61 results about "Population genetics" patented technology

The invention discloses a polar region environment-oriented two-stage micro-siting optimization method for a wind generating set, and relates to the technical field of polar region renewable energy planning and wind power generation, the optimization method comprises the following steps: polar region environment parameter initialization and scene modeling; the first stage is grid primary selection based on mixed integer linear programming; the second stage is coordinate refinement based on a multi-population genetic algorithm; and scheme output and efficiency evaluation. According to the method, a sector reweighting mechanism of extremely cold correction parameters is realized through reweighting of biochemical parameters and scenes in an environment special for a polar region, the extremely cold correction parameters are directly embedded into a wind regime scene set and a power model, and the problem that a conventional land model can obviously underestimate or overestimate single-machine power and wake flow propagation distance under extremely low temperature and low roughness conditions, so that the reliability of the model is improved is solved. Therefore, the power prediction and wake flow loss evaluation are more practical under the polar region conditions such as the south pole, so that the engineering reliability of site selection decision and the accuracy of generating capacity prediction are improved.

The invention discloses a compression and decompression method based on generic genome expression, and relates to the technical field of compression and decompression of DNA next-generation sequencing data, in particular to the compression and decompression method based on generic genome expression. The method aims at solving the problems that in the prior art, the capacity of processing population genetic diversity is insufficient, original sequencing quality information cannot be effectively restored during decompression, and memory occupation is too high during large-scale data processing. Obtaining a to-be-compressed sequencing sequence data file, a reference genome sequence and a thousand-person genome variation sample; obtaining a haplotype list, a variation list and a haplotype offset list corresponding to each window block; storing the window number, the haplotype number, the haplotype offset, the head and tail unmatched sequences, the current sequence name and the quality score character string into a single compression block; carrying out binding storage; completing the compression processing of the mass fraction; and obtaining each to-be-compressed sequencing sequence based on the result of the compressed part.

This invention discloses an artificial intelligence-based method and system for predicting and intelligently replenishing SPD consumable demand, belonging to the field of medical consumable supply chain management technology. It obtains key influencing factors of SPD consumables by clustering analysis of historical SPD consumable demand correlation data and identifying influencing factors. Furthermore, through the acquisition and training of an initial SPD consumable demand prediction model, an accurate SPD consumable demand prediction model is obtained. This model is then used to predict real-time SPD consumable demand correlation data, outputting SPD consumable demand prediction results that better match actual needs and applications. In addition, the replenishment objective function is iteratively optimized using a multi-population genetic algorithm to obtain optimal SPD control parameters, thereby automating the generation of intelligent replenishment strategies.

The application discloses a high-throughput genotype intelligent analysis method, which comprises data acquisition and preprocessing, molecular marker identification and prediction of genetic relationship and hybridization advantage; high-throughput genotype data are subjected to standardization treatment, three quality evaluation standards of coverage, transversion / transversion ratio and error rate are established, and batch effect is corrected through a position effect index; then genetic similarity matrix between samples is calculated based on the pretreated data, a label SNP with high centrality is identified as a molecular marker through linkage disequilibrium network analysis; the population genetic relationship is estimated by using the marker, and a phylogenetic tree is constructed, and the hybridization advantage is predicted based on the relationship index of heterozygosity and genetic distance. The application significantly improves the quality of genotype data, optimizes the screening of molecular markers, accurately estimates the population genetic relationship and accurately predicts the hybridization advantage, and provides an efficient bioinformatics solution for modern breeding.

The application provides an analysis method for complex evolutionary history based on deep learning, comprising: according to a preset species evolutionary history simulation sequence data, respectively as a model training set and a test set; determining the topological structure of the training set data, and labeling the training data in different topological structure proportions; constructing a convolutional neural network, training and testing the convolutional neural network with the data set, so that the error between the data prediction value and the label value is minimized; based on the trained convolutional neural network, analyzing real genomic sequence data, and combining other population genetics analysis methods, determining the evolutionary relationship and introgression site between different biological groups. The application uses comparative genome or population genome data, infers the topological structure between sequences through a deep learning algorithm, further evaluates the evolutionary relationship at the genome level, and identifies local introgression signals through the difference of the topological structure between different regions.

