52 results about "Genotyping by sequencing" patented technology

The invention discloses RT-qPCR-HRM (real-time quantitative polymerase chain reaction-high-resolution melting) detection primers and a detection method for identifying five different subtype avian influenza viruses, and belongs to the technical field of biology. The invention discloses an RT-qPCR-HRM detection method for identifying five different subtypes of avian influenza viruses, which comprises the following steps: designing a specific primer based on a highly conserved region of an AIV M gene, and simultaneously carrying out genetic typing on five subtypes of AIV strains H3, H5, H6, H7 and H9 in combination with an HRM technology; by comparing melting curve characteristics of M gene segments of different subtypes of AIV, an AIV detection method with good sensitivity and specificity is established. According to the method, the five AIVs of H3, H5, H6, H7 and H9 can be accurately typed, the defect of missing detection of a traditional AIV detection method is overcome, and the method has a wide application prospect.

This invention discloses a reagent, detection system, and method for HPA genotyping in the Chinese population. The invention employs a multiplex PCR technique based on fluorescent probe melting curves, arranging and combining specific primers and fluorescently labeled probes for different HPA systems. This ultimately enables simultaneous genotyping of 14 HPA antigen systems in the Chinese population using only three reaction tubes in a single test. Furthermore, the detection system of this invention is not only simple and rapid but also accurate and efficient, possessing high practical value.

The invention relates to methods of identifying and characterizing a Cannabis spp. plant with respect to a flower to leaf ratio trait comprising genotyping the plant for a quantitative trait locus (QTL) associated with a flower to leaf ratio trait, and to methods of producing plants having a flower to leaf ratio trait of interest based on defined allelic states of polymorphisms defining the QTL. Also provided are Cannabis spp. plants having a flower to leaf ratio trait of interest comprising defined allelic states of polymorphisms defining the QTL and plants identified, characterized or produced by the methods described herein. The invention further relates to marker assisted selection and marker assisted breeding methods, in particular using a combination of specific markers provided, for obtaining plants having a flower to leaf ratio trait of interest or for modulating the flower to leaf ratio of cannabis plants.

The invention relates to the technical field of molecular detection, and particularly discloses a police dog 10K liquid phase chip, a design method and application thereof and a kit, and genetic typing sites of the police dog 10K liquid phase chip comprise 10463 SNP sites; the physical positions of the 10463 SNP loci are determined based on the comparison of the whole genome sequence of the canine reference genome CanFam 3.1, and the 10463 SNP loci are shown in the table 1. The 10463 SNP loci disclosed by the invention are obtained by screening based on a DNA sample of the police dog, and the obtained 10463 SNP loci can be used as a basis for genetic typing of the police dog; the liquid chip designed according to 10463 SNP loci can quickly realize genotyping of the target SNP loci, and obtained genotyping data can be used for variety identification of police dogs and population diversity analysis of police dogs.

The application discloses a high-throughput KASP molecular marker significantly related to plant height of Gossypium hirsutum and application, and belongs to the technical field of cotton molecular breeding. The KASP marker is successfully developed based on cotton plant type related genes and resequencing data of germplasm resources. Through genotyping and phenotype correlation analysis in 246 natural Gossypium hirsutum populations, four KASP markers (PH-TK1-PH-TK4) significantly related to plant height in three environments are screened. The regulation effect and aggregation effect of the markers on plant height are verified in a separation population. Experiments prove that the KASP marker can be used for high-throughput and accurate genotyping of plant height in early cotton breeding, and provides an effective tool for molecular marker assisted selection of cotton ideal plant type, and helps to accelerate the breeding process of cotton varieties suitable for mechanical harvesting.

The invention discloses a wheat haploid accurate identification and breeding method based on molecular markers, and belongs to the technical field of agricultural biology. The method comprises the following steps: hybridizing a created multifunctional haploid induction line HIP-Plus serving as a male parent with a target female parent, and saving immature embryos to obtain seedlings; a three-stage identification system comprising visual preliminary screening, molecular confirmation and early selection is adopted to carry out accurate screening on seedlings: firstly, preliminary screening is carried out based on embryo color, then haploid confirmation and transgenic component detection are carried out by utilizing TaMTL allele specific markers, and finally genetic typing is carried out through important character function markers to screen out elite haploids; and carrying out chromosome doubling to obtain a double haploid homozygous line. According to the method, the haploid identification accuracy is improved, the breeding period is shortened, the early directional selection of the target agronomic traits in the haploid stage is realized, and the breeding efficiency and accuracy are greatly improved.

