40 results about "SNP genotyping" patented technology

The invention belongs to the technical field of aquatic product breeding, and particularly relates to a KASP molecular marker related to high temperature resistance character of patinopecten yessoensis and application of the KASP molecular marker in genetic breeding. On the basis of genome re-sequencing of 200 patinopecten yessoensis, a PySNP587919 locus obviously associated with the patinopecten yessoensis high-temperature-resistant character is screened by combining a whole genome SNP genotype and whole genome association analysis of the patinopecten yessoensis high-temperature-resistant character, and after the reliability of the locus is verified through Sanger sequencing, the locus is developed into a KASP marker, and the KASP marker can be used for identifying the high-temperature-resistant character of the patinopecten yessoensis and identifying the high-temperature-resistant character of the patinopecten yessoensis. The screening method can be used for screening the high-temperature-resistant comb shells. Furthermore, the invention also establishes a method for screening the high-temperature-resistant patinopecten yessoensis, and the method is efficient and accurate. Therefore, the technical scheme provided by the invention is suitable for molecular marker-assisted breeding work, rapid and effective screening of parents can be realized by typing the PySNP587919 site, and the breeding efficiency is improved.

The application discloses a method for screening superior parents of carp with high total content of polyunsaturated fatty acids. The method comprises obtaining training characteristic data and training target data, wherein the training characteristic data comprises SNP genotype information of training samples, and the training target data comprises total content information of polyunsaturated fatty acids of the training samples; training a ridge regression model by using the training characteristic data and the training target data to obtain a prediction model; obtaining SNP genotype information of a to-be-tested sample; obtaining a breeding value of the to-be-tested sample according to the SNP genotype information of the to-be-tested sample and the prediction model; and screening superior parents of carp with high total content of polyunsaturated fatty acids according to the breeding value. By the method, the breeding value of the to-be-tested sample can be directly obtained according to the SNP genotype information of the to-be-tested sample and the prediction model, and then the superior parents of carp with high content of polyunsaturated fatty acids can be screened from the to-be-tested sample, thereby providing excellent materials for new germplasm identification and breeding of carp.

The invention provides a method for screening candidate genes and SNP (Single Nucleotide Polymorphism) loci related to residual feed intake of Sahu hybrid sheep, which is characterized by comprising the following steps: S1, collecting jugular vein blood samples of the Sahu hybrid sheep, and extracting genomic DNA (Deoxyribose Nucleic Acid) of the blood samples for quality detection; the method comprises the following steps: S1, extracting DNA, S2, carrying out whole genome re-sequencing on the extracted DNA and carrying out genotyping to obtain SNP genotype data, and S3, carrying out reference genome comparison, SNP detection and genotype quality control. And S4, carrying out whole genome association analysis on the residual feed intake character of the Sahu hybrid sheep to obtain a significant SNP site. The nucleotide sequence of the SNP site obviously related to the residual feed intake of the Sahu hybrid sheep, which is obtained by the method provided by the invention, is as shown in SEQ ID NO.1, the basic group R at the 51st site of the sequence is A or G, the gene mutation causes the nucleotide of the sequence to generate polymorphism, and when the marker is mutated into G, the Sahu hybrid sheep shows lower residual feed intake.

This application relates to the technical field of biological gene detection, specifically disclosing a miniature pig SNP molecular marker combinatorial system and its application. The miniature pig SNP molecular marker combinatorial system disclosed in this application includes at least one of 221 SNP molecular markers. The physical locations of these 221 SNP molecular markers are determined based on sequence alignment during 10× coverage whole-genome sequencing of miniature pigs. The site information of the 221 SNP molecular markers is shown in Table 1. The miniature pig SNP molecular marker combinatorial system provided in this application is used for detecting SNP genotyping in miniature pigs and possesses novel, stable, cost-effective, and efficient properties.