The present disclosure discloses a method for reconstructing the working face of coal mine based on search space pruning and multi-population dynamic adjustment, which involves the technical field of working face reconstruction of coal mine under incomplete projection conditions, comprising: based on prior knowledge of the working face reconstruction model structure, an initial grid partitioning of the exploration area is performed. Subsequently, multi-scale grid partitioning is achieved through search space pruning, guided by the sum of ray intercepts within each grid unit; to meet the requirements of population diversity and rapid convergence in the multi-population genetic algorithm, a multi-scale reconstruction objective function is constructed based on the partitioned multi-scale grids, this objective function is then solved using a dynamic multi-population genetic algorithm. Therefore, the above-mentioned method for reconstructing the working face of coal mine based on search space pruning and multi-population dynamic adjustment may dynamically adjust and optimize the number of populations, to ensure that the diversity of populations may be maintained, and the search efficiency may be improved, thereby improving the stability and convergence speed of the working face reconstruction operation.

The application discloses a kind of integrated hybrid information purebred genome prediction method, belong to animal genetic breeding and propagation technical field.The population genetic dataset comprising purebred population A, B and hybrid population CB is constructed, and the population genetic differentiation is verified by principal component analysis and genetic differentiation index;After the genotypes of purebred and hybrid population CB are phased, the ancestral information inference method is used to determine the origin information of each allele and process missing sites;Based on the origin information of allele, additive effect partial kinship correlation matrix and dominant effect partial kinship correlation matrix are constructed;The above matrix is integrated into three-trait mixed linear model, forming the prediction model that simultaneously incorporates purebred and hybrid population genetic information;The application distinguishes the breed origin of allele and quantifies its additive and dominant effect, significantly improves the prediction accuracy of purebred genome breeding value, is suitable for the traits difficult to directly determine in purebred population, and provides reliable technical support for animal breeding.

The invention discloses an application of an SNP (Single Nucleotide Polymorphism) site CLA25328 and a detection primer pair of the SNP site CLA25328 in identifying clematis hispida. The SNP site CLA25328 is located at the 182nd site of SEQ ID NO: 1, the polymorphism of the SNP site is C / T, and two genotypes of CC and TT coexist. The detection primer pair is composed of DNA molecules as shown in SEQ ID NO: 2 and SEQ ID NO: 3. PCR amplification and first-generation sequencing are carried out on genomic DNA of 15 clematis plants by adopting the primer pair, and it is found that only clematis angulata is of a TT genotype, and the other clematis plants are of a CC genotype. Therefore, the clematis hispida and other 14 clematis plants can be effectively distinguished by utilizing the SNP site and the detection primer pair provided by the invention. The method disclosed by the invention plays an important role in resource census, efficient evaluation of population genetic diversity and rapid identification of a seedling stage of clematis hispida.

The invention discloses an SNP (Single Nucleotide Polymorphism) marker primer pair for distinguishing mandarin fish groups in Heilongjiang and Beijing water systems, a kit, application and a method. According to the invention, an SNP (Single Nucleotide Polymorphism) marker is found, the site is lgr4p.D874V and is located at the base 14537718 of a chromosome 1, and the base mutation type is T / A; different genotypes are shown in the two groups, and group verification shows that the site has remarkable group genetic differentiation characteristics and can be used as an effective molecular marker for subsequent group identification. On the basis, the invention also discloses a primer pair of the SNP marker, a kit containing the primer pair, and application of the SNP marker in molecular traceability, germplasm resource identification or population genetic characteristic analysis of a mandarin fish population. The invention further discloses a method for distinguishing siniperca chuatsi group sources in Heilongjiang and Beijing water systems and a molecular monitoring method for siniperca chuatsi local germplasm resources. The method can quickly and accurately identify the population source of the mandarin fish, judge the genetic background and guide the germplasm resource protection and improved variety breeding of the mandarin fish.

