Aegilops speltoides,the closest ancestor of the wheat B subgenome,has been well studied genomically.However,the epigenetic landscape of Ae.speltoides and the effects of epigenetics on its growth and development remain...Aegilops speltoides,the closest ancestor of the wheat B subgenome,has been well studied genomically.However,the epigenetic landscape of Ae.speltoides and the effects of epigenetics on its growth and development remain poorly understood.Here,we present a comprehensive multi-omics atlas of leaves and roots in Ae.speltoides,encompassing transcriptome,DNA methylation,histone modifications,and small RNA profiling.Divergent DNA methylation levels were detected between leaves and roots,and were associated with differences in accumulated 24-nt siRNAs.DNA methylation changes in promoters and gene bodies showed strong connections with altered expression between leaves and roots.Transcriptional regulatory networks(TRN)reconstructed between leaves and roots were driven by tissue-specific TF families.DNA methylation and histone modification act together as switches that shape root and leaf morphogenesis by modulating the binding of tissue-specific TFs to their target genes.The TRNs in leaves and roots reshaped during wheat polyploidization were associated with alterations in epigenetic modi-fications.Collectively,these results not only shed light on the critical contribution of epigenetic regulation in the morphogenesis of leaves and roots in Ae.speltoides but also provide new insights for future investigations into the complex interplay of genetic and epigenetic factors in the developmental biology of common wheat.展开更多
Bread wheat provides an essential fraction of the daily calorific intake for humanity.Due to its huge and complex genome,progress in studying on the wheat genome is substantially trailed behind those of the other two ...Bread wheat provides an essential fraction of the daily calorific intake for humanity.Due to its huge and complex genome,progress in studying on the wheat genome is substantially trailed behind those of the other two major crops,rice and maize,for at least a decade.With rapid advances in genome assembling and reduced cost of high-throughput sequencing,emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research.Here,we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome.New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress,genomic variations at multiple scales contributing to the diversity of wheat germplasm,and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat.Genomics databases and bioinformatics tools meeting the urgent needs of wheat ge-nomics research are also summarized.The ever-increasing omics data,along with advanced tools and well-structured databases,are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.展开更多
The MADS-box gene plays an important role in regulating plant growth and development.In this study,a SEP3-like MADS-box gene TaSEP3-1 was isolated from bread wheat.The expression patterns of the three homoeologs TaSEP...The MADS-box gene plays an important role in regulating plant growth and development.In this study,a SEP3-like MADS-box gene TaSEP3-1 was isolated from bread wheat.The expression patterns of the three homoeologs TaSEP3-A1,TaSEP3-B1,and TaSEP3-D1 were similar,and higher expression levels were detected in floral organs and developing kernels.TaSEP3-D1 was located in the nucleus and cytoplasm and possessed transactivation activity in yeast.Homoeolog sequence polymorphism analysis identified four,three,and four haplotypes of TaSEP3-A1,TaSEP3-B1,and TaSEP3-D1,respectively,and the haplotypes of TaSEP3-D1 had larger effects on agronomic traits than those of TaSEP3-A1 and TaSEP3-B1.D1_h4,significantly associated with heading date,plant height,and other yield-related traits,was the favored haplotype of TaSEP3-D1.Transgenic wheat genotypes overexpressing TaSEP3-D1 exhibited delayed heading and reduced plant height,indicating a role in regulating heading date and plant development.These results shed light on the role of TaSEP3-D1 in wheat plant development.The favored haplotype of TaSEP3-D1 can be applied in breeding to improve plant architecture and yield in wheat.展开更多
