Agrobacterium tumefaciens mediated plant transformation is a versatile tool for plant genetic engineering following its discovery nearly half a century ago.Numerous modifications were made in its application to increa...Agrobacterium tumefaciens mediated plant transformation is a versatile tool for plant genetic engineering following its discovery nearly half a century ago.Numerous modifications were made in its application to increase efficiency,especially in the recalcitrant major cereals plants.Recent breakthroughs in transformation efficiency continue its role as a mainstream technique in CRISPR/Cas-based genome editing and gene stacking.These modifications led to higher transformation frequency and lower but more stable transgene copies with the capability to revolutionize modern agriculture.In this review,we provide a brief overview of the history of Agrobacterium-mediated plant transformation and focus on the most recent progress to improve the system in both the Agrobacterium and the host recipient.A promising future for transformation in biotechnology and agriculture is predicted.展开更多
In the current issue of The Crop Journal,Chen et al.[1]reports map-based cloning of a wheat gene that showed temperaturedependent pleiotropic effects on multiple traits including plant height,leaf shape,spike and grai...In the current issue of The Crop Journal,Chen et al.[1]reports map-based cloning of a wheat gene that showed temperaturedependent pleiotropic effects on multiple traits including plant height,leaf shape,spike and grain morphology,and accordingly was named WPA1 for Wheat Plant Architecture 1.The mutant was first observed among EMS-treated plants and repeatedly appeared in multiple occasions.展开更多
MicroRNAs （miRNAs） are important post-transcriptional regulators of their target genes in plants and animals, miRNAs are usually 20-24 nucleotides long. Despite their unusually small sizes, the evolutionary history ...MicroRNAs （miRNAs） are important post-transcriptional regulators of their target genes in plants and animals, miRNAs are usually 20-24 nucleotides long. Despite their unusually small sizes, the evolutionary history of miRNA gene families seems to be similar to their protein-codingcounterparts. In contrast to the small but abundant miRNA families in the animal genomes, plants have fewer but larger miRNA gene families. Members of plant miRNA gene families are often highly similar, suggesting recent expansion via tandem gene duplication and segmental duplication events. Although many miRNA genes are conserved across plant species, the same gene family varies significantly in size and genomic organization in different species, which may cause dosage effects and spatial and temporal differences in target gene regulations. In this review, we summarize the current progress in understanding the evolution of plant miRNA gene families.展开更多
Single-guide RNA(sg RNA) is one of the two core components of the CRISPR(clustered regularly interspaced short palindromic repeat)/Cas(CRISPR-associated) genome-editing technology. We established an in vitro Traffic L...Single-guide RNA(sg RNA) is one of the two core components of the CRISPR(clustered regularly interspaced short palindromic repeat)/Cas(CRISPR-associated) genome-editing technology. We established an in vitro Traffic Light Reporter(TLR) system, which is designated as the same colors as traffic lights such as green, red and yellow were produced in cells. The TLR can be readily used in maize mesophyll protoplast for a quick test of promoter activity. The TLR assay indicates the variation in transcription activities of the seven Pol III promoters, from 3.4%(U6-1) to over 21.0%(U6-6). The U6-2 promoter, which was constructed to drive sg RNA expression targeting the Zm Wx1 gene, yielded mutation efficiencies ranging from 48.5% to 97.1%. Based on the reported and unpublished data, the in vitro TLR assay results were confirmed to be a readily system and may be extended to other plant species amenable to efficient genome editing via CRISPR/Cas. Our efforts provide an efficient method of identifying native Pol III-recognized promoters for RNA guide-based genome-editing systems in maize.展开更多
MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA f...MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.展开更多
The CRISPR/Cas9 technology is evolved from a type II bacterial immune system and represents a new generation of targeted genome editing technology that can be applied to nearly all organisms. Site-specific modificatio...The CRISPR/Cas9 technology is evolved from a type II bacterial immune system and represents a new generation of targeted genome editing technology that can be applied to nearly all organisms. Site-specific modification is achieved by a single guide RNA(usually about 20nucleotides) that is complementary to a target gene or locus and is anchored by a protospaceradjacent motif. Cas9 nuclease then cleaves the targeted DNA to generate double-strand breaks(DSBs), which are subsequently repaired by non-homologous end joining(NHEJ) or homology-directed repair(HDR) mechanisms. NHEJ may introduce indels that cause frame shift mutations and hence the disruption of gene functions. When combined with double or multiplex guide RNA design, NHEJ may also introduce targeted chromosome deletions,whereas HDR can be engineered for target gene correction, gene replacement, and gene knock-in. In this review, we briefly survey the history of the CRISPR/Cas9 system invention and its genome-editing mechanism. We also describe the most recent innovation of the CRISPR/Cas9 technology, particularly the broad applications of modified Cas9 variants, and discuss the potential of this system for targeted genome editing and modification for crop improvement.展开更多