The present disclosure provides a combination of single sequence repeat (SSR) molecular marker for Procapra przewalskii, a primer combination, a kit, and use, and relates to the technical field of molecular biology. In the present disclosure, design of SSR primers and screening of SSR loci are conducted based on a whole-genome sequencing data of Procapra przewalskii. 26 pairs of obtained SSR primers can stably amplify a target product, and are highly polymorphic, and can be used for population genetic diversity detection, population genetic structure analysis, evolution, and kinship research of the Procapra przewalskii. A combination of polymorphic SSR molecular marker of Procapra przewalskii selected can be used for individual identification of the Procapra przewalskii with a high accuracy. The experimental results show that the combination of SSR molecular marker of Procapra przewalskii can meet the needs of individual identification.

The invention belongs to the technical field of molecular genetics and biology, and particularly relates to a cynomolgus monkey specific SNP site combination, a liquid chip and application of the cynomolgus monkey specific SNP site combination in individual recognition and paternity identification. The invention provides a combination of 1508 specific SNP (Single Nucleotide Polymorphism) sites of cynomolgus monkeys with high polymorphism. By utilizing the site combination, the invention further develops a high-throughput liquid phase chip which is suitable for efficient genetic analysis of cynomolgus monkeys. Experiments prove that when the liquid chip is used for detecting 383 cynomolgus monkey samples from three different groups, the average site detection rate reaches 99.47%, the recorded parent-child relationship can be accurately restored, and it is proved that the site combination and the liquid chip have extremely high accuracy and reliability in paternity identification. According to the technical scheme provided by the invention, the genetic detection efficiency and identification accuracy of the cynomolgus monkeys can be remarkably improved, and a powerful technical tool is provided for scientific breeding management, population genetic structure optimization and genetic resource protection of the cynomolgus monkeys.

The invention belongs to the technical field of biology, and discloses a plateau dairy cow liquid phase breeding chip and application thereof, and detection objects of the liquid phase chip comprise 75939 SNP sites positioned on a common cow reference genome AR-UCD 1.2. The liquid chip provided by the invention can ensure comprehensive coverage and genetic information representativeness of bovine genomes, and provides a reliable basis for subsequent molecular identification, population structure analysis and molecular breeding application. The gene not only has population genetic polymorphism, but also covers a gene functional region and a non-functional region. Practicality and representativeness of the chip are guaranteed, stability and functional correlation of genetic markers can be considered, and a reliable tool is provided for molecular breeding and genetic improvement.

The invention discloses a human haplogroup hierarchical tracking and macro haplogroup normalization method, and relates to the field of group genetics and bioinformatics software methods. Comprising the following steps: establishing an adjacency list data structure based on an authoritative phylogenetic tree; constructing a synonym normalization dictionary for processing the heterogeneity problem of haplogroup naming; a hierarchical path backtracking algorithm is realized, backtracking is performed from a target haplogroup node to a root node based on a depth-first search principle, a complete evolutionary path is generated, the hierarchical path backtracking algorithm comprises a path integrity verification mechanism, a broken path or a circular reference error is automatically detected and reported, and the biological rationality of the generated path is ensured; a path output interface is provided, and a positive-sequence path representation mode and a negative-sequence path representation mode are supported. The method has the advantages of being high in standardization degree, high in automation level, high in reproducibility, good in universality and good in user experience.

The application relates to a method for evaluating meat quality traits of Sichuan yak. Two SNP sites of g.40461124A>G and g.40460948A>C are found in the IFI47 gene of the Sichuan yak, and population genetic analysis shows that the two SNP sites are low polymorphism. Association analysis proves that the two sites are significantly associated with postmortem pH (affecting tenderness and water holding capacity) and backfat thickness, two key meat quality traits of the Sichuan yak. Important basis is provided for early selection and genetic improvement of the meat quality traits of the Sichuan yak.

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.

