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Histological,transcriptomic,and gene functional analyses of flower transition in lily 认领 引用
1
作者 Dandan Liu Jiahui Liang +5 位作者 Wenqiang Pan Mingfang Zhang Fengping Yang Shiyin Yu Zhixuan Zhang Yunpeng Du 《Ornamental Plant Research》 2025年第1期418-429,共12页
Lilies are globally cultivated ornamental flowers and an economic crop,whose flower bud initiation is regulated by a complex interplay of intrinsic factors and external environmental conditions;however,this mechanism ... Lilies are globally cultivated ornamental flowers and an economic crop,whose flower bud initiation is regulated by a complex interplay of intrinsic factors and external environmental conditions;however,this mechanism remains largely unknown.In the present study,RNA sequencing(RNA-seq)coupled with histological and gene functional data were employed to reveal the differences in flower bud initiation between various lily cultivars.The results exhibited that the floral buds of the O-series'Brasilia'and'Hachi'differentiated quickly,the LA-series'Purple Marble'and the OA-series'Hotel California'were slower compared to the O-series.Additionally,the T-series'Yellow Planet'and OT-series'Red Morning'floral buds differentiated later.By comparing'Yellow Planet'and'Red Morning'with the'Brasilia,''Hachi,''Purple Marble',and OA-series'Hotel California',5,829 upregulated genes,1,010 downregulated genes,and some differentially expressed genes(DEGS)involved in pathways such as photoperiod,gibberellin,age,vernalization,autonomous,and temperature were identified.A flowering transition-related gene,FCA,was identified,and the effectiveness of the virus-induced gene silencing(VIGS)system was validated.The results showed the expression of LtFCA was successfully knocked down using the VIGS system,leading to compromised flower bud initiation in silenced lily plants.This observation underscores a potential correlation between the expression patterns of flowering regulatory genes and the distinct species within the lily series.In conclusion,this research provides a basis for understanding the regulatory mechanisms of flower bud transition in lilies. 展开更多
关键词 flower bud flower transition histological gene functional data floral buds transcriptomic analysis histological analysis gene functional analysis lily
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A simple and efficient gene functional analysis method for studying the growth and development of peach seedlings 认领 引用 被引量：2
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作者 Jun Cheng Yun Shao +11 位作者 Xinyue Hu Liying Gao Xianbo Zheng Bin Tan Xia Ye Wei Wang Haipeng Zhang Xiaobei Wang Xiaodong Lian Zhiqian Li Jiancan Feng Langlang Zhang 《Horticulture Research》 SCIE CSCD 2024年第7期379-387,共9页
Stable genetic transformation of peach[Prunus persica(L.)Batsch]still faces many technical challenges,and existing transient expression methods are limited by tissue type or developmental stage,making it difficult to ... Stable genetic transformation of peach[Prunus persica(L.)Batsch]still faces many technical challenges,and existing transient expression methods are limited by tissue type or developmental stage,making it difficult to conduct functional analysis of genes regulating shoot growth.To overcome this dilemma,we developed a three-step method for efficient analysis of gene functions during peach seedling growth and development.This method resulted in transformation frequencies ranging from 48 to 87%,depending on the gene.From transformation of germinating seeds to phenotyping of young saplings took just 1.5 months and can be carried out any time of year.To test the applicability of this method,the function of three tree architecture-related genes,namely PpPDS,PpMAX4,and PpWEEP,and two lateral root-related genes,PpIAA14–1 and−2,were confirmed.Since functional redundancy can challenge gene functional analyses,tests were undertaken with the growth-repressor DELLA,which has three homologous genes,PpDGYLA(DG),PpDELLA1(D1),and−2(D2),in peach that are functionally redundant.Silencing using a triple-target vector(TRV2-DG-D1-D2)resulted in transgenic plants taller than those carrying just TRV2-DG or TRV2.Simultaneously silencing the three DELLA genes also attenuated the stature of two dwarf genotypes,‘FHSXT’and‘HSX’,which normally accumulate DELLA proteins.Our study provides a method for the functional analysis of genes in peach and can be used for the study of root,stem,and leaf development.We believe this method can be replicated in other woody plants. 展开更多
