30 results about "Functional genomics" patented technology

The invention relates to an application of a FaPDHE1alpha gene or an encoding protein thereof in prevention and control of strawberry gray mold, and belongs to the field of plant genetic engineering and the field of prevention and control of postharvest diseases of fruits and vegetables. The invention discloses a key positive regulation and control effect of FaPDHE1alpha in regulation and control of strawberry gray mold resistance. By constructing a 35S:: FaPDHE1alpha overexpression vector and a FaPDHE1alpha RNAi interference vector, according to transient gene overexpression and RNA interference silencing tests, it is verified that high expression of the FaPDHE1alpha gene can obviously enhance the resistance of strawberry fruits to botrytis cinerea, and silencing of the gene causes reduction of the disease resistance of the fruits. Mechanism studies show that after the FaPDHE1alpha gene is activated, mitochondrial energy metabolism and controlled ROS signal generation are promoted, antioxidant enzyme activity is enhanced, and defense related gene expression is induced, so that the disease resistance of fruits is improved. By means of functional genomics, the key function of the FaPDHE1alpha gene in prevention and control of gray mold after strawberry harvest is illuminated for the first time, and the FaPDHE1alpha gene can be used for screening disease-resistant breeding materials or developing biological prevention and control preparations for postharvest diseases and has important application value.

This invention discloses the application of the wheat gene TaPSS2 in improving plant drought resistance, belonging to the field of functional genomics. The nucleotide sequence of the wheat gene TaPSS2 is shown in SEQ ID NO: 2. Transforming this gene into the model plant Arabidopsis thaliana can significantly improve the drought resistance of Arabidopsis. If the wheat gene TaPSS2 is transformed into wheat, rice, maize, cauliflower, and other plants, it is possible to obtain new germplasm with drought-resistant characteristics, which is of great significance for the breeding of superior crop varieties and their widespread application in production.

The invention relates to the technical field of biology, in particular to application of an RhUNE10 gene to regulation and control of root cancer resistance of Chinese roses and a regulation and control method. The nucleotide sequence of the RhUNE10 gene is as shown in SEQ ID NO. 1. The application mode is that the RhUNE10 gene is silenced and knocked out, or the expression of the protein coded by the RhUNE10 gene is inhibited; and the amino acid sequence of the protein coded by the RhUNE10 gene is as shown in SEQ ID NO. 3. After the RhUNE10 gene is silenced, the resistance of the Chinese rose to agrobacterium tumefaciens is remarkably reduced, which indicates that the RhUNE10 gene has important biological functions, is beneficial to promoting Chinese rose functional genomics research, gene editing breeding and transgenic breeding research, excavates and cultivates new varieties of high-resistance Chinese roses, and has wide application prospects. And a certain theoretical basis and key gene resources are provided for comprehensive prevention and treatment of root cancer and cultivation of a new variety of Chinese rose.

The application discloses a chrysanthemum constitutive high-expression promoter and application thereof in gene editing. The nucleotide sequence of the promoter CmUbi is shown as SEQ ID NO. 4. Through double luciferase reporter experiments and stable genetic transformation experiments, it is proved that the expression activity of the CmUbi promoter in chrysanthemum protoplast and callus is significantly higher than that of commonly used CaMV 35S, AtRPS5a and corn ZmUbi promoters. A CRISPR / Cas9 gene editing vector is constructed by using the promoter, and a key gene of branch of hexaploid chrysanthemum is edited BRC1b , and a plurality of allele simultaneous mutation complete editing strains are successfully obtained, and the number of branches of the mutants is significantly increased. The endogenous high-activity promoter of the chrysanthemum provided by the application effectively solves the problems of low expression activity of an existing heterologous promoter in the chrysanthemum and poor gene editing efficiency of a polyploid, and provides an efficient and adaptive expression regulation element for chrysanthemum molecular breeding and functional genomics research.