In the past decade we witnessed a revolutionary development of wheat genomics and functional genomics, thanks to the development of next generation sequencing (NSG) technology.Wheat, as one of the most important crops...In the past decade we witnessed a revolutionary development of wheat genomics and functional genomics, thanks to the development of next generation sequencing (NSG) technology.Wheat, as one of the most important crops in China and the world and with a huge, repetitive, and polyploid genome,was unconquerable in the past and is now catching up with other crops due to the availability of an increasing number of resources and platforms.Wheat researchers in China have worked unostentatiously during the last decade after The National High Technology Research and Development Program of China first set up the wheat functional genomics program in 2005. Since then many papers on wheat were published in a wide range of international journals demonstrating significant progress in wheat functional genomics.展开更多
Bread wheat is not only an important cereal crop but also a model for study of an allopolyploid plant with a large, highly repetitive genome. Advances in next-generation sequencing(NGS) technology provide needed throu...Bread wheat is not only an important cereal crop but also a model for study of an allopolyploid plant with a large, highly repetitive genome. Advances in next-generation sequencing(NGS) technology provide needed throughput to conquer the enormous size of the wheat genome. Multiple high quality reference genome sequences will soon be available. Full-scale wheat functional genomics studies are dawning. In this review we highlight the available tools and methodologies for wheat functional genomics research developed with the assistance of NGS technology and recent progress, particularly the concerted effort in generating multiple reference genomes, strategies to attain genome-wide genetic variation, genome-wide association studies, mutant population generation, and NGS-supported gene cloning and functional characterization. These resources and platforms lay a solid foundation for wheat research, leading to a new era of wheat functional genomics that will bridge the gap between genotype and phenotype.Dissection of wheat genomes and gene functions should assist in genomics-assisted selection and facilitate breeding of elite varieties for sustainable agriculture in China and the world.展开更多
Hexaploid wheat has triplicated homoeologs for most of the genes that are located in subgenomes A, B, and D. GASR7, a member of the Snakin/GASA gene family, has been associated with grain length development in wheat. ...Hexaploid wheat has triplicated homoeologs for most of the genes that are located in subgenomes A, B, and D. GASR7, a member of the Snakin/GASA gene family, has been associated with grain length development in wheat. However, little is known about divergence of its homoeolog expression in wheat polyploids. We studied the expression patterns of the GASR7 homoeologs in immature seeds in a synthetic hexaploid wheat line whose kernels are slender like those of its maternal parent(Triticum turgidum, AABB, PI 94655) in contrast to the round seed shape of its paternal progenitor(Aegilops tauschii, DD, AS2404). We found that the B homoeolog of GASR7 was the main contributor to the total expression level of this gene in both the maternal tetraploid progenitor and the hexaploid progeny, whereas the expression levels of the A and D homoeologs were much lower. To understand possible mechanisms regulating different GASR7 homoeologs, we firstly analyzed the promoter sequences of three homoeologous genes and found that all of them contained gibberellic acid(GA) response elements, with the TaG ASR7 B promoter(pT aG ASR7B) uniquely characterized by an additional predicted transcriptional enhancer. This was confirmed by the GA treatment of spikes where all three homoeologs were induced, with a much stronger response for TaG ASR7 B. McrB C enzyme assays showed that the methylation status at pT aG ASR7 D was increased during allohexaploidization, consistent with the repressed expression of TaG ASR7 D. For pT aG ASR7 A, the distribution of repetitive sequence-derived 24-nucleotide(nt) small interfering RNAs(siR NAs) were found which suggests possible epigenetic regulation because 24-nt siR NAs are known to mediate RNA-dependent DNA methylation. Our results thus indicate that both genetic and epigenetic mechanisms may be involved in the divergence of GASR7 homoeolog expression in polyploid wheat.展开更多