关键词 transformation frequencies stable genetic transformation gene functional analysis functional analysis peach seedlings analysis gene functions transient expression methods
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Cucurbitaceae genome evolution,gene function,and molecular breeding 认领 引用 被引量：21
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作者 Lili Ma Qing Wang +12 位作者 Yanyan Zheng Jing Guo Shuzhi Yuan Anzhen Fu Chunmei Bai Xiaoyan Zhao Shufang Zheng Changlong Wen Shaogui Guo Lipu Gao Donald Grierson Jinhua Zuo Yong Xu 《Horticulture Research》 SCIE CSCD 2022年第1期108-131,共24页
Cucurbitaceae is one of the most genetically diverse plant families in the world.Many of them are important vegetables or medicinal plants and are widely distributed worldwide.The rapid development of sequencing techn... Cucurbitaceae is one of the most genetically diverse plant families in the world.Many of them are important vegetables or medicinal plants and are widely distributed worldwide.The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species.This has greatly facilitated research on gene identification,genome evolution,genetic variation,and molecular breeding of cucurbit crops.So far,genome sequences of 18 different cucurbit species belonging to tribes Benincaseae,Cucurbiteae,Sicyoeae,Momordiceae,and Siraitieae have been deciphered.This review summarizes the genome sequence information,evolutionary relationships,and functional genes associated with important agronomic traits(e.g.fruit quality).The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed. 展开更多
关键词 bioinformatic algorithms genome sequences gene function genome evolution cucurbitaceae medicinal plants sequencing technologies molecular breeding
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An effective method for studying gene function of Chinese cabbage 认领 引用
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作者 Tongkun Liu 《Vegetable Research》 2023年第1期267-268,共2页
Heading Chinese cabbage(Brassica rapa ssp.pekinensis),a cruciferous family species,is a common leafy vegetable crop native to northern China.Pan-genome and population variome analysis of B.rapa have been completed in ... Heading Chinese cabbage(Brassica rapa ssp.pekinensis),a cruciferous family species,is a common leafy vegetable crop native to northern China.Pan-genome and population variome analysis of B.rapa have been completed in recent years,laying a foundation for the study of gene functions in Chinese cabbage.In the current era of functional genomics,large-scale,high-throughput genome sequencing technologies are frequently used to study gene functions,and mutants are important materials for conducting related gene studies. 展开更多
关键词 study gene functions pan genome functional genomicslarge scalehigh throughput Brassica rapa ssp pekinensis population variome population variome analysis gene function Chinese cabbage
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Efficient isolation and transformation of protoplasts in coconut endosperm and leaves for gene function studies 认领 引用 被引量：3
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作者 Qinghui Guo Yaning Wang +2 位作者 Jixin Zou Huang Jing Dongdong Li 《Tropical Plants》 2023年第1期77-84,共8页
To establish a rapid and efficient method for isolating and transforming protoplasts in coconut endosperm,coconut liquid endosperm and young leaves were utilized as starting materials.By comparing factors such as enzy... To establish a rapid and efficient method for isolating and transforming protoplasts in coconut endosperm,coconut liquid endosperm and young leaves were utilized as starting materials.By comparing factors such as enzyme digestion time,quantity,activity,cell and nucleus morphology,ploidy,and subcellular localization,it was discovered that the optimal conditions for achieving the highest protoplast yield and activity were 45 min of enzyme digestion for liquid endosperm and 2.5 h for leaves.Furthermore,the endosperm cells were found to be 2−3 times larger than leaf cells and exhibited triploid characteristics.Moreover,DAPI staining and subcellular localization revealed the presence of significantly enlarged nuclei in protoplasts from coconut liquid endosperm,occupying nearly the entire cell.Using PEG-mediated transformation,the exogenous gene NAC96 was successfully overexpressed in protoplasts derived from both coconut leaves and endosperm.This study has established an efficient method for isolating and transforming protoplasts in coconut while identifying the distinct characteristics of protoplasts in liquid endosperm.These findings provide a crucial experimental platform for verifying coconut gene function and exploring gene expression regulation. 展开更多
