9 results about "Plant genomics" patented technology

The invention relates to the technical field of crossing of bioinformatics, artificial intelligence and plant genomics, and discloses a plant single cell gene expression prediction method, system, device and medium. A plant single cell gene expression prediction model realizes dynamic feature fusion of a DNA sequence and chromatin accessibility signals through a gated cross attention mechanism; the problem that a traditional single-mode model cannot model regulation and control dynamic association is effectively solved, and the result interpretability is enhanced; a hybrid expert system and a load balancing design are adopted to significantly improve the recognition capability of the model for rare cell types, and a decoupling prediction head design supports efficient transfer learning; a DNA long sequence processing mechanism and nucleosome scale feature coding ensure cross-species compatibility; an end-to-end automatic process and a dynamic parameter optimization framework greatly improve the practicability; a'prediction-verification 'closed-loop support system can be constructed for molecular breeding, and high-precision and interpretable prediction of plant single-cell gene expression is realized.

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.

Provided herein are highly transformable maize plants, referred to as HI-NA plants, and methods of their production and use. A HI-NA plant, as disclosed herein, is homozygous for a loss-of-function mutant allele in the patatin-like phospholipase A2α (MATL) gene and at least heterozygous for one or more QTL and / or gene alleles that are responsible for increased haploid induction and / or transformation frequency in plants. A HI-NA plant, as disclosed herein, may also have a cytotype A background, which may render it highly transformable. Also provided are methods of producing I-NA plants and methods of using a HI-NA plant for editing plant genomic DNA.

The invention relates to the technical field of biology, in particular to a method for regulating and controlling the methylation level of a plant genome DNA specific region by using a Cas12i system. The invention provides a fusion protein. The fusion protein sequentially comprises a first nuclear localization signal peptide, a methylation modification structural domain, a connecting peptide, a nuclease activity-free Cas12i protein and a second nuclear localization signal peptide from an N terminal to a C terminal, the methylation modification structural domain is OsSUVH2 protein capable of up-regulating the methylation level or a functional active fragment of the OsSUVH2 protein; the amino acid sequence of the OsSUVH2 protein is as shown in SEQ ID NO: 1; the amino acid sequence of the nuclease activity-free Cas12i protein is as shown in SEQ ID NO: 3. The invention also provides a CRISPR-dCas12i system constructed on the basis of the fusion protein. According to the CRISPR-dCas12i system, the methylation modification efficiency of the plant genome DNA is remarkably improved.

The invention discloses a construction method and application of a plant CircRNA overexpression vector, and the construction method comprises the following steps: aiming at multi-exon CircRNA, taking plant genome DNA as a template, designing specific primers in a segmented manner, amplifying a target CircRNA looping region, splitting the target CircRNA into a plurality of target segments according to genome sequence characteristics, amplifying intron flanking sequences on two sides of a looping site, and constructing the plant CircRNA overexpression vector. Meanwhile, introducing an intron sequence among 1-3 exons, and connecting and cloning an amplified ring formation region fragment into a vector through a multi-fragment homologous recombinase and verifying; an efficient cyclization expression vector is transferred to promote reverse splicing and cyclization of the CircRNA in plant cells and detection of expression and cyclization efficiency in plants. By introducing the intron sequence between exons, the reverse splicing process is optimized, the cyclization efficiency is high, and the method can be applied to CircRNA expression of model plants such as grapes and tobaccos and commercial crops.

The present invention belongs to the field of molecular biology technology, and specifically relates to a method for screening broad-spectrum disease-resistant genes in plants and the application of the broad-spectrum disease-resistant gene HSP1 in preventing and controlling plant diseases. The screening method comprises: comparing the CDS sequences of N target pathogens to obtain homologous gene sequences; N is a natural number ≥2; comparing the protein sequences of the N target pathogens to obtain homologous protein sequences; comparing the coding sequences of the homologous gene sequences and the homologous protein sequences, taking the intersection, and obtaining conserved genes; comparing the conserved genes with plant genomic DNA, eliminating highly homologous genes, and obtaining broad-spectrum disease-resistant genes in plants. The screening method provided by the present invention is a broad-spectrum disease-resistant gene screening system applicable to different types of crops and corresponding to different types of crop pathogens, providing a new gene cloning idea for plant disease-resistant molecular breeding.

The invention discloses a plant genome DNA rapid crude extract and an extraction method based on the crude extract. The DNA crude extract is prepared from the following components: 60 to 150 mM of Tris-HCl and 5 to 12 mM of EDTA (Ethylene Diamine Tetraacetic Acid), and the pH (Potential of Hydrogen) of the DNA crude extract is 7.5 to 8.5. The extraction method based on the crude extract comprises the following steps: adding a plant tissue sample and a DNA extracting solution into a centrifugal tube or a deep-hole plate, grinding the sample, and carrying out warm bath on the sample to obtain the crude extract DNA. The coarsely extracted DNA can be directly used for PCR amplification without dilution. According to the DNA crude extraction method disclosed by the invention, the crude extraction DNA can be obtained only by adding liquid once, high-temperature treatment is not needed, sample pollution possibly caused by multiple times of liquid adding and high-temperature treatment is avoided, and the operation is simple, convenient, rapid and efficient.

The invention relates to the technical field of crossing of bioinformatics and plant genomics, and discloses a method and system for constructing a rice root single cell type annotation model, which adopt a double standardization strategy to integrate rice root single cell sequencing data from different data sources, can eliminate batch effect in multi-source data integration, and can improve the accuracy of the rice root single cell type annotation model. Optimizing the specific high-noise characteristics of the plants, and accurately dividing the single cell type dynamic continuous pedigree of the rice roots; a gradient lifting decision tree is utilized to train the model to learn rice root single cell sequencing data of different types of rice root single cells through an ordered lifting strategy and a classification feature processing mechanism, the problems of class imbalance and high-dimensional sparsity are effectively solved, a high-precision rice root single cell type annotation model is obtained, and the accuracy of rice root single cell type annotation is improved. The probability that the rice root single cell to be detected belongs to a certain cell type can be accurately identified, cell type annotation is carried out, the rice root single cell type annotation efficiency, accuracy and automation degree are improved, and research of plant cells is promoted.

The invention relates to the technical field of plant genome DNA extraction, in particular to a safe, non-toxic and rapid plant genome DNA extraction method which comprises the following steps: step 1, selecting fresh plant leaves as a sample, placing the sample in liquid nitrogen for rapid freezing, and then fully grinding the sample in the liquid nitrogen into fibrous powder; step 2, rapidly transferring 100mg of the ground fibrous powder into a centrifugal tube filled with 400mu L of Buffer mLP1 and 5mu L of DNAseA (deoxyribonucleic acid sease) in advance; 3, the plant genome DNA extraction kit is subjected to column dividing, program selecting and running, the plant genome DNA extraction method is matched with the plant genome DNA extraction kit, genome nucleic acid can be conveniently, rapidly and easily obtained from plant samples, operation is easy, multiple samples can be extracted at a time, rapid diagnosis is achieved, safety and non-toxicity are achieved, and the method is suitable for large-scale popularization and application. The vacancy of the automatic high-throughput plant sample genome extraction kit in the current market is filled up.