The aBIOTECH journal is pleased to announce that it will publish a Feature Issue on“AI in Crop Breeding”.In this issue,submission of articles addressing the following research areas would be welcomed.
Special Issue“AI in Crop Breeding”The aBIOTECH journal is pleased to announce that it will publish a Feature Issue on“AI in Crop Breeding”.In this issue,submission of articles addressing the following research are...Special Issue“AI in Crop Breeding”The aBIOTECH journal is pleased to announce that it will publish a Feature Issue on“AI in Crop Breeding”.In this issue,submission of articles addressing the following research areas would be welcomed。展开更多
The aBIOTECH journal is pleased to announce that it will publish a Feature Issue on"AI in 0 Crop Breeding".In this issue,submission of articles addressing the following research areas would be welcomed:Integ...The aBIOTECH journal is pleased to announce that it will publish a Feature Issue on"AI in 0 Crop Breeding".In this issue,submission of articles addressing the following research areas would be welcomed:Integration of multi-omic big data.展开更多
Plant metabolites are crucial for the growth,development,environmental adaptation,and nutritional quality of plants.Plant metabolomics,a key branch of systems biology,involves the comprehensive analysis and interpreta...Plant metabolites are crucial for the growth,development,environmental adaptation,and nutritional quality of plants.Plant metabolomics,a key branch of systems biology,involves the comprehensive analysis and interpretation of the composition,variation,and functions of these metabolites.Advances in technology have transformed plant metabolomics into a sophisticated process involving sample collection,metabolite extraction,high-throughput analysis,data processing,and multidimensional statistical analysis.In today’s era of big data,the field is witnessing an explosion in data acquisition,offering insight into the complexity and dynamics of plant metabolism.Moreover,multiple omics strategies can be integrated to reveal interactions and regulatory networks across different molecular levels,deepening our understanding of plant biological processes.In this review,we highlight recent advances and challenges in plant metabolomics,emphasizing the roles for this technique in improving crop varieties,enhancing nutritional value,and increasing stress resistance.We also explore the scientific foundations of plant metabolomics and its applications in medicine,and ecological conservation.展开更多
Soil salinization is a severely detrimental environmental problem that affects the seed germination,growth and yield of wheat.To excavate salt-tolerant genes and breed salt-tolerant wheat varieties are of great signif...Soil salinization is a severely detrimental environmental problem that affects the seed germination,growth and yield of wheat.To excavate salt-tolerant genes and breed salt-tolerant wheat varieties are of great significance for ensuring global food security.In this study,we have successfully developed a novel salt-tolerant wheat cultivar,KD808,which is shown to have remarkable salt tolerance through multiple phenotypic analyses.RNA-seq coupled with RT-qPCR analyses reveal that the expression of TaSGR-5B is up-regulated by salt stress treatment in the salt-sensitive wheat varieties such as KN199 and Fielder,whereas the salt-induction of TaSGR-5B is abolished in our salt-tolerant variety KD808.More importantly,we found that the loss-of-function Tasgr-aabbdd mutants exhibit significantly salt-tolerant phenotypes without penalties in major agronomic traits.This study not only provides valuable insights into the molecular mechanisms of salt tolerance in wheat but also offers substantial potential for improving wheat cultivation in saline-alkali soils,thereby contributing to sustainable agricultural production.展开更多
Potato common scab(CS)is a worldwide disease,caused by Streptomyces spp.,and its presence reduces the market value of potatoes.A nontoxic and potentially effective approach in many control strategies is the use of ant...Potato common scab(CS)is a worldwide disease,caused by Streptomyces spp.,and its presence reduces the market value of potatoes.A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents.In this study,Bacillus atrophaeus DX-9 was isolated and assessed for its ability to protect against CS.Through integrated metagenomic and metabolomic analyses,changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX-9 on CS.These studies revealed that DX-9 inoculation could significantly decrease CS disease rate,disease index,and the number of CS pathogens,along with an increase in soil N and P content.Our metagenomic assays identified 102 phyla and 1154 genera,and DX-9 inoculation increased the relative abundances of the phyla Pseudomonadota,Chloroflexota and Gemmatimonadota.Additionally,an increase in the relative abundance of genera,such as Bradyrhizobium,Agrobacterium,and Nitrobacter,were significantly and positively correlated with soil N and P.Metabolomic analysis revealed that DX-9 inoculation significantly increased the soil levels of phytolaccoside A,7,8-dihydropteroic acid,novobiocin,and azafrin.These compounds were enriched in microbe pathway metabolites,including xenobiotic biodegradation and metabolism,biosynthesis of other secondary metabolites,and metabolism of cofactors and vitamins.In summary,the use of Bacillus atrophaeus DX-9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties.This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.展开更多
