),agricultural crops(e.g.,Oryza sativa),and bioenergy crops(e.g.,Populus spp.).It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants.In this review,we summarize current technical advancements in plant scRNA-seq,including sample preparation,sequencing,and data analysis,to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples.We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research.Finally,we discuss the challenges and opportunities for the application of scRNA-seq in plants.展开更多
基金Funding in the Van der Knaap laboratory is from the National Science Foundation(IOS 1564366,IOS 1732253,and USDA 2017-67013-26199).
文摘Directed breeding of horticultural crops is essential for increasing yield,nutritional content,and consumer-valued characteristics such as shape and color of the produce.However,limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches.Natural genetic changes in cisregulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression.Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner.The advent of CRISPR/Cas-mediated cis-regulatory region engineering(cis-engineering)provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement.Here,we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops.We describe strategies and limitations for its use in crop improvement,including de novo cis-regulatory element(CRE)discovery,precise genome editing,and transgene-free genome editing.In addition,we discuss the challenges and prospects regarding current technologies and achievements.CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.
基金This work was supported by the Natural Science Foundation of Hebei Province(C2021204015)the 2021 Project for the Introduction of Oversea Students in Hebei Province(C20210510)+4 种基金science and technology research projects of colleges and universities in Hebei Province(ZD2022111)the Introduction of Talents Start-up fund of the State Key Laboratory of North China Crop Improvement and Regulation(NCCIR2020RC-13)the Introduction of Talents Start-up fund of Hebei Agricultural University(YJ2020067)the Hebei Fruit Vegetables Seed Industry Science and Technology Innovation Team Project(21326309D)the Vegetable Innovation Team Project of Hebei Modern Agricultural Industrial Technology System(HBCT2018030203).
文摘Fleshy fruit shape is an important external quality trait influencing the usage of fruits and consumer preference.Thus,modification of fruit shape has become one of the major objectives for crop improvement.However,the underlying mechanisms of fruit shape regulation are poorly understood.In this review we summarize recent progress in the genetic basis of fleshy fruit shape regulation using tomato,cucumber,and peach as examples.Comparative analyses suggest that the OFP-TRM(OVATE Family Protein-TONNEAU1 Recruiting Motif)and IQD(IQ67 domain)pathways are probably conserved in regulating fruit shape by primarily modulating cell division patterns across fleshy fruit species.Interestingly,cucumber homologs of FRUITFULL(FUL1),CRABS CLAW(CRC)and 1-aminocyclopropane-1-carboxylate synthase 2(ACS2)were found to regulate fruit elongation.We also outline the recent progress in fruit shape regulation mediated by OFP-TRM and IQD pathways in Arabidopsis and rice,and propose that the OFP-TRM pathway and IQD pathway coordinate regulate fruit shape through integration of phytohormones,including brassinosteroids,gibberellic acids,and auxin,and microtubule organization.In addition,functional redundancy and divergence of the members of each of the OFP,TRM,and IQD families are also shown.This review provides a general overview of current knowledge in fruit shape regulation and discusses the possible mechanisms that need to be addressed in future studies.
基金supported by funding from USDA NIFA AFRI 2016-05951by a scholarship from the Fulbright Garcia-Robles program.
文摘Within large-fruited germplasm,fruit size is influenced by flat and globe shapes.Whereas flat fruits are smaller and retain better marketability,globe fruits are larger and more prone to cuticle disorders.Commercial hybrids are often developed from crosses between flat and globe shaped parents because flat shape is thought to be dominant and fruit size intermediate.The objectives of this study were to determine the genetic basis of flat/globe fruit shape in large-fruited fresh-market tomato germplasm and to characterize its effects on several fruit traits.Twenty-three advanced single plant selections from the Fla.8000×Fla.8111B cross were selectively genotyped using a genome-wide SNP array,and inclusive composite interval mapping identified a single locus on the upper arm of chromosome 12 associated with shape,which we termed globe.A 238-plant F 2 population and 69 recombinant inbred lines for this region from the same parents delimited globe to approximately 392-kilobases.A germplasm survey representing materials from multiple breeding programs demonstrated that the locus explains the flat/globe shape broadly.A single base insertion in an exon of Solyc12g006860,a gene annotated as a brassinosteroid hydroxylase,segregated completely with shape in all populations tested.CRISPR/Cas9 knock out plants confirmed this gene as underlying the globe locus.In silico analysis of the mutant allele of GLOBE among 595 wild and domesticated accessions suggested that the allele arose very late in the domestication process.Fruit measurements in three genetic backgrounds evidenced that globe impacts fruit size and several fruit shape attributes,pedicel length/width,and susceptibility of fruit to weather check.The mutant allele of GLOBE appears mostly recessive for all traits except fruit size where it acts additively.