The invention provides a method and system for gene expression quantitative trait locus analysis, and relates to the technical field of genomics, the method comprises the following steps: carrying out sample and locus level quality control on input genotype data, and generating a standardized genotype matrix; performing standardization processing and low expression gene filtering on the input gene expression data to generate a standardized expression quantity matrix; performing principal component analysis according to the standardized genotype matrix to obtain a group structure covariable; carrying out implicit factor analysis on the basis of the standardized expression quantity matrix to obtain a technical batch effect covariable; quantitative character site correlation analysis is carried out through a standardized genotype matrix, a standardized expression quantity matrix, a population structure covariable and a technical batch effect covariable. The method is suitable for functional genomics research, complex disease genetic mechanism analysis and precision medical related functional genetic variation mining scenes.

The invention discloses a genetic transformation method based on pear somatic embryogenesis, and belongs to the technical field of genetic engineering and molecular breeding. In order to solve the problems that existing pear genetic transformation is low in transformation efficiency, high in chimera rate, long in period, difficult to obtain gene editing regeneration plants and the like, the invention provides two paths: 1, immature zygotic embryos 30-60 days after pear flowering are taken as explants, resistant plants are directly induced through a somatic embryo regeneration path, and the transformation efficiency within 40-60 days reaches 73.91%; secondly, the embryogenic callus with the consistent genetic background is used as an explant for infection, the embryogenic property is maintained and the proliferation efficiency is improved by optimizing a culture medium formula, and a resistant plant with the consistent genetic background can be obtained within 30-50 days. The method overcomes the defect that regeneration plants are difficult to obtain through existing callus transformation, remarkably shortens the breeding period, is high in transformation efficiency, low in chimera rate and controllable in genetic background consistency, and provides technical support for pear functional genomics research and molecular breeding.

The invention relates to the technical field of agriculture, in particular to an efficient ABE base editing tool based on Cas12i3 and application of the efficient ABE base editing tool. The Cas12i3-based efficient ABE base editing tool provided by the invention comprises a protein expression cassette and an RNA (Ribonucleic Acid) expression cassette, the protein expression cassette comprises a promoter, a 2 * BP NLS nuclear localization signal fragment, a 2 * adenine deaminase TadA8e, a connecting peptide, a Cas12i3 notch enzyme fragment and a terminator, the RNA expression cassette comprises a promoter, a crRNA sequence and a terminator; wherein the crRNA sequence is composed of a DR sequence and a target specific spacer sequence. The tool realizes efficient and specific single base substitution of A-to-G in a rice genome by utilizing the targeted binding characteristic of Cas12i3 and the efficient deamination activity of 2 * TadA8e, has the advantages of high editing efficiency, low off-target rate, wide application range and the like, provides an efficient and accurate technical means for plant functional genome research and molecular breeding, and has a wide application prospect. The creation of excellent rice varieties can be accelerated.

Aspects of the technology relate to methods and compositions for multiplexed assessment of perturbations with single cell molecular resolution using a regulatable Cas enzyme with intrinsic RNase activity.

The invention relates to a method for rapidly carrying out BSA (Bovine Serum Albumin) gene localization by utilizing a space mutation mutant. The method comprises the following steps: firstly, carrying propagules such as seeds through an aerospace craft, and constructing a broad-spectrum mutant library by utilizing space environment mutagenesis; returning to the ground, culturing and screening M1-generation mutants with target excellent characters, and hybridizing / backcrossing with a wild type to construct a character segregation population; by adopting a group separation analysis (BSA) strategy, selecting phenotype polar differentiation individuals, and respectively mixing the phenotype polar differentiation individuals to form a high-value pool and a low-value pool; and finally, carrying out whole genome high-throughput sequencing on the double pools and the parents, rapidly locking a genome region linked with a target character by combining bioinformatics analysis such as SNP-index and the like, and verifying candidate genes through gene annotation, molecular marking and gene editing. According to the invention, the broad spectrum of space mutagenesis and the high efficiency of the BSA-seq technology are integrated, the period from mutation creation to gene identification is remarkably shortened, and an innovative technical scheme is provided for crop genetic improvement and functional genomics research.

