Soybean [Glycine max(L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding...Soybean [Glycine max(L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding for many useful agronomic traits. Next-generation sequence data available in public databases provides valuable information and offers new insights for rapid and efficient development of molecular markers. In this study, we attempted to show the feasibility and facility of using genomic resequencing data as raw material for identifying putative In Del markers. First, we identified 17,613 In Del sites among 56 soybean accessions and obtained 12,619 primer pairs. Second, we constructed a genetic map with a random subset of 2841 primer pairs and aligned 300 polymorphic markers with the 20 consensus linkage groups(LG). The total genetic distance was 2347.3 c M and the number of mapped markers per LG ranged from 10 to 23 with an average of 15 markers. The largest and smallest genetic distances between adjacent markers were 52.3 c M and 0.1 cM, respectively. Finally, we validated the genetic map constructed by newly developed In Del markers by QTL analysis of days to flowering(DTF) under different environments. One major QTL(qDTF4) and four minor QTL(qDTF20, qDTF13, qDTF12,and q DTF11) on 5 LGs were detected. These results demonstrate the utility of the In Del markers developed in this work for map-based cloning and molecular breeding in soybean.展开更多
Flowering time is an important agronomic trait for soybean yield and adaptation. However, the genetic basis of soybean adaptation to diverse latitudes is still not clear. Four NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED...Flowering time is an important agronomic trait for soybean yield and adaptation. However, the genetic basis of soybean adaptation to diverse latitudes is still not clear. Four NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED 2(LNK2) homeologs of Arabidopsis thaliana LNK2 were identified in soybean. Three single-guide RNAs were designed for editing the four LNK2 genes. A transgene-free homozygous quadruple mutant of the LNK2 genes was developed using the CRISPR(clustered regularly interspaced short palindromic repeats)/Cas9(CRISPR-associated protein 9). Under long-day(LD) conditions, the quadruple mutant flowered significantly earlier than the wild-type(WT). Quantitative real-time PCR(q RT-PCR)revealed that transcript levels of LNK2 were significantly lower in the quadruple mutant than in the WT under LD conditions. LNK2 promoted the expression of the legume-specific E1 gene and repressed the expression of FT2 a. Genetic markers were developed to identify LNK2 mutants for soybean breeding.These results indicate that CRISPR/Cas9-mediated targeted mutagenesis of four LNK2 genes shortens flowering time in soybean. Our findings identify novel components in flowering-time control in soybean and may be beneficial for further soybean breeding in high-latitude environments.展开更多
Flowering time is a key agronomic trait that directly affect the adaptation and yield of soybean.After whole genome duplications,about 75%of genes being represented by multiple copies in soybean.There are four TERMINA...Flowering time is a key agronomic trait that directly affect the adaptation and yield of soybean.After whole genome duplications,about 75%of genes being represented by multiple copies in soybean.There are four TERMINAL FLOWER 1(TFL1)genes in soybean,and the TFL1b(Dt1)has been characterized as the determinant of stem growth habit.The function of other TFL1 homologs in soybean is still unclear.Here,we generated knockout mutants by CRISPR/Cas9 genome editing technology and found that the tfl1c/tfl1d double mutants flowered significantly earlier than wild-type plants.We investigated that TFL1c and TFL1d could physically interact with the b ZIP transcription factor FDc1 and bind to the promoter of APETALA1a(AP1a).RNA-seq and q RT-PCR analyses indicated that TFL1c and TFL1d repressed the expressions of the four AP1 homologs and delayed the flowering time in soybean.The two genes play important roles in the regulation of flowering time in soybean and mainly act as the flowering inhibitors under long-day conditions.Our results identify novel components in the flowering-time regulation network of soybean and will be invaluable for molecular breeding of improved soybean yield.展开更多