Brassinosteroids(BRs),a class of plant-specific steroidal hormones,play crucial roles in regulating various plant physiological functions,such as growth,development,and adaptability to the environment.Despite this bro...Brassinosteroids(BRs),a class of plant-specific steroidal hormones,play crucial roles in regulating various plant physiological functions,such as growth,development,and adaptability to the environment.Despite this broader role of BRs,previously published reviews mainly focused on the molecular mechanisms of BR-mediated regulation of vegetative and reproductive growth of model plants like Arabidopsis and some food crops,such as rice,maize,and wheat.While horticultural plants hold significant economic importance in modern agriculture,less attention has been paid to understanding the role of BRs in regulating the physiological functions of these plants.Given the lack of relevant reviews,this article aims to discuss the major roles of BRs in horticultural plants,particularly fruit and leaf development,whole plant architecture,and adaptive stress response.We also highlight key challenges and provide some future research directions for genetically improving horticultural plants by altering the BR signaling pathway.展开更多
Meeting the increasing demand for food and industrial products by the growing global population requires targeted efforts to improve crops,livestock,and microorganisms.Modern biotechnology,particularly genetic modific...Meeting the increasing demand for food and industrial products by the growing global population requires targeted efforts to improve crops,livestock,and microorganisms.Modern biotechnology,particularly genetic modification(GM)and genome-editing(GE)technologies,is crucial for food security and environmental sustainability.China,which is at the forefront of global biotechnological innovation and the rapid advancements in GM and GE technologies,has prioritized this field by implementing strategic programs such as the National High-tech Research&Development Program in 1986,the National Genetically Modified Organism New Variety Breeding Program in 2008,and the Biological Breeding-National Science and Technology Major Project in 2022.Many biotechnological products have been widely commercialized in China,including biofertilizers,animal feed,animal vaccines,pesticides,and GM crops such as cotton(Gossypium hirsutum),maize(Zea mays),and soybean(Glycine max).In this review,we summarize progress on the research and utilization of GM and GE organisms in China over the past 3 decades and provide perspectives on their further development.This review thus aims to promote worldwide academic exchange and contribute to the further development and commercial success of agricultural biotechnology.展开更多
RXLR effectors are pathogenic factors secreted from oomycetes to manipulate the immunity of the host.Typical RXLR effectors contain an RXLR-dEER motif at the N-terminus,whereas atypical RXLRs show variations on this m...RXLR effectors are pathogenic factors secreted from oomycetes to manipulate the immunity of the host.Typical RXLR effectors contain an RXLR-dEER motif at the N-terminus,whereas atypical RXLRs show variations on this motif.The oomycete Phytophthora cactorum is known to infect over 200 plant species,resulting in significant agricultural economic losses.Although genome-wide identification and functional analyses of typical RXLRs from P.cactorum have been performed,little is known of atypical PcaRXLRs.Here,we identified RXLRs,both typical and atypical,in P.cactorum and compared them with those of other oomycete pathogens.Fewer RXLRs were identified in P.cactorum compared with other Phytophthora species,possibly due to fewer duplication events of RXLRs.In contrast,the percentage of atypical RXLRs was higher in P.cactorum than in other species,suggesting significant roles in P.cactorum pathogenesis.Analysis of RXLR gene expression showed that most were transcribed,suggesting their functionality.Transient expression of two atypical RXLRs in Nicotiana benthamiana showed that they induced necrosis dependent on host SGT1 and HSP90.Furthermore,two additional atypical RXLRs suppressed the defense response in N.benthamiana and promoted P.cactorum infection.These results demonstrate the vital role of atypical RXLRs in P.cactorum and provide valuable information on their evolutionary patterns and interactions with host plants.展开更多
Correction:aBIOTECH(2024)5:309-324 https://doi.org/10.1007/s42994-024-00176-2 The article Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza,written by Honggang Dai,Yaxin Fan,Yichao Mei,...Correction:aBIOTECH(2024)5:309-324 https://doi.org/10.1007/s42994-024-00176-2 The article Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza,written by Honggang Dai,Yaxin Fan,Yichao Mei,Ling-Ling Chen,Junxiang Gao,was originally published Online First without Open Access.After publication in volume 5,issue 3,pages 309–324 the authors decided to opt for Open Choice and to make the article an Open Access publication.展开更多
Recessive resistance mediated by mutations in the eukaryotic translation initiation factor 4E(eIF4E),has proven effective against diverse potyviruses and is extensively utilized in breeding programs.However,the rise o...Recessive resistance mediated by mutations in the eukaryotic translation initiation factor 4E(eIF4E),has proven effective against diverse potyviruses and is extensively utilized in breeding programs.However,the rise of resistance-breaking(RB)strains and emerging potyviral species necessitates the development of more durable and broad-spectrum resistance strategies.In this study,our field survey in Yunnan,China,identified potato virus Y(PVY)RB isolates,as well as the prevalence of tobacco vein banding mosaic virus(TVBMV)and chilli veinal mottle virus(ChiVMV),in tobacco carrying the recessive va locus,which lacks the eIF4E1-S susceptibility gene,due to a chromosomal deletion.Protein interaction and viral infection assays demonstrated that both eIF4E1-S and eIFiso4E-T are used by PVY RB as susceptibility factors for infection,with the combined inactivation of these genes confering durable resistance.Similarly,the knockout of eIFiso4E-S,in the va genetic background,provided effective resistance to TVBMV and reduced susceptibility to ChiVMV.Notably,pyramiding mutations in eIFiso4E-S and eIFiso4E-T,in va tobacco,generated plants exhibiting robust,broad-spectrum resistance,to all three viruses,without compromising plant development.These findings underscore the potential of stacking eIF4E mutations to engineer durable,broad-spectrum resistance to potyviruses in tobacco,offering a promising strategy for crop improvement.展开更多