The application discloses a kind of molecular breeding methods of apricot flower chicken for optimizing meat quality, it is related to molecular assisted selection, the method comprises: the index correlation analysis is carried out to the chicken of selected variety;Statistical meat quality trait target characteristic value is inconsistent with the first occurrence frequency ratio of the first selected chicken trait record data of variety in the index of feeding condition;Statistical meat quality trait target characteristic value is consistent with the second occurrence frequency ratio of the first selected chicken trait record data of variety in the index of feeding condition, the average of second occurrence frequency ratio is third occurrence frequency ratio;When the first occurrence frequency ratio or third occurrence frequency ratio is greater than or equal to occurrence frequency ratio threshold value, add variety chicken into SNP genotyping chicken;According to SNP genotyping variety chicken, apricot flower chicken molecular breeding is carried out.Solve the problem that the existing breeding method carries out genotyping detection to each variety of apricot flower chicken, determines the correlation of trait and genotype, selects variety and then optimizes apricot flower chicken meat quality, resulting in low efficiency.

The invention discloses a gene expression profile prediction method and device, electronic equipment and a storage medium, and relates to the technical field of artificial intelligence. Specific genetic variation and regulation region sequences in a peripheral blood sample are detected, and a standardized SNP genotype matrix and a regulation annotation vector are obtained; constructing a gene-pathway-disease-drug four-layer regulation and control network based on multi-source heterogeneous data, and determining a core node gene based on the constructed network; obtaining LD structure information and chromatin accessibility characteristics corresponding to the core node gene; and taking the standardized SNP genotype matrix corresponding to the core node gene, the regulation and control annotation vector, the LD structure information and chromatin accessibility characteristics as input of a pre-trained gene expression profile prediction model to obtain a gene expression profile prediction value of an individual corresponding to the peripheral blood sample in a specified brain region. Therefore, an accurate mapping relation between the blood gene expression data and the gene expression data of the targeted CNS tissue is established.

The application discloses an application of a GhSCAR4 gene related to oil content and protein quality of Gossypium hirsutum L.The application provides a cDNA sequence SEQ ID NO.1 and a genome sequence SEQ ID NO.2 of the gene in tetraploid Gossypium hirsutum L.The gene is obtained by resequencing and whole genome association analysis of Gossypium hirsutum L.varieties, and is significantly related to oil content and protein content of cotton seeds.The gene is used for distinguishing high-quality and low-quality haplotypes by using whether methylation variation and SNP genotypes of the gene occur.The varieties population is classified according to the haplotypes, and statistical analysis is carried out in combination with quality traits, and it is also proved that the GhSCAR4 gene is significantly related to the oil content and protein content of cotton seeds.The above results show that the gene has important research value and application prospect in efficient identification of high-oil and high-protein cotton varieties, improvement of the oil content and protein content of cotton and cultivation of new cotton varieties with high oil content and high protein content.

This application provides a method, apparatus, and electronic device for evaluating the effectiveness of SNP genotyping based on silhouette coefficients, relating to the field of SNP genotyping technology, and alleviating the technical problems in evaluating the effectiveness of SNP genotyping. The method includes: acquiring endpoint fluorescence intensity data for a target SNP locus; performing clustering based on the endpoint fluorescence intensity data using a clustering algorithm to obtain a first clustering result; filtering samples in the first clustering result using individual silhouette coefficients and a preset silhouette coefficient threshold to obtain a sample filtering result; and clustering the sample filtering result using the clustering algorithm to obtain a second clustering result.

This invention discloses molecular markers related to the number of ears per unit area in wheat and their applications. This invention belongs to the field of biotechnology, specifically relating to molecular markers related to the number of ears per unit area in wheat and their applications. The method for identifying or assisting in the identification of the number of ears per acre in wheat includes detecting the genotype of a SNP locus in the genome of the wheat to be tested, and identifying or assisting in the identification of the number of ears per acre based on the genotype. The SNP locus is a single SNP locus on wheat chromosome 4A, with nucleotide type G or T, and is the 51st nucleotide of sequence 4 in the sequence listing. The number of ears per acre in the tested wheat with the SNP genotype TT is higher or a candidate higher than that in the tested wheat with the SNP genotype GG. The identification method and its primer composition of this invention can be used in wheat breeding and have broad application prospects.

The invention relates to a method for applying an AK4 gene molecular marker to duck high sperm curve rate early breeding, and belongs to the technical field of biology, SNP genetic typing is carried out by utilizing a sequencing technology, the AK4 gene molecular marker obviously related to sperm curve rate is obtained through whole genome association analysis and screening, and in breeding, according to a breeding target, the AK4 gene molecular marker is applied to duck high sperm curve rate early breeding. By eliminating G / A genotype and A / A genotype individuals and retaining G / G genotype individuals, the reproductive performance of the breeding ducks is improved, the artificial insemination efficiency is optimized, and the breeding progress is accelerated.