Grain size is one of the determinants of grain yield,and identifying the genetic loci that control grain size will be helpful for increasing grain yield.In our previous study,a quantitative trait locus(QTL)for grain l...Grain size is one of the determinants of grain yield,and identifying the genetic loci that control grain size will be helpful for increasing grain yield.In our previous study,a quantitative trait locus(QTL)for grain length(GL),QGl.cau-2D.1,was identified from an F2 population developed from the cross between the natural(TAA10)and synthetic(XX329)allohexaploid wheat.In the present study,we mainly fine mapped and validated its genetic effects.To this end,multiple near-isogenic lines(NILs)were obtained through marker-assisted selection with TAA10 as the recurrent parent.The secondary populations derived from 25 heterozygous recombinants were used for fine mapping of QGl.cau-2D.1,and the allele from XX329 significantly increased GL,thousand-grain weight(TGW),total spikelet number per spike(TSN)and spike compactness(SC).Using NILs for XX329(2D+)and TAA10(2D−),we determined the genetic and pleiotropic effects of QGl.cau-2D.1.The target sequences were aligned with the wheat reference genome RefSeq v2.1 and spanned an~0.9 Mb genomic region.TraesCS2D03G0114900(ortholog of Os03g0594700)was predicted as the candidate gene based on whole-genome re-sequencing and expression analyses.In summary,the map-based cloning of QGl.cau-2D.1 will be useful for improving grain weight with enhanced GL and TSN.展开更多
A complete reference genome assembly is crucial for biological research and genetic improvement. Owing to its large size and highly repetitive nature, there are numerous gaps in the globally used wheat Chinese Spring ...A complete reference genome assembly is crucial for biological research and genetic improvement. Owing to its large size and highly repetitive nature, there are numerous gaps in the globally used wheat Chinese Spring (CS) genome assembly. In this study, we generated a 14.46 Gb near-complete assembly of the CS genome, with a contig N50 of over 266 Mb and an overall base accuracy of 99.9963%. Among the 290 gaps that remained (26, 257, and 7 gaps from the A, B, and D subgenomes, respectively), 278 were extremely high-copy tandem repeats, whereas the remaining 12 were transposable-element-associated gaps. Four chromosome assemblies were completely gap-free, including chr1D, chr3D, chr4D, and chr5D. Extensive annotation of the near-complete genome revealed 151 405 high-confidence genes, of which 59 180 were newly annotated, including 7602 newly assembled genes. Except for the centromere of chr1B, which has a gap associated with superlong GAA repeat arrays, the centromeric sequences of all of the remaining 20 chromosomes were completely assembled. Our near-complete assembly revealed that the extent of tandem repeats, such as simple-sequence repeats, was highly uneven among different subgenomes. Similarly, the repeat compositions of the centromeres also varied among the three subgenomes. With the genome sequences of all six types of seed storage proteins (SSPs) fully assembled, the expression of ω-gliadin was found to be contributed entirely by the B subgenome, whereas the expression of the other five types of SSPs was most abundant from the D subgenome. The near-complete CS genome will serve as a valuable resource for genomic and functional genomic research and breeding of wheat as well as its related species.展开更多
The introduction of Reduced height(Rht)genes into wheat varieties has been pivotal in developing semidwarf plant architectures,significantly improving lodging resistance and harvest indices.Therefore,identifying new R...The introduction of Reduced height(Rht)genes into wheat varieties has been pivotal in developing semidwarf plant architectures,significantly improving lodging resistance and harvest indices.Therefore,identifying new Rht gene resources for breeding semi-dwarf wheat cultivars has been a key strategy for ensuring high and stable grain yields since the 1960s.In this study,we report the map-based cloning of TaERF-A1,which encodes an AP2/ERF(APETALA2/ethylene responsive