Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases.In recent years,the study of DNA m...Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases.In recent years,the study of DNA methylation in regulating the growth and development of plants and animals has become a key area of research.This review describes the regulatory mechanisms of DNA cytosine methylation in plants.It summarizes studies on epigenetic modifications of DNA methylation in fruit ripening,development,senescence,plant height,organ size,and under biotic and abiotic stresses in horticultural crops.The review provides a theoretical basis for understanding the mechanisms of DNA methylation and their relevance to breeding,genetic improvement,research,innovation,and exploitation of new cultivars of horticultural crops.展开更多
The freshness phenotype of fruit and vegetables is a critical determinant of consumer satisfaction,selection,and public health,which plays a pivotal role in postharvest quality management.This paper presents a review ...The freshness phenotype of fruit and vegetables is a critical determinant of consumer satisfaction,selection,and public health,which plays a pivotal role in postharvest quality management.This paper presents a review of the definition and detection techniques used to assess and maintain this vital freshness phenotype.Advanced intel-ligent packaging technologies,that incorporate sensors,indicators,and data carrier systems,and their roles in dynamically monitoring the freshness phenotype during storage and transportation are discussed.The integration of nondestructive testing(NDT)methods such as near-infrared spectroscopy(NIR),hyperspectral imaging(HSI),machine vision,and light detection and ranging(LiDAR)offers real-time,precise assessments of the freshness phenotype without compromising the integrity of the produce.By understanding the underlying mechanisms of the fruit and vegetable freshness phenotype,this paper discusses the definition,detection technologies,and gaps that require further research.The integration of advanced quantitative models with NDT and intelligent pack-aging solutions has the potential to reduce food waste.This advancement will lead to better quality control,extended shelf life,and increased consumer confidence in fresh produce,driving innovation and application within the food industry.展开更多
DNA methylation is typically regarded as a repressive epigenetic marker for gene expression.Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and de...DNA methylation is typically regarded as a repressive epigenetic marker for gene expression.Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence(MEMS) in the promoter of the DNA demethylase gene ROS_1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS_1 expression. How DNA methylation in the MEMS region promotes ROS_1 expression is not known. Here, we show that several Su(var)3-9 homologs(SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS_1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS.Mutations in the SUVHs lead to decreased ROS_1 expression, causing DNA hypermethylation at more than 1,000 genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation.展开更多
Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression.The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethy...Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression.The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at 1000 s of genomic regions in Arabidopsis.How ROS1 is regulated and targeted to specific genomic regions is not well understood.Here,we report the discovery of an Arabidopsis protein complex that contains ROS1,regulates ROS1 gene expression,and likely targets the ROS1 protein to specific genomic regions.ROS1 physically interacts with a WD40 domain protein(RWD40),which in turn interacts with a methyl-DNA binding protein(RMB1)as well as with a zinc finger and homeobox domain protein(RHD1).RMB1 binds to DNA that is methylated in any sequence context,and this binding is necessary for its function in vivo.Loss-of-function mutations in RWD40,RMB1,or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1.Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter,plants mutated in RWD40,RMB1,or RHD1 show increased ROS1 expression.Importantly,ROS1 binding to the ROS1 promoter requires RWD40,RMB1,and RHD1,suggesting that this complex dictates ROS1 targeting to this locus.Our results demonstrate that ROS1 forms a protein complex with RWD40,RMB1,and RHD1,and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.展开更多
The widely used Streptococcus pyogenes Cas9(SpCas9)requires NGG as a protospacer adjacent motif(PAM)for genome editing.Although Sp Cas9 is a powerful genome-editing tool,its use has been limited on the targetable geno...The widely used Streptococcus pyogenes Cas9(SpCas9)requires NGG as a protospacer adjacent motif(PAM)for genome editing.Although Sp Cas9 is a powerful genome-editing tool,its use has been limited on the targetable genomic locus lacking NGG PAM.The Sp Cas9 variants xCas9 and Cas9-NG have been developed to recognize NG,GAA,and GAT PAMs in human cel s.Here,we show that xCas9 cannot recognize NG PAMs in tomato,and Cas9-NG can recognize some of our tested NG PAMs in the tomato and Arabidopsis genomes.In addition,we engineered BrSp Cas9(XNG-Cas9)based on mutations from both xCas9 and Cas9-NG,and found that XNG-Cas9 can efficiently mutagenize endogenous target sites with NG,GAG,GAA,and GAT PAMs in the tomato or Arabidopsis genomes.The PAM compatibility of XNG-Cas9 is the broadest reported to date among Cas9 s(SpCas9 and Cas9-NG)active in plant.展开更多
Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal feed.mi R396 genes have been shown to negatively regulate grain size in ri...Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal feed.mi R396 genes have been shown to negatively regulate grain size in rice,but whether mi R396 family members may function in a similar manner in soybean is unknown.Here,we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean mi R396genes through genome editing with clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas)12SF01 in the elite soybean cultivar Zhonghuang 302(ZH302).Four triple mutants(mir396aci,mir396acd,mir396adf,and mir396cdf),two quadruple mutants(mir396-abcd and mir396acfi),and two quintuple mutants(mir396abcdf and mir396bcdfi)were characterized.We found that plants of all the mir396 mutants produced larger seeds compared to ZH302 plants.Field tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower latitude.In contrast,mir396abcdf and mir396bcdfiplants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues,but they are suited for low latitude growth zones with increased yield without lodging problems.Taken together,our study demonstrated that loss-of-function of mi R396 genes leads to significantly enlarged seed size and increased yield in soybean,providing valuable germplasms for breeding high-yield soybean.展开更多
Soybean(Glycine max(L.)Merr.)is a major source of vegetable protein and oil in human diet and animal nutrition.Soybean seeds have been extensively used in various food products and snacks.Taste quality,particularly th...Soybean(Glycine max(L.)Merr.)is a major source of vegetable protein and oil in human diet and animal nutrition.Soybean seeds have been extensively used in various food products and snacks.Taste quality,particularly the aroma,affects cooking and eating,and ultimately influences consumer preference.Soy milk is particularly popular in China and has been gaining popularity in many other countries in the world.展开更多
Dear Editor,Soybean(Glycine max)is one of the world’s most important economic and oilseed crops.It plays a critical role in food security,livestock feed supply,and the vegetable oil industry.1 Genetic transformation ...Dear Editor,Soybean(Glycine max)is one of the world’s most important economic and oilseed crops.It plays a critical role in food security,livestock feed supply,and the vegetable oil industry.1 Genetic transformation is a fundamental technology in soybean gene function research and molecular breeding.However,conventional soybean transformation methods rely on plant tissue culture,which is labor-intensive,time-consuming,costly,low in efficiency,and highly genotype dependent.展开更多
GABA,a non-proteinogenic amino acid with anti-hypertensive properties,holds health-beneficial potential when enriched in crops.Previous studies have established that targeted disruption of the calmodulin-binding domai...GABA,a non-proteinogenic amino acid with anti-hypertensive properties,holds health-beneficial potential when enriched in crops.Previous studies have established that targeted disruption of the calmodulin-binding domain(CaMBD)of the tomato glutamate decarboxylase 3(SlGAD3)enhances GABA biosynthesis.In this study,we used CRISPR/Cas9-mediated gene editing to precisely modify the CaMBD coding sequence of SlGAD3 in three elite tomato varieties(SFT1,SFT2,and SFT3).Under our experimental conditions,targeted editing of SlGAD3 led to substantial accumulation of GABA in all three varieties without compromising key agronomic traits such as fruit size and number.Although flowering was delayed in SFT2 and SFT3 mutants,SFT1 mutants had higher GABA levels but also maintained a wild-type flowering time.This result highlights the critical importance of selecting specific varieties,such as SFT1,to minimize pleiotropic effects.By identifying varieties that can accumulate high levels of GABA without major reductions in growth and yield potential,this work bridges a critical gap between plant metabolic-engineering research and practical applications in commercial crop-improvement programs.展开更多
基金This work was supported by the National Natural Science Foundation of China(32270367)the Office of Education of Anhui Province for Distinguished Young Scholars(2022AH020061)the National Key Research and Development Program of China(2021YFA1300401 and NK2022010301).
文摘Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases.In recent years,the study of DNA methylation in regulating the growth and development of plants and animals has become a key area of research.This review describes the regulatory mechanisms of DNA cytosine methylation in plants.It summarizes studies on epigenetic modifications of DNA methylation in fruit ripening,development,senescence,plant height,organ size,and under biotic and abiotic stresses in horticultural crops.The review provides a theoretical basis for understanding the mechanisms of DNA methylation and their relevance to breeding,genetic improvement,research,innovation,and exploitation of new cultivars of horticultural crops.