关键词 protoplast isolation coconut endosperm transforming protoplasts protoplast transformation young leaves gene function studies coconut leaves liquid endosperm
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Predicting Arabidopsis thaliana Gene Function by Transitiving Co-expression in Shortest-path 认领 引用 被引量：1
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作者 SHI Feng-li HUANG Ji-feng 《Agricultural Science & Technology》 CAS 2010年第5期1-4,21,共4页
The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co... The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co-expression among genes can be used as an important attribute to link genes of the same biological pathway. The genes from the same biological pathway with similar functions are strongly correlated in expression. Moreover,the function of unknown genes can be predicted by the known genes where they are strongly correlated in expression lying on the same shortest-path from the biological pathway. Analyzing the Arabidopsis thaliana from the biological pathway,this study showed that this method can reliably reveal function of the unknown Arabidopsis thaliana genes and the approach of predicting gene function by transitiving co-expression in shortest-path is feasible and effective. 展开更多
关键词 Shortest-path Pathway Co-expression Gene function Arabidopsis thaliana
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A callus transformation system for gene functional studies in soybean 认领 引用
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作者 XU Kun ZHANG Xiao-mei +5 位作者 FAN Cheng-ming CHEN Fu-lu ZHU Jin-long ZHANG Shi-long CHEN Qing-shan FU Yong-fu 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2017年第9期1913-1922,共10页
Obtaining transgenic plants is a common method for analyzing gene function.Unfortunately,stable genetic transformation is difficult to achieve,especially for plants(e.g.,soybean),which are recalcitrant to genetic tran... Obtaining transgenic plants is a common method for analyzing gene function.Unfortunately,stable genetic transformation is difficult to achieve,especially for plants(e.g.,soybean),which are recalcitrant to genetic transformation.Transient expression systems,such as Arabidopsis protoplast,Nicotiana leaves,and onion bulb leaves are widely used for gene functional studies.A simple method for obtaining transgenic soybean callus tissues was reported recently.We extend this system with simplified culture conditions to gene functional studies,including promoter analysis,expression and subcellular localization of the target protein,and protein-protein interaction.We also evaluate the plasticity of this system with soybean varieties,different vector constructs,and various Agrobacterium strains.The results indicated that the callus transformation system is efficient and adaptable for gene functional investigation in soybean genotype-,vector-,and Agrobacterium strain-independent modes.We demonstrated an easy set-up and practical homologous strategy for soybean gene functional studies. 展开更多
关键词 soybean callus gene function studies transformation
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Application of Transgenic Technology in Identification for Gene Function on Grasses 认领 引用
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作者 Lijun Zhang Ying Liu +1 位作者 Yushou Ma Xinyou Wang Qinghai 《Phyton-International Journal of Experimental Botany》 SCIE 2024年第8期1913-1941,共29页
Perennial grasses have developed intricate mechanisms to adapt to diverse environments,enabling their resistance to various biotic and abiotic stressors.These mechanisms arise from strong natural selection that contri... Perennial grasses have developed intricate mechanisms to adapt to diverse environments,enabling their resistance to various biotic and abiotic stressors.These mechanisms arise from strong natural selection that contributes to enhancing the adaptation of forage plants to various stress conditions.Methods such as antisense RNA technology,CRISPR/Cas9 screening,virus-induced gene silencing,and transgenic technology,are commonly utilized for investigating the stress response functionalities of grass genes in both warm-season and cool-season varieties.This review focuses on the functional identification of stress-resistance genes and regulatory elements in grasses.It synthesizes recent studies on mining functional genes,regulatory genes,and protein kinase-like signaling factors involved in stress responses in grasses.Additionally,the review outlines future research directions,providing theoretical support and references for further exploration of(i)molecular mechanisms underlying grass stress responses,(ii)cultivation and domestication of herbage,(iii)development of high-yield varieties resistant to stress,and(iv)mechanisms and breeding strategies for stress resistance in grasses. 展开更多