factor)transcription factor that acts as a positive regulator of wheat stem elongation,as a novel gene that regulates plant height and spike length.The natural variant,TaERF-A1^(JD6),features a Phe(derived from’Nongda3338’)to Ser(derived from’Jingdong6’)substitution at position 178,which significantly reduces the stability of the TaERF-A1 protein.This substitution leads to partially attenuated transcriptional activation of downstream target genes,including TaPIF4(Triticum aestivum Phytochrome Interacting Factor 4),thereby restricting stem and spike elongation.Importantly,the introgression of the semi-dwarfing allele TaERF-A1^(JD6)into wheat can significantly enhance lodging resistance,particularly in dense cropping systems.Therefore,our study identifies TaERF-A1^(JD6)as a new Rht gene resource for breeding semi-dwarf wheat varieties with increased yield stability.展开更多
Nitrogen fertilization has increased wheat yields since the Green Revolution,but these gains have plateaued.Excessive nitrogen application reduces nitrogen use efficiency by promoting nonproductive tillers,and balanci...Nitrogen fertilization has increased wheat yields since the Green Revolution,but these gains have plateaued.Excessive nitrogen application reduces nitrogen use efficiency by promoting nonproductive tillers,and balancing nitrogen uptake with tillering in wheat remains a challenge.Here,we demonstrate that TaNLP3 is a master regulator of nitrate signaling that,together with the SWl/SNF complex,regulates chromatin accessibility to fine-tune nitrate uptake and tiller formation through a temporal transcriptional cascade.In short-term nitrate signaling,TaNLP3 activates the expression of primary nitrate response genes,including TaNRT2.1,to promote nitrate uptake.In long-term nitrate signaling,TaLBD38 is induced by TaNLP3 and represses TaNRT2.1,limiting nitrate uptake and promoting tillering by inhibiting TaCKX4/5,negative modulators of tillering.Furthermore,we identified elite haplotypes of TaNLP3-3B,TaLBD38-4A,andTaNRT2.1-6B4 that enable higher yields under equivalent nitrogen supply.Taken together,our findings reveal the dynamic coordination between nitrate uptake and tillering under fluctuating nitrogen conditions,offering valuable resources for breeding wheat varieties with improved nitrogen use efficiency and productivity.展开更多
To the Editor:Diabetes mellitus(DM)is a chronic disease that endangers human health and can lead to different complications.[1]Coronary artery,disease is one of the most serious complications in DM patients.
基金supported by the National Key Research and Development Program of China(2023YFD1200403).
文摘Aegilops speltoides,the closest ancestor of the wheat B subgenome,has been well studied genomically.However,the epigenetic landscape of Ae.speltoides and the effects of epigenetics on its growth and development remain poorly understood.Here,we present a comprehensive multi-omics atlas of leaves and roots in Ae.speltoides,encompassing transcriptome,DNA methylation,histone modifications,and small RNA profiling.Divergent DNA methylation levels were detected between leaves and roots,and were associated with differences in accumulated 24-nt siRNAs.DNA methylation changes in promoters and gene bodies showed strong connections with altered expression between leaves and roots.Transcriptional regulatory networks(TRN)reconstructed between leaves and roots were driven by tissue-specific TF families.DNA methylation and histone modification act together as switches that shape root and leaf morphogenesis by modulating the binding of tissue-specific TFs to their target genes.The TRNs in leaves and roots reshaped during wheat polyploidization were associated with alterations in epigenetic modi-fications.Collectively,these results not only shed light on the critical contribution of epigenetic regulation in the morphogenesis of leaves and roots in Ae.speltoides but also provide new insights for future investigations into the complex interplay of genetic and epigenetic factors in the developmental biology of common wheat.
基金supported by the National Natural Science Foundation of China(32272124,31991210)and the 2115 Talent Development Program.
