18 results about "Genomewide association" patented technology

This invention relates to the fields of genomics, molecular biology, bioinformatics, and genome-wide selection breeding, specifically a 20k liquid-phase breeding chip for the whole genome of *S. esculenta* and its applications. The liquid-phase chip contains background SNPs and functional SNPs located on the *S. esculenta* reference genome; wherein the background SNPs are uniformly distributed within the genome; and the functional SNPs are associated with important economic traits of *S. esculenta*; these important economic traits include one or more of the following: saponin content, polysaccharide content, and heat tolerance. The chip can be applied to the assessment of genetic diversity in *S. esculenta*, identification of germplasm resources and phylogenetic relationships, genome-wide association analysis of important economic traits, and genome-wide selection breeding. This chip has advantages such as high throughput, high region coverage, high locus detection rate, and high flexibility, providing powerful tool support for molecular breeding of *S. esculenta*.

The application provides a molecular marker related to cold tolerance of arrowhead pea on chromosome 1 and application, and belongs to the technical field of biology. Through whole genome association analysis, an InDel site is located in the arrowhead pea and named as Vs_Chr1_34169935, and the nucleotide sequence of the insertion or deletion fragment is shown in the sequence table SEQ ID NO. 3. A primer pair for amplifying the molecular marker is shown in the nucleotide sequences of SEQ ID NO. 1-2. The molecular marker and the primer pair thereof can identify or assist in identifying the cold tolerance of the arrowhead pea. Meanwhile, the application also provides a method for rapidly identifying the cold tolerance of the arrowhead pea by using the molecular marker. The method is simple and fast, the identification result is accurate, and has a good popularization and application prospect.

The invention provides a genome method and an SNP (Single Nucleotide Polymorphism) marker combination for a pig to adapt to related traits in a high-temperature and high-humidity environment, and belongs to the technical field of genome prediction, the method comprises the following steps: taking a local pig SNP marker combination as a prior fixing effect; standard miscalculation of a p value, a beta value and a beta value based on whole genome association analysis; performing interval dimension reduction based on linkage imbalance; searching an optimal parameter by using a genetic algorithm, and adaptively grouping the SNPs; performing weighted summation on the G matrix; the SNP marker combination is used as a fixed effect, the weighted G matrix is used as a random effect, a genetic evaluation model is configured, and genome prediction is carried out on target characters. According to the method, the large-effect SNP and the minor-effect multi-gene effect which are causally associated with the target prediction character can be accurately captured, redundant information is removed through dimension reduction in the interval, the optimal parameter combination is found through the genetic algorithm, and the calculation speed is greatly increased while the accuracy of genome prediction is improved.

The application discloses a kind of molecular marker related to oat salt tolerance and its application, belong to molecular biology technical field.The application takes 144 forages oat as material, by whole genome resequencing and germination rate phenotype determination under salt stress, carries out whole genome association analysis, identifies one SNP site significantly related to oat salt tolerance, which is located at the 375175364 base of chromosome chr1D, and the polymorphism is G / A.According to the SNP site, the application further develops KASP primer combination.Using the molecular marker and primer combination, the salt tolerance of oat seed stage can be quickly identified: oat material with genotype GG has higher germination rate under salt stress, and shows strong salt tolerance, and material with genotype AA is contrary.The method in the application is stable, and has good repeatability, and can be used for early salt tolerance screening and molecular assisted breeding, to significantly improve breeding efficiency and accuracy.

The invention provides a construction method and application of a chrysanthemum aphid resistance prediction system based on whole genome selection. According to the method, SNP loci remarkably related to the aphid resistance of the chrysanthemum are identified through whole genome association analysis, the influence of different statistical models and SNP markers with different densities on the whole genome prediction precision is compared, the method for rapidly, efficiently and accurately predicting the aphid resistance of the chrysanthemum based on GWAS-assisted whole genome selection is established, and the prediction accuracy can reach 0.882. The whole genome selection system constructed based on the method can realize early selection of the aphid resistance of the chrysanthemum, accelerates the breeding process of the excellent new variety of aphid resistance of the chrysanthemum, saves the breeding cost, effectively overcomes the technical problems that the field aphid resistance identification work is tedious, long in period and easy to be influenced by environmental factors and human subjective factors and the like, and improves the identification efficiency of the aphid resistance of the chrysanthemum. The method has important theoretical and practical significance.

