90 results about "Genotyping by sequencing" patented technology

The invention discloses a method for identifying Yushan black pigs by adopting an SNP (Single Nucleotide Polymorphism) molecular marker technology, and particularly relates to the technical field of molecular detection.The method comprises the following steps: S1, sample preparation: collecting any one of ear tissues, tail tips or blood samples of to-be-detected pig individuals, and extracting to obtain genome DNA (Deoxyribose Nucleic Acid); the genome DNA is used as a template, amplification detection is conducted through a first primer pair, a second primer pair, a third primer pair and a fourth primer pair corresponding to the first SNP site, the second SNP site and the fourth SNP site, and the nucleotide sequences of the first primer pair, the second primer pair and the fourth primer pair are sequentially SEQ ID NO.5-SEQ ID NO.12. By detecting the specific single nucleotide polymorphic sites in the Yushan black pig genome and carrying out genetic typing comparison, the Yushan black pigs and the filial generation thereof can be quickly and accurately identified.

The invention discloses an SNP (Single Nucleotide Polymorphism) molecular marker associated with a pig backfat thickness character and application. The nucleotide sequence of the SNP molecular marker is as shown in SEQ ID NO: 1; one SNP molecular marker site A / G is arranged at the 254bp position of the sequence of the SNP molecular marker. Genetic typing is carried out by utilizing a gene chip technology, whole genome association analysis is carried out in combination with the character of correcting the 100 kg backfat thickness of a large white pig, one SNP molecular marker remarkably related to the character is screened out, and a new marker resource is provided for molecular breeding of the growth character of the breeding pig.

The invention discloses an SNP (Single Nucleotide Polymorphism) molecular marker related to disease resistance of ricefield eel and application of the SNP molecular marker, and relates to the technical field of molecular biology. The nucleotide sequence of the SNP molecular marker is as shown in SEQ ID NO.3, and SNP sites, namely G / A mutation and A / C mutation, exist at the 143rd and 413th basic groups of the SNP molecular marker. According to the invention, SNP loci in LamR genes in a ricefield eel group are screened out through sequence alignment, and genotyping is carried out on the SNP loci; and comparing the differences of the disease resistance of the genotypes, and screening to obtain the genotype with the strongest disease resistance, thereby providing an effective molecular marker for detecting the disease resistance of the ricefield eel. The SNP molecular marker provided by the invention is associated with the disease resistance of the ricefield eel, and provides effective technical support for breeding of disease-resistant ricefield eel varieties.

The invention discloses a reagent, a detection system and a method for HPA genotyping detection of Chinese population. 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 a relatively high practical value.

The invention discloses an SNP molecular marker combination related to disease resistance of ricefield eels and application of the SNP molecular marker combination, and relates to the technical field of molecular biology. The SNP molecular marker combination comprises the following molecular markers (1)-(3): (1) a molecular marker with a nucleotide sequence as shown in SEQ ID NO.7; (2) a molecular marker with a nucleotide sequence as shown in SEQ ID NO.8; and (3) a molecular marker with a nucleotide sequence as shown in SEQ ID NO.9. According to the invention, an SNP locus in a TLR7 gene in a monopterus albus group is screened through sequence alignment, and genotyping is carried out on the SNP locus; and comparing the differences of the disease resistance of the genotypes, and screening to obtain the genotype with the strongest disease resistance, thereby providing an effective molecular marker for detecting the disease resistance of the ricefield eel. The molecular marker combination provided by the invention is associated with the disease resistance of the monopterus albus, and provides effective technical support for breeding of disease-resistant monopterus albus varieties.

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.

The present disclosure provides methods and systems for classifying microsatellite and minor alleles in a sample. Also, the present disclosure provides methods and systems for generating classifiers for conditions based on microsatellite loci and for performing pan-cancer assays. The methods and systems can involve next-generation sequencing of nucleic acid samples from subjects and genotyping microsatellite loci in the samples.

The application belongs to the technical field of pig molecular marker, and particularly discloses a SNP molecular marker related to the litter size of sows and application thereof. SLC22A12 A SNP site significantly related to the litter size of Landrace sows is screened out by using second-generation gene sequencing and gene chip technology for genotyping and whole genome association analysis of 732 Landrace sows, the SNP site is located on the upstream of a gene on chromosome 2 of pigs, corresponding to the 7565970th nucleotide on chromosome 2 of the international pig 11.1 version reference genome, and can be used for predicting or assisting breeding of the litter size of sows.

The invention discloses a molecular marker related to disease resistance of ricefield eel and application of the molecular marker, and relates to the biological field of aquaculture and molecular marker screening. According to the invention, SNP loci in SFRP2 and TC1A gene coding regions in a ricefield eel group are screened through sequence alignment, and the two genes and a combination thereof are subjected to genetic typing; and comparing the differences of the disease resistance of the genotypes, and screening to obtain the genotype with the strongest disease resistance and the combination thereof, thereby providing an effective molecular marker for detecting the disease resistance of the ricefield eel. According to the monopterus albus disease resistance screening method developed based on the molecular marker, monopterus albus varieties with excellent disease resistance can be screened by utilizing SNP differences of disease-resistant genes, and then the monopterus albus varieties are used for disease resistance breeding. Effective technical support is provided for breeding of disease-resistant ricefield eel varieties.

