In plants,numerous non-Mendelian inherited dominant effects,including over-,incomplete-,and codominance,are frequently observed,yet they remain insufficiently understood.A novel phenotype has been identified in specif...In plants,numerous non-Mendelian inherited dominant effects,including over-,incomplete-,and codominance,are frequently observed,yet they remain insufficiently understood.A novel phenotype has been identified in specific soybean transformants overexpressing a single 35S::GmFT2a copy:superearly flowering dominance is exclusively observed in hemizygotes,not in homozygotes.Homozygous individual exhibits si RNA-mediated DNA methylation,causing epigenetic transcriptional silencing,whereas no such effect occurs in hemizygotes.Intriguingly,two distinct rounds of DNA methylation establishment occur,each mediated by a different mechanism.The homozygotes that derived from the hemizygous mother plants carrying 35S::GmFT2a locus was associated with the initiation of CHHcontext DNA methylation at 35S promoters mediated by 21 and 22 nucleotide(nt)si RNAs.Subsequently,24 nt si RNAs contribute to additional CHG-and CG-context DNA methylation at 35S promoters during the homozygosity of genes in plants already homozygous in maternal lineage.Reducing DNA methylation levels can be achieved by generating a hemizygous genotype through a crossing experiment with a recessive genotype.This research has unveiled a phenomenon:hemizygote-dependent dominance resulting from transcriptional silencing in homozygote offsprings.It provides new insights into the molecular mechanism underlying dominant effects.展开更多
Leaves provide substances and signals for pod and seed development in soybean.However,the regulatory feedbacks of pod and seed to leaf development remain unclear.We investigated the effects of pod and seed on leaf sen...Leaves provide substances and signals for pod and seed development in soybean.However,the regulatory feedbacks of pod and seed to leaf development remain unclear.We investigated the effects of pod and seed on leaf senescence by conducting pod removal and seed injury experiments.Pod removal and seed injury delayed leaf senescence and caused the staygreen phenotype of leaves.There were dosage effects of pod number on the extent of staygreen in depodded plants.The concentrations of chlorophyll(SPAD value,an index of relative chlorophyll content),soluble protein,and soluble sugar in the leaves of depodded plants were higher than those of intact plants.During seed development,the content of IAA decreased,while that of ABA increased.This trend was more pronounced in intact than in depodded and seed-injured plants.The GA3/ABA ratio decreased gradually in all treatments.The content of GA3 was relatively stable and was higher in intact than in depodded plants.The expression levels of four senescence-related genes,Gm SARK,Gm SGR1,Gm CYN1,and Gm NAC,declined in depodded or seed-injured treatments and were positively correlated with the number of leaves retained on plants.Gm FT2 a,the major flowering-promoting gene,was expressed at a higher level while E1,a key flowering inhibitory gene,was expressed at a lower level in depodded than in intact plants.We propose that the pod or seed can regulate leaf development.When the seed is aborted owing to disease infection or pest attack,the leaves stay green because of the absence of the seed signals for senescence.展开更多
Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and breeding.Uncovering the uni...Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and breeding.Uncovering the unique genomic features of popular cultivars will help to understand how soybean genomes have been modified through breeding.We re-sequenced 134 soybean cultivars that were released and most widely planted over the last century in China.Phylogenetic analyses established that these cultivars comprise two geographically distinct sub-populations:Northeast China (NE) versus the HuangHuai-Hai River Valley and South China (HS).A total of 309 selective regions were identified as being impacted by geographical origins.The HS sub-population exhibited higher genetic diversity and linkage disequilibrium decayed more rapidly compared to the NE sub-population.To study the association between phenotypic differences and geographical origins,we recorded the vegetative period under different growing conditions for two years,and found that clustering based on the phenotypic data was closely correlated with cultivar geographical origin.By iteratively calculating accumulated genetic diversity,we established a platform panel of cultivars and have proposed a novel breeding strategy named "Potalaization"for selecting and utilizing the platform cultivars that represent the most genetically diversity and the highest available agronomic performance as the "plateau"for accumulating elite loci and traits,breeding novel widely adapted cultivars,and upgrading breeding technology.In addition to providing new genomic information for the soybean research community,the "Potalaization"strategy that we devised will also be practical for integrating the conventional and molecular breeding programs of crops in the post-genomic era.展开更多