The application discloses a dyslipidemia risk prediction device and terminal equipment, method and storage medium, and relates to the technical field of medical detection equipment. The device comprises an acquisition module, a first processing module and a second processing module which are connected with each other. The first processing module is used for inputting SNP genotype data of a to-be-predicted object into a pre-constructed scoring model, obtaining a polygenic risk score, and inputting an actual age and a phenotype age into a pre-constructed age linear regression model after obtaining the phenotype age based on clinical biochemical marker data and the actual age of the to-be-predicted object, so as to obtain a phenotype age acceleration value. The second processing module is used for inputting the polygenic risk score, the phenotype age acceleration value and individual characteristic data into a pre-constructed integrated model, obtaining a prediction result set, and taking a mode of the prediction result set as a prediction result of the to-be-predicted object. The device can be used for more comprehensive and accurate prediction and can improve processing efficiency.

The invention discloses an efficient and accurate wheat parent matching method and system based on the distance between a core germplasm and a genome, and belongs to the technical field of cross breeding. The matching method comprises the following steps: acquiring whole genome SNP genotype data of a breeding population, constructing a core germplasm of which the sample size is smaller than that of an original population but the original genetic diversity is greater than or equal to 95%, analyzing the population genetic structure of the core germplasm, calculating the genome distance between individuals of the core germplasm, and selecting the whole genome SNP genotype data of the breeding population. And screening Top N combinations with maximum and minimum genome distances by taking parents from different genetic subgroups as a primary condition and taking an interval from the top quartile to the maximum value of the genome distance as a primary screening range, and outputting a recommended hybrid combination list. According to the method, quantitative indexes of the genetic population structure and the genome distance are innovatively coupled through an algorithm model, double screening of subpopulation complementation and distance optimization is achieved, decision logic is more scientific, and prediction accuracy is higher.

The invention belongs to the technical field of biological detection, and particularly relates to a probe-free multiple SNP (Single Nucleotide Polymorphism) typing method, a kit and application thereof. The invention provides a method for realizing multiple SNP (Single Nucleotide Polymorphism) typing without using a probe, and the method takes a melting temperature (Tm) as a discrimination index to distinguish different allele specific PCR (Polymerase Chain Reaction) products for adjusting the Tm through differential tailing so as to identify allele types of each SNP. Compared with an existing method, the reagent cost, the experiment time and the workload are greatly reduced, and meanwhile high accuracy and stability are kept. The method has the characteristics of high efficiency, expandability and economical efficiency, and is expected to play an important role in the fields of large-scale gene screening, crop breeding, clinical typing analysis and the like, so that the method has a good practical application value.

The application belongs to the technical field of molecular marker assisted breeding, and particularly relates to a specific SNP molecular marker for rapidly identifying the genetic sex of Pelochelys cantonensis and application thereof, the SNP molecular marker is selected from at least one of JB_SNP1-3, is located at the 337th, 363rd and / or 392th base of the nucleotide sequence shown in SEQ ID NO. 3 and / or 4, and when being GG, CC and / or TT genotype respectively, the to-be-tested Pelochelys cantonensis individual is male, and when being GT, CA and / or TC genotype respectively, the to-be-tested Pelochelys cantonensis individual is female. The application provides an important molecular tool for the sex identification and sex determination mechanism research of Pelochelys cantonensis, can convert the judgment of the sex of Pelochelys cantonensis into the judgment of the SNP genotype, is favorable for the sex identification of Pelochelys cantonensis in the early growth stage, and has the advantages of rapidness and high efficiency, short sex detection period, large detection flux, small environmental factor interference, high accuracy and reliability of detection results and the like.

The application belongs to the field of plant development biology and crop molecular genetic breeding technology, and discloses a molecular marker closely linked to a major QTL site qLL.A02 for regulating the length of a rape rosette leaf and application thereof. A stable major QTL site qLL.A02 for regulating the length of a rape rosette leaf is identified through whole genome correlation analysis. A key SNP variation closely linked to qLL.A02 is identified through co-segregation analysis of a lead SNP genotype and a phenotype between populations, which is located at a SNP site at 9828644 bp of a chromosome A02 of a rape ZS11.v10 reference genome, and the G base variation genotype is a rosette leaf length dominant genotype, and is also highly related to leaf area and seedling stage biomass dominance. A KASP molecular marker developed for the variation can efficiently and accurately identify and explore excellent materials with leaf dominance in a rape germplasm resource population, and provides a key, reliable and efficient idea and method for rape variety improvement and molecular design breeding at the level of seedling stage nutrient growth.