基金supported by earmarked funds for China Agriculture Research System (CARS-09)the Agricultural Science and Technology Innovation Program (ASTIP)
文摘Rice bean(Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop.Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers.In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides(17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT(14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean.However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice bean and other Vigna species.
文摘A high-density inferred consensus map for 13homoeologous groups of cotton was constructedthrough the integration of three genetic maps(At,Dt and D)of homoeologous chromosomes.The consensus map included 2843 markers andspanned about 2242 cM in 13 linkage groups.1777 mapped probes were sequenced andcompared to the Arabidopsis using the
基金supported by the National Natural Science Foundation of China(grant nos.32388201 and 32372126)Fundamental Research Funds for the Central Universities(YDZX2024041).
文摘Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold over the past 60 years,the continually growing global population necessitates further increases in soybean production.In the past,especially in the last decade,significant progress has been made in both functional genomics and molecular breeding.However,many more challenges should be overcome to meet the anticipated future demand.Here,we summarize past achievements in the areas of soybean omics,functional genomics,and molecular breeding.Furthermore,we analyze trends in these areas,including shortages and challenges,and propose new directions,potential approaches,and possible outputs toward 2035.Our views and perspectives provide insight into accelerating the development of elite soybean varieties to meet the increasing demands of soybean production.
基金support of the Neogen Land Grant Prize,an endowed grant program administered by the Office of Research and Innovation at Michigan State University(MSU),which supports graduate students in translating their research into real-world applications that positively impact society and the US economyfunded by a National Science Foundation(NSF)-IMPACTS Training Grant(DGE-1828149)+6 种基金funded by NSF Dimensions of Biodiversity(DEB 1737898)supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number T32 GM110523the US Department of Energy Great Lakes Bioenergy Research Center Cooperative Agreement DESC0018409funding from the Department of Biochemistry and Molecular Biology at MSU and support from AgBioResearch(MICL02454)supported in part by the National Science Foundation under Grant number 1737898funding from the University of Georgia,the Georgia Research Alliance,and Georgia Seed Developmentsupport from the NSF under grant number ISO-2029959.
文摘Teucrium chamaedrys,commonly known as wall germander,is a small woody shrub native to the Mediterranean region.Its name is derived from the Greek words meaning‘‘ground oak,’’as its tiny leaves resemble those of an oak tree.Teucrium species are prolific producers of diterpenes,endowing them with valuable properties widely utilized in traditional and modern medicine.Sequencing and assembly of the 3-Gbp tetraploid T.chamaedrys genome revealed 74 diterpene synthase genes,with a substantial number of these genes clustered at four synteny genomic loci,each harboring a copy of a large diterpene biosynthetic gene cluster.Comparative genomics revealed that this cluster is conserved in the closely related species Teucrium marum.Along with the presence of several cytochrome p450 sequences,this region is among the largest biosynthetic gene clusters identified.Teucrium is well known for accumulating clerodane-type diterpenoids,which are produced from a kolavenyl diphosphate precursor.To elucidate the complex biosynthetic pathways of these medicinal compounds,we identified and functionally characterized several kolavenyl diphosphate synthases from T.chamaedrys.The remarkable chemical diversity and tetraploid nature of T.chamaedrys make it a valuable model for studying genomic evolution and adaptation in plants.
文摘Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.
基金the National Key Research and Development Plan(2016YFD0101005,2016YFD0100201,and 2016YFD0100304)the National Natural Science Foundation of China(31871705 and 31422041)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences,and the Central Public-Interest Scientific Institution Basal Research Fund(Y2016JC13).
