42 results about "Genetic architecture" patented technology

The invention relates to the technical field of information, and provides a cross-platform global weed gene database unified building method which comprises the following steps: screening out a weed population having gene exchange characteristics with a target crop, identifying gene segments of gene exchange between the crop and weeds by adopting a gene comparison method, and determining a transmission path of resistance genes in interspecific hybridization; according to a gene comparison result, extracting transmission path data of the resistance gene, and analyzing the influence of resistance gene transmission on the genetic structure of the weed population in combination with the genetic structure characteristics of the weed population; calculating the frequency distribution of the resistance genes in different weed populations, judging the diffusion trend of the resistance genes in the weed populations according to the frequency distribution, generating a resistance gene diffusion map, and predicting the variation trend of the future weed population genetic structure based on a weed population genetic structure variation trend chart and the resistance gene diffusion map. And a global weed gene database is established, so that an effective weed management strategy can be formulated.

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 discloses a Dazu black goat gene polymorphism and lambing trait association analysis method, and relates to the field of genes. Comprising the following steps: sample collection and data collection: collecting Dazu black goats as well as blood samples and ovary samples of the Dazu black goats, respectively collecting the lambing number and birth weight of the black goats, and then calculating the average birth weight of the first birth and the average lambing number of the first three births; extracting blood DNA, namely extracting the blood DNA by adopting a traditional phenol-chloroform method; designing a PCR primer and an amplification system; and analyzing a population genetic structure, and carrying out genetic analysis and screening on SNP sites of the goat AMH gene. The molecular marker-assisted technology is utilized to screen out the marker of the targeted gene polymorphic site which is strongly related to the breeding traits of the Dazu black goats, the breeding period can be shortened in molecular breeding, the breeding and breeding efficiency can be effectively improved, and the economic value of the Dazu black goats is further improved.

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 present invention provides a Przewalski's gazelle SSR molecular marker combination, a primer combination, a kit and an application, and relates to the technical field of molecular biology. Based on the whole genome sequencing data of Przewalski's gazelle, the present invention performs SSR primer design and SSR site screening, and the obtained 26 pairs of SSR primers can stably amplify the target product and are highly polymorphic, and can be used for the detection of genetic diversity of Przewalski's gazelle population, the analysis of population genetic structure, and the study of evolution and kinship. The polymorphic SSR molecular marker combination of Przewalski's gazelle obtained by screening can be used for individual identification of Przewalski's gazelle with high accuracy. The experimental results show that the SSR molecular marker combination of Przewalski's gazelle of the present invention can meet the needs of individual identification, and 33 fecal samples of Przewalski's gazelle subadults are individually identified, which come from 24 different individuals, which is consistent with the number of Przewalski's gazelle subadults in the Jiangxigou Przewalski's gazelle rescue center.

Compositions and methods for detecting genetic structural variations (SVs) in a gene of interest, involved in disease pathologies commonly found in large Mendelian genomics programs; or for genetic mapping of mobile transposable elements, involved in genetic disease, cancer, and aging are disclosed. The methods include: (i) contacting a sample comprising genomic DNA with a DNA endonuclease for an effective amount of time to cleave the genomic DNA into fragments, the genomic DNA has not been crosslinked, (ii) subjecting the fragments obtained from step (b) to a DNA ligase to obtain circularized DNA, (iii) subjecting the circularized DNA to inverse PCR amplification comprising inverse primers, wherein the inverse primers are designed to align with anticipated wild-type sequences, adjacent to a suspected mutation locus in a gene, and (iv) sequencing the amplified product. Exemplary conditions include Bardet-Biedl syndrome; Severe upper and lower limb defects; Retinitis pigmentosa; Syndromic microcephaly; Spastic paraplegia; and atypical hemolytic uremic syndrome.

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 present invention relates to the field of information technology, and provides a method for uniformly constructing a global weed gene database across platforms, including: screening out weed populations with gene exchange characteristics with target crops, using gene alignment methods to identify gene fragments of gene exchange between crops and weeds, and determining the transmission path of resistance genes in interspecific hybridization; according to the gene alignment results, extracting the transmission path data of resistance genes, and combining with the genetic structure characteristics of the weed population, analyzing the impact of the transmission of resistance genes on the genetic structure of the weed population; calculating the frequency distribution of resistance genes in different weed populations, judging the diffusion trend of resistance genes in the weed population according to the frequency distribution, generating a resistance gene diffusion map, and based on the weed population genetic structure change trend map and the resistance gene diffusion map, predicting the future change trend of the weed population genetic structure, uniformly constructing a global weed gene database, which helps to formulate effective weed management strategies.

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.

The invention discloses a model and method for predicting biological characters by integrating genetic background and variation information, and the model comprises an embedded Siamese network which generates and extracts genetic background and genetic correlation information between samples, and builds an embedded vector for each sample to represent the genetic background information; the genetic variation embedded network is used for extracting complex high-order information and establishing an embedded vector by using a deep learning network and the whole genome variation information of each sample so as to characterize the cumulative effect of genetic variation on characters; and the fusion and character prediction module organically fuses embedded vectors output by the two modules to realize accurate prediction of characters. According to the method, the problem that genetic background information and genome variation information cannot be effectively fused in the prior art can be solved, the nonlinear effect between genes is effectively captured, and the accuracy of genome selection and the genetic architecture analysis capability of complex characters are greatly improved.

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.