Plant-pathogenic fungi significantly affect crop yield and quality.Understanding pathogenic mechanisms and reducing yield losses from plant diseases are therefore crucial for global food security.Epigenetics has becom...Plant-pathogenic fungi significantly affect crop yield and quality.Understanding pathogenic mechanisms and reducing yield losses from plant diseases are therefore crucial for global food security.Epigenetics has become a central focus in fungal biology research,and recent refinements in high-throughput sequencing technologies have drawn attention to the role of histone methylation in fungal pathogenicity.Due to their diversity and complexity,histone methylations play crucial roles in epigenetic and transcriptional regulation.In this review,we summarize recent progress in understanding histone methylation in plant-pathogenic fungi and examine how these modifications influence fungal pathogenicity.Ultimately,we aim to offer insight for creating fungal disease control strategies through the lens of histone methylation.展开更多
The advent of genome editing technologies,particularly CRISPR/Cas9,has significantly advanced the generation of legume mutants for reverse genetic studies and understanding the mechanics of the rhizobial symbiosis.The...The advent of genome editing technologies,particularly CRISPR/Cas9,has significantly advanced the generation of legume mutants for reverse genetic studies and understanding the mechanics of the rhizobial symbiosis.The legume–rhizobia symbiosis is crucial for sustainable agriculture,enhancing nitrogen fixation and improving soil fertility.Numerous genes with a symbiosis-specific expression have been identified,sometimes exclusively expressed in cells forming infection threads or in nitrogen-fixing nodule cells.Typically,mutations in these genes do not affect plant growth.However,in some instances,germline homozygous mutations can be lethal or result in complex pleiotropic phenotypes that are challenging to interpret.To address this issue,a rhizobia-inducible and cell-type-specific CRISPR/Cas9 strategy was developed to knock-out genes in specific legume transgenic root tissues.In this review,we discuss recent advancements in legume genome editing,highlighting the cell-type-specific CRISPR system and its crucial applications in symbiotic nitrogen fixation and beyond.展开更多
Correction:aBIOTECH https://doi.org/10.1007/s42994-025-00214-7 The original article contained several errors caused in the production process of the article:In this article the affiliation‘State Key Laboratory of See...Correction:aBIOTECH https://doi.org/10.1007/s42994-025-00214-7 The original article contained several errors caused in the production process of the article:In this article the affiliation‘State Key Laboratory of Seed Innovation,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,Beijing,100101,China’for Author Jia Yuan was missing.Greek letters and other symbols were missing in Figs.1 and 4 have now been included.展开更多
Cis-regulatory elements(CREs)are the genetic DNA fragments bound by transcription factors(TFs).CREs function as molecular switches that precisely modulate the dosage and spatiotemporal patterns of gene expression.The ...Cis-regulatory elements(CREs)are the genetic DNA fragments bound by transcription factors(TFs).CREs function as molecular switches that precisely modulate the dosage and spatiotemporal patterns of gene expression.The systematic identification of CREs not only facilitates the annotation of the functional non-coding genome but also provides essential insights into the architecture of gene regulatory networks and sheds light on an accurate selection of the target sites for genetic engineering of crops.In this review,we summarize the current high-throughput methodologies used for identifying CREs,illustrate the associations between CREs and agronomic traits in horticultural crops,and discuss how CREs can be exploited to facilitate crop breeding.展开更多
Pearl millet(Pennisetum glaucum)is a major staple food in arid and semi-arid regions of sub-Saharan Africa,India,and South Asia.However,how epigenetic mechanisms regulate tissue-specific gene expression in this crop r...Pearl millet(Pennisetum glaucum)is a major staple food in arid and semi-arid regions of sub-Saharan Africa,India,and South Asia.However,how epigenetic mechanisms regulate tissue-specific gene expression in this crop remains poorly understood.In this study,we profiled multiple epigenetic features in the young panicles and roots of pearl millet using RNA-seq,ATAC-seq,whole-genome bisulfite sequencing,and ChIP-seq(H3K4me3 and H3K36me3).We identified thousands of genes that were differentially expressed between these two tissues.Root-specific genes were enriched for plant hormone signaling,oxidative phosphorylation,and stress responses.Analysis of chromatin accessibility revealed that root-specific accessible chromatin regions(ACRs)were enriched in binding motifs for stress-responsive transcription factors(e.g.,NAC,WRKY),whereas ACRs in young panicles were enriched in motifs for developmental regulators(e.g.,AP2/ERF).DNA methylation profiling revealed 25,141 tissue-specific differentially methylated regions,with CHH methylation—rather than CG or CHG methylation—showing the strongest tissue specificity.Promoters of root-specific genes had higher levels of CHH methylation compared to those of young panicle–specific genes,suggesting that the roles of CHH methylation in regulating transcription might be tissue dependent.Notably,promoter-associated H3K4me3 marked panicle-specific genes,whereas root-specific expression was primarily linked to chromatin accessibility,suggesting a transcription factor–mediated regulatory mechanism.Together,our findings highlight the distinct epigenetic frameworks governing tissue-specific gene expression in pearl millet and provide valuable insights for advancing the genetic improvement of this crop.展开更多
