103 results about "Plant genomes" patented technology

The invention relates to the technical field of collaborative prediction, in particular to a plant polygene stress resistance collaborative prediction method and system based on a federal map neural network. The method comprises the following steps: modeling a multilayer heterogeneous graph according to acquired plant genome data; constructing a dynamic graph neural network model based on time sequence perception; training a dynamic graph neural network model by using the multi-layer heterogeneous graph, and performing distributed privacy calculation on the multi-layer heterogeneous graph by using a federated graph neural network; generalization training is carried out on the small sample scene data based on multi-task learning and a cross-species migration mechanism; and obtaining a gene function prediction result. Through a multi-layer heterogeneous graph fusion technology and a dynamic graph neural network design of time sequence perception, multi-dimensional biological information such as gene regulation, protein interaction, metabolic pathways and stress response can be captured at the same time, and time sequence change characteristics of gene expression in the plant stress response process can be captured at the same time.

The invention provides a method for realizing fixed-point activation of a plant genome by directionally inserting an enhancer, and particularly, by inserting a short enhancer (STE) in a specific region of a target gene promoter, a target gene can be efficiently activated, the expression level of the target gene can be enhanced by about 2000 times, and the enhancement multiple can be flexibly adjusted as required. The site-specific activation method for the plant genome has high efficiency, wide applicability and stable heredity, and has outstanding application value in plant research and breeding.

The invention discloses an RNA (Ribonucleic Acid) aptamer and application thereof in improving the salt tolerance of rice. The aptamer sequence eApt-2 with high affinity to eIF4A is obtained through enrichment by using a phylogenetic screening technology of the nucleic acid aptamer, and the aptamer sequence eApt-2 can inhibit the RNA helicase activity of eIF4A and selectively block a 5'cap-dependent translation initial process. After the eApt-2 coding sequence is introduced into a rice cell, the transgenic rice shows significantly enhanced salt tolerance under a salt stress condition: the growth condition is improved, and the biomass and the photosynthetic efficiency are both higher than those of a control plant. Compared with a traditional strategy of improving the salt tolerance through gene overexpression or knockout, the method does not need permanent modification of animal and plant genomes, accurate and reversible regulation and control of translation initiation factors are carried out through aptamers, optimization of stress response protein synthesis is achieved, and higher specificity and safety are achieved. The invention provides a novel and efficient technical approach for cultivating salt-tolerant crops, and has a wide application prospect.

The invention discloses a method for site-specific replacement or insertion of DNA fragments in a plant genome, and belongs to the technical field of biology. The method disclosed by the invention comprises the following steps: editing a genome of a plant protoplast by adopting a CRISPR / Cas9 system and taking a double-stranded DNA repair template as a donor template to obtain an edited protoplast; and carrying out culture regeneration on the edited protoplast by utilizing a plant protoplast transformation method to obtain a site-directed mutagenesis plant in the genome so as to realize site-directed mutagenesis of the target plant genome. The method disclosed by the invention can be used for accurately replacing DNA in a plant genome at a fixed point. According to the invention, a recognition sequence of recombinase can be accurately inserted into a genome at a fixed point through homologous recombination, and then accurate fixed-point replacement of a gene large fragment is realized by virtue of a specific recombinase system.

The invention belongs to the field of gene engineering, and relates to a plant genome directional editing tool based on transposon-coded nuclease. The invention aims to solve the technical problem that the application range of a plant genome editing tool based on CRISPR-Cas9 and Cas12a is limited to a great extent due to the fact that CRISPR-Cas9 and Cas12a are large in protein size and difficult to deliver. The invention provides transposon nuclease suitable for plant genome editing. The transposon nuclease is IsDge10, IsAam1 or enIscB subjected to codon preference optimization; and a gene editing system containing the three transposon nuclease is constructed. The gene editing system can be suitable for editing a coding region, a non-coding region and the like; the method can be widely applied to monocotyledonous plants, dicotyledonous plants, gymnosperm and the like.