The Q gene in common wheat encodes an APETALA2(AP2) transcription factor that causes the free threshing attribute. Wheat spikelets bearing several florets are subtended by a pair of soft glumes that allow free liberat...The Q gene in common wheat encodes an APETALA2(AP2) transcription factor that causes the free threshing attribute. Wheat spikelets bearing several florets are subtended by a pair of soft glumes that allow free liberation of seeds. In wild species, the glumes are tough and rigid,making threshing difficult. However, the nature of these "soft glumes", caused by the domestication allele Q is not clear. Here, we found that over expression of Q in common wheat leads to homeotic florets at glume positions. We provide phenotypic, microscopy, and marker genes evidence to demonstrate that the soft glumes of common wheat are in fact lemma-like organs, or so-called sterile-lemmas. By comparing the structures subtending spikelets in wheat and other crops such as rice and maize, we found that AP2 genes may play conserved functions in grasses by manipulating vestigial structures, such as floret-derived soft glumes in wheat and empty glumes in rice. Conversion of these seemingly vegetative organs to reproductive organs may be useful in yield improvement of crop species.展开更多
Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology ...Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here,we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST,synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. WheatGene is available at http://wheatgene.agrinome.org.展开更多
In recent years, wheat yield per hectare appears to have reached a plateau, leading to concerns for future food security with an increasing world population. Since its invention, synthetic hexaploid wheat （SHW） has ...In recent years, wheat yield per hectare appears to have reached a plateau, leading to concerns for future food security with an increasing world population. Since its invention, synthetic hexaploid wheat （SHW） has been shown to be an effective genetic resource for transferring agronomically important genes from wild relatives to common wheat. It provides new sources for yield potential, drought tolerance, disease resistance, and nutrient-use efficiency when bred conventionally with modern wheat varieties. SHW is becoming more and more important for modern wheat breeding. Here, we review the current status of SHW generation, study, and application, with a particular focus on its contribution to wheat breeding. We also briefly introduce the most recent progress in our understanding of the molecular mechanisms for growth vigor in SHW. Advances in new technologies have made the complete wheat reference genome available, which offers a promising future for the study and applications of SHW in wheat improvement that are essential to meet global food demand.展开更多
Multicoloured languages play an irreplaceable role in the whole world as a useful communication tool. With the development of technology and science, varieties of languages have an ideal prospective tendency to evolut...Multicoloured languages play an irreplaceable role in the whole world as a useful communication tool. With the development of technology and science, varieties of languages have an ideal prospective tendency to evolution during the long and wonderful history. Will they be thriving or decaying? To begin with, aimed to gain general tendency about the quantity of languages' speakers, we employ the Grey prediction to capture associative curve which can be seen in Figure 1. From the trend of this vivid figure, we not only can come to the conclusion that the number of English and Chinese users tend to increase but also find that Spanish development will reach the period of stagnation. Secondly, for further improvement, we take birth rate, death rate, economic factors and the immigration into consideration and establish the language communication model. This model is deduced from the population prediction model and virus transmission model. After data normalization, the eventual curve indicates that current top-ten languages seem to be replaced by other languages. This transformation phenomenon also occurs among such top-ten languages. For instance, Hindustani will replace Spanish in the future when seen from Table 1. What's more, after predicting the migration pattern, we can draw the conclusion that some range of languages' dissemination has obvious change. As show in vivid Figure 14, we know English will popularize widely among neighboring countries such as Canada, Mexico, Cuba and Russia. Moreover, with regard to how to manage international offices' quantity and locations in the world, we construct the efficiency model with combination of the Bayes' probability theory and Fussy comprehensive assessment. As a result, we obtain 9 optimal plans to establish the international offices. Intelligible result is showed in Table 4 and Table 5. In short, our model is reasonable and feasible, which can accommodate to different situation.展开更多
