21 results about "Genetic architecture" patented technology

The invention discloses a sesbania SSR primer combination developed based on a shallow genome sequence and application thereof, and belongs to the technical field of molecular markers. The invention develops an SSR primer combination based on a shallow genome sequence of sesbania, and the SSR primer combination comprises 23 pairs of SSR primer pairs. The SSR primer pair developed by the invention has the advantages of high polymorphism, rich polymorphic information content, stable amplification result, high resolution, accuracy and the like, can quickly and accurately judge the source and variety of sesbania, is beneficial to the research of germplasm resource identification, germplasm resource genetic diversity analysis, genetic structure analysis and the like of sesbania, and has wide application prospects. The method has important significance in promoting conservation and utilization of sesbania germplasm resources and promoting industrial development.

Compositions and methods for detecting structural variations (SVs) in target genes or for genetic mapping of movable transposable elements are disclosed, the target genes relating to disease pathologies commonly found in large Mendelian genomics projects, and the movable transposable elements relating to genetic diseases, cancer, and aging. The method comprises: (i) contacting a sample containing genomic DNA with a DNA endonuclease for an effective amount of time to cleave the genomic DNA into fragments, the genomic DNA being uncrosslinked; (ii) subjecting the fragments obtained from step (b) to a DNA ligase to obtain circularized DNA; (iii) subjecting the circularized DNA to reverse PCR amplification containing a reverse primer, wherein the reverse primer is designed to match a expected wild-type sequence near a suspected mutant locus in the gene; and (iv) sequencing the amplified products. Exemplary conditions include Bardet-Biedel syndrome; severe upper and lower limb defects; retinitis pigmentosa; syndromic microcephaly; spastic paraplegia; and atypical hemolytic uremic syndrome.

The invention discloses an oryzias chinensis SSR molecular marker primer group and application, and belongs to the technical field of molecular biology. The oryzias chinensis SSR molecular marker primer group provided by the invention comprises 10 pairs of primers, and the primer sequences of the primers are sequentially shown as SEQ ID NO.1-20. The oryzias chinensis SSR molecular marker primer group can be used for polymorphism analysis of an oryzias chinensis population in combination with a PCR amplification technology, and a basis is provided for construction of a genetic structure and a genetic map of the oryzias chinensis population.

The invention discloses an SSR (Simple Sequence Repeat) primer composition for evaluating genetic diversity of channel catfish breeding population and an application method of the SSR primer composition, and belongs to the technical field of fish genetic breeding. The method comprises the following steps: modifying 5'ends of forward primers of the primers by using FAM fluorophores respectively, amplifying genome DNA of each breeding group by using the 10 pairs of microsatellite site primers respectively, analyzing amplification products, reading genotypes, analyzing parameters, and determining the genotype of the breeding group. The analysis result is used for evaluating the population polymorphism, the variation condition of the population genetic structure and the genetic differentiation degree among the populations. By applying the evaluation method disclosed by the invention, the population genetic diversity and genetic structure of continuous breeding generations of channel catfish can be systematically evaluated. The SSR primer and the genetic diversity evaluation method can be used for genetic improvement and new variety breeding of channel catfish.

The invention belongs to the field of biological detection, and relates to an SNP (Single Nucleotide Polymorphism) combination for identifying hybrid lineage of foreign varieties and northeast local beef cattle and an application method of the SNP combination. A whole genome re-sequencing technology is utilized, northeast local beef Yanbian cattle is taken as a target group, European common cattle is taken as a reference group, Asian common cattle is taken as a transition group, and variation sites and a group genetic structure of northeast local beef cattle are analyzed; it is found that hybrid individuals of lizan or simmental and Yanbian cattle of foreign varieties exist in local beef cattle groups in northeast China. By calculating inter-population differentiation index (Fst), linkage imbalance (LD) and allele frequency (AF) of variation sites in the population, 1640 SNP sites are screened, and the lineage of Yanbian cattle can be identified.

This invention provides SSR molecular markers for Hibiscus rosa-sinus and their applications, belonging to the field of molecular marker technology. The invention comprises 15 molecular markers, with corresponding primer sequences shown in SEQ ID NO. 1~30. Testing revealed that this series of markers exhibits a 100% polymorphism rate, excellent polymorphism information content, marker index, and resolution, and strong genetic stability. The molecular marker primers of this invention can efficiently distinguish Hibiscus rosa-sinus germplasm materials, clearly revealing the population's genetic structure and phylogenetic relationships. They are suitable for Hibiscus rosa-sinus germplasm resource identification, genetic diversity analysis, molecular fingerprinting construction, and assisted breeding, possessing the characteristics of high specificity, high resolution, and wide applicability.