The invention relates to an HPA genotyping detection reagent based on a melting curve analysis method, a detection method and application, in particular to a detection reagent for HPA genotyping detection of Chinese population, a detection method and application. According to the invention, a multiplex PCR technology based on a fluorescent probe melting curve is adopted, specific primers of different HPA systems and fluorescent labeled probes are arranged and combined, and finally, only three reaction tubes are used for simultaneously carrying out genotyping on 14 HPA antigen systems of Chinese population at a time. In addition, the detection system disclosed by the invention is simple, convenient, rapid, accurate and efficient, and has relatively high practical value and clinical transformation prospect.

The invention discloses a method for auxiliary identification of Duroc pig growth traits based on a BTG1 region SNP marker, and belongs to the technical field of animal genetic breeding and reproduction. Comprising the following steps: step S1, acquiring a growth trait record of a Duroc pig to be detected, performing data preprocessing, and calculating genetic correlation and phenotypic correlation between heritability and growth traits based on a pedigree; step S2, performing genetic typing on the Duroc pig to be detected, and detecting genotypes of the Duroc pig in a BTG1 region and other key SNP sites; s3, carrying out auxiliary identification on the growth traits of the to-be-detected Duroc pigs on the basis of a pre-established relationship between genotypes and the growth traits; and S4, selecting a corresponding individual as a breeding object according to an auxiliary identification result. The method can be used for early screening and genetic improvement of growth traits such as different day-age weights and staged average daily gain of Duroc pigs, and is suitable for breeding pig breeding practice of large-scale pig farms, live pig breeding enterprises and scientific research institutions.

The invention discloses a haplotype molecular marker related to cotton fiber strength and application of a detection primer of the haplotype molecular marker, and relates to the technical field of plant molecular biology and genetic breeding. The haplotype molecular marker is located in 112, 985, 431-112, 990 and 059bp regions of A06 chromosome of a cotton reference genome, a haplotype block is formed by nine closely linked SNP (Single Nucleotide Polymorphism) sites, the incidence relation between three haplotypes Hap1, Hap2 and Hap3 in the block and fiber strength is defined, and a new molecular target is provided for cotton fiber quality breeding. Compared with a single SNP marker, the haplotype molecular marker provided by the invention has higher stability and phenotype prediction accuracy under a complex genetic background. Genetic typing can be carried out in the cotton seedling stage based on the marker, fiber maturation does not need to be waited, the breeding period is greatly shortened, and the field screening cost is reduced.

The application discloses a DEL molecular marker related to a chilling requirement trait of peaches, a primer pair and application, and the nucleotide sequence of the DEL molecular marker is shown as SEQ ID NO. 1. The application selects 550 natural groups of different chilling requirements of peaches to carry out whole genome resequencing, and then performs genotyping and data quality control in sequence, removes sites with a deletion rate of more than 20% and sites with a minor allele frequency of less than 5%; LD decay evaluates the height of marker density; and the prediction of population structure is beneficial to the selection of a suitable association analysis model, and finally, association analysis is carried out. Finally, a 30bp deletion variation closely linked to the chilling requirement is identified. The application verifies the relationship between the variation and the chilling requirement in 88 peach varieties with different chilling requirements, and the results show that the genotypes of medium and high chilling requirement (>= 400h) varieties do not contain 30bp deletion, and the genotypes of low chilling requirement (<400h) varieties all contain 30bp deletion, and the accuracy reaches 100%.

The invention discloses a method for identifying the purity of a coconut strain. The method comprises the following steps: collecting DNA of a target sample; constructing a DNA library of the target sample, and performing whole genome re-sequencing; filtering data in the DNA library to obtain an impurity-removed DNA sequence; comparing the DNA sequence subjected to impurity removal with a reference genome, carrying out variation detection, generating SNP and INDEL marker files, then carrying out genetic typing, and constructing a variety identification model; comparing and analyzing whole genome SNPs of the two groups, and screening specific sites capable of identifying and distinguishing the two groups in the genome; and inputting the DNA of the target sample into the variety identification model, detecting the SNP specific site of the gene, and judging the variety result to realize the identification of the purity of the coconut variety. The identification accuracy of the identification method can reach 99% and is far higher than that of a traditional morphological method, rapid identification can be conducted in the seedling stage, and the identification period is greatly shortened.