The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding programs.In this study,we used a multi-omic approach to analyze the transcripto...The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding programs.In this study,we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages,revealing co-ordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition.We constructed a core transcriptional regulatory network(TRN)that drives wheat spike formation and experimentally validated a multi-layer regulatorymodule involving TaSPL15,TaAGLG1,and TaFUL2.By integrating the TRN with genome-wide association studies,we identified 227 transcription factors,including 42 with known functions and 185 with unknown functions.Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time,such as TaMYC2-A1,TaMYB30-A1,and TaWRKY37-A1.Of particular interest,TaMYB30-A1,downstream of and repressed by WFzP,was found to regulate fertile spikelet number.Notably,the excellent haplotype of TaMYB30-A1,which contains a C allele at the WFzP binding site,was enriched during wheat breeding improvement in China,leading to improved agronomic traits.Finally,we constructed a free and open access Wheat Spike Multi-Omic Database(http://39.98.48.156:8800/#/).Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development,with practical value forwheat breeding.展开更多
Clustered regularly interspaced short palindromic repeats(CRISPR)-Cas systems can be engineered as programmable transcription factors to either activate(CRISPRa)or inhibit transcription.Apomixis is extremely valuable ...Clustered regularly interspaced short palindromic repeats(CRISPR)-Cas systems can be engineered as programmable transcription factors to either activate(CRISPRa)or inhibit transcription.Apomixis is extremely valuable for the seed industry in breeding clonal seeds with pure genetic backgrounds.We report here a CRISPR/dCas9-based toolkit equippedwith dCas9-VP64 andMS2-p65-HSF1 effectors that may specifically target genes with high activation capability.We explored the application of in vivo CRISPRa targeting of maize BABY BOOM2(ZmBBM2),acting as a fertilization checkpoint,as a means to engineer parthenogenesis.We detected ZmBBM2 transcripts only in egg cells but not in other maternal gametic cells.Activation of ZmBBM2 in egg cells in vivo caused maternal cell-autonomous parthenogenesis to produce haploid seeds.Our work provides a highly specific gene-activation CRISPRa technology for target cells and verifies its application for parthenogenesis induction in maize.展开更多
Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we...Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we identify a wheat TaPRR95 gene by genome-wide association studies to be associated with plant height.Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height,particularly the peduncle,with an earlier heading date.The longer peduncle is mainly caused by the increased cell elon-gation at its upper section,whilst the early heading date is accompanied by elevated expression of flow-ering genes,such as TaFT and TacO1.A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAAVAux genes for auxin signaling inpr95abad plants that may act as a regulatory mechanism to promote robust plant growth.A haplotype analysis identifies a TaPRR95-B haplotype(Hap2)to be closely associated with reduced plant height and increased thousand-grain weight.Moreover,the Hap2 frequency is higher in cultivars than that in landraces,suggesting the artifi-cial selection on the allele during wheat breeding.These findings suggest that TaPRR95 is a regulator for plant height and heading date,thereby providing an important target for wheat yield improvement.展开更多
Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement,which is still poorly understood in wheat.In this study,we exome sequenc...Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement,which is still poorly understood in wheat.In this study,we exome sequenced 287 wheat accessions that were collected in the past 100 years.Population genetics analysis identified that 6.7%of the wheat genome falls within the selective sweeps between landraces and cultivars,which harbors the genes known for yield improvement.These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected.Genome-wide association study(GWAS)identified genomic loci associated with traits for yield potential,and two underlying genes,TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-proteinγ-subunit,were located and characterized to pleiotropically regulate both plant height and grain weight.Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding.Interestingly,we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus,leading to propose a“Green Revolution”-based working model for historical wheat breeding.Collectively,our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community.展开更多
基金financial assistance provided by the High-End Foreign Expert Recruitment Program(G2022051003L)National Natural Science Foundation of China(32201878)+3 种基金Hainan Yazhou Bay Seed Lab(B21HJ0215)Agricultural Science and Technology Innovation Program of CAAS(CAASZDRW202002,CAAS-ZDRW202201)Hebei Natural Science Foundation(C2021205013)Long Mao is also a“Yellow River Delta Scholar”in Sino-Agro Experimental Station for Salt Tolerant Crops(SAESSTC),Dongying,Shandong,China.