The invention relates to a penaeus chinensis 40K liquid phase chip, a probe combination and application thereof, and belongs to the technical field of aquatic molecular breeding biology. The liquid-phase chip comprises probes corresponding to 40 and 803 SNP (Single Nucleotide Polymorphism) loci, and the loci are uniformly distributed on a reference genome ASM1920278v2, are comprehensive in coverage and good in polymorphism, and are particularly closely related to key characters such as growth, stress resistance and disease resistance. Various application requirements of molecular identification, genome selection, functional gene research and the like of the Chinese prawns can be met at the same time, and the method can be used for germplasm resource evaluation and variety identification, population genetic structure research and protection, genome selective breeding, whole genome association analysis, candidate gene mining and the like.

This invention discloses a pleiotropic gene sharing genetic structure with obesity and mental disorders, along with its screening method and applications, belonging to the field of biomedical technology. The pleiotropic gene includes RERE, NEGR1, DENND1B, CTNNB1, TMEM106B, SP4, TSNARE1, DENND1A, CNNM2, NT5C2, BMAL1, MPHOSPH9, CCDC92, YLPM1, TAOK2, RTN4RL1, and ARFGEF2. The process includes collecting GWAS summary statistics on obesity-related phenotypes and mental disorders, assessing genetic correlation, screening pleiotropic genetic loci and candidate pleiotropic genes, using TWAS to screen pleiotropic genes, functional analysis and drug target prediction, and bidirectional causal association genetic validation. These methods are used to prepare drugs for the treatment of obesity and mental disorders or to construct a risk prediction model for obesity-mental disorder comorbidity.

The application belongs to the field of animal and plant breeding prediction, and discloses a fast and accurate genomic prediction method based on a genetic force model, which calculates the minor allele frequency and linkage disequilibrium score of a marker; obtains an optimal SNP genetic force model through a SNP genetic force model; selects an optimal number of layers; obtains layer genotype data formed by the genotype data of all individuals in a corresponding layer of a to-be-predicted data set; calculates the estimated genetic force of each layer of SNPs based on the optimal SNP genetic force model, and assigns the estimated genetic force to a corresponding diagonal weight matrix of the layer; calculates the kinship matrix between individuals in the corresponding layer genotype data of each layer; fits a multi-random mixed model to obtain the genomic estimated breeding value of each phenotype of all individuals in the to-be-tested data set. The application is based on a linear model framework, has low calculation complexity, and the key steps can be processed in parallel, so the calculation speed is fast; the application constructs a trait-specific SNP genetic force model, optimizes the model representation of the genetic structure of a complex trait, and thus improves the prediction performance.

The application belongs to the technical field of genetic breeding, and specifically discloses a method for constructing a pure line of ptilophogus percussor, which mainly utilizes microsatellite amplification, gene sequencing and typing, and family grouping after analyzing the genetic structure of a group; finally, after expansion, subculture, and two generations, the inbreeding coefficient is calculated, and if the inbreeding coefficient is less than 0.01 and the inbreeding increment of generations is less than 0.003, it is indicated that the construction of the pure line is successful. Compared with the prior art, the application can quickly homozygous ptilophogus percussor, keep the purity of the genetic resource variety, guarantee the genetic polymorphism of ptilophogus percussor, lay a foundation for genetic resource protection, effectively avoid the inbreeding depression of ptilophogus percussor, and lay a foundation for the development and utilization of ptilophogus percussor genetic resources and the cultivation of new matching lines.

The invention provides a polyploidy genome apparent data resolution analysis method which comprises the following steps: S1, acquiring original data, removing linkers and filtering low-quality sequences; s2, carrying out single-ended comparison on the reference genome by using bowtie2 software and taking-k'n 'as a parameter, and screening comparison results; s3, recording double-end matched Reads and matched chromosome numbers; s4, dividing the reference genome into a plurality of sets, and independently constructing a reference genome index for each set of genome; s5, extracting sequences according to the records obtained in the step S3, and distributing the sequences to corresponding subgenomes according to chromosome numbers; and S6, comparing each group of sequences with corresponding sub-genomes according to a double-end comparison process, and finally identifying peaks information of each group of genomes, thereby completing the polyploidy genome apparent data resolution analysis. According to the method, by optimizing comparison parameters and adding a subsequent sequence identification screening strategy, apparent data between homologous chromosomes are accurately distinguished, and accurate distinguishing of genetic structures is achieved.