The key factors for genome-editing in plants using CRISPR/Cas9,such as the Cas9 nuclease and guide RNA(gRNA)are typically expressed from a construct that is integrated into the plant genome.However,the presence of for...The key factors for genome-editing in plants using CRISPR/Cas9,such as the Cas9 nuclease and guide RNA(gRNA)are typically expressed from a construct that is integrated into the plant genome.However,the presence of foreign DNA in the host genome causes genetic and regulatory concerns,particularly for commercialization.To address this issue,we developed an accelerated pipeline for generating transgene-free genome-edited sorghum(Sorghum bicolor)in the T0 generation.For proof-of-concept,we selected the Phytoene desaturase(PDS)gene as the target due to its visible phenotype(albinism)upon mutation.Following microprojectile-mediated co-transformation with a maize(Zea mays)-optimized Cas9 vector and a guide RNA(gRNA)cassette with a geneticin(G418)resistance gene,we divided tissue derived from immature embryos into two groups(with and without antibiotic selection)and cultured them separately as parallel experiments.In regenerated plants cultured on medium containing MS basal nutrition(to allow albino plants to survive),we detected higher rates of albinism in the non-selection group,achieving editing rates of 11.1–14.3%compared with 4.2–8.3%in the antibiotic selection group.In the T0 generation,22.2–38.1%of albino plants from the non-selection group were identified as transgene-free,whereas only 0–5.9%from the selection group were transgene-free.Therefore,our strategy efficiently produced transgene-free genome-edited plants without the need for self-crossing or outcrossing,demonstrating the feasibility of achieving transgene-free genome-edited sorghum plants within a single generation.These findings pave the way for commercializing transgene-free genome-edited lines,particularly for vegetatively propagated crops like pineapple,sugarcane,and banana.展开更多
Synonymous mutations have traditionally been regarded as functionally neutral because they do not alter protein sequences.However,growing evidence suggests these variants can affect gene expression,RNA structure,and p...Synonymous mutations have traditionally been regarded as functionally neutral because they do not alter protein sequences.However,growing evidence suggests these variants can affect gene expression,RNA structure,and protein function,ultimately influencing phenotypes.A recent study by Xin et al.(2025)provides strong evidence that synonymous mutations can exert regulatory effects through epitranscriptomic mechanisms,particularly m^(6)A RNA methylation.The authors identify a synonymous 1287C>T mutation in the ACS2 gene that reduces m^(6)A methylation at the adjacent A^(1286)site.This reduction alters RNA secondary structure,creating a more compact conformation that impairs translation efficiency,leading to decreased ACS2 protein levels and promoting fruit elongation in cultivated cucumbers.The mutation lies within a domestication sweep region and ACS2^(1287C)is exclusively found in wild cucumber populations,suggesting that ACS2^(1287T)has been favored during domestication for its agronomic benefits.Notably,the study also uncovers a genotype-dependent interaction between ACS2 and the m^(6)A reader protein YTH1,which binds only to methylated transcripts,further illustrating how genetic background modulates epitranscriptomic regulation.These findings challenge the long-standing assumption that synonymous variants are biologically irrelevant and introduce RNA methylation as a key,dynamic regulatory layer in crop domestication and breeding,offering new opportunities for RNA-based precision breeding.展开更多
The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical...The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical limitations persist in current computational tools for quantifying editing efficiency-particularly concerning data processing capabilities,analytical throughput,and operational flexibility.This research presents SuperDecode,a novel computational framework designed to address these methodological constraints.The SuperDecode offers key advantages,including local processing capabilities,large-size sequencing files,batch-processing,and diversified operational functions.展开更多
Varieties with a semi-dwarf compact plant architecture may increase yield per unit area in rapeseed(Brassica napus)by allowing high-density cultivation and mechanical harvesting while conferring lodging resistance.Mut...Varieties with a semi-dwarf compact plant architecture may increase yield per unit area in rapeseed(Brassica napus)by allowing high-density cultivation and mechanical harvesting while conferring lodging resistance.Mutation of ERECTA(ER),which encodes a receptor-like protein kinase,generates a compact and upright plant architecture in Arabidopsis thaliana;however,there have been no reports on the roles of the ER family(ERf)in B.napus.In this study,we used the CRISPR/Cas9 system to generate mutants in each of the two homoeologs of B.napus ERf members BnaER and ER-Like 1(BnaERL1),and in the single BnaERL2 gene,resulting in the homozygous mutants BnaA09.er/BnaC08.er,BnaA06.erl1/BnaC03.erl1,and BnaA10.erl2.Under greenhouse conditions,BnaA09.er/BnaC08.er plants were shorter than the wild type,with a compact inflorescence and shorter siliques.In addition,BnaA09.er/BnaC08.er plants produced significantly more branches and total siliques than the wild type,with no significant changes in the number of ovules per silique or thousand-seed weight.Under field conditions,the BnaA09.er/BnaC08.er mutant plant showed a phenotype comparable to that under greenhouse conditions,but with a notable drop in thousand-seed weight.These results indicate that the BnaA09.er/BnaC08.er mutant offers a valuable germplasm resource for breeding rapeseed with ideal plant architecture.展开更多
文摘The aBIOTECH journal is pleased to announce that it will publish a Feature Issue on“AI in Crop Breeding”.In this issue,submission of articles addressing the following research areas would be welcomed.
