Allelic diversity in the wild grass Aegilops tauschii is vastly greater than that in the D genome of common wheat(Triticum aestivum), of which Ae. tauschii is the source. Since the 1980 s,there have been numerous effo...Allelic diversity in the wild grass Aegilops tauschii is vastly greater than that in the D genome of common wheat(Triticum aestivum), of which Ae. tauschii is the source. Since the 1980 s,there have been numerous efforts to harness a much larger share of Ae. tauschii^ extensive and highly variable gene pool for wheat improvement. Those efforts have followed two distinct approaches: production of amphiploids, known as "synthetic hexaploids," between T. turgidum and Ae. tauschii,and direct hybridization between 丁. aestiuum and Ae. tauschii;both approaches then involve backcrossing to 丁. aestiuum. Both synthetic hexaploid production and direct hybridization have led to the transfer of numerous new genes into common wheat that confer improvements in many traits. This work has led to release of improved cultivars in China, the United States, and many other countries. Each approach to D-genome improvement has advantages and disadvantages. For example, production of synthetic hexaploids can incorporate useful germplasm from both T. turgidum and Ae.tauschii, thereby enhancing the A, B, and D genomes; on the other hand, direct hybridization rapidly restores the recurrent parent's A and B genomes and avoids incorporation of genes with adverse effects on threshability, hybrid necrosis, vernalization response, milling and baking quality, and other traits, which are often transferred when T. turgidum is used as a parent. Choice of method will depend in part on the type of wheat being developed and the target environment. However, more extensive use of the so-far underexploited direct hybridization approach is especially warranted.展开更多
[Objectives] The identification of salt tolerant genetic loci in rice can provide a research basis for the molecular mechanism of salt tolerance and gene resources for improving salt tolerant cultivars. [Methods] Reco...[Objectives] The identification of salt tolerant genetic loci in rice can provide a research basis for the molecular mechanism of salt tolerance and gene resources for improving salt tolerant cultivars. [Methods] Recombinant inbred lines(RILs) derived from Zhaxima, an indica landrace variety from Yunnan Province and Nanjing 46, an elite japonica variety with superior grain quality from Jiangsu Province were used. The salt tolerance at seeding stage in the RIL population was investigated as the phenotypic value. [Results] Combined with the linkage map, a total of 4 QTLs were detected: qSST-1, qSST-3, qSST-5 and qSST-11, located in rice chromosomes 1, 3, 5 and 11, respectively. All positive alleles were from the parent Nanjing 46. Three QTLs among them were not included in chromosome intervals the same as cloned rice salt tolerance genes, and thus were described as new candidate gene loci associated with seeding-stage salt tolerance. [Conclusions] This study provides important information for further exploration and utilization of new salt tolerant QTLs in rice. It is of great significance for improving the utilization of saline land in China and ensuring the stable rice production.展开更多
ChinaMu is the largest sequence-indexed Mutator(Mu)transposon insertional library in maize(Zea mays).In this study,we made significant improvements to the size and quality of the ChinaMu library.We developed a new Mu-...ChinaMu is the largest sequence-indexed Mutator(Mu)transposon insertional library in maize(Zea mays).In this study,we made significant improvements to the size and quality of the ChinaMu library.We developed a new Mu-tag isolation method Mu-Tn5-seq(MuT-seq).Compared to the previous method used by ChinaMu,MuT-seq recovered 1/3 more germinal insertions,while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time.Using MuT-seq,we identified 113,879 germinal insertions from 3,168 Mu-active F1 families.We also assembled a high-quality genome for the Mu-active line Mu-starter,which harbors the initial active MuDR element and was used as the pollen donor for the mutation population.Using the Mu-starter genome,we recovered 33,662(15.6%)additional germinal insertions in 3,244(7.4%)genes in the Mu-starter line.The Mu-starter genome also improved the assignment of 117,689(54.5%)germinal insertions.The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions.These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes,including 23,006(80.4%)core genes shared by the two genomes.As a test model,we investigated Mu insertions in the pentatricopeptide repeat(PPR)superfamily,discovering insertions for 92%(449/487)of PPR genes in ChinaMu,demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.展开更多