The invention provides a crop insect resistance character high-throughput screening method based on transboundary RNA stability, and the method comprises the following steps: firstly, inoculating standardized aphids to crop leaves to be detected, and limiting feeding time; then, time sequence sampling is carried out at a specific time point after the aphids are removed; then, extracting total RNA (Ribonucleic Acid) of a plant, and detecting abundance of target transboundary RNA by utilizing an aphid specific primer through a real-time fluorescent quantitative PCR (Polymerase Chain Reaction) technology; then, calculating the stability index of the transboundary RNA, calculating the resistance index of the crop based on the established mathematical model, and judging the resistance grade according to the resistance index; and finally, integrating the steps on a high-throughput automatic platform, and further applying the obtained resistance phenotype data to whole genome association analysis so as to mine resistance gene loci.

The application provides a genetic sexing strain of the ayu based on whole genome association analysis and an application thereof. A GWAS analysis is performed on 426 ayu groups by using a GCTA and GEMMA double algorithm, and a core SNP marker verified by statistics is screened out. The marker can be used for precise selection of seeds at the fry stage, shortens the breeding and screening period, and promotes the industrialization of high-efficiency molecular design breeding of the ayu.

The application provides a snowflake black cattle breeding method and system based on whole genome association analysis, relates to the technical field of black cattle breeding, and comprises the following steps: extracting PacBio long read HiFi sequencing data and second-generation whole genome resequencing data in a blood sample, and extracting Hi-C chromosome conformation capture sequencing data and multi-tissue full-length transcriptome sequencing data in a tissue sample; performing genome assembly to obtain a chromosome-level reference genome sequence; performing gene structure annotation on the reference genome sequence; detecting a whole genome SNP marker data set of a breeding population; screening whole genome SNP marker data meeting a preset significance threshold; performing functional annotation to obtain molecular markers for snowflake black cattle breeding. The application provides reliable and practically functional molecular marker support for the directional breeding of snowflake black cattle meat quality-related key economic traits.

The application discloses an AhFMO gene for regulating peanut seed size and kernel weight and application thereof, relates to the technical field of bioengineering, and has the technical scheme as follows: 1. An AhFMO gene for regulating peanut seed size and kernel weight and application thereof, wherein the gene sequence is SEQ ID 1; 2. A method for screening candidate genes, wherein the method is realized by combining whole genome association analysis (GWAS) and genetic map positioning linkage analysis (QTL mapping) joint analysis, combining transcriptome analysis gene differential expression, homology analysis and overexpression verification; and 3. Application of the AhFMO gene for regulating peanut seed size and kernel weight, wherein the gene can regulate the size and kernel weight of seeds.

The invention belongs to the field of gene chips, and discloses a tetraploid crassostrea gigas 40K breeding liquid phase chip as well as a preparation method and application thereof. The breeding liquid phase chip disclosed by the invention comprises a probe for detecting 41270 SNP (Single Nucleotide Polymorphism) sites; the position information of the 41270 SNP loci is determined by performing sequence alignment on the basis of a reference version of a pacific oyster genome, and the reference version of the pacific oyster genome is GCA011032805.1. The gene chip can be applied to genotyping, genome selection or whole genome association analysis of tetraploid crassostrea gigas. The breeding liquid chip can effectively reduce the genotyping and breeding cost of tetraploid crassostrea gigas, improve the breeding accuracy and efficiency, and promote the development of tetraploid crassostrea gigas genome breeding.

The application discloses a gene marker combination for evaluating HLH risk and use thereof, and belongs to the technical field of gene detection. The gene marker combination is obtained by whole genome association analysis of whole exome sequencing, covers more extensive genetic information, solves the narrowness of the prior art, and provides more comprehensive analysis of the polygenic heterogeneity of HLH. Moreover, the cumulative effect of alleles is comprehensively considered, the genetic susceptibility characteristics of an individual to HLH can be more accurately reflected, and the sensitivity and specificity of gene detection can be improved.

The invention discloses a method and a system for integrating a chip and filling data to optimize genome selection, and belongs to the technical field of genome breeding. The method comprises the following steps: firstly, acquiring chip data and whole genome filling data; then executing a chip anchoring and filling expansion strategy: screening a core SNP set from chip data based on whole genome association analysis, and screening an additional significant SNP set from filling data; and finally, combining the two sets to form an optimized SNP set and carrying out genome selection analysis. The internal bottleneck that high-quality filling data is directly used for genome selection to cause reduction of accuracy is disclosed for the first time, through an innovative integration strategy, the prediction robustness is ensured by utilizing chip data, new genetic signals are explored by utilizing the filling data, advantage complementation is realized, the breeding value prediction accuracy is remarkably improved, and the breeding value prediction method is suitable for large-scale popularization and application. An effective scheme is provided for solving the application problem of high-density genotype data in breeding.