文摘Bread wheat provides an essential fraction of the daily calorific intake for humanity.Due to its huge and complex genome,progress in studying on the wheat genome is substantially trailed behind those of the other two major crops,rice and maize,for at least a decade.With rapid advances in genome assembling and reduced cost of high-throughput sequencing,emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research.Here,we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome.New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress,genomic variations at multiple scales contributing to the diversity of wheat germplasm,and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat.Genomics databases and bioinformatics tools meeting the urgent needs of wheat ge-nomics research are also summarized.The ever-increasing omics data,along with advanced tools and well-structured databases,are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
基金funded by the Basic Scientific Research Project of Chinese Academy of Agricultural Sciences (Y2019XK10)the National Key Research and Development Program of China (2016YFD0100102, 2016YFD0100302)。
文摘The MADS-box gene plays an important role in regulating plant growth and development.In this study,a SEP3-like MADS-box gene TaSEP3-1 was isolated from bread wheat.The expression patterns of the three homoeologs TaSEP3-A1,TaSEP3-B1,and TaSEP3-D1 were similar,and higher expression levels were detected in floral organs and developing kernels.TaSEP3-D1 was located in the nucleus and cytoplasm and possessed transactivation activity in yeast.Homoeolog sequence polymorphism analysis identified four,three,and four haplotypes of TaSEP3-A1,TaSEP3-B1,and TaSEP3-D1,respectively,and the haplotypes of TaSEP3-D1 had larger effects on agronomic traits than those of TaSEP3-A1 and TaSEP3-B1.D1_h4,significantly associated with heading date,plant height,and other yield-related traits,was the favored haplotype of TaSEP3-D1.Transgenic wheat genotypes overexpressing TaSEP3-D1 exhibited delayed heading and reduced plant height,indicating a role in regulating heading date and plant development.These results shed light on the role of TaSEP3-D1 in wheat plant development.The favored haplotype of TaSEP3-D1 can be applied in breeding to improve plant architecture and yield in wheat.
基金supported by the National Key Research and Development Program of China(32172069).
文摘Grain size is one of the determinants of grain yield,and identifying the genetic loci that control grain size will be helpful for increasing grain yield.In our previous study,a quantitative trait locus(QTL)for grain length(GL),QGl.cau-2D.1,was identified from an F2 population developed from the cross between the natural(TAA10)and synthetic(XX329)allohexaploid wheat.In the present study,we mainly fine mapped and validated its genetic effects.To this end,multiple near-isogenic lines(NILs)were obtained through marker-assisted selection with TAA10 as the recurrent parent.The secondary populations derived from 25 heterozygous recombinants were used for fine mapping of QGl.cau-2D.1,and the allele from XX329 significantly increased GL,thousand-grain weight(TGW),total spikelet number per spike(TSN)and spike compactness(SC).Using NILs for XX329(2D+)and TAA10(2D−),we determined the genetic and pleiotropic effects of QGl.cau-2D.1.The target sequences were aligned with the wheat reference genome RefSeq v2.1 and spanned an~0.9 Mb genomic region.TraesCS2D03G0114900(ortholog of Os03g0594700)was predicted as the candidate gene based on whole-genome re-sequencing and expression analyses.In summary,the map-based cloning of QGl.cau-2D.1 will be useful for improving grain weight with enhanced GL and TSN.
基金supported by the National Key Research and Development Program of China(2023YFF1000100)the National Natural Science Foundation of China(31991210,31921005,32020103004,and 32225038)+2 种基金the Pinduoduo-China Agricultural University Research Fund(PC2023A01004)the New Cornerstone Investigation Program(NCI202234)the 2115 Talent Development Program of China Agricultural University.
文摘A complete reference genome assembly is crucial for biological research and genetic improvement. Owing to its large size and highly repetitive nature, there are numerous gaps in the globally used wheat Chinese Spring (CS) genome assembly. In this study, we generated a 14.46 Gb near-complete assembly of the CS genome, with a contig N50 of over 266 Mb and an overall base accuracy of 99.9963%. Among the 290 gaps that remained (26, 257, and 7 gaps from the A, B, and D subgenomes, respectively), 278 were extremely high-copy tandem repeats, whereas the remaining 12 were transposable-element-associated gaps. Four chromosome assemblies were completely gap-free, including chr1D, chr3D, chr4D, and chr5D. Extensive annotation of the near-complete genome revealed 151 405 high-confidence genes, of which 59 180 were newly annotated, including 7602 newly assembled genes. Except for the centromere of chr1B, which has a gap associated with superlong GAA repeat arrays, the centromeric sequences of all of the remaining 20 chromosomes were completely assembled. Our near-complete assembly revealed that the extent of tandem repeats, such as simple-sequence repeats, was highly uneven among different subgenomes. Similarly, the repeat compositions of the centromeres also varied among the three subgenomes. With the genome sequences of all six types of seed storage proteins (SSPs) fully assembled, the expression of ω-gliadin was found to be contributed entirely by the B subgenome, whereas the expression of the other five types of SSPs was most abundant from the D subgenome. The near-complete CS genome will serve as a valuable resource for genomic and functional genomic research and breeding of wheat as well as its related species.