The transition from vegetative to reproductive growth is a vital step for the reproductive success of plants.In Arabidopsis thaliana,LEAFY(LFY)plays crucial roles in inflorescence primordium and floral organ developme...The transition from vegetative to reproductive growth is a vital step for the reproductive success of plants.In Arabidopsis thaliana,LEAFY(LFY)plays crucial roles in inflorescence primordium and floral organ development,but little is known about the roles of its homologs in crop plants such as soybean(Glycine max).Here,we investigated the expression patterns and functions of the two LFY genes(LFY1 and LFY2)in soybean.Both genes were predominantly expressed in unopened flowers and the shoot apical meristem,with LFY2 having the higher transcript abundance.In an in situ hybridization assay,LFY genes produced strong signals in the floral meristem.We next generated lfy1 and lfy2 knockout lines.The lfy2 mutants showed obvious changes in floral organ morphology,but the lfy1 mutants showed no obvious changes in floral organ morphology or pod development.The lfy1 lfy2 double mutants displayed more serious defects in floral organ development than lfy2,resulting in complete sterility.Gene expression analysis revealed differences in expression of the A-class APETALA(AP)genes AP1a and AP1b in the double mutant lines.These results suggest that LFY2 plays an important role in floral organ formation in soybean by regulating the expression of homeotic genes.Our findings increase the understanding of floral development,which could be useful for flower designs during hybrid soybean breeding.展开更多
Soybean(Glycine max) is an important legume crop that was domesticated in temperate regions.Soybean varieties from these regions generally mature early and exhibit extremely low yield when grown under inductive short-...Soybean(Glycine max) is an important legume crop that was domesticated in temperate regions.Soybean varieties from these regions generally mature early and exhibit extremely low yield when grown under inductive short-day(SD) conditions at low latitudes. The long-juvenile(LJ) trait, which is characterized by delayed flowering and maturity,and improved yield under SD conditions, allowed the cultivation of soybean to expand to lower latitudes. Two major loci control the LJ trait: J and E6. In the current study, positional cloning, sequence analysis, and transgenic complementation confirmed that E6 is a novel allele of J, the ortholog of Arabidopsis thaliana EARLY FLOWERING 3(ELF3). The mutant allele e6^(PG), which carries a Ty1/Copia-like retrotransposon insertion, does not suppress the legume-specific flowering repressor E1, allowing E1 to inhibit Flowering Locus T(FT) expression and thus delaying flowering and increasing yields under SD conditions. The e6^(PG)allele is a rare allele that has not been incorporated into modern breeding programs.The dysfunction of J might have greatly facilitated the adaptation of soybean to low latitudes. Our findings increase our understanding of the molecular mechanisms underlying the LJ trait and provide valuable resources for soybean breeding.展开更多
Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.I...Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.In this study,by combining whole-genome resequencing and genome-wide association studies we identified a novel locus,Time of Flowering 5(Tof5),which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean.By genomic,genetic and transgenic analyses we showed that Tof5 en-codes a homolog of Arabidopsis thaliana FRUITFULL(FUL).Importantly,further analyses suggested that different alleles of Tof5 have undergone parallel selection.The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean,while Tof5H2 allele was naturally selected in wild soybean,and in each case facilitating adaptation to high latitudes.Moreover,we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter.In turn,Tof5 physically associates with the promoters of two important FLOWERING LOCUS T(FT),FT2a and FT5a,to upregulate their transcription and promote flowering under long photoperiods.Collectively,ourfindings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.展开更多
基金supported by National Natural Science Foundation of China (31430065, 31571686, 31371643, 31071445)National Key Research and Development Program (2016YFD0100401)+4 种基金“Strategic Priority Research Program” of the Chinese Academy of Sciences (XDA08030108)the Open Foundation of the Key Laboratory of Soybean Molecular Design Breeding of Chinese Academy of Sciences“One-hundred Talents” Startup Funds from Chinese Academy of SciencesScientific Research Foundation for Returned Chinese Scholars of Heilongjiang Province, China (LC201417)the Science Foundation for Creative Research Talents of Harbin Science and Technology Bureau, China (2014RFQYJ046)