关键词 Grasses regulatory genes protein kinase-like signaling factors gene function identification resistance breeding
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Integrating Gene Ontology and Blast to predict gene functions 认领 引用
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作者 WANG Cheng-gang MO Zhi-hong 《Journal of Chongqing University》 2007年第3期151-154,共4页
A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology(GO)annotations together.The operation system was based on Debian Linux 3.1,with Apache as the web server and Mysql data... A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology(GO)annotations together.The operation system was based on Debian Linux 3.1,with Apache as the web server and Mysql database as the data storage system.FASTA files with GO annotations were taken as the sequence source for blast alignment,which were formatted by wu-formatdb program.The GoBlast system includes three Bioperl modules in Perl:a data input module,a data process module and a data output module.A GoBlast query starts with an amino acid or nucleotide sequence.It ends with an output in an html page,presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts.A simple click on a GO term leads to the detailed explanation of the specific gene function.This avails gene function prediction by Blast.GoBlast can be a very useful tool for functional genome research and is available for free at http://gffzzd23624d77401408chqu99ouuwwk5x6opf.ffgz.tsg.suse.edu.cn/goblast. 展开更多
关键词 gene ontology Blast gene function prediction
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Single and combined impacts of antibiotics on aerobic denitrification:Cell growth characteristics and functional genes expressions 认领 引用
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作者 Rong-Rong Chang Chang-Ze Shi +4 位作者 Yun-Jie Ruan Bao-Cheng Huang Ren-Cun Jin Ming Dong Wen-Bing Li 《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2026年第2期461-467,共7页
Antibiotic contamination has garnered significant attention,particularly given the growing pressures from aquaculture,a key contributor to environmental antibiotic loads.Addressing both antibiotic and nitrogen polluti... Antibiotic contamination has garnered significant attention,particularly given the growing pressures from aquaculture,a key contributor to environmental antibiotic loads.Addressing both antibiotic and nitrogen pollution in such ecosystems is critical.In this study,the aerobic denitrifying bacterium Marinobacter hydrocarbonoclasticus RAD-2,previously isolated in our laboratory,was subjected to a series of concentration gradients(0,20,40,60,80,100 mg/L)to evaluate the single and combined effects of tetracycline(TET)and chlortetracycline(CTC)on the aerobic denitrification process.Among them,the combined effects of antibiotics were set up in a full-factor experimental design(a total of 30 treatment combinations)on the basis of the single-factor experiments of TET and CTC.Results demonstrated that the inhibitory impact of both antibiotics intensified with increasing concentration,with CTC exerting a more pronounced inhibitory effect.Notably,RAD-2 was unable to proliferate at 100 mg/L of TET or 80 mg/L of CTC.High concentrations of either antibiotic significantly suppressed the expression of key denitrification functional genes,including nirX,napA,norB,and nosZ.Furthermore,simultaneous exposure to both antibiotics led to a rapid decline in nitrogen removal efficiency(TET or CTC>60 mg/L),alongside substantial inhibition of bacterial growth and functional gene expression,except for napA.Under specific concentration ranges,the combination of TET and CTC exhibits a certain degree of antagonistic effect.These findings provide critical insights into the restoration of wetland ecosystem health and inform strategies to mitigate the dual challenges of antibiotic and nitrogen pollution in aquaculture effluents. 展开更多