文摘Special Issue“AI in Crop Breeding”The aBIOTECH journal is pleased to announce that it will publish a Feature Issue on“AI in Crop Breeding”.In this issue,submission of articles addressing the following research areas would be welcomed。
文摘The aBIOTECH journal is pleased to announce that it will publish a Feature Issue on"AI in 0 Crop Breeding".In this issue,submission of articles addressing the following research areas would be welcomed:Integration of multi-omic big data.
基金financially supported by grants from the National Natural Science Foundation of China(No.32101662)Natural Science Foundation of Hainan Province(No.323RC421)+3 种基金Hainan Province Science and Technology Special Fund(No.ZDYF2022XDNY144)Hainan Provincial Academician Innovation Platform Project(No.HD-YSZX-202004)Hainan University Startup Fund(No.KYQD(ZR)21025)Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture,Hainan University(No.XTCX2022NYB06).
文摘Plant metabolites are crucial for the growth,development,environmental adaptation,and nutritional quality of plants.Plant metabolomics,a key branch of systems biology,involves the comprehensive analysis and interpretation of the composition,variation,and functions of these metabolites.Advances in technology have transformed plant metabolomics into a sophisticated process involving sample collection,metabolite extraction,high-throughput analysis,data processing,and multidimensional statistical analysis.In today’s era of big data,the field is witnessing an explosion in data acquisition,offering insight into the complexity and dynamics of plant metabolism.Moreover,multiple omics strategies can be integrated to reveal interactions and regulatory networks across different molecular levels,deepening our understanding of plant biological processes.In this review,we highlight recent advances and challenges in plant metabolomics,emphasizing the roles for this technique in improving crop varieties,enhancing nutritional value,and increasing stress resistance.We also explore the scientific foundations of plant metabolomics and its applications in medicine,and ecological conservation.
基金supported by the National Key Research and Development Program of China(2023YFF1000600,2023YFD1200403,2023YFF1000402)the Innovation Program of Chinese Academy of Agricultural Sciences.
文摘Soil salinization is a severely detrimental environmental problem that affects the seed germination,growth and yield of wheat.To excavate salt-tolerant genes and breed salt-tolerant wheat varieties are of great significance for ensuring global food security.In this study,we have successfully developed a novel salt-tolerant wheat cultivar,KD808,which is shown to have remarkable salt tolerance through multiple phenotypic analyses.RNA-seq coupled with RT-qPCR analyses reveal that the expression of TaSGR-5B is up-regulated by salt stress treatment in the salt-sensitive wheat varieties such as KN199 and Fielder,whereas the salt-induction of TaSGR-5B is abolished in our salt-tolerant variety KD808.More importantly,we found that the loss-of-function Tasgr-aabbdd mutants exhibit significantly salt-tolerant phenotypes without penalties in major agronomic traits.This study not only provides valuable insights into the molecular mechanisms of salt tolerance in wheat but also offers substantial potential for improving wheat cultivation in saline-alkali soils,thereby contributing to sustainable agricultural production.
基金supported by the Inner Mongolia Autonomous Region Key Technology Tackling Programmed(Grant number:2021GG0300)by Hebei Science and Technology Major Project(22287501Z)by the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant number:XDA28030202-3,XDA24020104).
文摘Potato common scab(CS)is a worldwide disease,caused by Streptomyces spp.,and its presence reduces the market value of potatoes.A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents.In this study,Bacillus atrophaeus DX-9 was isolated and assessed for its ability to protect against CS.Through integrated metagenomic and metabolomic analyses,changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX-9 on CS.These studies revealed that DX-9 inoculation could significantly decrease CS disease rate,disease index,and the number of CS pathogens,along with an increase in soil N and P content.Our metagenomic assays identified 102 phyla and 1154 genera,and DX-9 inoculation increased the relative abundances of the phyla Pseudomonadota,Chloroflexota and Gemmatimonadota.Additionally,an increase in the relative abundance of genera,such as Bradyrhizobium,Agrobacterium,and Nitrobacter,were significantly and positively correlated with soil N and P.Metabolomic analysis revealed that DX-9 inoculation significantly increased the soil levels of phytolaccoside A,7,8-dihydropteroic acid,novobiocin,and azafrin.These compounds were enriched in microbe pathway metabolites,including xenobiotic biodegradation and metabolism,biosynthesis of other secondary metabolites,and metabolism of cofactors and vitamins.In summary,the use of Bacillus atrophaeus DX-9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties.This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.
基金supported by the National Natural Science Foundation of China(grants 32030005,32470325,32400288)GuangDong Basic and Applied Basic Research Foundation(grant 2023A1515110339)internal funding from Guangzhou University.