This invention discloses a Panax notoginseng MYB transcription factor gene. PnMYB34 Its nucleotide sequence is as described in SEQ ID NO:1, encoding the MYB transcription factor. This invention confirms through molecular biology and functional genomics related technologies. PnMYB34 The gene has the ability to enhance the plant's resistance to viral infection, and the present invention will... PnMYB34 Genes were constructed into plant expression vectors and overexpressed in Panax notoginseng and tobacco, respectively. Experimental results showed that overexpression... PnMYB34 Genetically modified Panax notoginseng against Panax notoginseng A virus (GMO) Panax notoginseng virus A The resistance to ) was significantly enhanced, and overexpression PnMYB34 Genetically modified tobacco is susceptible to tobacco mosaic virus (BMP). Tobacco mosaic virus Its resistance was also significantly enhanced.

This invention belongs to the fields of microbiology and molecular biology, specifically relating to a homologous recombinase combination in myxobacteria and its application in gene editing. Specifically, this invention provides four pairs of homologous recombinase systems capable of efficiently mediating in vivo recombination in myxobacteria. Each pair includes a protein YqaJ with exonuclease function and a protein RecT with single-strand annealing function. This invention provides a method for myxobacterial gene editing: under the action of homologous recombinase pairs, mutant strains are obtained through positive screening using resistance tags. The resistance tags are then successfully removed through the combined action of the Cre / loxP system and the reverse screening gene galK. This method achieves a gene editing efficiency of up to 100%, has a short cycle time, requires no purification, and can be used for iterative deletion of multiple genes to achieve genome simplification in myxobacteria, or for inserting functional promoters and other elements to activate silent gene clusters. This method is of great significance for the bioexploration and functional genomics research of myxobacteria.

This invention discloses a wheat ultra-high-density gene chip probe and its preparation method, belonging to the fields of plant functional genomics, population genetics, and molecular breeding technology. Based on wheat pan-genome information, this invention uses resequencing data and exon capture sequencing data from large-scale natural wheat populations to perform variation analysis and obtain ultra-large-scale whole-genome variation information. High-quality SNPs and INDEL loci with population and individual representativeness are obtained through filtering and screening. Simultaneously, harmful mutation sites are identified, and publicly published genetic loci related to important wheat yield and quality traits are integrated and extracted. Polymorphic loci regions are determined by combining genome annotation and variation annotation. Finally, ultra-high-density liquid-phase probes are synthesized at the pan-genome level. Because this invention only sequences target gene regions, it reduces sequencing costs by more than 90% for the same gene sequencing depth.

This invention belongs to the field of plant genetic engineering technology, specifically relating to the application of the wheat TaMRS2-16 protein in regulating photosynthetic rate. The purpose of this invention is to provide a novel use for the wheat TaMRS2-16 gene, namely, its application in regulating wheat photosynthetic rate. Through functional genomics, this invention, for the first time, clarifies the positive regulatory role of the TaMRS2-16 gene in wheat photosynthetic rate, providing new target genes and molecular markers for molecular breeding of high-efficiency wheat.

The present application relates to the field of plant molecular biology and genetic engineering technology, and particularly relates to a transient expression method of orchid plants and application. The method provided by the present application successfully breaks through the infection barrier of the thick cuticle of orchid plants by optimizing the core parameters of vacuum-assisted Agrobacterium infection, screening the infection strains and optimizing the composition of the infection solution. The high activity of the leaf cells can be maintained for more than 9 days after infection, and the exogenous genes can realize stable and efficient expression. The method provided by the present application is simple to operate, does not require special instruments and equipment, is convenient to obtain materials, is not limited by the flowering season, can be carried out throughout the year, and the complete experimental cycle can be completed within 7 days. The present application effectively solves the long-standing technical problems in the field of genetic transformation of orchid plants, and provides an efficient and convenient gene function transient verification technology platform for the functional genomics research, gene function verification, promoter activity detection and precise molecular breeding of orchid and other orchid plants.