基金supported by grants from the National Natural Science Foundation of China(32101767 to L.C.and 31991210 to Q.S.)the Hainan Yazhou Bay Seed Laboratory(B21HJ0111 to Z.N.)the Pinduoduo-China Agricultural University Research Fund(PC2023A01003 to Z.N.).
文摘The introduction of Reduced height(Rht)genes into wheat varieties has been pivotal in developing semidwarf plant architectures,significantly improving lodging resistance and harvest indices.Therefore,identifying new Rht gene resources for breeding semi-dwarf wheat cultivars has been a key strategy for ensuring high and stable grain yields since the 1960s.In this study,we report the map-based cloning of TaERF-A1,which encodes an AP2/ERF(APETALA2/ethylene responsive factor)transcription factor that acts as a positive regulator of wheat stem elongation,as a novel gene that regulates plant height and spike length.The natural variant,TaERF-A1^(JD6),features a Phe(derived from’Nongda3338’)to Ser(derived from’Jingdong6’)substitution at position 178,which significantly reduces the stability of the TaERF-A1 protein.This substitution leads to partially attenuated transcriptional activation of downstream target genes,including TaPIF4(Triticum aestivum Phytochrome Interacting Factor 4),thereby restricting stem and spike elongation.Importantly,the introgression of the semi-dwarfing allele TaERF-A1^(JD6)into wheat can significantly enhance lodging resistance,particularly in dense cropping systems.Therefore,our study identifies TaERF-A1^(JD6)as a new Rht gene resource for breeding semi-dwarf wheat varieties with increased yield stability.
基金supported by the National Natural Science Foundation of China(nos.32572386 and U22A6009)the Hebei Key Science and Technology Support Program(242Q9911Z)+3 种基金the Guiding Special Fund for Central Universities to Build World-Class Universities(Disciplines)and Promote Characteristic Development(2025AC030)the National Key Research and Development Program of China(no.2023YFF1000601)the Chinese Universities Scientific Fund(no.2025TC135)the Agricultural Science and Technology Major Project.
文摘Nitrogen fertilization has increased wheat yields since the Green Revolution,but these gains have plateaued.Excessive nitrogen application reduces nitrogen use efficiency by promoting nonproductive tillers,and balancing nitrogen uptake with tillering in wheat remains a challenge.Here,we demonstrate that TaNLP3 is a master regulator of nitrate signaling that,together with the SWl/SNF complex,regulates chromatin accessibility to fine-tune nitrate uptake and tiller formation through a temporal transcriptional cascade.In short-term nitrate signaling,TaNLP3 activates the expression of primary nitrate response genes,including TaNRT2.1,to promote nitrate uptake.In long-term nitrate signaling,TaLBD38 is induced by TaNLP3 and represses TaNRT2.1,limiting nitrate uptake and promoting tillering by inhibiting TaCKX4/5,negative modulators of tillering.Furthermore,we identified elite haplotypes of TaNLP3-3B,TaLBD38-4A,andTaNRT2.1-6B4 that enable higher yields under equivalent nitrogen supply.Taken together,our findings reveal the dynamic coordination between nitrate uptake and tillering under fluctuating nitrogen conditions,offering valuable resources for breeding wheat varieties with improved nitrogen use efficiency and productivity.
基金National Natural Science Foundation of China(Nos. 81770331, 82000317, and 81500249)Top Talent Support Program for Young and Middle-aged People of Wuxi Health Committee(No. BJ2020018)Research Foundation from Wuxi Health Commission for the Youth(No. Q202034)。
文摘To the Editor:Diabetes mellitus(DM)is a chronic disease that endangers human health and can lead to different complications.[1]Coronary artery,disease is one of the most serious complications in DM patients.