The invention belongs to the technical field of gene engineering, and particularly relates to a negative-sense RNA virus plant genome editing system and application thereof. According to the genome editing system, a CRISPR-Cas9 gene editing technology is used, a plant cytoplasm rhabdovirus is used as a delivery carrier, the rhabdovirus is spread to a plant by means of entomophilous, a gene editing component is delivered to an axillary meristematic zone by utilizing RNA (Ribonucleic Acid) to move a motif, and a mutant lateral bud is obtained along with plant tillering. According to the method, plant gene editing can be completed without tissue culture, plant tissue culture dependence is overcome, the range of gene-editable strains is expanded, and pure mutants can be obtained only by one generation without hybridization and selfing processes.

The invention discloses application of novel reverse transcriptase and related fusion protein of the novel reverse transcriptase in plant-guided editing. Candidate RT protein is obtained through systematic mining from a public database, novel reverse transcriptase cl1 with activity is screened out in combination with a fluorescence report system, and a guided editing system suitable for plants is constructed. The system tests in wheat protoplast, and verifies the editing activity of cl1 to a plurality of endogenous targets. Further combining with protein structure prediction and rational design point mutation optimization, the cl1 mutant with higher editing efficiency is obtained, and the method can be applied to accurate and effective editing of plant genomes and plant breeding and improvement.

The disclosure relates to a plant that is tolerant or resistant to species of Ca. Liberibacter. Specifically exemplified are Citrus and solanaceous plants. Provided by the disclosure is a modified Citrus or solanaceous plant that is resistant or tolerant to Sec-dependent effectors secreted by bacteria. Also provided by the disclosure are methods of modifying a plant genome plant to provide tolerance or resistance to species of Ca. Liberibacter. Still further provided by the disclosure are methods conferring a population of plants with tolerance or resistance to species of Ca. Liberibacter and screening that population for the plants that are tolerant or resistant to species of Ca. Liberibacter.

The invention belongs to the field of gene engineering, and relates to nuclease generated based on AI and having a gene editing function and application of the nuclease. The technical problem to be solved by the invention is to develop more nuclease suitable for eukaryote gene editing. According to the technical scheme, nuclease AIGCprotein which is generated based on AI and has a gene editing function is obtained through the following steps that a plurality of protein amino acid sequences are generated through a known nuclease three-dimensional structure in a PDB database, the sequences are classified and compared, and a protein skeleton of the nuclease AIGCprotein is obtained through extraction; the known nuclease is Cas12. The invention provides nuclease which is generated on the basis of Protein MPNN AI and has a gene editing function, and the protein does not exist in the nature; the method can be used for constructing a plant genome editing system.

The present invention relates to a method for plant genome modification of at least one plant cell being in the developmental stage of a plant immature inflorescence meristem (IIM) cell, wherein the modification of the specific cell type is achieved by providing a genome modification or editing system, optionally together with at least one regeneration booster, preferably wherein the effector molecules are introduced by particle bombardment. To this end, new artificial and precisely controllable booster genes and proteins are provided. Further, the modified plant cells are regenerated in a direct or an indirect way. Finally, methods, tools, constructs and strategies are provided to effectively modify at least one genomic target site in a plant cell, to obtain the modified plant cell and to regenerate a plant tissue, organ, plant or seed from the modified plant cell.

The invention discloses a cytochrome P450 gene CYP71AF43, a polypeptide, a carrier and application of the cytochrome P450 gene CYP71AF43, the polypeptide and the carrier, and the CYP71AF43 gene is derived from alopecurus macrophysalis and has the effect of resisting fenoxaprop-p-ethyl. The nucleotide sequence of the gene is SEQ ID NO: 1 or a sequence with not less than 80% of identity compared with the SEQ ID NO: 1. On the basis, the invention further discloses a protein polypeptide coded by the CYP71AF43 gene. The invention further deeply relates to construction of a carrier containing the CYP71AF43 gene and an all-around application strategy in the breeding process of herbicide-resistant transgenic plants. Through systematic optimization of vector design and transgenic process, it is ensured that the CYP71AF43 gene can be stably and efficiently integrated into a plant genome, the function of giving herbicide resistance to plants is fully exerted, and breeding, popularization and application of new lines of herbicide-resistant transgenic plants are promoted.