[Objectives]This study was conducted to enhance the salt tolerance of current rice varieties at the seedling stage and fulfill the urgent requirement for salt-tolerant rice varieties in coastal tidal flats.[Methods]Fo...[Objectives]This study was conducted to enhance the salt tolerance of current rice varieties at the seedling stage and fulfill the urgent requirement for salt-tolerant rice varieties in coastal tidal flats.[Methods]Four high-generation stable rice lines with diverse salt tolerance were employed as test materials,and four NaCl concentration gradients were established for seed soaking treatment.[Results]The seedling survival rate of line 151465 underwent significant alterations after soaking with four different salt concentrations,and the survival rate was the highest after treatment with 1.8%NaCl for 1 d,reaching 65.2%.The average survival rate of other three lines with different salt tolerance reached 62%after soaking with 1.8%NaCl for 1 d,which was significantly higher than those of the 2.2%NaCl and 0%NaCl treatments.[Conclusions]This study provides a basis for reducing the effect of abiotic stress on rice growth and development and improving the utilization rate of saline-alkali land.展开更多
When plants are exposed to hypoxic conditions,the level of g-aminobutyric acid(GABA)in plant tissues increases by several orders of magnitude.The physiological rationale behind this elevation remains largely unanswere...When plants are exposed to hypoxic conditions,the level of g-aminobutyric acid(GABA)in plant tissues increases by several orders of magnitude.The physiological rationale behind this elevation remains largely unanswered.By combining genetic and electrophysiological approach,in this work we show that hypoxia-induced increase in GABA content is essential for restoration of membrane potential and preventing ROS-induced disturbance to cytosolic K+homeostasis and Ca^(2+)signaling.We show that reduced O_(2) availability affects H+-ATPase pumping activity,leading to membrane depolarization and K+loss via outward-rectifying GORK channels.Hypoxia stress also results in H_(2)O_(2) accumulation in the cell that activates ROS-inducible Ca^(2+)uptake channels and triggers self-amplifying"ROS-Ca hub,"further exacerbating K^(+)loss via non-selective cation channels that results in the loss of the cell’s viability.Hypoxia-induced elevation in the GABA level may restore membrane potential by pH-dependent regulation of H^(+)-ATPase and/or by generating more energy through the activation of the GABA shunt pathway and TCA cycle.Elevated GABA can also provide better control of the ROS-Ca^(2+)hub by transcriptional control of RBOH genes thus preventing over-excessive H_(2)O_(2) accumulation.Finally,GABA can operate as a ligand directly controlling the open probability and conductance of K+efflux GORK channels,thus enabling plants adaptation to hypoxic conditions.展开更多
Along with rapid advances in high-throughput-sequencing technology,the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic research.Desir...Along with rapid advances in high-throughput-sequencing technology,the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic research.Desirable molecular markers should be able to rapidly genotype tens of thousands of breeding accessions with tens to hundreds of markers.In this study,we developed a multiplex molecular marker,the haplotype-tag polymorphism(HTP),that integrates Maize6H-60K array data from 3,587 maize inbred lines with 6,375 blocks from the recombination block map.After applying strict filtering criteria,we obtained 6,163 highly polymorphic HTPs,which were evenly distributed in the genome.Furthermore,we developed a genome-wide HTP analysis toolkit,HTPtools,which we used to establish an HTP database(HTPdb)covering the whole genomes of 3,587 maize inbred lines commonly used in breeding.A total of 172,921 non-redundant HTP allelic variations were obtained.Three major HTPtools modules combine seven algorithms(e.g.,chain Bayes probability and the heterotic-pattern prediction algorithm)and a new plotting engine named“BCplot”that enables rapid visualization of the background information of multiple backcross groups.HTPtools was designed for big-data analyses such as complex pedigree reconstruction and maize heterotic-pattern prediction.The HTP-based analytical strategy and the toolkit developed in this study are applicable for high-throughput genotyping and for genetic mapping,germplasm resource analyses,and genomics-informed breeding in maize.展开更多
Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic ...Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.展开更多
Maize(Zea mays)is a cereal crop of global food importance.However,the deficiency of essential amino acids,more importantly lysine,methionine and tryptophan,in the major seed storage zein proteins makes corn nutritiona...Maize(Zea mays)is a cereal crop of global food importance.However,the deficiency of essential amino acids,more importantly lysine,methionine and tryptophan,in the major seed storage zein proteins makes corn nutritionally of low value for human consumption.The idea of improving maize nutritional value prompted the search for maize natural mutants harboring low zein contents and higher amount of lysine.These studies resulted in the identification of more than dozens of maize opaque mutants in the previous few decades,o2 mutant being the most extensively studied one.However,the high lysine contents but soft kernel texture and chalky endosperm halted the widespread application and commercial success of maize opaque mutants,which ultimately paved the way for the development of Quality Protein Maize(QPM)by modifying the soft endosperm of o2 mutant into lysine-rich hard endosperm.The previous few decades have witnessed a marked progress in maize zein research.It includes elucidation of molecular mechanism underlying the role of different zein genes in seed endosperm development by cloning different components of zein family,exploring the general organization,function and evolution of zein family members within maize species and among other cereals,and elucidating the cis-and trans-regulatory elements modulating the regulation of different molecular players of maize seed endosperm development.The current advances in high quality reference genomes of maize lines B73 and Mo17 plus the completion of ongoing pan genome sequencing projects of more maize lines with NGS technologies are expected to revolutionize maize zein gene research in near future.This review highlights the recent advances in QPM development and its practical application in the post genomic era,genomic and physical composition and evolution of zein family,and expression,regulation and downstream role of zein genes in endosperm development.Moreover,recent genomic tools and methods developed for functional validation of maize zein genes are also discussed.展开更多
基金supported by the National Key Research and Development Program of China (2016YFD0100102-3)the Recruitment Program of High-end Foreign Experts of State Administration of Foreign Experts Affairs (GDT20163200028)the Independent Innovation of Agricultural Science and Technology of Jiangsu Province [CX(15)1001]
文摘Allelic diversity in the wild grass Aegilops tauschii is vastly greater than that in the D genome of common wheat(Triticum aestivum), of which Ae. tauschii is the source. Since the 1980 s,there have been numerous efforts to harness a much larger share of Ae. tauschii^ extensive and highly variable gene pool for wheat improvement. Those efforts have followed two distinct approaches: production of amphiploids, known as "synthetic hexaploids," between T. turgidum and Ae. tauschii,and direct hybridization between 丁. aestiuum and Ae. tauschii;both approaches then involve backcrossing to 丁. aestiuum. Both synthetic hexaploid production and direct hybridization have led to the transfer of numerous new genes into common wheat that confer improvements in many traits. This work has led to release of improved cultivars in China, the United States, and many other countries. Each approach to D-genome improvement has advantages and disadvantages. For example, production of synthetic hexaploids can incorporate useful germplasm from both T. turgidum and Ae.tauschii, thereby enhancing the A, B, and D genomes; on the other hand, direct hybridization rapidly restores the recurrent parent's A and B genomes and avoids incorporation of genes with adverse effects on threshability, hybrid necrosis, vernalization response, milling and baking quality, and other traits, which are often transferred when T. turgidum is used as a parent. Choice of method will depend in part on the type of wheat being developed and the target environment. However, more extensive use of the so-far underexploited direct hybridization approach is especially warranted.