文摘Agrobacterium tumefaciens mediated plant transformation is a versatile tool for plant genetic engineering following its discovery nearly half a century ago.Numerous modifications were made in its application to increase efficiency,especially in the recalcitrant major cereals plants.Recent breakthroughs in transformation efficiency continue its role as a mainstream technique in CRISPR/Cas-based genome editing and gene stacking.These modifications led to higher transformation frequency and lower but more stable transgene copies with the capability to revolutionize modern agriculture.In this review,we provide a brief overview of the history of Agrobacterium-mediated plant transformation and focus on the most recent progress to improve the system in both the Agrobacterium and the host recipient.A promising future for transformation in biotechnology and agriculture is predicted.
文摘In the current issue of The Crop Journal,Chen et al.[1]reports map-based cloning of a wheat gene that showed temperaturedependent pleiotropic effects on multiple traits including plant height,leaf shape,spike and grain morphology,and accordingly was named WPA1 for Wheat Plant Architecture 1.The mutant was first observed among EMS-treated plants and repeatedly appeared in multiple occasions.
文摘MicroRNAs （miRNAs） are important post-transcriptional regulators of their target genes in plants and animals, miRNAs are usually 20-24 nucleotides long. Despite their unusually small sizes, the evolutionary history of miRNA gene families seems to be similar to their protein-codingcounterparts. In contrast to the small but abundant miRNA families in the animal genomes, plants have fewer but larger miRNA gene families. Members of plant miRNA gene families are often highly similar, suggesting recent expansion via tandem gene duplication and segmental duplication events. Although many miRNA genes are conserved across plant species, the same gene family varies significantly in size and genomic organization in different species, which may cause dosage effects and spatial and temporal differences in target gene regulations. In this review, we summarize the current progress in understanding the evolution of plant miRNA gene families.
基金supported by the National Science Foundation of China(31771808)Ministry of Science and Technology(2015BAD02B0203)+1 种基金National Engineering Laboratory of Crop Molecular Breedingthe Chinese Academy of Agricultural Sciences(Y2017XM03)
文摘Single-guide RNA(sg RNA) is one of the two core components of the CRISPR(clustered regularly interspaced short palindromic repeat)/Cas(CRISPR-associated) genome-editing technology. We established an in vitro Traffic Light Reporter(TLR) system, which is designated as the same colors as traffic lights such as green, red and yellow were produced in cells. The TLR can be readily used in maize mesophyll protoplast for a quick test of promoter activity. The TLR assay indicates the variation in transcription activities of the seven Pol III promoters, from 3.4%(U6-1) to over 21.0%(U6-6). The U6-2 promoter, which was constructed to drive sg RNA expression targeting the Zm Wx1 gene, yielded mutation efficiencies ranging from 48.5% to 97.1%. Based on the reported and unpublished data, the in vitro TLR assay results were confirmed to be a readily system and may be extended to other plant species amenable to efficient genome editing via CRISPR/Cas. Our efforts provide an efficient method of identifying native Pol III-recognized promoters for RNA guide-based genome-editing systems in maize.
基金supported in part by a grant from Northern Illinois University Foundation to Long MAONational Institutes of Health(NIH)grant to Mitrick JOHNS and Long MAO(No.44-G1A62164)a grant from the National Natural Science Foundation of China for oversea young scholars to Long MAO(No.30228022).
文摘MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.
基金supported in part by the Key Transgenic Breeding Program of the Ministry of Agriculture of China(ZX2014X08009-001 and ZX2016X08009-001)the Agricultural Science and Technology Innovation Program of CAAS
文摘The CRISPR/Cas9 technology is evolved from a type II bacterial immune system and represents a new generation of targeted genome editing technology that can be applied to nearly all organisms. Site-specific modification is achieved by a single guide RNA(usually about 20nucleotides) that is complementary to a target gene or locus and is anchored by a protospaceradjacent motif. Cas9 nuclease then cleaves the targeted DNA to generate double-strand breaks(DSBs), which are subsequently repaired by non-homologous end joining(NHEJ) or homology-directed repair(HDR) mechanisms. NHEJ may introduce indels that cause frame shift mutations and hence the disruption of gene functions. When combined with double or multiplex guide RNA design, NHEJ may also introduce targeted chromosome deletions,whereas HDR can be engineered for target gene correction, gene replacement, and gene knock-in. In this review, we briefly survey the history of the CRISPR/Cas9 system invention and its genome-editing mechanism. We also describe the most recent innovation of the CRISPR/Cas9 technology, particularly the broad applications of modified Cas9 variants, and discuss the potential of this system for targeted genome editing and modification for crop improvement.