关键词 Antibiotics Aerobic denitrification Synergistic effects Functional genes inhibition
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Functional genes associated with the occurrence of mycotoxins produced by Aspergillus in foods 认领 引用
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作者 Mei Gu Can Liu +4 位作者 Xiaofeng Yue Du Wang Xiaoqian Tang Qi Zhang Peiwu Li 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2026年第2期585-601,共17页
Aspergillus species are ubiquitous fungi that produce mycotoxins(secondary metabolites)known as sterigmatocystin and aflatoxins in many different kinds of foods,which leads to serious contamination in agricultural pro... Aspergillus species are ubiquitous fungi that produce mycotoxins(secondary metabolites)known as sterigmatocystin and aflatoxins in many different kinds of foods,which leads to serious contamination in agricultural products,thereby endangering human health.Extensive studies on Aspergillus fungi have been conducted on growth and development,aflatoxin biosynthesis,and their interactions with environment.Here,we summarized a series of functional genes of the main Aspergillus fungi relative to toxins occurrence in foods,which revealed the signal transduction mechanisms of their involvement in growth and development,toxin production,and response to light,anticipating providing theoretical guidance on developing control and prevention technologies for mycotoxin contamination in agricultural products to ensure food safety. 展开更多
关键词 functional genes Aspergillus aflatoxin development
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Evolutionary plasticity of MADS-box genes in ornamental plants:from floral development to horticultural improvement 认领 引用
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作者 Xinyi Zhou Meiyi She +10 位作者 Feng Wang Xiaojun Chang Biwei Hong Zhengjia Wang Giorgio Perrella D.Blaine Marchant Qiaomei Wang Kejun Cheng Zhonghua Chen Xiaohui Wen Liangsheng Zhang 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第8期1729-1746,共18页
The MADS-box gene family,particularly the ABCE-class genes,plays a pivotal role in regulating floral development and reproductive processes in angiosperms.Expansion of the MADS-box gene family through ancient whole-ge... The MADS-box gene family,particularly the ABCE-class genes,plays a pivotal role in regulating floral development and reproductive processes in angiosperms.Expansion of the MADS-box gene family through ancient whole-genome duplications and lineage-specific duplication events has generated extensive regulatory flexibility across flowering plants.This review summarizes current findings on the evolutionary expansion and functional diversification of MADS-box genes,with a focus on the evolution of the ABCE-class in ornamental plants.We highlight how differential gene retention,expression divergence,and functional specialization have shaped the remarkable morphological diversity of floral organs across flowering plants.Comparative analyses across angiosperms reveal a lineage-dependent distinction between phylogenetic A-class genes and the developmental A-function:while AP1 represents the canonical A-class gene in core eudicots,AGL6-like genes fulfill ancestral A-function roles in early-diverging angiosperms,magnoliids,and monocots.Lineage-specific expansion and rewiring of ABCE gene networks,as observed in Orchidaceae,Asteraceae,and Rosaceae,have enabled reassembly of MADS-box protein complexes and rebalancing of expression domains,driving innovative floral forms.Beyond floral development,numerous MADS-box genes have diversified to function in flowering-time regulation and environmental stress responses,highlighting their broader adaptive significance beyond reproduction.This review provides an integrated evolutionary and functional perspective on MADS-box genes plasticity,and offers valuable insights for ornamental plant breeding and horticultural improvement. 展开更多
关键词 ABCE model MADS-box Gene family expansion Gene function divergence Flower adaptability Biotic and abiotic stress
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Constitution and function of intergenic genome regions in cultivated versus annual wild soybean in China 认领 引用
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作者 Xiaoshuai Hao Xinyang Hu +9 位作者 Yongpeng Pan Qi Zhang Ran Ou Fenfen Jiang Fangdong Liu Jiaoping Zhang Wubin Wang Guangnan Xing Junyi Gai Jianbo He 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2026年第7期2105-2127,共23页
