442 results about "Haplotype" patented technology

The invention discloses an SNP (Single Nucleotide Polymorphism) molecular marker for identifying drought tolerance of wheat, haplotypes, primers and application. Belongs to the technical field of biological breeding. Research finds that three SNP loci exist on a wheat ARF20-B gene, a wheat drought-enduring haplotype ARF20-BHapI is developed based on the SNP loci, the first locus is located at the 3616bp position of the ARF20-B gene, and the A / G nucleotide polymorphism is A; the second site is located at the 5623bp position of the ARF20-B gene, and G is in the G / A nucleotide polymorphism; the third site is located at the 9795bp position of the ARF20-B gene, and G is in the G / A nucleotide polymorphism. The wheat carrying the ARF20-BHapI haplotype has the advantage that the drought tolerance of the wheat carrying the ARF20-BHapI haplotype is higher. The invention further provides a KASP primer group for detecting the ARF20-BHapI haplotype, and successful detection of the drought tolerance of the wheat is achieved.

The invention relates to the technical field of plant genetic engineering, and discloses a haplotype identification marker of a rice flood-resistant gene ARF9 and application of the haplotype identification marker. The molecular marker is derived from an exon of an ARF9 gene, is located at the 22009082bp and 22010019bp of a No.4 chromosome of rice, and has a basic group of C. The SNP molecular marker is related to the waterflooding resistance of a male parent oryza longistaminate of perennial rice, and the waterflooding resistance of the male parent oryza longistaminate with a locus genotype of CC is obviously higher than that of rice with a locus genotype of non-AA type. Therefore, the invention provides the loop-mediated isothermal amplification primer group for rapidly identifying the ARF9 gene haploid molecular marker, and the loop-mediated isothermal amplification primer group is used for identifying the ARF9 gene haploid molecular marker so as to rapidly screen out waterflooding-resistant rice. The invention provides a group of primers, the flood-resistant rice can be quickly identified by adopting the primers to perform loop isothermal reaction, the detection cost is low, the detection speed is high, the flood-resistant germplasm can be quickly screened in the rice seedling stage by adopting the method provided by the invention, a time-consuming flooding test does not need to be performed in the later stage, and the breeding process is greatly accelerated.

A haplotype genome assembly method and device, and related applications. The method comprises: acquiring short-read-length data and long-read-length data obtained by sequencing the same biological sample to be detected; performing error correction on the long-read-length data according to the short-read-length data to obtain error-corrected long-read-length data; performing genome assembly according to the error-corrected long-read-length data to obtain a preliminary assembly sequence; and optimizing the preliminary assembly sequence according to the short-read-length data to obtain a target assembly sequence. The method addresses the technical problem in the related art where obtaining high-quality genome assembly requires the use of three types of sequencing data, resulting in excessive data usage.

The invention relates to haplotypes of cobia fatness degree related SNP sites, a primer group and application of the haplotypes and the primer group, and belongs to the technical field of molecular markers, seven SNP sites related to cobia fatness degree are screened, primers for amplifying the SNP sites are provided, breeding of new varieties with fatness degree characters can be assisted by utilizing the SNP sites or the primers, and breeding of cobia fatness degree characters is facilitated. The method can greatly shorten the breeding period, reduce the dependence on phenotypic characters, improve the selective breeding efficiency, and have good application prospects.

Compositions, methods, kits, systems, and software are provided for non-invasive prenatal testing for autosomal recessive diseases. Next generation sequencing is used to sequence maternal and fetal DNA isolated from maternal plasma by probe capture. The fetal fraction of the sequencing reads for DNA isolated from maternal plasma is estimated by counting single nucleotide polymorphisms (SNPs) for which an allele is detected that is present in the paternal haplotype but absent in the maternal haplotype, based on the assumption that SNPs having a paternal allele belong to the fetal DNA. The fetal fraction is bioinformatically enriched by excluding sequencing reads over a specified length via in-silico size selection, which increases fetal genotype prediction accuracy. Parental haplotype information together with the read ratios observed at the linked SNPs is used to predict the fetal genotype at a site of a mutation linked to the autosomal recessive disease.