基金supported partly by the National Key R&D Program for Crop Breeding of China to L.M. (No. 2016YFD0101004)
文摘In the past decade we witnessed a revolutionary development of wheat genomics and functional genomics, thanks to the development of next generation sequencing (NSG) technology.Wheat, as one of the most important crops in China and the world and with a huge, repetitive, and polyploid genome,was unconquerable in the past and is now catching up with other crops due to the availability of an increasing number of resources and platforms.Wheat researchers in China have worked unostentatiously during the last decade after The National High Technology Research and Development Program of China first set up the wheat functional genomics program in 2005. Since then many papers on wheat were published in a wide range of international journals demonstrating significant progress in wheat functional genomics.
基金supported in part by the National Key R&D Program of China (2016YFD0101004,2016YFD0100300)
文摘Bread wheat is not only an important cereal crop but also a model for study of an allopolyploid plant with a large, highly repetitive genome. Advances in next-generation sequencing(NGS) technology provide needed throughput to conquer the enormous size of the wheat genome. Multiple high quality reference genome sequences will soon be available. Full-scale wheat functional genomics studies are dawning. In this review we highlight the available tools and methodologies for wheat functional genomics research developed with the assistance of NGS technology and recent progress, particularly the concerted effort in generating multiple reference genomes, strategies to attain genome-wide genetic variation, genome-wide association studies, mutant population generation, and NGS-supported gene cloning and functional characterization. These resources and platforms lay a solid foundation for wheat research, leading to a new era of wheat functional genomics that will bridge the gap between genotype and phenotype.Dissection of wheat genomes and gene functions should assist in genomics-assisted selection and facilitate breeding of elite varieties for sustainable agriculture in China and the world.
基金supported by the Chinese National Natural Science Foundation (31271716)National High Technology Research and Development Program (2012AA10A308)National Key Program on Transgenic Research (2013ZX009-001)
文摘Hexaploid wheat has triplicated homoeologs for most of the genes that are located in subgenomes A, B, and D. GASR7, a member of the Snakin/GASA gene family, has been associated with grain length development in wheat. However, little is known about divergence of its homoeolog expression in wheat polyploids. We studied the expression patterns of the GASR7 homoeologs in immature seeds in a synthetic hexaploid wheat line whose kernels are slender like those of its maternal parent(Triticum turgidum, AABB, PI 94655) in contrast to the round seed shape of its paternal progenitor(Aegilops tauschii, DD, AS2404). We found that the B homoeolog of GASR7 was the main contributor to the total expression level of this gene in both the maternal tetraploid progenitor and the hexaploid progeny, whereas the expression levels of the A and D homoeologs were much lower. To understand possible mechanisms regulating different GASR7 homoeologs, we firstly analyzed the promoter sequences of three homoeologous genes and found that all of them contained gibberellic acid(GA) response elements, with the TaG ASR7 B promoter(pT aG ASR7B) uniquely characterized by an additional predicted transcriptional enhancer. This was confirmed by the GA treatment of spikes where all three homoeologs were induced, with a much stronger response for TaG ASR7 B. McrB C enzyme assays showed that the methylation status at pT aG ASR7 D was increased during allohexaploidization, consistent with the repressed expression of TaG ASR7 D. For pT aG ASR7 A, the distribution of repetitive sequence-derived 24-nucleotide(nt) small interfering RNAs(siR NAs) were found which suggests possible epigenetic regulation because 24-nt siR NAs are known to mediate RNA-dependent DNA methylation. Our results thus indicate that both genetic and epigenetic mechanisms may be involved in the divergence of GASR7 homoeolog expression in polyploid wheat.