文摘Brassinosteroids(BRs),a class of plant-specific steroidal hormones,play crucial roles in regulating various plant physiological functions,such as growth,development,and adaptability to the environment.Despite this broader role of BRs,previously published reviews mainly focused on the molecular mechanisms of BR-mediated regulation of vegetative and reproductive growth of model plants like Arabidopsis and some food crops,such as rice,maize,and wheat.While horticultural plants hold significant economic importance in modern agriculture,less attention has been paid to understanding the role of BRs in regulating the physiological functions of these plants.Given the lack of relevant reviews,this article aims to discuss the major roles of BRs in horticultural plants,particularly fruit and leaf development,whole plant architecture,and adaptive stress response.We also highlight key challenges and provide some future research directions for genetically improving horticultural plants by altering the BR signaling pathway.
基金Biological Breeding-National Science and Technology Major Project(2022ZD04021).
文摘Meeting the increasing demand for food and industrial products by the growing global population requires targeted efforts to improve crops,livestock,and microorganisms.Modern biotechnology,particularly genetic modification(GM)and genome-editing(GE)technologies,is crucial for food security and environmental sustainability.China,which is at the forefront of global biotechnological innovation and the rapid advancements in GM and GE technologies,has prioritized this field by implementing strategic programs such as the National High-tech Research&Development Program in 1986,the National Genetically Modified Organism New Variety Breeding Program in 2008,and the Biological Breeding-National Science and Technology Major Project in 2022.Many biotechnological products have been widely commercialized in China,including biofertilizers,animal feed,animal vaccines,pesticides,and GM crops such as cotton(Gossypium hirsutum),maize(Zea mays),and soybean(Glycine max).In this review,we summarize progress on the research and utilization of GM and GE organisms in China over the past 3 decades and provide perspectives on their further development.This review thus aims to promote worldwide academic exchange and contribute to the further development and commercial success of agricultural biotechnology.
基金funded by the Liaoning Applied Basic Research Program(2022JH2/101300284)Liaoning Agricultural Science and Technology Innovation Fund(2022XTCX0503 and 2023QN2417).
文摘RXLR effectors are pathogenic factors secreted from oomycetes to manipulate the immunity of the host.Typical RXLR effectors contain an RXLR-dEER motif at the N-terminus,whereas atypical RXLRs show variations on this motif.The oomycete Phytophthora cactorum is known to infect over 200 plant species,resulting in significant agricultural economic losses.Although genome-wide identification and functional analyses of typical RXLRs from P.cactorum have been performed,little is known of atypical PcaRXLRs.Here,we identified RXLRs,both typical and atypical,in P.cactorum and compared them with those of other oomycete pathogens.Fewer RXLRs were identified in P.cactorum compared with other Phytophthora species,possibly due to fewer duplication events of RXLRs.In contrast,the percentage of atypical RXLRs was higher in P.cactorum than in other species,suggesting significant roles in P.cactorum pathogenesis.Analysis of RXLR gene expression showed that most were transcribed,suggesting their functionality.Transient expression of two atypical RXLRs in Nicotiana benthamiana showed that they induced necrosis dependent on host SGT1 and HSP90.Furthermore,two additional atypical RXLRs suppressed the defense response in N.benthamiana and promoted P.cactorum infection.These results demonstrate the vital role of atypical RXLRs in P.cactorum and provide valuable information on their evolutionary patterns and interactions with host plants.
文摘Correction:aBIOTECH(2024)5:309-324 https://doi.org/10.1007/s42994-024-00176-2 The article Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza,written by Honggang Dai,Yaxin Fan,Yichao Mei,Ling-Ling Chen,Junxiang Gao,was originally published Online First without Open Access.After publication in volume 5,issue 3,pages 309–324 the authors decided to opt for Open Choice and to make the article an Open Access publication.
基金supported by National Natural Science Foundation of China(31860490)YNTC funds(2023530000241007 and 2017YN02)+1 种基金Yunnan Daguan Lab(YNDG202302ZY01)CLZ is supported by the Postdoctoral Fellowship Program of CPSF under grant number GZC20241527。
文摘Recessive resistance mediated by mutations in the eukaryotic translation initiation factor 4E(eIF4E),has proven effective against diverse potyviruses and is extensively utilized in breeding programs.However,the rise of resistance-breaking(RB)strains and emerging potyviral species necessitates the development of more durable and broad-spectrum resistance strategies.In this study,our field survey in Yunnan,China,identified potato virus Y(PVY)RB isolates,as well as the prevalence of tobacco vein banding mosaic virus(TVBMV)and chilli veinal mottle virus(ChiVMV),in tobacco carrying the recessive va locus,which lacks the eIF4E1-S susceptibility gene,due to a chromosomal deletion.Protein interaction and viral infection assays demonstrated that both eIF4E1-S and eIFiso4E-T are used by PVY RB as susceptibility factors for infection,with the combined inactivation of these genes confering durable resistance.Similarly,the knockout of eIFiso4E-S,in the va genetic background,provided effective resistance to TVBMV and reduced susceptibility to ChiVMV.Notably,pyramiding mutations in eIFiso4E-S and eIFiso4E-T,in va tobacco,generated plants exhibiting robust,broad-spectrum resistance,to all three viruses,without compromising plant development.These findings underscore the potential of stacking eIF4E mutations to engineer durable,broad-spectrum resistance to potyviruses in tobacco,offering a promising strategy for crop improvement.
基金supported by Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding(2021C02064)the National Natural Science Foundation of China(32370200).