The application discloses a Zm00001eb038700 gene for regulating corn plant height and application thereof. The nucleotide sequence of the gene is shown as SEQ ID NO:1, and the expression amount of the gene is positively correlated with the corn plant height. The amino acid sequence of the protein coded by the gene is shown as SEQ ID NO:2, the protein codes a conserved C2H2 type zinc finger protein Bud20, and the protein may be involved in the development regulation of the internode part so as to affect the corn plant height. The SNP1-206,628,704 site is located at the downstream 3801bp of the gene; when the genotype of the site is CC, the corn shows a dwarf trait; and when the genotype is changed into AA, the corn shows a high-stalk dominant trait. The application firstly discloses the dose-effect relationship between the expression level of the Zm00001eb038700 gene and the corn plant height, the associated SNP can explain 3.57% of the plant height phenotype variation. The application develops a molecular marker combination combining the SNP genotype and the gene expression amount, and the prediction accuracy of the plant height is obviously improved. Therefore, the results of the application provide technical support for breeding corn varieties with suitable plant type and high yield.

The invention is suitable for the technical field of computational biology and parasitic molecule epidemiology, and provides a whole genome machine learning method and system for toxoplasma gondii population structure analysis. According to the method, an SNP genotype probability matrix is constructed by using whole genome sequencing data, an optimal group structure is identified in combination with unsupervised clustering, and then multi-site sequence typing and rapid classification prediction of toxoplasma gondii are realized through supervised tag integration and supervised learning models. According to the method, a closed-loop mechanism of'unsupervised clustering-semi-supervised labeling-supervised learning 'is formed, and interpretability and expandability are achieved while high precision (the average accuracy is about 97%) is kept. According to the method, core information sites are obtained through screening based on progressive feature selection of feature importance, high robustness and accuracy can still be kept under the background of low sequencing depth and metagenome mixing, support is provided for genetic differentiation evaluation, epidemiological traceability and the like, modules are clear and easy to integrate, and efficient landing is achieved.

This invention belongs to the field of molecular biology, specifically relating to a molecular marker associated with stem diameter in alfalfa under salt stress and its application. The technical problem this invention addresses is that the selection of alfalfa varieties with ideal stem diameter under salt stress primarily relies on multi-year phenotypic measurements, a time-consuming and labor-intensive process heavily influenced by the environment, resulting in insufficient selection efficiency and accuracy. The technical solution of this invention is a molecular marker associated with stem diameter in alfalfa under salt stress, with the following locus information: chromosome: chr5; location: 58795369; SNP genotype: G / T. This invention also provides a primer set for amplifying the aforementioned molecular marker. This invention can be used for early prediction of stem diameter in alfalfa under salt stress and for marker-assisted breeding.

The invention discloses a portunus trituberculatus 43K SNP (Single Nucleotide Polymorphism) chip and application thereof. According to the invention, 43314 SNP loci with high quality, high polymorphism and uniformly distributed chromosomes are obtained through screening, and a probe is designed aiming at the 43314 SNP markers, so that the 43K SNP chip of the portunus trituberculatus is obtained. The Portunus trituberculatus 43K SNP chip is excellent in overall performance, high in genotype detection rate, high in genotype accuracy and good in stability, and can be completely used for SNP genotyping detection of different Portunus trituberculatus samples. The method can be widely applied to different application scenes such as germplasm resource identification and genetic diversity evaluation of the portunus trituberculatus, genetic map construction and QTL positioning, whole genome association analysis and genome selective breeding, and has important significance in improving the breeding efficiency of the portunus trituberculatus and promoting high-quality development of the portunus trituberculatus industry in China.