Soybean is one of the world's most important oil and protein crops. Efficient transformation is a key factor for the improvement of soybean by genetic modification. We describe an optimized protocol for the Agroba...Soybean is one of the world's most important oil and protein crops. Efficient transformation is a key factor for the improvement of soybean by genetic modification. We describe an optimized protocol for the Agrobacterium rhizogenes-mediated transformation of soybean and the induction of hairy root development in vitro. Cotyledons with 0.5-cm hypocotyls were cut from 5-day-old seedlings and used as explants. After infection and co-cultivation,hairy roots were produced in induction culture medium after 10–12 days. Using this method, 90%–99% of the infected explants of five different cultivars produced hairy roots within one month. Observations using reporter constructs showed that 30%–60% of the hairy roots induced were transformed. Based on high transformation efficiency and short transformation period, this method represents an efficient and rapid platform for study of soybean gene function.展开更多
Bioactive components are partially responsible for the nutritional and health benefits of soybeans. Four major bioactive components: isoflavones, oligosaccharides, phospholipids,and saponins, were quantified in 763 so...Bioactive components are partially responsible for the nutritional and health benefits of soybeans. Four major bioactive components: isoflavones, oligosaccharides, phospholipids,and saponins, were quantified in 763 soybean samples collected from widely distributed regions across China from 2010 to 2013. A majority of the tested bioactive components showed generally declining trends from the north(high latitude) to the south(low latitude).A positive relationship between total oligosaccharides(TO) and altitude was observed. Total isoflavones(TI), phospholipids(TP) and TO were negatively correlated with cumulative temperature above or equal to 15 °C(AT15) and mean daily temperature(MDT), but positively correlated with diurnal temperature range(DTR) and hours of sunshine(HS).Total saponins(TS) were negatively correlated with MDT but positively correlated with rainfall(RF), whereas TO were negatively correlated with RF. Path-coefficient analysis showed that, besides genotype differences, temperature and HS during the reproductive period influenced TI and TP contents, while temperature and RF influenced TS and TO. The effects of weather factors on soybean bioactive components in diverse regions of China were characterized. These findings will be helpful in promoting soybean production for functional food purposes.展开更多
Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nev...Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.展开更多
Soybean(Glycine max[L.]Merr.)is a food and oil crop whose growth and yield are influenced by root and nodule development.In the present study,Gm NMHC5 was found to promote the formation of nodules in overexpressing mu...Soybean(Glycine max[L.]Merr.)is a food and oil crop whose growth and yield are influenced by root and nodule development.In the present study,Gm NMHC5 was found to promote the formation of nodules in overexpressing mutants.In contrast,the number of nodules in Gmnmhc5 edited with CRISPR/Cas9 decreased sharply.In 35 S:Gm NMHC5 mutants,expression levels of genes involved in nodulation were significantly up-regulated.Both in vitro and in vivo biochemical analyses showed that Gm NMHC5 directly interacted with Gm GAI(a DELLA protein),and the content of gibberellin 3(GA_(3))in overexpressing mutants was lower than that in the wild type.These results revealed that Gm NMHC5 participates in the classical GA signaling pathway,and may regulate the content of GA_3 to match the optimal concentration required for nodule formation,thereby promoting nodulation by directly interacting with Gm GAI.A model illustrating the mechanism by which Gm NMHC5 promotes soybean nodulation is presented.展开更多
Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequ...Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.展开更多
Wild soybean is a typical short-day plant that begins flowering when the days are shorter than its critical photoperiod, Soybean was domesticated in the temperate region of East Asia at the relatively high latitude, a...Wild soybean is a typical short-day plant that begins flowering when the days are shorter than its critical photoperiod, Soybean was domesticated in the temperate region of East Asia at the relatively high latitude, and the breeding and release of soybean varieties have historically centered on mid- and high-latitude temperate regions. Low-latitude areas with tropical and sub- tropical climates were previously considered unsuitable for soy- bean production because most temperate soybean varieties ex- hibited precocious flowering and early maturity and suffered from low yields.展开更多
基金supported by grants from the National Key Research and Development Program of China(2023YFD120300)the National Natural Science Foundation of China(32201869)the Earmarked Fund for China Agriculture Research System(CARS-04)。