Botrytis blight is a major disease in the cultivation of Rosa hybrida, which seriously threatens the quality and yield of cut rose. In order to effectively deal with this disaster stress affecting the yield and quality of rose, 192 pairs of SSR primers were used to amplify the DNA of parents 'Jinmali' and 'Beijinghong' and six randomly selected offspring. Among the parents, 35 pairs of primers showed genetic differences. Further, the DNA of the offspring was amplified using the 35 pairs of primers, and the electrophoresis bands were detected by PAGE electrophoresis and converted into '0, 1 matrix' for genotyping. Through the correlation regression analysis, the optimal subset selection was carried out, and finally three primers related to the resistance to Botrytis blight were successfully screened: Geno-BC-1, Geno-BC-2, Geno-BC-3. The above findings provide an important theoretical basis for molecular marker-assisted breeding of disease resistance in rose, and are expected to promote the early identification of disease-resistant plants, thereby shortening the breeding cycle and improving the breeding efficiency.

The invention discloses a cotton fiber length KASP molecular marker and application, and relates to the technical field of cotton molecular breeding, a specific KASP primer group is designed according to a site sequence, nucleotide sequences of the specific KASP primer group are respectively shown as SEQ ID NO.1, SEQ ID NO.2 and SEQ ID NO.3, a genome molecular marker with polymorphism is screened from segregation population offspring, and the molecular marker is used for detecting cotton fiber length. And a single cotton plant can be subjected to genetic typing at the functional site. When the genotype is G: G, the single plant is indicated to have relatively long fiber length potential; the method can accurately track and locate a target gene and efficiently screen the fiber length character, is high in typing accuracy, low in cost and simple and convenient to operate, can be used for auxiliary selection of the fiber length character in early generation of cotton breeding, and further can be used for molecular design breeding.

The present invention provides a method for constructing a Map3k3I441M mutation knock-in transgenic mouse model and a use. The method comprises: replacing the region from exon 1 to part of intron 2 of a mouse with a mutant gene fragment, wherein the sequence of the mutant gene fragment is as shown in SED ID NO: 1 in the sequence listing; using a BCA clone as a template to amplify a homologous arm-containing mouse genome fragment as a targeting vector; co-injecting Cas9 and gRNA as well as the targeting vector into fertilized eggs; allowing the fertilized eggs to develop to obtain positive F0 generation samples; co-housing the positive F0 generation samples for breeding to obtain F1 generation samples; performing genotyping on the F1 generation samples to screen for Map3k3I441M samples; and mating the Map3k3I441M samples from the F1 generation samples with a Cdh5-CreERT tool sample to produce F2 generation samples. A model constructed by the construction method can accurately reflect the real situation in a mouse.

A computerized system and method are provided for assessing a number of gene-gene interactions between the HLA and IRF5 gene regions. At least one computing device enrolls subjects in a registry, including SLE patients having met classification criteria for SEE and Sjogren's patients having met AECG criteria. Moreover, at least one computing device can perform genotyping for the subjects and healthy control subjects, for submission to a genotyping platform. Further, at least one computing device can develop HLA risk factor models for each of a plurality of stages, and perform statistical analysis for each of the plurality of stages.

The invention belongs to the field of molecular biotechnology and livestock breeding, and discloses an rs323970378 site SNP molecular marker related to pig birth litter weight and application of the rs323970378 site SNP molecular marker. According to the invention, DNA samples of 617 large white pigs are subjected to genetic typing by using a low-depth (1 *) whole genome re-sequencing technology, and an SNP site significantly related to the litter weight character of the pigs is finally screened out through GWAS (whole genome association analysis). The SNP molecular marker is located at the 26902856th nucleotide of a chromosome 14 in an Ensembl Sscrofa11.1 reference genome version, and Cgt exists in the SNP molecular marker; g is subjected to base mutation. A research result shows that when the genotype of the locus is C / C, the birth litter weight of a large white pig individual is the highest. The invention provides a new marker for genetic improvement and molecular marker-assisted breeding in the aspect of pig birth litter weight traits.