The invention relates to a gracilaria cpSSR (simple sequence repeat) marker primer combination and application thereof. The SSR molecular marker primer combination comprises the following five pairs of primer combinations: CpSSR-6-451, CpSSR-11-97, CpSSR-11-485, CpSSR-10-162 and CpSSR-12-86. The gracilaria cpSSR marker primer combination provided by the invention has the beneficial effects that a group of SSR loci with high polymorphism and high resolution and specific primers thereof are screened from chloroplast genomes, so that the resolving power and stability of the existing molecular marker are remarkably improved; the marker combination can provide objective and accurate identification basis for gracilaria species from genetic essence, effectively distinguish species with similar forms, solve the problem of difficult identification of traditional methods, can be used for gracilaria DNA fingerprint spectrum construction, germplasm resource identification, genetic relationship analysis and population genetic diversity research, and has wide application prospects. And a reliable technical means is provided for protection, development and improved variety breeding of gracilaria germplasm resources.

The application discloses a coal mine working face reconstruction method based on search space pruning and multi-population dynamic adjustment, relates to the technical field of coal mine working face reconstruction under incomplete projection conditions, and comprises prior knowledge based on a working face reconstruction model structure, preliminary grid division of a working face exploration area, and multi-scale grid division through search space pruning according to the sum of ray intercepts in each network; on the basis of considering the population diversity and fast convergence requirements of a multi-population genetic algorithm, a multi-scale reconstruction objective function is constructed based on the divided multi-scale grid, and is solved through a dynamic multi-population genetic algorithm. Therefore, the coal mine working face reconstruction method based on search space pruning and multi-population dynamic adjustment can dynamically adjust and optimize the number of populations, so that the diversity of the population can be maintained, the search efficiency is improved, and the stability and convergence speed of working face reconstruction operation are improved.

The invention discloses a common sassafras in-situ germplasm resource library conservation method which comprises the following steps: (1) selecting a forest stand on which common sassafras grows from natural forest stands, and forming an in-situ conservation group of the common sassafras by all common sassafras single plants in the selected forest stand; in the selected forest stand, the number of single common sassafras plants is larger than or equal to 300; (2) investigating the tree height, diameter at breast height and fruiting amount of single sassafras plants in the in-situ conservation group; and (3) selecting a sampling single plant from the sassafras single plants of the in-situ conservation group according to the survey result in the step (2), and carrying out leaf collection on the sampling single plant. According to the method provided by the invention, a common sassafras germplasm resource collection and preservation strategy is provided around a common sassafras natural population genetic variation distribution pattern, and construction of a common sassafras in-situ germplasm resource library can be guided.

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 discloses a method for rapidly identifying male and female cannabis sativa plants based on a specific DNA (Deoxyribose Nucleic Acid) sequence. Based on high-quality haplotype genome data of the cannabis sativa, population genetic differentiation indexes and allele frequency difference analysis are adopted, the fact that the cannabis sativa belongs to an XX / XY type sex determination system is determined, the sex chromosome of the cannabis sativa is positioned to be a 10 # chromosome, and a specific linkage region on a Y chromosome is positioned in a 28.17-118.28 Mb region. A Y specific gene sequence is identified, a specific PCR primer is further designed, and a rapid PCR amplification system is established. Compared with a traditional phenotype-dependent identification method, the method can simply, efficiently, accurately and rapidly screen the plants with the target gender in the seedling stage, remarkably saves field planting space and management cost, and is suitable for accurate screening of cannabis sativa with different purposes. The method can improve the breeding efficiency and economic benefits of the cannabis industry, provides technical support for sex control production of the cannabis, and has industrial application prospects.