文摘In plants,numerous non-Mendelian inherited dominant effects,including over-,incomplete-,and codominance,are frequently observed,yet they remain insufficiently understood.A novel phenotype has been identified in specific soybean transformants overexpressing a single 35S::GmFT2a copy:superearly flowering dominance is exclusively observed in hemizygotes,not in homozygotes.Homozygous individual exhibits si RNA-mediated DNA methylation,causing epigenetic transcriptional silencing,whereas no such effect occurs in hemizygotes.Intriguingly,two distinct rounds of DNA methylation establishment occur,each mediated by a different mechanism.The homozygotes that derived from the hemizygous mother plants carrying 35S::GmFT2a locus was associated with the initiation of CHHcontext DNA methylation at 35S promoters mediated by 21 and 22 nucleotide(nt)si RNAs.Subsequently,24 nt si RNAs contribute to additional CHG-and CG-context DNA methylation at 35S promoters during the homozygosity of genes in plants already homozygous in maternal lineage.Reducing DNA methylation levels can be achieved by generating a hemizygous genotype through a crossing experiment with a recessive genotype.This research has unveiled a phenomenon:hemizygote-dependent dominance resulting from transcriptional silencing in homozygote offsprings.It provides new insights into the molecular mechanism underlying dominant effects.
基金supported by the China Agriculture Research System (No.CARS-04)the Agricultural Science and Technology Innovation Program to T.F.Hanthe National Major Project for Breeding of Transgenic Crops (No.2016ZX08004002) to C.H.Guo
文摘Leaves provide substances and signals for pod and seed development in soybean.However,the regulatory feedbacks of pod and seed to leaf development remain unclear.We investigated the effects of pod and seed on leaf senescence by conducting pod removal and seed injury experiments.Pod removal and seed injury delayed leaf senescence and caused the staygreen phenotype of leaves.There were dosage effects of pod number on the extent of staygreen in depodded plants.The concentrations of chlorophyll(SPAD value,an index of relative chlorophyll content),soluble protein,and soluble sugar in the leaves of depodded plants were higher than those of intact plants.During seed development,the content of IAA decreased,while that of ABA increased.This trend was more pronounced in intact than in depodded and seed-injured plants.The GA3/ABA ratio decreased gradually in all treatments.The content of GA3 was relatively stable and was higher in intact than in depodded plants.The expression levels of four senescence-related genes,Gm SARK,Gm SGR1,Gm CYN1,and Gm NAC,declined in depodded or seed-injured treatments and were positively correlated with the number of leaves retained on plants.Gm FT2 a,the major flowering-promoting gene,was expressed at a higher level while E1,a key flowering inhibitory gene,was expressed at a lower level in depodded than in intact plants.We propose that the pod or seed can regulate leaf development.When the seed is aborted owing to disease infection or pest attack,the leaves stay green because of the absence of the seed signals for senescence.
基金supported by the National Key Research and Development Program of China (2017YFD0101400)China Agriculture Research System (CARS-04)+1 种基金the Agricultural Science and Technology Innovation Program of CAASsupported by a grant from the Hong Kong Research Grants Council Area of Excellence Scheme (Ao E/M-403/16) awarded to HonMing Lam。
文摘Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and breeding.Uncovering the unique genomic features of popular cultivars will help to understand how soybean genomes have been modified through breeding.We re-sequenced 134 soybean cultivars that were released and most widely planted over the last century in China.Phylogenetic analyses established that these cultivars comprise two geographically distinct sub-populations:Northeast China (NE) versus the HuangHuai-Hai River Valley and South China (HS).A total of 309 selective regions were identified as being impacted by geographical origins.The HS sub-population exhibited higher genetic diversity and linkage disequilibrium decayed more rapidly compared to the NE sub-population.To study the association between phenotypic differences and geographical origins,we recorded the vegetative period under different growing conditions for two years,and found that clustering based on the phenotypic data was closely correlated with cultivar geographical origin.By iteratively calculating accumulated genetic diversity,we established a platform panel of cultivars and have proposed a novel breeding strategy named "Potalaization"for selecting and utilizing the platform cultivars that represent the most genetically diversity and the highest available agronomic performance as the "plateau"for accumulating elite loci and traits,breeding novel widely adapted cultivars,and upgrading breeding technology.In addition to providing new genomic information for the soybean research community,the "Potalaization"strategy that we devised will also be practical for integrating the conventional and molecular breeding programs of crops in the post-genomic era.