The invention provides a lysis solution for rapidly extracting animal and plant genomes and an application method thereof.The lysis solution is prepared from, by mass, 20-25 parts of Tris-Hcl, 10-15 parts of LICI, 5-10 parts of EDTA, 1-3 parts of 3-sulfopropyl hexadecyl dimethyl betaine, 1-3 parts of (NH4) 2SO4 and 30-40 parts of ddH2O. The 3-sulfopropyl hexadecyl dimethyl betaine and (NH4) 2SO4 in the formula of the lysis solution can effectively destroy cell membranes and nuclear membranes; the lysate prepared by the method is clear in component and simple to prepare, DNA precipitation or column purification can be directly carried out after lysis, meanwhile, the lysate is suitable for various sample types including animal tissues and plant tissues, a formula does not need to be adjusted according to different sample types, and compared with a traditional lysate, the lysate has the advantages that the cost is low, and the efficiency is high. The optimized formula has the advantages of high splitting efficiency, wide application range, high DNA purity, high extraction speed and good DNA integrity.

The present invention discloses a plant gene editing method for insufficiently editing a target gene, and belongs to the field of plant genetic engineering. The present invention provides a method for plant gene editing, which can achieve insufficient editing of the plant genome by using a promoter that functions after the callus enters the differentiation period to drive the expression of a gene editing functional element, thereby being able to be used to create a heterozygous mutant in the plant. The present invention also provides a promoter sequence for incomplete editing of the plant genome, a nucleic acid protein composition, and a method for creating a plant heterozygous mutant.

The present invention relates to a method for preparing a MAGEA8-Fc transgenic plant. Through a platform using a tobacco plant, a recombinant protein MAGEA8-Fc, in which a human IgG Fc fragment is fused to a MAGEA8 protein, can be stably expressed. The method of the present invention enables high-level expression efficiency and stable protein production by introducing a target gene into a plant genome using an Agrobacterium binary vector. By directly isolating and purifying the recombinant protein from the transgenic tobacco plant, large-scale production can be easily achieved. Compared to conventional microbial or animal cell-based expression systems, the method provides economic efficiency and scalability, and thus can be usefully applied as a platform for producing fusion proteins.

The disclosure relates to a plant that is tolerant or resistant to species of Ca. Liberibacter. Specifically exemplified are Citrus and solanaceous plants. Provided by the disclosure is a modified Citrus or solanaceous plant that is resistant or tolerant to Sec-dependent effectors secreted by bacteria. Also provided by the disclosure are methods of modifying a plant genome plant to provide tolerance or resistance to species of Ca. Liberibacter. Still further provided by the disclosure are methods conferring a population of plants with tolerance or resistance to species of Ca. Liberibacter and screening that population for the plants that are tolerant or resistant to species of Ca. Liberibacter.

Compositions containing chimeric RNA molecules which comprise meristem targeting sequences that are fused to RNA cargo sequences that include gene editing molecules are provided. Methods of using the compositions to efficiently edit plant genomes without intervening tissue culture steps are also provided. The solutions described here relate to engineered RNA molecules useful in producing plants with altered genomes. As such, it relates to substantially purified compositions, vectors, systems, as well as genomes of plants.

The application discloses a plant genome DNA extraction reagent, which comprises Buffer 1 lysate, Buffer 2 precipitate and Buffer 3 combination liquid; the Buffer 1 lysate comprises sodium chloride, PVP40, sodium metabisulfite and SDS; wherein the concentration of the sodium chloride is 250-1200 mM; the mass percentage of the PVP40 is 0.5%-3%; the concentration of the sodium metabisulfite is 50-150 mM; and the mass percentage of the SDS is 0.7%-2.5%; the Buffer 2 precipitate comprises acetate; wherein the concentration of the acetate is 2.2-4.3 M; and the Buffer 3 combination liquid comprises guanidine hydrochloride; wherein the concentration of the guanidine hydrochloride is 0.5-2.5 M. The extraction reagent does not contain organic solvents such as phenol and chloroform, and can improve the removal rate of polyphenols.

Methods arc provided for making a plant genome having a desired nucleic acid sequence. One example method includes identifying genomic segments of a plant that include at least one desired nucleic acid sequence, using a trained neural network, which is biology-informed through first pre-training connections between a genetic data layer and at least one intermediate layer and second pre-training connection between the at least one intermediate layer and a phenotypic layer. The method also includes recombining the at least one at least one desired nucleic acid sequence with a second nucleic acid sequence to form a target plant genome.