The present application relates to pig breed molecular identification, and discloses a SNP molecular marker combination for Wannan flower pig identification, the combination is composed of the following 11 SNP sites, the physical position and allele information of each SNP site is determined based on pig reference genome Sscrofa11.1: rs342792776, located at 103395244bp of chromosome 4, the allele thereof is A / G; rs343665183, located at 104083270bp of chromosome 4, the allele thereof is G / A; novel_WNS1, located at 5240118bp of chromosome 7, the allele thereof is G / A.The present application is based on whole genome resequencing and population genetics analysis, 11 Wannan flower pig specific SNP sites are screened out, and unified REF / ALT unification, 0 / 1 / 2 numerical coding, standardization processing and threshold determination rules are combined, so that the detection process is clear, the repeatability is strong, and the standardized implementation between different detection platforms and laboratories is facilitated.

The invention discloses a carya illinoensis KASP primer combination, a kit and application of the carya illinoensis KASP primer combination. The primer combination is used for detecting a plurality of different SNP (Single Nucleotide Polymorphism) sites located at the 351th site of any sequence of SEQ ID NO: 1-23. The polymorphism information content of the detected SNP site is concentrated in the range of 0.3-0.4, the minimum allele frequency is mainly distributed in the range of 0.4-0.5, genetic variation in a group can be effectively reflected, and the genetic diversity of the group is represented. Meanwhile, based on the carya illinoensis KASP primer combination, identification, differentiation and genetic background analysis of carya illinoensis germplasm resources can be effectively realized, and the further screened core KASP primer combination only contains 9 groups of primers, so that the identification and analysis efficiency and economy can be greatly improved. On the other hand, a DNA fingerprint spectrum can be further constructed based on the carya illinoensis core KASP primer combination, and a new tool is provided for molecular breeding of carya illinoensis.

The invention relates to the technical field of molecular identification of pig varieties, and discloses an SNP molecular marker combination for identification of Huoshou black pigs, the combination is composed of the following 27 SNP sites, and the physical position and allele information of each SNP site are determined based on a pig reference genome Sscrofa11.1: rs3473390918 located at 229783932bp of a chromosome 1, the allele of which is C / T; the rs690957272 is located at the 230954563bp position of the chromosome 1, and the allele of the rs690957272 is T / C; and the rs337901794 is located at the 231278598bp position of the chromosome 1, and the allele of the rs337901794 is T / A. According to the invention, through whole genome re-sequencing and population genetics analysis (FST screening), in combination with partial least squares regression importance evaluation, PLS-DA modeling, cross validation and linkage imbalance redundancy elimination, 27 Houshou black pig specific SNP loci are finally optimized.

This invention discloses a wheat ultra-high-density gene chip probe and its preparation method, belonging to the fields of plant functional genomics, population genetics, and molecular breeding technology. Based on wheat pan-genome information, this invention uses resequencing data and exon capture sequencing data from large-scale natural wheat populations to perform variation analysis and obtain ultra-large-scale whole-genome variation information. High-quality SNPs and INDEL loci with population and individual representativeness are obtained through filtering and screening. Simultaneously, harmful mutation sites are identified, and publicly published genetic loci related to important wheat yield and quality traits are integrated and extracted. Polymorphic loci regions are determined by combining genome annotation and variation annotation. Finally, ultra-high-density liquid-phase probes are synthesized at the pan-genome level. Because this invention only sequences target gene regions, it reduces sequencing costs by more than 90% for the same gene sequencing depth.

The invention discloses a dairy cow genetic evaluation method based on big data, and aims to solve the problems of single data dimension and insufficient evaluation accuracy and efficiency of an existing method. The method comprises the following steps: firstly, collecting multi-dimensional data such as pedigree, production performance, microbiome, metabolome and the like, and after cleaning, standardization and heterogeneity fusion, constructing a pedigree network, a phenotype-environment interaction network and a microbe-metabolome association network and fusing into a multi-modal comprehensive association network; extracting genetic feature vectors through a graph attention network, estimating genetic parameters by using a Bayesian hierarchical model, and predicting an individual comprehensive genetic evaluation value; and determining core breeding individuals and outputting hybridization suggestions by combining genetic stability screening and inbreeding risk control. According to the method, multi-source heterogeneous data and an innovative algorithm are integrated, complex trait evaluation accuracy and breeding efficiency are improved, population genetic diversity is guaranteed, and technical support is provided for precise breeding of dairy cows.