The application discloses a model and method for predicting biological traits by comprehensively integrating genetic background and variation information, and the model comprises: a Siamese network which generates and extracts genetic background and genetic correlation information between samples, establishes an embedding vector for each sample to represent the genetic background information; a genetic variation embedding network which uses a deep learning network to extract complex high-order information using whole genome variation information of each sample, establishes an embedding vector to represent the cumulative effect of genetic variation on traits; and a fusion and trait prediction module which realizes accurate prediction of traits by organically fusing the embedding vectors output by the above two modules. The application can solve the problem that genetic background information and genomic variation information cannot be effectively fused in the prior art, effectively capture the nonlinear effect between genes, and greatly improve the accuracy of genomic selection and the genetic architecture analysis capability of complex traits.

In certain aspects, the technology relates to methods of selecting and / or treating subjects having cancer, where the subjects are identified as having at least one genetic structural variant associated with, or adjacent to, the PTPRD gene, the CD274 gene and / or the CD273, wherein the subject having cancer for potential responsiveness to treatment with a PTPRD-targeted therapeutic and / or an immune checkpoint blockade.

The invention belongs to the technical field of molecular biology, and provides polymorphic primers of Chinese hippophae rhamnoides genome SSR molecular markers and application of the polymorphic primers. The SSR molecular marker is composed of 20 pairs of SSR molecular marker polymorphic primers, and the nucleotide sequences of the primers are as shown in SEQ ID NO.1-SEQ ID NO.40. The SSR molecular marker comprises 20 pairs of SSR molecular marker polymorphic primers. A large number of SSR sequences are mined by using transcriptomes, SSR capillary electrophoresis technology is combined, SSR loci with high measurement indexes Na value, I value and PIC value of genetic difference and front 20 of the sequence are screened, and Chinese sea-buckthorn molecular identity information is made and applied to Chinese sea-buckthorn geographic source identification. The SSR molecular marker is good in polymorphism primer specificity and high in polymorphism, and when the SSR molecular marker is applied to Chinese hippophae rhamnoides population genetic structure and resource genetic diversity analysis, the diversity and genetic structure of hippophae rhamnoides genetic level in China can be revealed more comprehensively, and a foundation is laid for formulating a genetic protection strategy.

The invention discloses a deep learning genome prediction method and system based on a retrieval enhancement mechanism. The method comprises the following steps: acquiring genome data; generating an individual embedding representation through a gene feature extraction network, and optimizing embedding space distribution by using a gene specific discriminator to capture a potential genetic structure; retrieving a reference individual most related to the target sample based on the similarity of the embedded space; performing weighted fusion on the retrieved reference sample features and the target sample to form enhanced representation; and finally predicting the phenotypic value of the target sample through the regression network. According to the method, a retrieval enhancement mechanism is introduced, so that the model can dynamically utilize information of genetic related individuals in a prediction process, and genetic related characteristics of an individual level are extracted from a group. Different from a traditional genome prediction model which is only based on independent sample learning, the method provided by the invention structurally fuses genetic similarity among individuals, and can more accurately model a complex nonlinear genetic effect.

The invention belongs to the technical field of molecular biology, and particularly relates to a phyllostachys pubescens SSR molecular marker primer group and application thereof. The phyllostachys pubescens SSR molecular marker primer group provided by the invention comprises six pairs of primers, namely SSR-49, SSR-7, SSR-42, SSR-4, SSR-28 and SSR-11, wherein the nucleotide sequences of the six pairs of primers are shown as SEQ ID NO.1-2, SEQ ID NO.3-4, SEQ ID NO.5-6, SEQ ID NO.7-8, SEQ ID NO.9-10 and SEQ ID NO.11-12. The phyllostachys pubescens SSR molecular marker primer group provided by the invention can be used for detecting phyllostachys pubescens. The developed polymorphic SSR marker systematically evaluates the genetic diversity of 19 kinds of moso bamboos and variants of the moso bamboos, indicates the medium genetic diversity level and significant genetic structure differentiation of moso bamboos populations, constructs the SSR-based moso bamboos digital fingerprint spectrum, provides an important tool for moso bamboos germplasm resource protection, variety identification and molecular breeding, and has a wide application prospect. The method has positive significance in promoting sustainable development of the bamboo industry.