The subgenus Soja,including annual wild(Glycine soja)and cultivated soybean(Glycine max),is the primary germplasm source of soybeans.We analyzed the genome constitution of 750 wild and cultivated accessions from the C... The subgenus Soja,including annual wild(Glycine soja)and cultivated soybean(Glycine max),is the primary germplasm source of soybeans.We analyzed the genome constitution of 750 wild and cultivated accessions from the Chinese Soybean Germplasm Population(CSGP),covering~20.42%genic and~79.58%intergenic regions.Most previous genomic studies focused on gene compositions and functions,with intergenic regions being nonemphasized yet.Our results showed:(i)We defined48,465 gene blocks(2–23 alleles/gene block)in the genic region.For intergenic region partitioning,the linkage-disequilibrium(LD)confidence interval(CI)method performed the best,identifying 137,104 SNP LD blocks(SNPLDBs,2–24 haplotypes/SNPLDB).(ii)Wild and cultivated accessions shared 98.5%/80.9%genes/alleles and 88.0%/80.8%SNPLDBs/haplotypes,indicating high wild genomic contribution to the cultivated genome;genic and intergenic regions exhibit distinct allele/haplotype dynamics during domestication.(iii)We proposed the threecase restricted two-stage multi-locus multi-allele genome-wide association study(three-case RTMGWAS),identifying 82 day-to-flowering(DTF)maineffect genes and 47 intergenic-SNPLDB-impacted genes(by 34 SNPLDBs)(total 129 genes,746 alleles).These explained 98.87%of phenotypic variance(PV),with main-effect and SNPLDB-impacted genes accounting for 68.61%and 30.26%PV,respectively;gene-allele(s)impacted by SNPLDB-haplotype(one/both sides)were also identified.(iv)Domestication process excluded more large-effect positive alleles that shorten DTF in cultivated accessions,enhancing DTFÂs transgressive recombination potential in earliness.This study provides insights into genic/intergenic genome regions,offering a novel understanding of soybean functional genomics. 展开更多
关键词 annual wild soybean Glycine soja Sieb.&Zucc cultivated soybean Glycine max(L.)Merr days to flowering gene function intergenic impact linkage disequilibrium three-case RTM-GWAS
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Functional characterization of OsLT9 in regulating rice leaf thickness 认领 引用
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作者 Jian Wang Dagang Chen +9 位作者 Haifei Hu Yamei Ma Tifeng Yang Jie Guo Ke Chen Chanjuan Ye Juan Liu Xinqiao Zhou Chuanguang Liu Junliang Zhao 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2026年第2期223-233,共11页
Leaf thickness in rice critically influences photosynthetic efficiency and yield,yet its genetic basis remains poorly understood,with few functional genes previously characterized.In this study,we employ a pangenome-w... Leaf thickness in rice critically influences photosynthetic efficiency and yield,yet its genetic basis remains poorly understood,with few functional genes previously characterized.In this study,we employ a pangenome-wide association study(Pan-GWAS)on 302 diverse rice accessions from southern China,identifying 49 quantitative trait loci(QTLs)associated with leaf thickness.The most significant locus,qLT9,is fine-mapped to a 79-kb region on chromosome 9.Transcriptomic and genomic sequence analyses identify LOC_Os09g33480,which encodes a protein belonging to Multiple Organellar RNA Editing Factor family,as the key candidate gene.Overexpression and complementation transgenic experiments confirm LOC_Os09g33480(OsLT9)as the functional gene underlying qLT9,demonstrating a 24-bp Indel in its promoter correlates with the expression levels and leaf thickness.Notably,OsLT9 overexpression lines show not only thicker leaf,but also significantly enhanced photosynthetic efficiency and grain yield,establishing a link between leaf thickness modulation and yield enhancement.Population genomic analyses indicate strong selection for OsLT9 during domestication and breeding,with modern cultivars favoring thick leaf haplotype of OsLT9.This study establishes OsLT9 as a key regulator controlling leaf thickness in rice,and provides a valuable genetic resource for molecular breeding of high-yielding rice through optimization of plant architecture. 展开更多
关键词 Rice Leaf thickness GWAS Functional gene OsLT9
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Stabilization of plant-derived carbon from different green manure species mediated by carbon-decomposition genes 认领 引用