基金This work was supported by the Shanghai Agricultural Science and Technology Innovation Project(T2023315)Authors also thank the financial support from National Natural Science Foundation of China(32102451)Shanghai Rising-Star Program(22QB1404100).
文摘The freshness phenotype of fruit and vegetables is a critical determinant of consumer satisfaction,selection,and public health,which plays a pivotal role in postharvest quality management.This paper presents a review of the definition and detection techniques used to assess and maintain this vital freshness phenotype.Advanced intel-ligent packaging technologies,that incorporate sensors,indicators,and data carrier systems,and their roles in dynamically monitoring the freshness phenotype during storage and transportation are discussed.The integration of nondestructive testing(NDT)methods such as near-infrared spectroscopy(NIR),hyperspectral imaging(HSI),machine vision,and light detection and ranging(LiDAR)offers real-time,precise assessments of the freshness phenotype without compromising the integrity of the produce.By understanding the underlying mechanisms of the fruit and vegetable freshness phenotype,this paper discusses the definition,detection technologies,and gaps that require further research.The integration of advanced quantitative models with NDT and intelligent pack-aging solutions has the potential to reduce food waste.This advancement will lead to better quality control,extended shelf life,and increased consumer confidence in fresh produce,driving innovation and application within the food industry.
文摘DNA methylation is typically regarded as a repressive epigenetic marker for gene expression.Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence(MEMS) in the promoter of the DNA demethylase gene ROS_1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS_1 expression. How DNA methylation in the MEMS region promotes ROS_1 expression is not known. Here, we show that several Su(var)3-9 homologs(SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS_1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS.Mutations in the SUVHs lead to decreased ROS_1 expression, causing DNA hypermethylation at more than 1,000 genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation.
基金supported by the Chinese Academy of SciencesNational Nature Science Foundation of China(32002046)Natural Science Foundation of Jiangsu Province(BK20200948)。
文摘Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression.The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at 1000 s of genomic regions in Arabidopsis.How ROS1 is regulated and targeted to specific genomic regions is not well understood.Here,we report the discovery of an Arabidopsis protein complex that contains ROS1,regulates ROS1 gene expression,and likely targets the ROS1 protein to specific genomic regions.ROS1 physically interacts with a WD40 domain protein(RWD40),which in turn interacts with a methyl-DNA binding protein(RMB1)as well as with a zinc finger and homeobox domain protein(RHD1).RMB1 binds to DNA that is methylated in any sequence context,and this binding is necessary for its function in vivo.Loss-of-function mutations in RWD40,RMB1,or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1.Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter,plants mutated in RWD40,RMB1,or RHD1 show increased ROS1 expression.Importantly,ROS1 binding to the ROS1 promoter requires RWD40,RMB1,and RHD1,suggesting that this complex dictates ROS1 targeting to this locus.Our results demonstrate that ROS1 forms a protein complex with RWD40,RMB1,and RHD1,and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.
基金supported by the National Key Research and Development Program(2018YFD1000200)(Z.L.)Major Project of Transgenic Crops of China(2019ZX08010003-002-006)(Y.L.)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27040000)(Z.L.)。
文摘The widely used Streptococcus pyogenes Cas9(SpCas9)requires NGG as a protospacer adjacent motif(PAM)for genome editing.Although Sp Cas9 is a powerful genome-editing tool,its use has been limited on the targetable genomic locus lacking NGG PAM.The Sp Cas9 variants xCas9 and Cas9-NG have been developed to recognize NG,GAA,and GAT PAMs in human cel s.Here,we show that xCas9 cannot recognize NG PAMs in tomato,and Cas9-NG can recognize some of our tested NG PAMs in the tomato and Arabidopsis genomes.In addition,we engineered BrSp Cas9(XNG-Cas9)based on mutations from both xCas9 and Cas9-NG,and found that XNG-Cas9 can efficiently mutagenize endogenous target sites with NG,GAG,GAA,and GAT PAMs in the tomato or Arabidopsis genomes.The PAM compatibility of XNG-Cas9 is the broadest reported to date among Cas9 s(SpCas9 and Cas9-NG)active in plant.