This invention discloses a method for SNP site screening in DNA fingerprinting and its application. The method includes: acquiring and standardizing SNP genotype data; calculating a comprehensive quality score for each site based on four dimensions: deletion rate, minor allele frequency, Hardy-Weinberg balance, and genetic diversity index, using preset weights; pre-screening based on the quality scores to obtain a candidate site set; optimizing the candidate sites using a multi-algorithm fusion strategy combining a greedy algorithm and a genetic algorithm, where the greedy algorithm progressively adds sites with the greatest discriminative power, and the genetic algorithm performs a global search in the solution space; merging the results of the two algorithms, selecting the optimal SNP site combination based on the comprehensive score; and generating a DNA fingerprint based on the optimal combination. This invention achieves maximum sample discriminative power with the fewest number of sites, significantly improving the efficiency and accuracy of DNA fingerprinting construction, and can be widely applied in fields such as crop variety identification and germplasm resource management.

The invention discloses a genome prediction method and system based on small sample adaptive deep learning, and the method comprises the steps: obtaining to-be-predicted gene data belonging to the same biological individual, carrying out the preprocessing of the to-be-predicted gene data, and obtaining SNP genotype data and gene expression data; respectively carrying out feature extraction on the SNP genotype data and the gene expression data to obtain SNP gene features and gene expression features; performing feature fusion on the SNP gene features and the gene expression features to obtain fusion features; performing regularization processing on the fused features through a feature enhancement module subjected to Gaussian diffusion training to obtain enhanced features; the enhanced features are input into a multi-head self-attention Transform encoder, and deep feature representation is obtained; and inputting the deep feature representation into a multi-task prediction module to obtain a genome prediction result. Therefore, the heterogeneous omics data can be deeply fused, the strong generalization ability is kept under the small sample condition, and the method has the advantages of good robustness and interpretability.

The present invention provides a method for the identification and characterization of chromosomal rearrangements, particularly reciprocal translocations, segregating in a plant mapping population, including a biparental mapping population of a polyploid plant species, based on the identification of allelic dosage imbalances in SNP genotyping data. Further, the invention provides a method allowing the deciphering of true aneuploid genotypes and tracking segregation thereof in a given population. Finally, the invention provides plant cells and materials and the use of suitable SNP genotyping data sets corresponding to or allowing the identification of single individuals being a carrier of the translocation and / or in addition an interesting aneuploid genotype.

The invention discloses a molecular marker related to millet plant height and application of the molecular marker. The technical problem to be solved by the invention is to identify or assist in identifying the millet plant height. According to the application of the substance for detecting the polymorphism or genotype of the SNP in identifying or assisting in identifying the plant height of the foxtail millet, or preparing products for identifying or assisting in identifying the plant height of the foxtail millet, or breeding the foxtail millet or preparing products for breeding the foxtail millet, the SNP is a single nucleotide polymorphism site of a foxtail millet genome, is the 196th nucleotide of a sequence 1 in a sequence table, and is G or A. A variety of millet genomes are detected to find that the height of millet plants with the SNP genotype being GG is higher than that of millet plants with the SNP genotype being AA, or candidate millet plants are higher than that of millet plants with the SNP genotype being AA, and the method can be used for genetic breeding of millet plants.

The invention relates to the technical field of animal breeding, and particularly discloses a beef cattle genome matching method integrating genetic advantages and defects and application, the method comprises the following steps: S1, respectively extracting beef cattle individual DNA samples from to-be-matched breeding bulls and to-be-matched cows for genetic typing, and obtaining individual SNP genotype data; s2, calculating an additive genetic relationship matrix according to a VanRaden algorithm to obtain genome estimation breeding values of beef cattle individuals on important economic characters, and calculating comprehensive selection indexes of the individuals; s3, according to the comprehensive selection index value of the individual, the SNP genotype data, the inbreeding coefficient and the economic value corresponding to each part, constructing a beef cattle economic scoring model; s4, based on the beef cattle economic scoring model, calculating economic scores of all possible pairing combinations between the to-be-mated breeding bulls and the to-be-mated cows, and performing maximum solution to generate an optimal mating scheme; through genome breeding value evaluation and economic scoring model construction, beef cattle genome matching with genetic advantages and defects is realized.