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作者 Tingyu Li Wei Feng +3 位作者 Tianshu Wang Yili Meng Shuihong Yao Xinhua Peng 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2026年第6期2545-2555,共11页
The integration of green manure(GM)crops into traditional cropping systems has regained attention for its potential to improve soil organic carbon(SOC)content in an environmentally sustainable way.However,the effects ... The integration of green manure(GM)crops into traditional cropping systems has regained attention for its potential to improve soil organic carbon(SOC)content in an environmentally sustainable way.However,the effects of carbon(C)input from different GM species on the SOC accumulation and recalcitrant C fractions across soil profile remain inadequately understood.This three-year field study in the North China Plain assessed SOC changes and C fractions of easily oxidizable carbon(EOC)and recalcitrant organic carbon(ROC)in fallow,rye,rapeseed,and vetch systems,with δ13C analysis for GM-derived C fraction and microbial C-decomposition functional genes.Our results showed that SOC was significantly increased by GMs.Rapeseed was the only species that improved SOC at 20–40 cm,the rapeseed-derived C contributed 2.48%of the SOC.Rye enhanced EOC and ROC at topsoil,rapeseed increased ROC at 20–60 cm,and vetch increased EOC at 40–60 cm.At the topsoil,the abundances of cellulose-and pectin-decomposition genes were increased in vetch and decreased in rye.At 20–40 cm,the pectin-and lignin-decomposition genes were markedly improved by rapeseed,while at 40–60 cm,the chitin-decomposition gene was increased in vetch,indicating the microbial promoting effects by deep roots of vetch and rapeseed.Our results suggest GM species infiuence SOC deposition depth and the recalcitrance of SOC decomposition,thereby affecting the distribution of SOC accumulation through microbial-driven C decomposition activities. 展开更多
关键词 green manure SOC storage C recalcitrance C functional genes
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Developing a homology-driven gene silencing system in Iris japonica:a versatile tool for comparative functional studies 认领 引用
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作者 Cheng Luo Zhiyan Wu +3 位作者 Lingmei Shao Jiaping Zhang Yiping Xia Danqing Li 《Ornamental Plant Research》 2025年第1期81-92,共12页
Iris japonica,an evergreen ornamental species known for its beautiful flowers and year-round evergreen foliage,is difficult to genetically manipulate due to the lack of an efficient genetic transformation system.This ... Iris japonica,an evergreen ornamental species known for its beautiful flowers and year-round evergreen foliage,is difficult to genetically manipulate due to the lack of an efficient genetic transformation system.This limitation hinders the functional verification of key genes in I.japonica.To address this,a Virus-Induced Gene Silencing(VIGS)system based on Tobacco rattle virus(TRV)was developed,enabling efficient,transient gene silencing in I.japonica.In this system,the phytoene desaturase(PDS)gene,a common reporter gene used for VIGS,was selected to assess the silencing efficiency.The recombinant vector pTRV2-IjPDS was used to infect I.japonica plants.The PDS gene silencing resulted in distinct photobleaching symptoms,demonstrating the successful silencing of the target gene.The presence of the TRV vector was verified by using a GFP-tagged pTRV2-GFP vector,and GFP expression was detected using fluorescence visualization under ultraviolet(UV)light and confirmed by laser confocal microscopy.Real-time PCR was used to quantify the reduction in IjPDS gene expression,confirming the successful silencing.The study further optimized the VIGS system by evaluating the impact of seedling ages on silencing efficiency,identifying one-year-old seedlings as the most effective for gene silencing(36.67%).This TRV-based VIGS system provides a robust tool for functional gene analysis in I.japonica and offers a new approach to studying the rules of key genes in its biological processes,with potential applications in ornamental plant breeding and genomics research. 展开更多
关键词 iris japonicaan tobacco rattle virus phytoene desaturase pds genea gene silencing genetic transformation systemthis functional verification key genes tobacco rattle virus trv virus induced gene silencing
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Ion Channel Genes and Epilepsy:Functional Alteration,Pathogenic Potential,and Mechanism of Epilepsy 认领 引用 被引量：28