基金supported by the National Key Program for Transgenic Crop Cultivation (2016ZX09001-001)The CAAS Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission (CAAS-XTCX2016)
文摘The Q gene in common wheat encodes an APETALA2(AP2) transcription factor that causes the free threshing attribute. Wheat spikelets bearing several florets are subtended by a pair of soft glumes that allow free liberation of seeds. In wild species, the glumes are tough and rigid,making threshing difficult. However, the nature of these "soft glumes", caused by the domestication allele Q is not clear. Here, we found that over expression of Q in common wheat leads to homeotic florets at glume positions. We provide phenotypic, microscopy, and marker genes evidence to demonstrate that the soft glumes of common wheat are in fact lemma-like organs, or so-called sterile-lemmas. By comparing the structures subtending spikelets in wheat and other crops such as rice and maize, we found that AP2 genes may play conserved functions in grasses by manipulating vestigial structures, such as floret-derived soft glumes in wheat and empty glumes in rice. Conversion of these seemingly vegetative organs to reproductive organs may be useful in yield improvement of crop species.
基金financially supported by National Key Research and Development Program of China (2016YFD0101004)Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciencessupported by the Chinese Government Scholarship。
文摘Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here,we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST,synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. WheatGene is available at http://wheatgene.agrinome.org.
基金The work related to synthetic wheat is supported by National Natural Science Foundation of China （31661143007 and 31571665） and the Major Breeding Program from Ministry of Science and Technology of China （2016YFD0101004 and 2016YFD0102002）.
文摘In recent years, wheat yield per hectare appears to have reached a plateau, leading to concerns for future food security with an increasing world population. Since its invention, synthetic hexaploid wheat （SHW） has been shown to be an effective genetic resource for transferring agronomically important genes from wild relatives to common wheat. It provides new sources for yield potential, drought tolerance, disease resistance, and nutrient-use efficiency when bred conventionally with modern wheat varieties. SHW is becoming more and more important for modern wheat breeding. Here, we review the current status of SHW generation, study, and application, with a particular focus on its contribution to wheat breeding. We also briefly introduce the most recent progress in our understanding of the molecular mechanisms for growth vigor in SHW. Advances in new technologies have made the complete wheat reference genome available, which offers a promising future for the study and applications of SHW in wheat improvement that are essential to meet global food demand.
文摘Multicoloured languages play an irreplaceable role in the whole world as a useful communication tool. With the development of technology and science, varieties of languages have an ideal prospective tendency to evolution during the long and wonderful history. Will they be thriving or decaying? To begin with, aimed to gain general tendency about the quantity of languages' speakers, we employ the Grey prediction to capture associative curve which can be seen in Figure 1. From the trend of this vivid figure, we not only can come to the conclusion that the number of English and Chinese users tend to increase but also find that Spanish development will reach the period of stagnation. Secondly, for further improvement, we take birth rate, death rate, economic factors and the immigration into consideration and establish the language communication model. This model is deduced from the population prediction model and virus transmission model. After data normalization, the eventual curve indicates that current top-ten languages seem to be replaced by other languages. This transformation phenomenon also occurs among such top-ten languages. For instance, Hindustani will replace Spanish in the future when seen from Table 1. What's more, after predicting the migration pattern, we can draw the conclusion that some range of languages' dissemination has obvious change. As show in vivid Figure 14, we know English will popularize widely among neighboring countries such as Canada, Mexico, Cuba and Russia. Moreover, with regard to how to manage international offices' quantity and locations in the world, we construct the efficiency model with combination of the Bayes' probability theory and Fussy comprehensive assessment. As a result, we obtain 9 optimal plans to establish the international offices. Intelligible result is showed in Table 4 and Table 5. In short, our model is reasonable and feasible, which can accommodate to different situation.
基金supported by the National Natural Science Foundation of China(31921005)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24010204)+1 种基金the National Key Research and Development Program of China(2021YFD1201500)the Major Basic Research Program of Shandong Natural Science Foundation of China(ZR2019ZD15).