文摘Soybean [Glycine max(L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding for many useful agronomic traits. Next-generation sequence data available in public databases provides valuable information and offers new insights for rapid and efficient development of molecular markers. In this study, we attempted to show the feasibility and facility of using genomic resequencing data as raw material for identifying putative In Del markers. First, we identified 17,613 In Del sites among 56 soybean accessions and obtained 12,619 primer pairs. Second, we constructed a genetic map with a random subset of 2841 primer pairs and aligned 300 polymorphic markers with the 20 consensus linkage groups(LG). The total genetic distance was 2347.3 c M and the number of mapped markers per LG ranged from 10 to 23 with an average of 15 markers. The largest and smallest genetic distances between adjacent markers were 52.3 c M and 0.1 cM, respectively. Finally, we validated the genetic map constructed by newly developed In Del markers by QTL analysis of days to flowering(DTF) under different environments. One major QTL(qDTF4) and four minor QTL(qDTF20, qDTF13, qDTF12,and q DTF11) on 5 LGs were detected. These results demonstrate the utility of the In Del markers developed in this work for map-based cloning and molecular breeding in soybean.
基金supported by National Key Research and Development Program of China(2017YFD0101305)the National Natural Science Foundation of China(31930083,31901568,31801384,31725021,and 31771815)。
文摘Flowering time is an important agronomic trait for soybean yield and adaptation. However, the genetic basis of soybean adaptation to diverse latitudes is still not clear. Four NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED 2(LNK2) homeologs of Arabidopsis thaliana LNK2 were identified in soybean. Three single-guide RNAs were designed for editing the four LNK2 genes. A transgene-free homozygous quadruple mutant of the LNK2 genes was developed using the CRISPR(clustered regularly interspaced short palindromic repeats)/Cas9(CRISPR-associated protein 9). Under long-day(LD) conditions, the quadruple mutant flowered significantly earlier than the wild-type(WT). Quantitative real-time PCR(q RT-PCR)revealed that transcript levels of LNK2 were significantly lower in the quadruple mutant than in the WT under LD conditions. LNK2 promoted the expression of the legume-specific E1 gene and repressed the expression of FT2 a. Genetic markers were developed to identify LNK2 mutants for soybean breeding.These results indicate that CRISPR/Cas9-mediated targeted mutagenesis of four LNK2 genes shortens flowering time in soybean. Our findings identify novel components in flowering-time control in soybean and may be beneficial for further soybean breeding in high-latitude environments.
基金supported by the National Natural Science Foundation of China(32022062,32001503)the Science and Technology Innovation Team of Soybean Modern Seed Industry in Hebei(21326313D)。
文摘Flowering time is a key agronomic trait that directly affect the adaptation and yield of soybean.After whole genome duplications,about 75%of genes being represented by multiple copies in soybean.There are four TERMINAL FLOWER 1(TFL1)genes in soybean,and the TFL1b(Dt1)has been characterized as the determinant of stem growth habit.The function of other TFL1 homologs in soybean is still unclear.Here,we generated knockout mutants by CRISPR/Cas9 genome editing technology and found that the tfl1c/tfl1d double mutants flowered significantly earlier than wild-type plants.We investigated that TFL1c and TFL1d could physically interact with the b ZIP transcription factor FDc1 and bind to the promoter of APETALA1a(AP1a).RNA-seq and q RT-PCR analyses indicated that TFL1c and TFL1d repressed the expressions of the four AP1 homologs and delayed the flowering time in soybean.The two genes play important roles in the regulation of flowering time in soybean and mainly act as the flowering inhibitors under long-day conditions.Our results identify novel components in the flowering-time regulation network of soybean and will be invaluable for molecular breeding of improved soybean yield.