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 an SNP (Single Nucleotide Polymorphism) molecular marker associated with correction of a 100kg backfat thickness character of a pig and application of the SNP molecular marker. The SNP molecular marker is located on a pig chromosome 2 and contains six SNP molecular marker sites. Genetic typing is carried out by utilizing a gene chip technology, whole genome association analysis is carried out in combination with the 100kg backfat thickness correction character of the landrace, six SNP molecular markers obviously related to the character are screened out, and a new marker resource is provided for molecular breeding of the growth character of the boar.

The invention relates to the field of plant genetic breeding, and discloses an SNP molecular marker related to corn drought resistance and application of the SNP molecular marker. Two markers ZMDRI291441904 and ZMDRI159118475 which are obviously associated with the corn drought tolerance index are mined through whole genome association analysis, the marker sites are A / G and T / C respectively, the two markers are used for performing genetic typing on the corn inbred line, and the drought tolerance indexes of the corn inbred line of the two genotypes of each marker respectively follow the following conditions: GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, GGgt, , AA, CCgt; tT. Experiments show that the maize inbred line with relatively high drought tolerance index can be found by detecting the SNP site. The invention provides a new method for corn molecular marker-assisted selective breeding, and has important significance in drought-resistant screening of corn inbred lines and breeding of drought-resistant new varieties.

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 present invention discloses a SNP molecular marker related to the feed conversion rate of Large White pigs and its application, belonging to the technical field of molecular marker-assisted selection. The present invention discloses a SNP molecular marker related to the feed conversion rate of Large White pigs. The DNA samples of 5256 Large White pigs were genotyped using the Porcine 80K SNP high-density chip, and a SNP site significantly correlated with the feed conversion rate of pigs was finally screened out through genome-wide association analysis (GWAS). The site genomic version of the SNP molecular marker corresponds to position 263045504 on chromosome 1 of the Ensembl Sscrofa 11.1 reference genome. The polymorphic site is G or A. When the genotype of the site is G / G, the pig has a higher feed utilization rate.

The invention discloses application of a KASP molecular marker in identification of muskmelon tendril traits, and belongs to the technical field of molecular markers. According to the application, a BSA-seq technology is used for preliminarily positioning a gene interval related to the muskmelon tendril-free character, a KASP marker is further designed for fine positioning, and a key gene for controlling the character is finally determined to be MELO3C022091. The key gene has an InDel site with polymorphism between a parent HMC-1226 without tendrils and a parent hornhoney with tendrils, and the InDel site is shown as an insertion difference of five basic groups. The genotype and phenotype of the InDel site of the KASP molecular marker have significant correlation, wherein when the basic group is T, tendrils exist, and when the basic group is TATTAT, tendrils do not exist. The KASP molecular marker developed on the basis of the InDel site can efficiently and accurately perform genetic typing on a muskmelon population, early prediction of whether a filial generation has a tendril character or not is realized, the breeding selection efficiency is remarkably improved, and an important technical means is provided for muskmelon molecular marker-assisted breeding.

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 present disclosure provides a method for using reticulocytes derived from recipients of gene-edited hematopoietic stem cells (HSCs) to evaluate the results of gene editing in a transplanted population of gene-edited HSCs. Provided herein are methods and compositions relating to the use of single-cell RNA sequencing to evaluate the results of gene editing in a transplanted population of gene-edited hematopoietic stem cells. Although RBCs derived from gene-edited HSCs have had their nuclei removed and are therefore unavailable for genotyping, reticulocytes are immature RBCs that still contain some RNA that can be used to evaluate allele correction.

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.

The invention belongs to the technical field of biology, and relates to a micro-fluidic sample pretreatment chip for detecting different genotype viruses of African swine fever as well as a construction method and application of the micro-fluidic sample pretreatment chip. The invention firstly provides an African swine fever gene I type, II type and I / II recombinant virus detection target gene SNP locus combination; secondly, providing an LAMP (loop-mediated isothermal amplification) system for specific amplification of African swine fever gene I type, II type and I / II recombinant virus detection target gene SNP (single nucleotide polymorphism) site combinations, and constructing a microfluidic sample pretreatment chip; finally, a sample for identifying the genotype of the African swine fever virus is added into the micro-fluidic sample pretreatment chip for amplification, ASFV genotyping can be carried out on an amplification product by detecting the SNP site combination on the genotyping dot matrix chip, and finally, detection, identification and monitoring of African swine fever gene I type, II type and I / II recombinant viruses are achieved.

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.

This invention discloses a method utilizing Breast Milk A method for identifying the red coat color phenotype in cattle using an 8403 bp gene sequence. Analysis of third-generation sequencing data from domestic cattle samples with different coat color phenotypes identified, for the first time, a gene significantly associated with the red coat color phenotype. Breast Milk An 8403bp structural variation in the gene sequence overlaps with a LINE-1 transposon, leading to... Breast Milk Gene transcripts produce different mRNA isoforms. This invention achieves the detection of bovine mRNA using two pairs of primers. Breast Milk Gene detection and accurate genotyping can be performed, enabling marker-assisted selection of the red coat color trait in cattle at the DNA level.