The present invention provides high-content and high-resolution in vivo screening for the analysis of the function of multiple genes. In the functional screening of the present invention, genetic perturbations are delivered to CRISPR-expressing transgenic systems by specific AAV vectors fully compatible with the Perturb-seq platform. This screening enables in vivo functional genomics analysis in a variety of tissues, cell types, and model organisms with high-throughput single-cell readout.

The invention discloses a negative pressure fixation and micro-injection combined cotton virus-induced gene silencing inoculation method. The method comprises the following steps: (1) constructing a virus-induced gene silencing vector; (2) preparing an agrobacterium suspension; (3) fixing under negative pressure; (4) performing micro-injection inoculation; and (5) subsequent culture: culturing the inoculated plant under the conditions that the temperature is 22-25 DEG C, the illumination period is 16h illumination / 8h darkness, the illumination intensity is 100-200 and the relative humidity is 60-80%, and observing the gene silencing phenotype after 7-14 days. The method solves the problems that a traditional virus-induced gene silencing inoculation method is complex in operation, low in success rate and large in leaf damage, has the advantages of being easy and convenient to operate, high in inoculation success rate, small in leaf damage, high in gene silencing efficiency and the like, and is suitable for cotton functional genomics research and gene function verification.

The invention discloses a targeted senile degenerative bone disease key lesion regulation factor mRNA therapy recommendation evaluation model method, and the model comprises a data input layer which receives bone disease genetic association and regulation data, including GWAS summary data, space transcriptome and single cell transcriptome data; the intervention target priority ordering module is used for integrating the obtained genetic evidence, regulation evidence and network evidence and carrying out priority ordering on intervention targets; and the intervention target identification network module is used for predicting a key intervention target according to an intervention target network generated by acquiring a gene interaction relationship from the pathway, and obtaining a potential mRNA intervention therapy. The genetic evidence comprises a genetic risk site set annotated through multi-modal regulation genomics data; the regulation evidence comprises functional genomics data related to diseases; the network evidence comprises a high-credibility protein interaction relationship. And the intervention target identification network module is used for analyzing an intervention target network and further comprises disturbance removal analysis and regulation and control hierarchy analysis.

The invention belongs to the field of plant molecular biology and functional genomics, and particularly relates to a method for identifying a barren-resistant index gene of a tea tree based on WGCNA analysis and application. The invention discloses a method for identifying a barren-resistant related gene of a tea tree, which comprises the following steps: firstly, selecting tea tree varieties with different growth vigor, and measuring the root biomass under the same condition; performing low-nitrogen treatment on the seedlings, extracting RNA (Ribonucleic Acid) from root tissues, establishing a cDNA (Complementary Deoxyribonucleic Acid) library, and performing high-throughput sequencing; screening a gene set with high expression and large variable coefficient based on sequencing data, constructing a gene co-expression network by using WGCNA, and identifying a green module highly related to root biomass; 14 core candidate genes which are stably and highly expressed in varieties with strong growth vigor are screened out as barren-resistant potential candidate molecular indexes, are used for germplasm resource evaluation, early screening of low-fertilizer-resistant varieties and molecular marker-assisted breeding, and have important theoretical values and application prospects.

This invention belongs to the field of bioinformatics, specifically relating to a hierarchical transposon classification method based on dynamically gated multi-scale features. First, K-mer frequencies and one-hot encoded bimodal features are extracted from the DNA sequence. Second, these features are encoded separately using a gated multi-scale convolutional network and a DNA-specific convolutional pyramid. Then, adaptive feature fusion is performed using an attention-gating mechanism conditioned on sequence features. Finally, a top-down hierarchical decision is made in the classification tree based on probability thresholds. This invention overcomes the shortcomings of existing methods in feature capture, fusion, and hierarchical decision-making, achieving high-precision and high-efficiency transposon classification, providing a more accurate and reliable analytical tool for genome annotation, evolutionary research, and functional genomics.