基金Supported by National Key Technology R&D Program(2015BAD01B01)
文摘[Objectives] The identification of salt tolerant genetic loci in rice can provide a research basis for the molecular mechanism of salt tolerance and gene resources for improving salt tolerant cultivars. [Methods] Recombinant inbred lines(RILs) derived from Zhaxima, an indica landrace variety from Yunnan Province and Nanjing 46, an elite japonica variety with superior grain quality from Jiangsu Province were used. The salt tolerance at seeding stage in the RIL population was investigated as the phenotypic value. [Results] Combined with the linkage map, a total of 4 QTLs were detected: qSST-1, qSST-3, qSST-5 and qSST-11, located in rice chromosomes 1, 3, 5 and 11, respectively. All positive alleles were from the parent Nanjing 46. Three QTLs among them were not included in chromosome intervals the same as cloned rice salt tolerance genes, and thus were described as new candidate gene loci associated with seeding-stage salt tolerance. [Conclusions] This study provides important information for further exploration and utilization of new salt tolerant QTLs in rice. It is of great significance for improving the utilization of saline land in China and ensuring the stable rice production.
文摘ChinaMu is the largest sequence-indexed Mutator(Mu)transposon insertional library in maize(Zea mays).In this study,we made significant improvements to the size and quality of the ChinaMu library.We developed a new Mu-tag isolation method Mu-Tn5-seq(MuT-seq).Compared to the previous method used by ChinaMu,MuT-seq recovered 1/3 more germinal insertions,while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time.Using MuT-seq,we identified 113,879 germinal insertions from 3,168 Mu-active F1 families.We also assembled a high-quality genome for the Mu-active line Mu-starter,which harbors the initial active MuDR element and was used as the pollen donor for the mutation population.Using the Mu-starter genome,we recovered 33,662(15.6%)additional germinal insertions in 3,244(7.4%)genes in the Mu-starter line.The Mu-starter genome also improved the assignment of 117,689(54.5%)germinal insertions.The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions.These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes,including 23,006(80.4%)core genes shared by the two genomes.As a test model,we investigated Mu insertions in the pentatricopeptide repeat(PPR)superfamily,discovering insertions for 92%(449/487)of PPR genes in ChinaMu,demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.
基金Supported by Saline-alkali Land Control and Soil Fertility Improvement Technology"Jiebangguashuai"Project of Jiangsu Coastal Development Group Co.,Ltd.(2022YHTDJB02).
文摘[Objectives]This study was conducted to enhance the salt tolerance of current rice varieties at the seedling stage and fulfill the urgent requirement for salt-tolerant rice varieties in coastal tidal flats.[Methods]Four high-generation stable rice lines with diverse salt tolerance were employed as test materials,and four NaCl concentration gradients were established for seed soaking treatment.[Results]The seedling survival rate of line 151465 underwent significant alterations after soaking with four different salt concentrations,and the survival rate was the highest after treatment with 1.8%NaCl for 1 d,reaching 65.2%.The average survival rate of other three lines with different salt tolerance reached 62%after soaking with 1.8%NaCl for 1 d,which was significantly higher than those of the 2.2%NaCl and 0%NaCl treatments.[Conclusions]This study provides a basis for reducing the effect of abiotic stress on rice growth and development and improving the utilization rate of saline-alkali land.
基金supported by the National Natural Science Foundation of China(31572169)the project of International Cooperation and Exchanges of NSFC(31961143001)+3 种基金the project of Basic and Applied Basic Research of Guangdong Province(2019A1515110856)China National Distinguished Expert Project(WQ20174400441)grant 31961143001for Joint Research Projects between Pakistan Science Foundation and National Natural Science Foundation of Chinafunding from Australian Research Council.
文摘When plants are exposed to hypoxic conditions,the level of g-aminobutyric acid(GABA)in plant tissues increases by several orders of magnitude.The physiological rationale behind this elevation remains largely unanswered.By combining genetic and electrophysiological approach,in this work we show that hypoxia-induced increase in GABA content is essential for restoration of membrane potential and preventing ROS-induced disturbance to cytosolic K+homeostasis and Ca^(2+)signaling.We show that reduced O_(2) availability affects H+-ATPase pumping activity,leading to membrane depolarization and K+loss via outward-rectifying GORK channels.Hypoxia stress also results in H_(2)O_(2) accumulation in the cell that activates ROS-inducible Ca^(2+)uptake channels and triggers self-amplifying"ROS-Ca hub,"further exacerbating K^(+)loss via non-selective cation channels that results in the loss of the cell’s viability.Hypoxia-induced elevation in the GABA level may restore membrane potential by pH-dependent regulation of H^(+)-ATPase and/or by generating more energy through the activation of the GABA shunt pathway and TCA cycle.Elevated GABA can also provide better control of the ROS-Ca^(2+)hub by transcriptional control of RBOH genes thus preventing over-excessive H_(2)O_(2) accumulation.Finally,GABA can operate as a ligand directly controlling the open probability and conductance of K+efflux GORK channels,thus enabling plants adaptation to hypoxic conditions.