The invention belongs to the field of biological detection, and particularly relates to a fluorescent quantitative PCR (polymerase chain reaction) detection method of KIR2DS5 mRNA (messenger ribonucleic acid) as well as a detection kit, a primer and a design method of a probe. The method comprises the following steps: (1) performing KIR genetic typing on a DNA (deoxyribonucleic acid) sample by using a PCR-SSOP method, and screening out KIR2DS5 positive DNA; (2) carrying out PCR (Polymerase Chain Reaction) amplification and electrophoresis on the positive DNA sample; (3) extracting a KIR2DS5 specific DNA band, tapping rubber, purifying, connecting with a T vector, transforming, selecting flora, extracting plasmids, and sequencing; (4) comparing a sequencing result with a KIR / IPD database to confirm that the sequence is a characteristic gene sequence; and (5) designing a primer and a probe by using primer design software according to the characteristic KIR2DS5 gene sequence. And carrying out gene detection by using the designed primer and probe. According to the method, the specificity and accuracy of PCR detection are improved.

The invention provides a method for allele matching of donor mesenchymal stem cells and a receptor. The method comprises the following steps: S10, separating mesenchymal stem cells from perinatal tissue of a donor; s20, extracting genome DNA (deoxyribonucleic acid) of the mesenchymal stem cells, and performing HLA (human leukocyte antigen) genetic typing; s30, performing HLA (human leukocyte antigen) genetic typing on the DNA of the receptor; s40, performing allele spectrum comparison on the HLA gene of the receptor and the HLA gene of the mesenchymal stem cell, and calculating the matching degree; s50, judging the matching degree of the receptor and the mesenchymal stem cells according to the matching degree; and S60, storing the HLA genotyping result of the mesenchymal stem cells and the matching degree in a database, and establishing a matching library for matching the donor mesenchymal stem cells and the receptor. According to the method, a set of standardized system is established, compatibility evaluation of a donor and a receptor at the allele level is achieved, the immunological rejection risk caused by HLA mismatching is effectively predicted and avoided before treatment, and the in-vivo survival and implantation efficiency of MSCs is improved.

Techniques for generating a personalized reference sequence construct for an individual to align sequence reads obtained for the individual. The techniques include: obtaining a plurality of sequence reads for an individual; obtaining information identifying a plurality of locations; genotyping the plurality of sequence reads for the plurality of locations to obtain a first set of variants for the individual for at least some of the plurality of locations; identifying a second set of variants associated with the first set of variants; generating a personalized reference sequence construct using the second set of variants; and aligning the plurality of sequence reads to the personalized reference sequence construct.

We will develop a probe set that can process multiple samples simultaneously using sequence capture methods and comprehensively capture genes in the KIR region. [Solution] A probe set for KIR gene typing is provided, each consisting of oligonucleotides having a specific base sequence. Furthermore, a method for KIR gene typing using the probe set is provided.

The invention relates to the technical field of molecular markers, and particularly discloses a molecular marker primer group related to the stripe rust resistance character of wheat and application of the molecular marker primer group. The molecular marker Qyr.saas-4a is located on a long arm of a wheat 4A chromosome, and is closely linked with stripe rust resistant major QTL Qyr.saas-4A. The invention provides a specific KASP primer group for detecting the molecular marker, and the nucleotide sequence of the specific KASP primer group is shown as SEQ ID NO.1-3. The molecular marker is a co-dominant marker, can efficiently and accurately carry out genetic typing on the stripe rust resistance character of a wheat material through a fluorescent quantitative PCR technology, and is not limited by the environment and the growth stage. The invention also relates to an application of the primer group in molecular marker-assisted breeding for breeding a new variety of stripe rust resistant wheat, the breeding selection efficiency and success rate can be obviously improved, and the limitation that the traditional breeding depends on phenotypic selection is overcome.

The present application relates to the technical field of molecular detection, and specifically discloses a police dog 10K liquid chip, a design method, application and kit thereof, wherein the genotyping sites of the police dog 10K liquid chip include 10463 SNP sites; the physical positions of the 10463 SNP sites are determined based on the whole genome sequence alignment of the canine reference genome CanFam 3.1, wherein the 10463 SNP sites are shown in Table 1. The 10463 SNP sites of the present application are obtained by screening the DNA samples of police dogs, and the 10463 SNP sites can be used as the basis for genotyping the police dogs; the liquid chip designed according to the 10463 SNP sites can quickly realize the genotyping of target SNP sites, and the obtained genotyping data can be used for breed identification of the police dogs and analysis of the diversity of the police dog population.