基金supported by the Major Science and Technology Projects of China (2016ZX08010-004)the Ministry of Science and Technology of China (2016YFD0100504)the CAAS (Chinese Academy of Agriculture Sciences) Innovation Project
文摘Soybean is one of the world's most important oil and protein crops. Efficient transformation is a key factor for the improvement of soybean by genetic modification. We describe an optimized protocol for the Agrobacterium rhizogenes-mediated transformation of soybean and the induction of hairy root development in vitro. Cotyledons with 0.5-cm hypocotyls were cut from 5-day-old seedlings and used as explants. After infection and co-cultivation,hairy roots were produced in induction culture medium after 10–12 days. Using this method, 90%–99% of the infected explants of five different cultivars produced hairy roots within one month. Observations using reporter constructs showed that 30%–60% of the hairy roots induced were transformed. Based on high transformation efficiency and short transformation period, this method represents an efficient and rapid platform for study of soybean gene function.
基金supported by the National Key Research and Development Program of China(2017YFD0101400)China Agriculture Research System(CARS-04)Agricultural Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences
文摘Bioactive components are partially responsible for the nutritional and health benefits of soybeans. Four major bioactive components: isoflavones, oligosaccharides, phospholipids,and saponins, were quantified in 763 soybean samples collected from widely distributed regions across China from 2010 to 2013. A majority of the tested bioactive components showed generally declining trends from the north(high latitude) to the south(low latitude).A positive relationship between total oligosaccharides(TO) and altitude was observed. Total isoflavones(TI), phospholipids(TP) and TO were negatively correlated with cumulative temperature above or equal to 15 °C(AT15) and mean daily temperature(MDT), but positively correlated with diurnal temperature range(DTR) and hours of sunshine(HS).Total saponins(TS) were negatively correlated with MDT but positively correlated with rainfall(RF), whereas TO were negatively correlated with RF. Path-coefficient analysis showed that, besides genotype differences, temperature and HS during the reproductive period influenced TI and TP contents, while temperature and RF influenced TS and TO. The effects of weather factors on soybean bioactive components in diverse regions of China were characterized. These findings will be helpful in promoting soybean production for functional food purposes.
基金This work has been supported by the National Key Research and Development Program of China(2021YFF1200105)National Natural Science Foundation of China(62172125,62371161).
文摘Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.
基金supported by the National Natural Science Foundation of China(31271636)the China Agriculture Research System(CARS-04)。
文摘Soybean(Glycine max[L.]Merr.)is a food and oil crop whose growth and yield are influenced by root and nodule development.In the present study,Gm NMHC5 was found to promote the formation of nodules in overexpressing mutants.In contrast,the number of nodules in Gmnmhc5 edited with CRISPR/Cas9 decreased sharply.In 35 S:Gm NMHC5 mutants,expression levels of genes involved in nodulation were significantly up-regulated.Both in vitro and in vivo biochemical analyses showed that Gm NMHC5 directly interacted with Gm GAI(a DELLA protein),and the content of gibberellin 3(GA_(3))in overexpressing mutants was lower than that in the wild type.These results revealed that Gm NMHC5 participates in the classical GA signaling pathway,and may regulate the content of GA_3 to match the optimal concentration required for nodule formation,thereby promoting nodulation by directly interacting with Gm GAI.A model illustrating the mechanism by which Gm NMHC5 promotes soybean nodulation is presented.
基金supported by the Genetically Modified Organisms Breeding Major Projects of China (2016ZX08011-003)China Agriculture Research System (CARS-04)CAAS Agricultural Science and Technology Innovation Project
文摘Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.
文摘Wild soybean is a typical short-day plant that begins flowering when the days are shorter than its critical photoperiod, Soybean was domesticated in the temperate region of East Asia at the relatively high latitude, and the breeding and release of soybean varieties have historically centered on mid- and high-latitude temperate regions. Low-latitude areas with tropical and sub- tropical climates were previously considered unsuitable for soy- bean production because most temperate soybean varieties ex- hibited precocious flowering and early maturity and suffered from low yields.