The invention discloses an image phenotype-based wheat grain anthocyanin related gene detection method, which comprises the following steps: S1, collecting a wheat grain sample image, and carrying out automatic processing on the image; s2, extracting RGB color space features of the image, and converting the RGB color space features into a Lab color space to obtain an L value, an a value and a b value; s3, acquiring SNP (Single Nucleotide Polymorphism) genotype data; and S4, according to a correlation model of the L value, the a value, the b value and the SNP genotype of the wheat grains, judging whether the SNP locus is the anthocyanin-related gene locus or not. According to the method, the wheat grain anthocyanin character related color index is rapidly quantified, so that the method for detecting the anthocyanin related gene by applying the characteristic phenotype can provide an image phenotype index capable of being rapidly, stably and nondestructively detected for breeding of high-anthocyanin wheat, the related gene is efficiently screened, and the method has important significance on accelerating breeding.

The present invention relates to a DNA polymerase variant belonging to Family A and its use, and to a DNA polymerase variant that smoothly polymerizes when the base at the 3' end of a primer is complementary to a template, and polymerization is inhibited when the base at the 3' end of a primer is not complementary to a template, thereby easily discriminating between the two cases, and to a PCR method using the variant and a PCR kit containing the variant. The present invention is useful for single nucleotide polymorphism analysis (SNP genotyping) and somatic mutation detection, etc.

This invention belongs to the field of molecular biology, specifically relating to molecular markers related to crude protein content in alfalfa and their applications. The purpose of this invention is to screen molecular markers suitable for the rapid breeding of alfalfa varieties with superior quality traits. The technical solution of this invention is a molecular marker related to crude protein content in alfalfa, with the following specific information: Chromosome: Chr5; Location: 64978172; SNP genotyping: C / A. This invention also designs KASP genotyping primers for this locus, enabling genotyping screening at the seedling stage, allowing selection without waiting for plant maturity, significantly shortening the breeding cycle.

This invention discloses a method for evaluating rice yield based on KASP multi-site detection, belonging to the field of rice breeding technology. The method includes the following steps: (1) using the Japonica rice 'Nipponbare' genome IRGSP-1.0 as a reference genome, determining the SNP genotypes at the following locations: GW8 gene at chromosome 8 (26505387 bp), GNP1 gene at chromosome 3 (36150781 bp), GE gene at chromosome 7 (24714487 bp), GS3 gene at chromosome 3 (16733441 bp), and GL3.2 gene at chromosome 3 (17340602 bp); (2) the count of homozygous mutations at the above 5 SNP sites is 1, the count of heterozygous mutations is 0.5, and the count of no mutations is 0; if the total mutation count of the 5 SNP sites is ≥4.5, it is presumed to be a high-yielding material. This invention provides technical support for evaluating the yield of rice materials.

This invention belongs to the fields of molecular biotechnology and molecular marker technology, specifically relating to a lncRNA exon SNP molecular marker related to porcine meat production performance and its application. This marker corresponds to locus 94095216 on porcine chromosome 15 in the international reference genome Sscrofa 11.1. LOC110257192 is highly expressed in porcine muscle tissue, and a G>T base substitution exists at 1564 bp in the exon region of LOC110257192, leading to polymorphism. SNP genotyping and association analysis show that individuals with the TT genotype exhibit traits such as thick backfat at 100 kg body weight and small eye muscle area. This invention provides a novel marker for marker-assisted selection in porcines, which can be applied to genetic improvement to enhance porcine meat production capacity, accelerate the genetic selection process, and promote the genetic improvement and breeding of high-quality pig breeds.

The invention provides a digital intelligence breeding sheep genetic evaluation and cultivation management system, which collects individual physiological, behavior and environmental data in real time through RFID, an intelligent necklace and automatic weighing equipment, uploads the data to a cloud after edge preprocessing, performs genomic breeding value GEBV evaluation by adopting an SSGBLUP model in combination with pedigree, phenotype and 40K SNP genotype data, and provides a new breeding sheep genetic evaluation and cultivation management system. And an XGBoost algorithm is fused to improve the complexity prediction precision. The cloud intelligent module realizes oestrus early warning, health monitoring, accurate feeding and breeding optimization, analyzes a multi-target breeding decision through an NSGA-II algorithm, and ensures that key data cannot be tampered and the whole process is traceable in combination with a block chain technology. According to the system, the seed selection accuracy, the breeding efficiency and the breeding intelligence level are remarkably improved, and the system is suitable for digital transformation and genetic improvement of a large-scale sheep farm.