33 results about "Genetic architecture" patented technology

The invention relates to a method and primers for analyzing genetic diversity of nardostachyos root and rhizome based on ISSR molecular markers, and belongs to the technical field of molecular biology. The first technical problem solved by the invention is to provide an ISSR molecular marker primer for genetic diversity analysis of rhizoma nardostachyos. The sequences of the primers comprise UBC809, UBC823, UBC840, UBC842, UBC847 and UBC850, and the UBC840, the UBC842, the UBC847 and the UBC850 are The six ISSR primer sequences provided by the invention are stable in PCR amplification reaction in rhizoma nardostachyos, clear in amplified fragment and relatively good in stability and repeatability. The method for analyzing the genetic diversity of the rhizoma nardostachyos based on the ISSR molecular marker provides technical support for analysis of genetic structures and genetic relationships of different geographical populations and different characters of the rhizoma nardostachyos, can complete identification of test materials in a low-cost, large-batch and short-time manner, and provides a basis for protection of rhizoma nardostachyos resources and breeding of excellent varieties.

The invention belongs to the field of animal and plant breeding prediction, and discloses a rapid and accurate genome prediction method based on a heritability model, which comprises the following steps: calculating the frequency and linkage imbalance score of a marked secondary allele; refining the SNP heritability model to obtain an optimal SNP heritability model; selecting an optimal layering number; acquiring layer genotype data formed by genotype data of all individuals of the to-be-predicted data set in corresponding layers, calculating a diagonal weight matrix of each layer of SNP estimated heritability assignment to the corresponding layer based on the optimal SNP heritability model, and calculating a genetic relationship matrix between individuals of the layer genotype data corresponding to each layer; and fitting the multi-random hybrid model to obtain the genome estimation breeding value of each phenotype of all individuals in the data set to be tested. The method is based on a linear model framework, the calculation complexity is low, the key steps can be subjected to parallel processing, and the calculation speed is high; according to the method, the character specific SNP heritability model is constructed, and the model representation of a complex character genetic structure is optimized, so that the prediction performance is improved.

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 a gene combination for ASD evaluation and application thereof, and belongs to the technical field of gene detection. The gene combination for ASD evaluation is obtained on the basis that 1089 ASD cases are subjected to whole exome sequencing, the genetic structure of ASD is comprehensively analyzed, harmful variation in ASD related genes is comprehensively analyzed, 168 high-influence genes are obtained through comprehensive analysis and evaluation, the ASD related genes recorded in a part of a database are determined as low-influence genes, and the ASD related genes recorded in a part of a database are determined as low-influence genes. The detection rate of harmful variation of the high-influence gene combination in an ASD case group reaches 21.12%, which indicates that the high-influence gene combination can assist in improving the accuracy of ASD clinical diagnosis based on a genome level.

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 provides a genetic structure variation at the upstream of a GHR gene and application of the genetic structure variation. Specifically, the invention provides a structural variation molecular marker related to duck growth and development, the structural variation molecular marker is located at the upstream 80kb of a GHR gene on a chromosome ChrZ, and the nucleotide sequence of the structural variation molecular marker is as shown in SEQ ID NO: 1. The structural variation molecular marker can regulate and control the expression of the GHR gene so as to regulate and control the growth and development of ducks, provides a theoretical basis and a genetic basis for breeding or cultivating duck varieties with excellent growth traits, and is beneficial to improving the breeding efficiency and accelerating the duck breeding process.

The invention provides a genetic structure variation at the upstream of an FER gene and application thereof. Specifically, the invention provides a structural variation molecular marker, the structural variation molecular marker is located at the upstream 30kb of an FER gene on a chromosome ChrZ, and the nucleotide sequence of the structural variation molecular marker is as shown in SEQ ID NO: 1. The structural variation molecular marker mainly exists in domesticated ducks, can reduce expression of FER genes in livers, and can be used as a marker for distinguishing the domesticated ducks and wild ducks, so that the molecular marker provides a theoretical basis and a genetic basis for breeding or cultivating duck varieties with excellent economic characters, and is beneficial to improving the breeding efficiency and accelerating the duck breeding process.

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 present invention belongs to the technical field of molecular biology, and specifically discloses microsatellite loci of Platygyra daedalea. The microsatellite loci are one or more of JQ1026, JQ1086, JQ1610 and JQ55, and the nucleotide sequences of JQ1026, JQ1086, JQ1610 and JQ55 are SEQ ID NO.1-SEQ ID NO.4 respectively. The present invention also discloses the application of the above-mentioned microsatellite loci of Platygyra daedalea in population genetic structure analysis, paternity testing and / or molecular marker-assisted breeding.