The application discloses a method for screening complex disease drugs based on whole genome association signals, and comprises the following steps: screening and processing complex disease cells through a DESE algorithm based on whole genome association signals, so as to obtain a cell line of the complex disease; inducing and analyzing the cell line of the complex disease through drug blank control, so as to obtain a specific perturbation spectrum of the drug on the gene; and performing cyclic prediction analysis and calculation on the specific perturbation spectrum of the drug on the gene in combination with conditional data, so as to obtain a complex disease susceptible gene drug. Through the application, the screening range of complex disease candidate drugs can be reduced by predicting the drug for specifically perturbing multiple disease susceptible genes. The application can be widely applied to the technical field of high-throughput drug screening.

The invention relates to the technical field of lion-head goose breeding, and particularly discloses a whole genome association analysis method for lion-head goose egg laying performance. Comprising the following steps: S1, collecting genome DNA of lion-head geese; s2, performing whole genome re-sequencing on the genome DNA extracted in the step S1; s3, performing quality control, filtering and comparison on the original sequencing data in the S2, and detecting a single nucleotide polymorphism (SNP) site; s4, performing correlation analysis on the SNP loci detected in the step S3 and the egg laying traits of the lion-head geese by using a whole genome correlation analysis method; s5, based on a correlation analysis result obtained in the step S4, identifying SNP sites related to egg laying traits; and S6, screening candidate genes according to the SNP sites related to the egg laying traits obtained in the S5. The whole genome association screening can be used for breeding and breeding of lion-head geese, and has the advantages of being accurate in positioning, efficient in screening and high in guidance.

The invention discloses an efficient and rapid whole genome association analysis method based on a multi-site mixed model, and belongs to the field of plant and human disease gene mining, the method comprises the following steps: step 1, constructing a single-site mixed linear model, and determining candidate single nucleotide polymorphism sites potentially associated with target traits; step 2, constructing a multi-site mixed linear model by utilizing the obtained candidate single nucleotide polymorphic sites to determine a remarkably associated QTN (Quantitative Trait Networks); 3, determining the obtained SNP with the corrected P value smaller than or equal to the threshold value as the QTN significantly associated with the target character, and outputting the QTN. According to the method, unit point scanning and multi-site mixed model construction are integrated, so that rapid correlation analysis of a large-scale high-dimensional data set is realized, the calculation efficiency and the statistical effect of QTN detection are optimized, and the calculation speed and the detection robustness are balanced.

The invention provides a wheat quality trait gene positioning method and system based on correlation analysis. Comprising the following steps: acquiring whole genome typing data of an associated group; applying a standardized perturbation sequence to the associated population, and collecting a time-sequenced biological sample to obtain a dynamic molecular phenotype; performing parameterization processing on the dynamic molecular phenotype to obtain a group of quantitative dynamic response spectrum parameters including kinetic parameters and stress memory parameters; and taking the newly created parameters as phenotypes, and carrying out whole genome association analysis on the phenotypes and whole genome typing data so as to locate gene loci for controlling dynamic response characteristics. According to the method, the relation between laboratory dynamic response and field character stability can be established through causal intermediary analysis. According to the method, genetic loci for controlling a character dynamic process and environmental adaptability can be positioned, and a new technical approach is provided for precise breeding of crops.

The present application relates to the field of plant genetic engineering and molecular breeding technology, in particular to the application of corn ZmTAR4 gene in regulating callus related traits. The present application identifies a key gene ZmTAR4 through whole genome association analysis and weighted gene co-expression network analysis, which encodes a protein with tryptophan amino transferase activity. CRISPR / Cas9 knockout experiment proves that the gene is a gene necessary for positively regulating corn young embryo endogenous auxin (IAA) synthesis and embryogenic callus (EC) induction. Further, through overexpression experiment, it is proved that in corn materials with low induction rate, improving the expression level of ZmTAR4 can significantly improve the induction rate, growth amount and embryonic structure number of embryogenic callus, which fully verifies the positive regulation effect of the gene from the functional gain perspective.

The invention discloses a construction method and application of an SNP (Single Nucleotide Polymorphism) liquid phase chip for forest tree breeding, and belongs to the technical field of forest tree molecular breeding. The method comprises the steps that based on whole genome re-sequencing data of multiple germplasm resources of a target species, a high-quality candidate background site pool is obtained through primary screening of a first set of screening parameters, probe design feasibility and genome space distribution optimization are conducted on the high-quality candidate background site pool, and a uniformly-distributed and probe-feasible background site set is formed; secondly, based on a whole genome association analysis result, screening out a functional site set directly associated with breeding traits; and finally, combining the two types of site sets, and carrying out probe design and synthesis to prepare the liquid phase chip. The invention also provides the chip constructed by the method and application of the chip in forest genome selective breeding. According to the invention, the design limitation of a traditional chip is broken through, a special chip with high density and high breeding value can be systematically constructed, and the breeding efficiency is remarkably improved.