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作者 Feng Wei Li-Min Yan +6 位作者 Tao Su Na He Zhi-Jian Lin Jie Wang Yi-Wu Shi Yong-Hong Yi Wei-Ping Liao 《Neuroscience Bulletin》 SCIE CAS CSCD 2017年第4期455-477,共23页
Ion channels are crucial in the generation and modulation of excitability in the nervous system and have been implicated in human epilepsy. Forty-one epilepsyassociated ion channel genes and their mutations are system... Ion channels are crucial in the generation and modulation of excitability in the nervous system and have been implicated in human epilepsy. Forty-one epilepsyassociated ion channel genes and their mutations are systematically reviewed. In this paper, we analyzed the genotypes, functional alterations（funotypes）, and phenotypes of these mutations. Eleven genes featured loss-offunction mutations and six had gain-of-function mutations.Nine genes displayed diversified funotypes, among which a distinct funotype-phenotype correlation was found in SCN1A. These data suggest that the funotype is an essential consideration in evaluating the pathogenicity of mutations and a distinct funotype or funotype-phenotype correlation helps to define the pathogenic potential of a gene. 展开更多
关键词 Epilepsy Ion channel gene Epilepsy gene Genetics Gene function Pathogenic mechanism
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Research Progress on Functional Analysis of Rice WRKY Genes 认领 引用 被引量：36
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作者 SONG Yu AI Chong-rui +1 位作者 JING Shao-juan Yu Di-qiu 《Rice science》 2010年第1期60-72,共13页
Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription ... Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription factor gene families, was recently suggested to play important roles in plant development and stress response. In rice, the results of analyses of expression pattern and ectopic overexpressor lines also support this viewpoint, and the evidences implicate rice WRKY proteins in transcriptional reprogramming during biotic or abiotic stresses, senescence, sugar metabolites, and morphological architecture. In this paper, we review the advance in study of rice WRKY gene family and also propose unified nomenclature for rice WRKY factors to eliminate confusion. 展开更多
关键词 rice WRKYgene gene function transcription factor
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A Nimble Cloning-compatible vector system for high-throughput gene functional analysis in plants 认领 引用 被引量：8
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作者 Pu Yan Decai Tuo +3 位作者 Wentao Shen Haida Deng Peng Zhou Xinzheng Gao 《Plant Communications》 SCIE CSCD 2023年第2期65-76,共12页
Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding.The gene of interest is transferred to the vector by molecular cloning technology.Nimble Cloning is a newly develo... Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding.The gene of interest is transferred to the vector by molecular cloning technology.Nimble Cloning is a newly developed molecular cloning method with the advantages of simplicity,efficiency,and standardization.In this study,we developed a"pNC"vector system that contains 55 Nimble Cloning-compatible vectors for functional analysis of genes in plants.These vectors contain the NC frame flanked by unique adapters for one-step and standardized Nimble Cloning.We demonstrate that the pNC vectors are convenient and effective for the functional analysis of plant genes,including the study of gene ectopic expression,protein subcellular localization,protein-protein interaction,gene silencing(RNAi),virus-induced gene silencing,promoter activity,and CRISPR-Cas9-mediated genome editing.The"pNC"vector system represents a high-throughput toolkit that can facilitate the large-scale analysis of plant functional genomics. 展开更多
关键词 nimble cloning plant expression vector gene function ectopic expression genome editing
A Method of Gene-Function Annotation Based on Variable Precision Rough Sets 认领 引用 被引量：5
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作者 Zhi-li Pei Xiao-hu Shi +4 位作者 Meng Niu Xu-ning Tang Li-sha Liu Ying Kong Yan-chun Liang 《Journal of Bionic Engineering》 SCIE EI 2007年第3期177-184,共8页
It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotat... It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods. 展开更多
关键词 gene function annotation variable precision rough set GO BLAST
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