基金supported by grants from the 13th Five-Year National Key R&D Program of China(2017YFD0102001).
文摘Along with rapid advances in high-throughput-sequencing technology,the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic research.Desirable molecular markers should be able to rapidly genotype tens of thousands of breeding accessions with tens to hundreds of markers.In this study,we developed a multiplex molecular marker,the haplotype-tag polymorphism(HTP),that integrates Maize6H-60K array data from 3,587 maize inbred lines with 6,375 blocks from the recombination block map.After applying strict filtering criteria,we obtained 6,163 highly polymorphic HTPs,which were evenly distributed in the genome.Furthermore,we developed a genome-wide HTP analysis toolkit,HTPtools,which we used to establish an HTP database(HTPdb)covering the whole genomes of 3,587 maize inbred lines commonly used in breeding.A total of 172,921 non-redundant HTP allelic variations were obtained.Three major HTPtools modules combine seven algorithms(e.g.,chain Bayes probability and the heterotic-pattern prediction algorithm)and a new plotting engine named“BCplot”that enables rapid visualization of the background information of multiple backcross groups.HTPtools was designed for big-data analyses such as complex pedigree reconstruction and maize heterotic-pattern prediction.The HTP-based analytical strategy and the toolkit developed in this study are applicable for high-throughput genotyping and for genetic mapping,germplasm resource analyses,and genomics-informed breeding in maize.
基金supported by the National Natural Science Foundation of China (91531304, 31525018, 31370266, and 31788103)the “Strategic Priority Research Program” of the Chinese Academy of Sciences (XDA08000000)the State Key Laboratory of Plant Cell and Chromosome Engineering (PCCE-KF-2017-03)
文摘Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.
基金supported by Key Research and Development Program of Jiangsu Province(BE2017365)。
文摘Maize(Zea mays)is a cereal crop of global food importance.However,the deficiency of essential amino acids,more importantly lysine,methionine and tryptophan,in the major seed storage zein proteins makes corn nutritionally of low value for human consumption.The idea of improving maize nutritional value prompted the search for maize natural mutants harboring low zein contents and higher amount of lysine.These studies resulted in the identification of more than dozens of maize opaque mutants in the previous few decades,o2 mutant being the most extensively studied one.However,the high lysine contents but soft kernel texture and chalky endosperm halted the widespread application and commercial success of maize opaque mutants,which ultimately paved the way for the development of Quality Protein Maize(QPM)by modifying the soft endosperm of o2 mutant into lysine-rich hard endosperm.The previous few decades have witnessed a marked progress in maize zein research.It includes elucidation of molecular mechanism underlying the role of different zein genes in seed endosperm development by cloning different components of zein family,exploring the general organization,function and evolution of zein family members within maize species and among other cereals,and elucidating the cis-and trans-regulatory elements modulating the regulation of different molecular players of maize seed endosperm development.The current advances in high quality reference genomes of maize lines B73 and Mo17 plus the completion of ongoing pan genome sequencing projects of more maize lines with NGS technologies are expected to revolutionize maize zein gene research in near future.This review highlights the recent advances in QPM development and its practical application in the post genomic era,genomic and physical composition and evolution of zein family,and expression,regulation and downstream role of zein genes in endosperm development.Moreover,recent genomic tools and methods developed for functional validation of maize zein genes are also discussed.