The invention belongs to the field of gene engineering. Specifically, the invention relates to a method for inserting an exogenous sequence in a genome at a fixed point. Specifically, on the basis of a guided editing system (PE), two adjacent pegRNAs with partially overlapped sequences on a reverse transcription template are used, and efficient and accurate exogenous sequence fixed-point insertion is realized in a genome, especially a plant genome. The system is further coupled with a recombinase system such as Cre / Lox or FLP / FRT and the like, and large-fragment exogenous sequence fixed-point insertion is realized in genomes, especially plant genomes.

The invention provides a kit for extracting plant genome DNA based on magnetic beads and application. The kit is composed of a lysis solution, a binding solution, a washing solution I, a washing solution II, an eluent and magnetic beads. The cracking combination solution comprises at least one of lauryl sodium sulfate, cetyltrimethylammonium bromide, guanidine hydrochloride, guanidine isothiocyanate, citric acid, trisodium citrate, Tween 20, polyvinylpyrrolidone, sodium chloride, ethylenediamine tetraacetic acid and Tris-HCl; the cracking combination solution comprises at least one of sodium dodecyl sulfate, cetyltrimethylammonium bromide, guanidine hydrochloride, guanidine isothiocyanate, citric acid, trisodium citrate, Tween 20, polyvinylpyrrolidone, sodium chloride, ethylenediamine tetraacetic acid and Tris-HCl; the binding solution comprises at least one of isopropanol, ethanol, guanidine hydrochloride and polyethylene glycol; the washing liquid I is at least one of guanidine hydrochloride, guanidine isothiocyanate, absolute ethyl alcohol, ethylenediaminetetraacetic acid, sodium chloride and Tris-HCl, the washing liquid II is an ethanol aqueous solution, the eluent is a Tris-HCl and ethylenediaminetetraacetic acid aqueous solution, and the magnetic beads are hydroxyl magnetic beads or carboxyl magnetic beads.

The application discloses a kind of plant whole genome RNA-chromatin interaction detection methods, the method includes the interaction state of fixed RNA and chromatin, preparation double link, obtain nuclear, chromatin DNA fragment, RNA / linker / DNA chimera, RNA-DNA double-stranded complex in turn;Tn5 transposase fragmentization cuts double-stranded complex;PCR amplification forms DNA library.The application applies Tn5 transposase to the original RADICL-seq method, successfully to RNA-DNA complex is cut and library, greatly simplifies the process, experimental procedure is reduced by at least half, experimental period is shortened from 4-5 days to 3 days, the fragment size of DNA library produced is between 250bp-400bp, increase the length of final effective RNA / DNA fragment pair, thereby greatly improve the efficiency when aligning to plant genome in subsequent bioinformatics analysis, provide effective means for plant whole genome RNA-chromatin interaction detection.

Disclosed herein are methods of improving agronomic traits in crop plants through editing sequences within the 5′ untranslated region (UTR) of plant genomes.

The invention belongs to the technical field of agricultural biology, and particularly relates to a rice endogenous space-time specific promoter OsSULTR1; the invention discloses 3pro and application thereof. The promoter OsSULTR1 is characterized in that the promoter OsSULTR1 The nucleotide sequence of 3pro is as shown in SEQ ID NO. 1. The invention provides an OsSULTR1; 3pro is a space-time specific expression regulation element from rice, can efficiently and stably drive a target gene to be expressed in a plant callus, and can realize targeted efficient and stable expression in root and stem tissues in a plant vegetative growth period. The promoter can effectively replace a non-plant-source promoter commonly used in existing plant genetic engineering, has an important industrial application value in the field of plant genetic engineering, and not only can improve the targeting and stability of target gene expression in transgenic plants, but also can improve the yield of the transgenic plants. And the potential biological safety risk of the transgenic plant caused after the exogenous DNA is introduced into the plant genome can be obviously reduced.

The invention relates to the technical field of agriculture, in particular to an efficient CBE base editing tool based on Cas12i3 and application of the efficient CBE base editing tool. According to the Cas12i3-based efficient CBE base editing tool provided by the invention, the base editing tool comprises a protein expression cassette; the nucleotide sequence of the protein expression cassette is as shown in SEQ ID NO. 1. The tool can realize efficient, accurate and low-off-target C-to-T single base replacement in a plant genome, the editing efficiency and the target flexibility are remarkably improved, and an autonomous and controllable novel base editing platform is provided for crop functional gene research and molecular breeding.