文摘Plant-pathogenic fungi significantly affect crop yield and quality.Understanding pathogenic mechanisms and reducing yield losses from plant diseases are therefore crucial for global food security.Epigenetics has become a central focus in fungal biology research,and recent refinements in high-throughput sequencing technologies have drawn attention to the role of histone methylation in fungal pathogenicity.Due to their diversity and complexity,histone methylations play crucial roles in epigenetic and transcriptional regulation.In this review,we summarize recent progress in understanding histone methylation in plant-pathogenic fungi and examine how these modifications influence fungal pathogenicity.Ultimately,we aim to offer insight for creating fungal disease control strategies through the lens of histone methylation.
基金funded by the National Natural Science Foundation of China(32200208 to J-PG,and 32170250 to JDM)J-PG is supported by a grant to the University of Cambridge by the Bill&Melinda Gates Foundation and the UK Foreign,Commonwealth and Development Office(OPP1028264)known as the Enabling Nutrient Symbioses in Agriculture(ENSA)projectYS is supported by the China Scholarship Council(202208310095).
文摘The advent of genome editing technologies,particularly CRISPR/Cas9,has significantly advanced the generation of legume mutants for reverse genetic studies and understanding the mechanics of the rhizobial symbiosis.The legume–rhizobia symbiosis is crucial for sustainable agriculture,enhancing nitrogen fixation and improving soil fertility.Numerous genes with a symbiosis-specific expression have been identified,sometimes exclusively expressed in cells forming infection threads or in nitrogen-fixing nodule cells.Typically,mutations in these genes do not affect plant growth.However,in some instances,germline homozygous mutations can be lethal or result in complex pleiotropic phenotypes that are challenging to interpret.To address this issue,a rhizobia-inducible and cell-type-specific CRISPR/Cas9 strategy was developed to knock-out genes in specific legume transgenic root tissues.In this review,we discuss recent advancements in legume genome editing,highlighting the cell-type-specific CRISPR system and its crucial applications in symbiotic nitrogen fixation and beyond.
文摘Correction:aBIOTECH https://doi.org/10.1007/s42994-025-00214-7 The original article contained several errors caused in the production process of the article:In this article the affiliation‘State Key Laboratory of Seed Innovation,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,Beijing,100101,China’for Author Jia Yuan was missing.Greek letters and other symbols were missing in Figs.1 and 4 have now been included.
基金supported by the National Natural Science Foundation of China(32170554,32372666,32370582)the National Key Research and Development Program of China(2024YFC3407200)+1 种基金the Project of National Key Laboratory of Tropical Crop Breeding(NKLTCB-RC202402 and NKLTCBCXTD26)“Chu Ying”Young Talent Project of Fujian,Funding for High-level Overseas Personnel(Ministry of Human Resources and Social Security).
文摘Cis-regulatory elements(CREs)are the genetic DNA fragments bound by transcription factors(TFs).CREs function as molecular switches that precisely modulate the dosage and spatiotemporal patterns of gene expression.The systematic identification of CREs not only facilitates the annotation of the functional non-coding genome but also provides essential insights into the architecture of gene regulatory networks and sheds light on an accurate selection of the target sites for genetic engineering of crops.In this review,we summarize the current high-throughput methodologies used for identifying CREs,illustrate the associations between CREs and agronomic traits in horticultural crops,and discuss how CREs can be exploited to facilitate crop breeding.
基金supported by the National Key Research and Development Program of China(2024YFC3407200,2023YFF1000800)the National Natural Science Foundation of China(32170554,32370582)+2 种基金the Natural Science Foundation of Fujian(2023J01486)the“Chu Ying”young talent project of Fujian,and funding for High-level Overseas Personnel(Ministry of Human Resources and Social Security)the Department of Science and Technology of Xizang Autonomous Region(No.XZ202501ZY0021).
文摘Pearl millet(Pennisetum glaucum)is a major staple food in arid and semi-arid regions of sub-Saharan Africa,India,and South Asia.However,how epigenetic mechanisms regulate tissue-specific gene expression in this crop remains poorly understood.In this study,we profiled multiple epigenetic features in the young panicles and roots of pearl millet using RNA-seq,ATAC-seq,whole-genome bisulfite sequencing,and ChIP-seq(H3K4me3 and H3K36me3).We identified thousands of genes that were differentially expressed between these two tissues.Root-specific genes were enriched for plant hormone signaling,oxidative phosphorylation,and stress responses.Analysis of chromatin accessibility revealed that root-specific accessible chromatin regions(ACRs)were enriched in binding motifs for stress-responsive transcription factors(e.g.,NAC,WRKY),whereas ACRs in young panicles were enriched in motifs for developmental regulators(e.g.,AP2/ERF).DNA methylation profiling revealed 25,141 tissue-specific differentially methylated regions,with CHH methylation—rather than CG or CHG methylation—showing the strongest tissue specificity.Promoters of root-specific genes had higher levels of CHH methylation compared to those of young panicle–specific genes,suggesting that the roles of CHH methylation in regulating transcription might be tissue dependent.Notably,promoter-associated H3K4me3 marked panicle-specific genes,whereas root-specific expression was primarily linked to chromatin accessibility,suggesting a transcription factor–mediated regulatory mechanism.Together,our findings highlight the distinct epigenetic frameworks governing tissue-specific gene expression in pearl millet and provide valuable insights for advancing the genetic improvement of this crop.