文摘Improved soybean cultivars have been adapted to grow at a wide range of latitudes,enabling expansion of cultivation worldwide.However,the genetic basis of this broad adaptation is still not clear.Here,we report the identification of GmPRR3b as a major flowering time regulatory gene that has been selected during domestication and genetic improvement for geographic expansion.Through a genome-wide association study of a diverse soybean landrace panel consisting of 279 accessions,we identified 16 candidate quantitative loci associated with flowering time and maturity time.The strongest signal resides in the known flowering gene E2,verifying the effectiveness of our approach.We detected strong signals associated with both flowering and maturity time in a genomic region containing GmPRR3b.Haplotype analysis revealed that GmPRR3bH6 is the major form of GmPRR3b that has been utilized during recent breeding of modern cultivars.mRNA profiling analysis showed that GmPRR3bH6 displays rhythmic and photoperiod-dependent expression and is preferentially induced under long-day conditions.Overexpression of GmPRR3bH6 increased main stem node number and yield,while knockout of GmPRR3bH6 using CRISPR/Cas9 technology delayed growth and the floral transition.GmPRR3bH6 appears to act as a transcriptional repressor of multiple predicted circadian clock genes,including GmCCAIa,which directly upregulates J/GmELF3a to modulate flowering time.The causal SNP(Chr12:5520945)likely endows GmPRR3bH6 a moderate but appropriate level of activity,leading to early flowering and vigorous growth traits preferentially selected during broad adaptation of landraces and improvement of cultivars.
文摘Peanut （Arachis hypogaea; 2n = 4x = 40） is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facil- itate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide poiymorphisms （SNPs） were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic re- gions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone pos- itive selection. These observations provide key insights on the inclusion of new genetic diversity in culti- vated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.
基金supported by the National Key R&D Program of China(2021YFD1201601,2016YFD0100201,2020YFE0202300)the National Natural Science Foundation of China(32072091)+2 种基金the Platform of National Crop Germplasm Resources of China(2016-004,2017-004,2018-004,2019-04,2020-05)the Crop Germplasm Resources Protection(2016NWB036-05,2017NWB036-05,2018NWB03605,2019NWB036-05)the Agricultural Science and Technology Innovation Program(ASTIP)of Chinese Academy of Agricultural Sciences(CAASZDRW202109)。
文摘Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean(Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces(G. max(L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.
文摘Most plants are polyploid due to whole-genome duplications （WGD） and can thus have duplicated genes. Following a WGD, paralogs are often fractionated （lost） and few duplicate pairs remain. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high- resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, DNA methylation likely contributed to the elimination of ge- netic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit partic- ular genomic features as they are often associated with proximal transposable elements （TEs） and are pref- erentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.
基金supported by the Center for Bioenergy Innovation(CBI),which is a U.S.Department of Energy(DOE)Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science,and the DOE Genomic Science Program,as part of the Secure Ecosystem Engineering and Design Scientific(SEED)Focus Area.Oak Ridge National Laboratory is man-aged by UT-Battelle,LLC for the U.S.DOE under Contract Number DE-AC05-00OR22725This material is based on work supported by the U.S.Department of Energy,Ofice of Science,Biological and Environmental Research Program under Award Number DE-SC0023338 to CRB.
文摘Plants are complex systems hierarchically organized and composed of various cell types.To understand the molecular underpinnings of complex plant systems,single-cell RNA sequencing(scRNA-seq)has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity.Furthermore,scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology,which aims to modify plants genetically/epigenetically through genome editing,engineering,or re-writing based on rational design for increasing crop yield and quality,promoting the bioeconomy and enhancing environmental sustainability.In particular,data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects.To date,scRNA-seq has been demonstrated in a limited number of plant species,including model plants(e.g.,Arabidopsis thaliana),agricultural crops(e.g.,Oryza sativa),and bioenergy crops(e.g.,Populus spp.).It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants.In this review,we summarize current technical advancements in plant scRNA-seq,including sample preparation,sequencing,and data analysis,to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples.We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research.Finally,we discuss the challenges and opportunities for the application of scRNA-seq in plants.