Compositions and methods are provided for genome modification of a target sequence in the genome of a plant or plant cell. The methods and compositions employ a guide RNA / Cas endonuclease system to provide an effective system for modifying or altering target sites within the genome of a plant, plant cell or seed. Also provided are compositions and methods employing a guide polynucleotide / Cas endonuclease system for genome modification of a nucleotide sequence in the genome of a cell or organism, for gene editing, and / or for inserting or deleting a polynucleotide of interest into or from the genome of a cell or organism. Once a genomic target site is identified, a variety of methods can be employed to further modify the target sites such that they contain a variety of polynucleotides of interest. Breeding methods and methods for selecting plants utilizing a two component RNA guide and Cas endonuclease system are also disclosed. Compositions and methods are also provided for editing a nucleotide sequence in the genome of a cell.

To provide a method for genome editing of a plant with improved genome editing efficiency.SOLUTION: A method for genome editing of a plant, comprising: (1) introducing a CRISPR / Cas system into a meristematic tissue of a bud having shoot-forming ability of the plant by a particle bombardment method; and (2) culturing the meristematic tissue having the CRISPR / Cas system introduced in step (1) under a high temperature condition.SELECTED DRAWING: None

The present invention relates to a gap filling method based on a DL-GapFilling model. Comprising the following steps of: 1, pre-assembling an original genome by using a traditional tool to generate a sacffard file to obtain an assembling result 1; 2, performing deep learning on the data set by using a DFillingNet model network, predicting a gap sequence by using a BeamStar Control-Extension Algorithm (BSCEA) algorithm, and then performing genome assembly on the predicted gene sequence and an original genome together, so as to obtain an assembly result 2; and 3, using Quast, Exonerate and the like to compare the assembly results 1 and 2 to a reference genome, and optimizing the prediction sequence generated in the step 2 by constructing a PredictionFilter mechanism for screening and optimizing the prediction sequence. And finally, carrying out genome packaging on the screened prediction sequence and an original genome. According to the method, a new prediction sequence is provided for traditional software, a PredictionFilter mechanism aiming at the gene sequence is provided, and the gap filling rate and accuracy of the traditional software are improved.

The disclosure relates to methods of producing genome edited plant cells, genome edited plant calli, as well as genome edited plants. The methods comprise first introducing into a plant cell the polypeptide element(s) of a genome-editing system and, subsequently, introducing the polynucleotide element(s) of the genome-editing system into a plant cell that is already expressing the polypeptide element(s).

The invention provides a rice endogenous short enhancer capable of realizing fixed-point activation of a plant genome, and the rice endogenous short enhancer realizes efficient activation of a gene by directionally inserting into a promoter region of the plant gene. Specifically, 20 short enhancers with different activation multiples from rice are obtained through a large number of screening, the activation effect can be achieved in different reporter genes, and universality is achieved. The rice enhancer can be used for efficiently and flexibly regulating and controlling transcription of complex genes of plants such as rice.

The invention relates to the technical field of plant genomics and gene editing, in particular to an in-vitro genome editing technology aiming at wheat and other complex genome crops, and provides a plant genome repetitive sequence deletion technology and application thereof. According to the method, specific sgRNA is designed, and CAS9 / CAS12 enzyme is guided to precisely shear repetitive sequences in a target genome, so that redundant repetitive sequences in the genome are effectively removed, sequencing data redundancy is reduced, and the efficiency and precision of genome information analysis are improved. The method comprises the following steps: firstly, identifying and annotating a repetitive sequence region by analyzing genome data of crops such as wheat; then, designing an sgRNA sequence aiming at the repetitive sequence, and optimizing the specificity and amplification efficiency of the sgRNA sequence; then, synthesizing an sgRNA library by utilizing a high-throughput DNA synthesis technology, and carrying out an in-vitro shearing reaction together with CAS9 / CAS12 enzyme; and finally, sequencing the sheared genome through a high-throughput sequencing platform, and analyzing the shearing efficiency and accuracy. The technology not only improves the efficiency of genome simplification and redundant sequence removal, but also can provide powerful data support for genome research and application of crops such as wheat.