基金supported by Bel agen Biotechnology Inc.,and by the National Key Research and Development Program of China(No.NK2022010301)the Seed-Industrialized Development Program in Shandong Province,China(No.2021LZGC003)+3 种基金the Key Research&Development Program of Shandong Province,China(No.2021LZGC012)the Innovative research team of Anhui Education(No.2022AH010056)the National Natural Science Foundation of China(No.32270367)the Ph D Scientific Research and Innovation Foundation of Sanya Yazhou Bay Science and Technology City(No.HSPHDSRF-2023-11-007)。
文摘Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal feed.mi R396 genes have been shown to negatively regulate grain size in rice,but whether mi R396 family members may function in a similar manner in soybean is unknown.Here,we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean mi R396genes through genome editing with clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas)12SF01 in the elite soybean cultivar Zhonghuang 302(ZH302).Four triple mutants(mir396aci,mir396acd,mir396adf,and mir396cdf),two quadruple mutants(mir396-abcd and mir396acfi),and two quintuple mutants(mir396abcdf and mir396bcdfi)were characterized.We found that plants of all the mir396 mutants produced larger seeds compared to ZH302 plants.Field tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower latitude.In contrast,mir396abcdf and mir396bcdfiplants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues,but they are suited for low latitude growth zones with increased yield without lodging problems.Taken together,our study demonstrated that loss-of-function of mi R396 genes leads to significantly enlarged seed size and increased yield in soybean,providing valuable germplasms for breeding high-yield soybean.
基金supported by the National Natural Science Foundation of China(32188102 to J.-K.Z.)the Key R&D Program of Shandong Province,China(2021LZGC012-004 to H.X.)Bellagen Biotechnology Co.Ltd.,Jinan,China。
文摘Soybean(Glycine max(L.)Merr.)is a major source of vegetable protein and oil in human diet and animal nutrition.Soybean seeds have been extensively used in various food products and snacks.Taste quality,particularly the aroma,affects cooking and eating,and ultimately influences consumer preference.Soy milk is particularly popular in China and has been gaining popularity in many other countries in the world.
基金supported by Shandong Shunfeng Biotechnology Co.Ltd.,Jinan,China,the National Natural Science Foundation of China(32188102 and 32400338)the Shenzhen Science and Technology Program(KQTD20240729102038044)+1 种基金Guangdong S&T Program(2024B1111130001)the Basic Research Center,Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-BRC-AFIS-2025-03).
文摘Dear Editor,Soybean(Glycine max)is one of the world’s most important economic and oilseed crops.It plays a critical role in food security,livestock feed supply,and the vegetable oil industry.1 Genetic transformation is a fundamental technology in soybean gene function research and molecular breeding.However,conventional soybean transformation methods rely on plant tissue culture,which is labor-intensive,time-consuming,costly,low in efficiency,and highly genotype dependent.
基金supported by the National Key R&D Program of China(grant numbers:2022YFD2100101 and 2021YFA1300400)the National Natural Science Foundation of China(grant numbers:31671735 and 31970516)+3 种基金the Guangdong S&T Program(grant number:2024B1111130001)the Shenzhen Science and Technology Program(grant numbers:JCYJ20241202125311016 and KQTD20240729102038044)the Shandong Province Key R&D Program(Competitive Innovation Platform)(2023CXPT095)Shandong Shunfeng Biotechnology Co.Ltd.,Jinan,China.
文摘GABA,a non-proteinogenic amino acid with anti-hypertensive properties,holds health-beneficial potential when enriched in crops.Previous studies have established that targeted disruption of the calmodulin-binding domain(CaMBD)of the tomato glutamate decarboxylase 3(SlGAD3)enhances GABA biosynthesis.In this study,we used CRISPR/Cas9-mediated gene editing to precisely modify the CaMBD coding sequence of SlGAD3 in three elite tomato varieties(SFT1,SFT2,and SFT3).Under our experimental conditions,targeted editing of SlGAD3 led to substantial accumulation of GABA in all three varieties without compromising key agronomic traits such as fruit size and number.Although flowering was delayed in SFT2 and SFT3 mutants,SFT1 mutants had higher GABA levels but also maintained a wild-type flowering time.This result highlights the critical importance of selecting specific varieties,such as SFT1,to minimize pleiotropic effects.By identifying varieties that can accumulate high levels of GABA without major reductions in growth and yield potential,this work bridges a critical gap between plant metabolic-engineering research and practical applications in commercial crop-improvement programs.