The invention discloses an SNP (Single Nucleotide Polymorphism) typing and population genetics comprehensive analysis method and system based on Sanger sequencing, relates to the field of genetic engineering and the field of biological information analysis, mainly comprises two aspects of methods and systems, and comprises the steps and functions of SNP site interpretation and SNP typing, population genetic parameter calculation and analysis, result integration, report generation and the like. The method solves the problems of low manual interpretation efficiency, insufficient result accuracy, incomplete genetic information analysis and too redundant result files in a traditional SNP typing method, is suitable for multiple fields such as medical diagnosis, drug research and development, genetics research and the like, and has a wide application prospect.

The application discloses an application of an animal domestication behavior related RRM1 gene mutant. Through population genetics, comparative genomics and ancient genomics analysis, the cause variation of the strongest selected gene of goat domestication, namely, the RRM1 gene c.1020A>G mutation, is determined; through association analysis with a hybrid population with wild goat blood, it is found that the mutation is significantly related to the domestication behavior in the goat domestication process; and through construction of a mouse containing the RRM1 gene c.1020A>G mutation, it is proved that the corresponding mutant of the RRM1 gene obviously increases the domestication behavior of the mouse. The application provides a basis and lays a foundation for phenotype selection of the domestication behavior and preparation of a tame animal model.

The invention discloses an SNP (Single Nucleotide Polymorphism) site combination for identifying jujube tree germplasm resources and application of the SNP site combination, and belongs to the technical field of molecular marker-assisted breeding. According to the invention, 100 high-quality SNP markers are developed, and a core germplasm bank containing 92 parts of jujube germplasm resources is constructed. The 100 SNP molecular markers are used for carrying out genetic diversity analysis and jujube DNA fingerprint spectrum construction on core germplasm, different jujube germplasm can be accurately distinguished, and the genetic relationship of different germplasm can be determined. 23 KASP markers are further developed, the KASP markers are used for carrying out genetic typing detection on the core germplasm, and population genetic analysis and variety identification can be carried out based on the typing result. The jujube tree SNP site combination and the KASP marker combination provided by the invention can provide efficient genome typing technology and data reference for genetic diversity analysis, germplasm resource identification, marker-assisted breeding and the like of jujube trees.

The invention discloses a geographic bighead carp population tracing method based on a minimum feature allele combination, and belongs to the technical field of aquatic food tracing and population genetics. The method comprises the following steps: firstly, constructing a microsatellite initial database of a bighead carp group with a known geographic source; then, through a multi-stage screening process combining allele frequency filtering, Fst value screening and step-by-step discriminant analysis performed by using a specific F value threshold (entering 3.84, deleting 2.71), screening out a minimum feature allele combination with extremely small quantity and extremely strong discriminant force from a large number of allele; based on the combination, establishing a linear discriminant function by adopting linear discriminant analysis; for to-be-detected bighead carp individuals, rapid and low-cost geographical traceability can be completed only by detecting the genotype of the combination and calculating the distinguishing score of each group to which the bighead carp individuals belong. According to the method, the number of microsatellite sites which need to be detected is reduced from 15 to 5, the cost is saved by more than 60%, and the judgment accuracy rate reaches 100%.

The present application relates to the application of Hu sheep FGF1 gene and its coded protein, and belongs to the field of biotechnology. The application of Hu sheep FGF1 gene and its coded protein in regulating the level of oxidative stress, cell apoptosis or cell proliferation of ovary granulosa cells. The present application first systematically identifies the CDS and protein sequence of sheep FGF1 gene, and analyzes its physical and chemical properties, post-translational modification sites, secondary and tertiary structures and systematic evolution relationship, which provides a molecular basis for revealing the role of the gene in oxidative stress and cell fate regulation. In addition, the disclosed sequence information and variation data are helpful for evaluating population genetic diversity, and have important scientific value for the protection, development and evolution research of animal genetic resources.