The application discloses a method for transgene and / or gene editing of Brassica crops mediated by co-transformation strategy, and belongs to the technical field of genetic engineering.The method comprises the following steps: transforming a development regulator vector and a target gene vector into Agrobacterium rhizogenes K599 respectively to prepare a mixed bacteria solution of double strains; infecting a Brassica vegetable explant; inducing adventitious buds after co-culturing; and screening different types of transgenic buds through fluorescence labeling, phenotype observation and molecular identification.The method is simple and efficient, and can effectively avoid adverse phenotypes such as transgenic plant deformity caused by continuous overexpression of the development regulator, and can obtain a gene editing homozygous mutant in the T0 generation, so that the method has a wide application prospect in the research of Brassica crop functional genomics, gene editing and crop genetic improvement.

The invention discloses a female parent RNA interference method based on a parasitic wasp specific developmental window period, and relates to the technical field of insect functional genomics and genetic manipulation, and the method comprises the following steps: systematically comparing microinjection effects of a pre-pupal period and an adult period, determining an efficient and safe window of parasitic wasp female parent RNA interference in the adult period, the method comprises the following steps: selecting a conservative transform gene in an insect sex determination pathway as a target gene to prepare specific double-stranded RNA, and performing targeted microinjection on the belly of a female bee in an adult stage, so that efficient silencing of the target gene is realized on the premise of ensuring high survival rate and normal reproductive capacity of a female parent. According to the method, by defining an efficient and safe operation window of the parasitic wasp female parent RNAi in the adult stage, the technical problems of high death rate, developmental disorder, reproductive power decline and the like caused by injection in the pre-pupal stage are thoroughly solved, the cumulative survival rate of the female parent within 20 days is not lower than 50%, the operation repeatability is high, and a stable and reliable technical normal form is provided for research on the gene function of the parasitic wasp.

The invention discloses a method for realizing wheat whole genome large-scale mutation and germplasm creation by editing repetitive sequences. CRISPR / Cas9 target sites with the copy number higher than 20,000 in wheat genomes are screened, tandem repeat sequences and dispersed repeat sequences are edited in a targeted mode, and heritable large-scale variation, chromosome structure variation and agronomic character variation of the whole genome scale are induced and generated in progeny plants. By editing repetitive sequences, large-scale mutation with chromosome and subgenome specificity can be realized, the created mutant library not only provides heritable variation mutant types different from those of traditional physical and chemical mutagenesis methods, but also generates materials such as chromosome aneuploidy (such as monosome, tetrasome and whole-arm deletion) and the like. And a unique genetic resource is provided for wheat functional genomics research and germplasm improvement.

This invention discloses a Cyclophilin antibacterial protein gene from the Minjiang lily. LrCYP1 Its nucleotide sequence is as described in SEQ ID NO: 1, encoding a protein with the amino acid sequence shown in SEQ ID NO: 2. This invention confirms through functional genomics-related research. LrCYP1 The gene has the function of enhancing plant antifungal resistance, and the antifungal properties of this invention... LrCYP1 Genes were constructed into plant expression vectors and overexpressed in tobacco. The transgenic tobacco plants exhibited strong resistance to fungal infection, demonstrating the effectiveness of overexpression. LrCYP1 The genetically modified tobacco plants exhibit high levels of resistance to Alternaria alternata and Pseudomonas spp.