文摘The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding programs.In this study,we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages,revealing co-ordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition.We constructed a core transcriptional regulatory network(TRN)that drives wheat spike formation and experimentally validated a multi-layer regulatorymodule involving TaSPL15,TaAGLG1,and TaFUL2.By integrating the TRN with genome-wide association studies,we identified 227 transcription factors,including 42 with known functions and 185 with unknown functions.Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time,such as TaMYC2-A1,TaMYB30-A1,and TaWRKY37-A1.Of particular interest,TaMYB30-A1,downstream of and repressed by WFzP,was found to regulate fertile spikelet number.Notably,the excellent haplotype of TaMYB30-A1,which contains a C allele at the WFzP binding site,was enriched during wheat breeding improvement in China,leading to improved agronomic traits.Finally,we constructed a free and open access Wheat Spike Multi-Omic Database(http://39.98.48.156:8800/#/).Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development,with practical value forwheat breeding.
基金supported by the National Science Foundation of China(32001551 and 31771808)the China Postdoctoral Science Foundation(2020M680779)+1 种基金the Agricultural Science and Technology Innovation Program of the CAAS(S2022ZD03)Hainan Yazhou Bay Seed Laboratory(B21HJ0215).
文摘Clustered regularly interspaced short palindromic repeats(CRISPR)-Cas systems can be engineered as programmable transcription factors to either activate(CRISPRa)or inhibit transcription.Apomixis is extremely valuable for the seed industry in breeding clonal seeds with pure genetic backgrounds.We report here a CRISPR/dCas9-based toolkit equippedwith dCas9-VP64 andMS2-p65-HSF1 effectors that may specifically target genes with high activation capability.We explored the application of in vivo CRISPRa targeting of maize BABY BOOM2(ZmBBM2),acting as a fertilization checkpoint,as a means to engineer parthenogenesis.We detected ZmBBM2 transcripts only in egg cells but not in other maternal gametic cells.Activation of ZmBBM2 in egg cells in vivo caused maternal cell-autonomous parthenogenesis to produce haploid seeds.Our work provides a highly specific gene-activation CRISPRa technology for target cells and verifies its application for parthenogenesis induction in maize.
基金We are grateful for the funding from STI 2030-Major Projects(2023ZD0406802)the National Natural Science Foundation of China(32072066,32172050,3220151460)+2 种基金Hainan Yazhou Bay Seed Lab(B21HJ0215)CAAS Agricultural Science and Technology Innovation Program(CAAS-ZDRW202002,CAAS-ZDRW202201)Hebei Natural Science Foundation(C2021205013).
文摘Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we identify a wheat TaPRR95 gene by genome-wide association studies to be associated with plant height.Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height,particularly the peduncle,with an earlier heading date.The longer peduncle is mainly caused by the increased cell elon-gation at its upper section,whilst the early heading date is accompanied by elevated expression of flow-ering genes,such as TaFT and TacO1.A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAAVAux genes for auxin signaling inpr95abad plants that may act as a regulatory mechanism to promote robust plant growth.A haplotype analysis identifies a TaPRR95-B haplotype(Hap2)to be closely associated with reduced plant height and increased thousand-grain weight.Moreover,the Hap2 frequency is higher in cultivars than that in landraces,suggesting the artifi-cial selection on the allele during wheat breeding.These findings suggest that TaPRR95 is a regulator for plant height and heading date,thereby providing an important target for wheat yield improvement.
基金We acknowledge the financial support from the National Key Research and Development Program of China(2016YFD0101004,2016YFD0100300)National Natural Science Foundation of China(31830982,91731305,31661143007)CAAS Agricultural Science and Technology Innovation Program,China(CAAS-ZDRW202002).We thank the bioinformatics facility at the Institute of Crop Science,CAAS,China for providing the computing support.
文摘Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement,which is still poorly understood in wheat.In this study,we exome sequenced 287 wheat accessions that were collected in the past 100 years.Population genetics analysis identified that 6.7%of the wheat genome falls within the selective sweeps between landraces and cultivars,which harbors the genes known for yield improvement.These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected.Genome-wide association study(GWAS)identified genomic loci associated with traits for yield potential,and two underlying genes,TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-proteinγ-subunit,were located and characterized to pleiotropically regulate both plant height and grain weight.Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding.Interestingly,we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus,leading to propose a“Green Revolution”-based working model for historical wheat breeding.Collectively,our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community.