The invention provides a whole genome genetic effect estimation method and device and application, and belongs to the technical field of biological information. The method comprises the following steps: acquiring population whole genome data of a predetermined phenotype; performing section division on the population whole genome data; acquiring convergence parameters of each section based on the non-genetic contribution information of each section and the average genetic contribution information of the SNP; inputting the convergence parameter of each section into a machine learning model to obtain a genetic effect estimation result of each section; and combining the genetic effect estimation results of all the segments to obtain the whole genome genetic effect estimation result. The method is suitable for carrying out genetic effect estimation on population whole genome data, and individual data use limitation is avoided. According to the method, the problem of overfitting when the number of biomarker effects is too large is solved, the calculation efficiency and the model stability are improved, the multi-collinearity influence is reduced, and the flexibility of processing a complex genetic structure is enhanced.

This invention belongs to the field of animal molecular genetic detection and bioinformatics analysis technology, and relates to a method and application for constructing low-density SNP marker combinations for equine population attribution determination, population genetic structure assessment, and genetic correlation assessment. Specifically, based on equine whole-genome autosomal biallelic SNP data, a low-density differential information marker combination is obtained through multi-population differentiation information screening and supervised feature optimization. Results show that the marker combination maintains high population attribution determination performance in both outer cross-validation and external independent test sets, and can well reproduce the population genetic structure reflected by PCA, ADMIXTURE, and genomic relationship matrices; it is suitable for equine population attribution determination, genetic group identification, germplasm resource assessment, population genetic structure analysis, kinship determination, and the development of related molecular detection products.

The application discloses a kind of liquid chip for pedigree identification of Yudong goat and application thereof, belong to whole genome gene chip technical field.The chip contains 10,000 specific SNP sites, by analyzing the whole genome resequencing data of 231 individuals of Yudong goat, Boer goat and other 4 varieties, is obtained based on population differentiation index (FST) and polymorphism (MAF) screening.Using the chip, combined with targeted sequencing and bioinformatics analysis, a set of efficient, accurate pedigree identification and kinship analysis method is established.Experiment verification shows that the method is accurate to 100% for the pedigree identification of Yudong goat variety, and can quantitatively analyze individual pedigree composition, clearly analyze population genetic structure.The application solves the problems of insufficient specificity, low resolution accuracy and other problems in the application of existing general chip in Yudong goat, and provides key technical support for germplasm resource protection, core group management and precise genome breeding of the variety.

The invention relates to the technical field of agricultural biology, and discloses a method for identifying rice substantive derived varieties based on a whole genome SNP site set. The method comprises the following steps: carrying out whole genome sequencing and genotype analysis on a rice variety to be detected and a control variety, calculating the genetic similarity between the varieties by utilizing a set of pre-screened 15,772 core SNP site sets, and setting a unified judgment threshold value for indica rice and japonica rice subgroups based on the distribution of the site sets in a large-scale group. Therefore, the defects that in the prior art, site coverage is limited, steps are tedious, and subgroup genetic structure interference is caused are overcome, and efficient, stable and cross-subgroup applicable accurate judgment on rice substantive derived varieties is achieved.

The invention provides an identification method of Hu sheep environmental adaptability key genes and an application method in breeding. The method comprises the following steps: collecting Hu sheep blood samples in different environments, carrying out whole genome re-sequencing, identifying the key genes through the steps of data processing, population genetic structure analysis and selection signal detection, and verifying functions through a gene editing technology. In the application aspect, the identified key gene is used for Hu sheep breeding through a molecular marker-assisted selection technology, and the environmental adaptability of Hu sheep is improved. Compared with the prior art, the method can comprehensively and deeply excavate Hu sheep environment adaptability genes, accurately screen and breed excellent varieties, improve breeding benefits, reduce breeding risks and promote the Hu sheep industry to be transformed from tradition to modernization, and the problems that in the prior art, gene identification is not comprehensive, breeding efficiency is low, and breeding strategies are not targeted are solved.