Provided is the use of olfactory receptor BdorOR94bl as a target in the control of Bactrocera dorsalis. By means of functional genomics, electrophysiology, behavioristics, and traditional chemical ecology, the role of methyl eugenol in the mating behavior of Bactrocera dorsalis and the key olfactory receptor for male flies to recognize methyl eugenol are comprehensively analyzed. For the first time, the key olfactory receptor BdorOR94bl of Bactrocera dorsalis for recognizing methyl eugenol is identified, and the genomic coding region sequence and transcribed amino acid sequence information of the key olfactory receptor BdorOR94bl is obtained, which not only lays an important foundation for the subsequent screening of more stable and efficient structural analogs by taking the gene as a target, but also provides a foundation for the development of nucleic acid pesticides.

Machine learning-based methods, systems, and programming for training and deploying a multimodal, multi-masking-based deep learning model configured to predict cell type-specific functional genomic traits are described. The model utilizes a new training strategy comprising: (i) self-supervised learning on DNA sequence, and (ii) supervised learning on functional genomic data, along with the use of a multiscale loss function. A key feature of the disclosed methods and systems is the ability of the core deep learning model to be reconfigured for different functional genomics prediction applications by changing the masking strategy used during training and / or inference.

This invention provides a method, tool, and application for improving the gene editing efficiency of *Eimeria tenella*. The *Eimeria tenella* strain with KU80 deletion is obtained by knocking out the KU80 gene in *Eimeria tenella* using a CRISPR-Cas9 gene editing system. Compared with existing technologies, the tool and method of this invention can significantly improve gene-targeted integration efficiency, significantly reduce random integration events of exogenous DNA, and improve the accuracy and stability of gene editing. It is a universal gene editing platform that can be widely applied to gene knockout, gene knock-in, and endogenous marker research. The strain using this tool can significantly shorten the screening cycle for positive recombinant strains, improve experimental reproducibility, and provide important technical support for functional genomics research on *Eimeria tenella*.

The application discloses a method for constructing early non-invasive fluorescent screening zebrafish gene knockout homozygotes, two kinds of knock-in vectors containing different fluorescent markers are constructed for a target gene, and male and female lines expressing red or green fluorescence in the heart are obtained through microinjection and subculture; the two are crossed, and offspring embryos simultaneously present double-color heart fluorescence within 48 hpf, which are homozygotes. The method does not need tail cutting, PCR and sequencing, can identify in batches at one time, avoids loss of lethal mutations, saves time and cost, meets animal welfare, is suitable for any gene, and provides fast visual homozygous mutants for functional genomics and drug screening.

The invention belongs to the field of bioinformatics, and particularly relates to a transposon hierarchical classification method based on dynamic gating multi-scale features. The method comprises the following steps: firstly, extracting K-mer frequency and One-hot coding bimodal features from a DNA sequence; secondly, coding is carried out through a gated multi-scale convolutional network and a DNA specific convolutional pyramid; then, self-adaptive feature fusion is carried out by utilizing an attention gating mechanism taking sequence features as conditions; and finally, performing top-down hierarchical decision-making in the classification tree based on a probability threshold. According to the method, the defects of an existing method in feature capture, fusion and hierarchical decision making are overcome, high-precision and high-efficiency transposon classification is achieved, and a more accurate and reliable analysis tool is provided for genome annotation, evolutionary research and functional genomics.

The application discloses a method for constructing a large fragment deletion mutant library of Magnaporthe oryzae, and belongs to the field of agricultural biotechnology.The method comprises the step of adding DEB to the protoplast of the Magnaporthe oryzae for culture and inducing the production of conidia.The application utilizes the chemical mutagen DEB to obtain the Magnaporthe oryzae mutant at a high frequency on a whole genome scale, and provides a new technical path for the functional genomics research of the Magnaporthe oryzae.The method provided by the application is helpful to systematically analyze the pathogenic mechanism, the infection process and the environmental adaptation regulation network of the Magnaporthe oryzae, and provides support for mining new disease-resistant targets and disease-resistant mechanisms.The method has the advantages of high efficiency, low cost and short cycle, and has wide application potential in the genetic research of plant pathogenic fungi.