基金GRDC(Grains Research&Development Corporation)for funding the GRDC Better Sorghum with Larger Grain project(2018–2022).
文摘The key factors for genome-editing in plants using CRISPR/Cas9,such as the Cas9 nuclease and guide RNA(gRNA)are typically expressed from a construct that is integrated into the plant genome.However,the presence of foreign DNA in the host genome causes genetic and regulatory concerns,particularly for commercialization.To address this issue,we developed an accelerated pipeline for generating transgene-free genome-edited sorghum(Sorghum bicolor)in the T0 generation.For proof-of-concept,we selected the Phytoene desaturase(PDS)gene as the target due to its visible phenotype(albinism)upon mutation.Following microprojectile-mediated co-transformation with a maize(Zea mays)-optimized Cas9 vector and a guide RNA(gRNA)cassette with a geneticin(G418)resistance gene,we divided tissue derived from immature embryos into two groups(with and without antibiotic selection)and cultured them separately as parallel experiments.In regenerated plants cultured on medium containing MS basal nutrition(to allow albino plants to survive),we detected higher rates of albinism in the non-selection group,achieving editing rates of 11.1–14.3%compared with 4.2–8.3%in the antibiotic selection group.In the T0 generation,22.2–38.1%of albino plants from the non-selection group were identified as transgene-free,whereas only 0–5.9%from the selection group were transgene-free.Therefore,our strategy efficiently produced transgene-free genome-edited plants without the need for self-crossing or outcrossing,demonstrating the feasibility of achieving transgene-free genome-edited sorghum plants within a single generation.These findings pave the way for commercializing transgene-free genome-edited lines,particularly for vegetatively propagated crops like pineapple,sugarcane,and banana.
基金supported by the National Research Foundation Competitive Research Programme(grant no.NRFCRP22-2019-0001)intramural research support from Temasek Life Sciences Laboratory and National University of Singapore.
文摘Synonymous mutations have traditionally been regarded as functionally neutral because they do not alter protein sequences.However,growing evidence suggests these variants can affect gene expression,RNA structure,and protein function,ultimately influencing phenotypes.A recent study by Xin et al.(2025)provides strong evidence that synonymous mutations can exert regulatory effects through epitranscriptomic mechanisms,particularly m^(6)A RNA methylation.The authors identify a synonymous 1287C>T mutation in the ACS2 gene that reduces m^(6)A methylation at the adjacent A^(1286)site.This reduction alters RNA secondary structure,creating a more compact conformation that impairs translation efficiency,leading to decreased ACS2 protein levels and promoting fruit elongation in cultivated cucumbers.The mutation lies within a domestication sweep region and ACS2^(1287C)is exclusively found in wild cucumber populations,suggesting that ACS2^(1287T)has been favored during domestication for its agronomic benefits.Notably,the study also uncovers a genotype-dependent interaction between ACS2 and the m^(6)A reader protein YTH1,which binds only to methylated transcripts,further illustrating how genetic background modulates epitranscriptomic regulation.These findings challenge the long-standing assumption that synonymous variants are biologically irrelevant and introduce RNA methylation as a key,dynamic regulatory layer in crop domestication and breeding,offering new opportunities for RNA-based precision breeding.
文摘The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical limitations persist in current computational tools for quantifying editing efficiency-particularly concerning data processing capabilities,analytical throughput,and operational flexibility.This research presents SuperDecode,a novel computational framework designed to address these methodological constraints.The SuperDecode offers key advantages,including local processing capabilities,large-size sequencing files,batch-processing,and diversified operational functions.
基金supported by the National Key Researchand Development Program ofChina(2022YFD1200400)the National Natural Science Foundation of China(32072099,31971977).
文摘Varieties with a semi-dwarf compact plant architecture may increase yield per unit area in rapeseed(Brassica napus)by allowing high-density cultivation and mechanical harvesting while conferring lodging resistance.Mutation of ERECTA(ER),which encodes a receptor-like protein kinase,generates a compact and upright plant architecture in Arabidopsis thaliana;however,there have been no reports on the roles of the ER family(ERf)in B.napus.In this study,we used the CRISPR/Cas9 system to generate mutants in each of the two homoeologs of B.napus ERf members BnaER and ER-Like 1(BnaERL1),and in the single BnaERL2 gene,resulting in the homozygous mutants BnaA09.er/BnaC08.er,BnaA06.erl1/BnaC03.erl1,and BnaA10.erl2.Under greenhouse conditions,BnaA09.er/BnaC08.er plants were shorter than the wild type,with a compact inflorescence and shorter siliques.In addition,BnaA09.er/BnaC08.er plants produced significantly more branches and total siliques than the wild type,with no significant changes in the number of ovules per silique or thousand-seed weight.Under field conditions,the BnaA09.er/BnaC08.er mutant plant showed a phenotype comparable to that under greenhouse conditions,but with a notable drop in thousand-seed weight.These results indicate that the BnaA09.er/BnaC08.er mutant offers a valuable germplasm resource for breeding rapeseed with ideal plant architecture.