基金supported by the Open Competition Program of Top Ten Critical Priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province(2022SDZG05 to F.Kong,and B.Liu)the National Natural Science Foundation of China(32090064 to F.Kong,32330074 to B.Liu,and 32301874 to L.Wang)+1 种基金the Natural Science Foundation of Guangdong Province(2024A1515011314 to L.Wang)the Science and Technology Innovation Special Project of Modern Seed Industry(22326316D to F.Kong).
文摘The transition from vegetative to reproductive growth is a vital step for the reproductive success of plants.In Arabidopsis thaliana,LEAFY(LFY)plays crucial roles in inflorescence primordium and floral organ development,but little is known about the roles of its homologs in crop plants such as soybean(Glycine max).Here,we investigated the expression patterns and functions of the two LFY genes(LFY1 and LFY2)in soybean.Both genes were predominantly expressed in unopened flowers and the shoot apical meristem,with LFY2 having the higher transcript abundance.In an in situ hybridization assay,LFY genes produced strong signals in the floral meristem.We next generated lfy1 and lfy2 knockout lines.The lfy2 mutants showed obvious changes in floral organ morphology,but the lfy1 mutants showed no obvious changes in floral organ morphology or pod development.The lfy1 lfy2 double mutants displayed more serious defects in floral organ development than lfy2,resulting in complete sterility.Gene expression analysis revealed differences in expression of the A-class APETALA(AP)genes AP1a and AP1b in the double mutant lines.These results suggest that LFY2 plays an important role in floral organ formation in soybean by regulating the expression of homeotic genes.Our findings increase the understanding of floral development,which could be useful for flower designs during hybrid soybean breeding.
基金supported by the National Natural Science Foundation of China(31725021)funded by the Major Program of Guangdong Basic and Applied Research(2019B030302006)。
文摘Soybean(Glycine max) is an important legume crop that was domesticated in temperate regions.Soybean varieties from these regions generally mature early and exhibit extremely low yield when grown under inductive short-day(SD) conditions at low latitudes. The long-juvenile(LJ) trait, which is characterized by delayed flowering and maturity,and improved yield under SD conditions, allowed the cultivation of soybean to expand to lower latitudes. Two major loci control the LJ trait: J and E6. In the current study, positional cloning, sequence analysis, and transgenic complementation confirmed that E6 is a novel allele of J, the ortholog of Arabidopsis thaliana EARLY FLOWERING 3(ELF3). The mutant allele e6^(PG), which carries a Ty1/Copia-like retrotransposon insertion, does not suppress the legume-specific flowering repressor E1, allowing E1 to inhibit Flowering Locus T(FT) expression and thus delaying flowering and increasing yields under SD conditions. The e6^(PG)allele is a rare allele that has not been incorporated into modern breeding programs.The dysfunction of J might have greatly facilitated the adaptation of soybean to low latitudes. Our findings increase our understanding of the molecular mechanisms underlying the LJ trait and provide valuable resources for soybean breeding.
基金supported by the National Natural Science Foundation of China(grant nos.32090065 and 32001508 to L.D.,32090064 and 31725021 to F.K.,31930083 to B.L,31901568 to Q.C,32022062 to S.Lu.,32001502 to Y,Z)and also supported by the Major Program of Guangdong Basic and Applied FResearch(grant no.2019B030302006 to F.K.andB.L).
文摘Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.In this study,by combining whole-genome resequencing and genome-wide association studies we identified a novel locus,Time of Flowering 5(Tof5),which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean.By genomic,genetic and transgenic analyses we showed that Tof5 en-codes a homolog of Arabidopsis thaliana FRUITFULL(FUL).Importantly,further analyses suggested that different alleles of Tof5 have undergone parallel selection.The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean,while Tof5H2 allele was naturally selected in wild soybean,and in each case facilitating adaptation to high latitudes.Moreover,we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter.In turn,Tof5 physically associates with the promoters of two important FLOWERING LOCUS T(FT),FT2a and FT5a,to upregulate their transcription and promote flowering under long photoperiods.Collectively,ourfindings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.