The invention provides a method for constructing a genome selective breeding technical system of downy sheep, and relates to the technical field of genome selective breeding of downy sheep, the method comprises the following steps: constructing a reference group, selecting samples from downy sheep with multiple regions and multiple genetic backgrounds, collecting phenotypic data, and carrying out genetic typing; then establishing a genome selection model, processing genotype and phenotype data, and training by using GBLUP and Bayesian models; then, candidate groups are screened, a genome estimation breeding value is calculated, and individuals ranked in the first 20%-30% are selected; a breeding scheme is formulated, breeding is carried out without too large inbreeding coefficient, and progenies are determined and analyzed; and finally, collecting new data every year, and retraining the model every 2-3 years. Regional ecological differences of a reference group, a model algorithm, a convergence threshold value and candidate group phenotype evaluation index weights are limited, and the breeding effect of the villus sheep can be optimized.

The application provides a gene set and kit for evaluating the curative effect after allogeneic hematopoietic stem cell transplantation of hematopathy, and belongs to the field of gene detection. The application develops a new post-transplantation curative effect evaluation panel detection design method. The panel comprises: 1. single nucleotide polymorphism (SNP) sites characteristic of individual genetic characteristics, which can be used for graft implantation evaluation; 2. high-frequency mutation sites of blood tumor hotspot genes, which can be used for MRD detection and disease state evaluation; and 3. HLA gene characteristic SNP sites on the short arm of human chromosome 6, which can be used for HLA gene typing, combined with the state of graft implantation, to analyze the occurrence of HLA-loss. The technical scheme of the application can solve the above-mentioned multiple contents of post-transplantation curative effect evaluation at one time, is more accurate and sensitive than the previous detection method, and can greatly reduce the detection cost and shorten the clinical report time.

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 belongs to the technical field of pig molecular markers, and particularly discloses an SNP (Single Nucleotide Polymorphism) molecular marker related to the character of the number of live piglets born by pigs and application of the SNP molecular marker. Gene typing is carried out by utilizing a gene chip technology, whole genome association analysis is carried out on the basis of SNP molecular markers, and four SNP molecular markers related to the character of the live litter size of the pig are screened out through the analysis. The SNP molecular marker is located in a pig chromosome 2, is annotated to a PPP2R2B gene segment, and can be used for marker-assisted breeding of pig live birth number traits and heterosis utilization thereof.

The application discloses a KASP marker linked with a tomato green stem character and application, relates to the technical field of biology, and nucleotide sequence is SEQ ID NO:1; the development method is as follows: the Primer-BLAST function of NCBI is used, specific primers are designed according to upstream and downstream sequences on a SNP site; the application of the KASP marker is as follows: genomic DNA of a tomato sample to be detected is extracted, the genomic DNA is used as a template, PCR amplification is carried out by using the KASP marker special primer designed above, fluorescence data of PCR amplification products are read by using an enzyme label instrument, and genotyping is carried out. The application develops a KASP molecular marker KASP_ABCC5 which is co-segregated with the green stem character, accurate genotyping can be realized, and the breeding process is accelerated.

The invention relates to a set of primer combination for cherry variety identification and application thereof. The application of 26 SNP sites in a cherry genome in any one of the following steps: (1) preparing a cherry SNP site detection kit; (2) performing genetic typing on cherry germplasm resources or genetic populations; (3) constructing a DNA fingerprint spectrum of the cherry germplasm resource or variety; (4) identifying the variety of the cherry to be detected; the number of the 26 SNP sites is YTSNP01 to YTSNP26, and the number of the 26 SNP sites is 2. The cherry primer combination developed by the invention can be used for identifying the cherry variety to be detected, so that the operation of distinguishing the authenticity of the variety becomes accurate and convenient, and the primer combination spans the whole genome of the cherry, has a unique amplification stable point and is relatively strong in representativeness; the detection result of the method is stable and reliable, the operation is simple and rapid, and large-scale and standardized detection can be realized.

The invention relates to the technical field of molecular genetic breeding, in particular to an SNP (Single Nucleotide Polymorphism) molecular marker related to the weight and flowering phase of mung bean seeds and application. The SNP molecular marker disclosed by the invention is located on the No.3 chromosome Chr3-47757894 of a mung bean genome and has a base polymorphic site T / C; the seed weight of the individuals with the genotype TT is higher than that of the individuals with the genotype CC, and the flowering phase is earlier than that of the individuals with the genotype CC; the KASP marker associated with the weight and the flowering phase of the mung bean seeds is developed and subjected to genetic typing, the sample genetic typing effect is obvious, the weight and the flowering phase of the mung bean seeds can be sensitively and efficiently predicted at low cost, large-scale molecular marker screening and cultivation of high-yield and early-maturing mung bean varieties in the field are facilitated, and mung bean molecular breeding is assisted.