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 belongs to the technical field of gene and molecular breeding, and particularly relates to a picea koraiensis 40K genome liquid chip and application thereof. The picea koraiensis 40K genome liquid-phase chip provided by the invention comprises 40088 SNP loci, and compared with an existing European picea koraiensis 50K solid-phase chip, 170 QTL loci which are remarkably related to characters such as picea koraiensis wood property, insect resistance, tree height, diameter at breast height and the like are newly added to the picea koraiensis 40K genome liquid-phase chip; the method can be used for molecular breeding researches such as germplasm resource genetic evaluation, population genetic structure analysis, genetic relationship identification, quantitative character genetic positioning, whole-genome association analysis and whole-genome selection of spruces including picea koraiensis, and is helpful for promoting molecular marker-assisted breeding and genome selective breeding of precious tree species. The forest tree breeding period is shortened, and the selection precision and breeding efficiency are improved.

The present invention provides a combination of Psibalsk gazelle SSR molecular markers, a primer combination, a kit and uses, and relates to the technical field of molecular biology. Based on the whole-genome sequencing data of Psibalsk gazelle, SSR primer design and SSR loci were screened. The obtained 26 pairs of SSR primers can stably amplify the target product and are highly polymorphic, and can be used for detecting the genetic diversity of the Psibalsk gazelle population, analyzing the genetic structure of the population, and studying evolution and blood relationship. The combination of the screened Psibalsk gazelle polymorphic SSR molecular markers can identify individuals of Psibalsk gazelle with high accuracy. The experimental results show that the combination of Psibalsk gazelle SSR molecular markers of the present invention can meet the needs of individual identification, and individual identification was performed on 33 fecal samples of Psibalsk gazelle subadults derived from 24 different individuals, which is consistent with the number of Psibalsk gazelle subadults in the Jiangxigou Psibalsk gazelle rescue center.

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 invention discloses a triplophysa siluroides microsatellite marker as well as an amplification primer and application of the triplophysa siluroides microsatellite marker. According to the invention, 15 pairs of microsatellite molecular markers with high polymorphism are screened from triplophysa siluroides genome DNA for the first time, so that the problem of blank of triplophysa siluroides microsatellite markers is made up; in the provided 15 microsatellite molecular marker sites, 14 microsatellite molecular marker sites are 4-6 base repeated microsatellite molecular marker sites, slip bands and allele loss are not easy to occur, and during capillary electrophoresis typing, impure peaks are few, allele difference is obvious, reading is accurate, and mutation rate is higher. The microsatellite molecular marker screened by the invention can be used for analyzing the population genetic diversity and population genetic structure of triplophysa siluroides, and can provide a candidate molecular tool for the evaluation of the population genetic diversity of triplophysa siluroides, the development and protection of germplasm resources and the like.

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.

The application discloses a kind of endangered wild animals and its product geographical tracing method based on machine learning and DNA imprinting and application thereof, it is related to wild animal and product geographical tracing technical field.The method includes applying machine learning method to known geographical coordinates sample and establishing linear regression model, and the sample of unknown geographical coordinates is traced according to linear regression model two parts of content.The application discloses a kind of endangered wild animals and its product geographical tracing method based on machine learning and DNA imprinting and application thereof, by dimension reduction, the large amount of genetic markers obtained by original sequencing is simplified into a group of simplified features that cannot be directly compared, and each feature contains the geographical origin information of individual in sample;On this basis, linear regression model is established by training simplified features, which greatly reduces the training cost;The principal component with maximum variance is mapped to the geographical coordinates of individual, and the effect of tracing the geographical origin of individual is achieved through linear regression model.

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 provides a genetic structure variation of an IGF2BP1 gene regulatory region and application of the genetic structure variation. Specifically, the invention provides a structural variation molecular marker related to duck growth and development, the structural variation molecular marker is located at upstream 1.7 kb of an IGF2BP1 gene on a chromosome Chr28, and the structural variation molecular marker has a nucleotide sequence as shown in SEQ ID NO: 1. The structural variation molecular marker can up-regulate the expression of the IGF2BP1 gene so as to promote the growth and development of ducks, provides a theoretical basis and a genetic basis for breeding or cultivating duck varieties with excellent growth traits, and is beneficial to improving the breeding efficiency and accelerating the duck breeding process.

The invention discloses a specific oligonucleotide fluorescence in-situ hybridization probe library for accurately identifying tartary buckwheat chromosomes 5-8 and application, and belongs to the field of cytogenetics research. The method comprises the following steps: selecting single-copy oligonucleotide sequences of chromosomes 5-8 from a tartary buckwheat whole genome, and filtering out repetitive sequences to obtain a probe sequence library of each pair of chromosomes; and screening out specific single-copy oligonucleotide sequences of chromosomes 5-8, adding specific primers at two ends of the single-copy oligonucleotide sequences, and combining the probes into a specific oligonucleotide fluorescence in situ hybridization probe library of the tartary buckwheat chromosomes 5-8. The constructed single-copy oligonucleotide probe is combined with a fluorescence in-situ hybridization technology to be applied to tartary buckwheat chromosomes, the chromosomes 5-8 of tartary buckwheat can be accurately identified, and powerful cytological technical support is provided for research fields of karyotype characteristics and genetic structure variation of the tartary buckwheat chromosomes, tartary buckwheat cross breeding and the like.

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.