The invention discloses a sorghum brown midrib mutant gene bmr34 related to high digestibility and application of the sorghum brown midrib mutant gene bmr34. The haplotype of the mutant gene bmr34 can specifically reduce the lignin content by 2.99% without affecting the biological yield. The invention provides the KASP marker which can accurately locate the bmr34 gene of sorghum and is closely linked with the bmr34 gene of sorghum, so that the breeding efficiency can be greatly improved, the breeding process is accelerated, and the KASP marker has important theoretical and practical significance for improving the quality of sorghum feed.

The invention discloses a molecular marker of a brassica napus salt-tolerant gene BnaA07.GRP3 and application of the molecular marker, and belongs to the technical field of rape breeding. According to the invention, two haplotypes hap0 and hap1 of the salt-tolerant gene BnaA07. GRP3 are found for the first time, a corresponding molecular marker is provided for the optimal haplotype hap1 of the BnaA07. GRP3, and the optimal haplotype hap1 of the BnaA07. GRP3 is specifically amplified, so that the salt-tolerant material of the brassica napus is identified. The salt-resistant material of the brassica napus can be quickly and accurately identified, and the repeatability is good. The method is applied to auxiliary selective breeding of salt-resistant characters of the brassica napus, the breeding efficiency of the salt-resistant brassica napus can be greatly improved, the selection range of salt-resistant materials is expanded, the method has huge application potential and prospects, and an ideal way is provided for cultivating the salt-resistant brassica napus.

The invention belongs to the technical field of agricultural biology, and particularly discloses a molecular marker site related to gray mold resistance of Chinese roses and application of the molecular marker site. Specifically, the invention provides application of an SNP site in Chinese rose gray mold resistance molecular marker assisted breeding. The SNP loci are located at the 74bp site and the 108bp site from the 5'end of a sequence shown as SEQ ID NO.1, and when basic groups of the two loci present GT, the germplasm is judged as the germplasm with high gray mold resistance. Through analysis of a plurality of germplasm resources, it is found that the haplotype is GT, the germplasm has a smaller scab area and shows higher gray mold resistance, and the germplasm with high gray mold resistance is obtained. The method is mainly derived from genetic resources of Asian wild type and ancient Chinese varieties, and by means of the technical scheme, the breeding process can be accelerated, and Chinese rose germplasm with disease resistance can be rapidly obtained.

The invention relates to the technical field of virus traceability, and particularly discloses a coronavirus sample detection method which comprises the following steps: S1, acquiring high-throughput original sequencing data of a target sample; s2, inputting the original sequencing data into a dynamic learning type recognition model, and outputting each virus pedigree and the credibility of each pedigree; s3, performing noise perception variation detection on the original sequencing data; s4, aiming at each virus lineage, determining a variation point; s5, detecting a mixed infection indicator; s5, constructing a Bayesian network to determine the genetic relationship among the variation points, and generating a virus haplotype sequence; s6, calculating a genetic distance, and deducing a propagation path through a maximum likelihood method; and outputting a traceability report. The method solves the problem of frequency conflict when multiple pedigree coexist, is suitable for the situation that multiple pedigree viruses coexist to form mixed infection or co-infection, and avoids misjudgment of attribution of variation sites.

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.

Described herein are computer-implemented systems, methods, and devices for pharmacogenomic determination. The system includes a data processor configured to receive pharmacogenomic data representing at least one pharmacogenomic annotation in association with at least one gene; a database configuration engine configured to receive at least one genomic variation of the at least one gene and to search the pharmacogenomic data for at least one association with each genomic variation to return the associated data, the associated data being a haplotype or diplotype and a phenotype; a report generator configured to generate at least one report comprising the associated data with the genomic variation associated.

The invention discloses a haplotype analysis and assembly method and device for a polyploid genome. The invention develops a haplotype analysis support construction method which integrates HiC data and an assembly graph to improve accuracy, integrity and continuity. Key limitations of HiC are effectively overcome by utilizing graph connectivity derived from long read length overlap. The method is applied to complex polyploidy genomes, and compared with an existing tool, the method has the advantages that the sequence deletion rate is reduced by dozens of times, the sequence error rate is reduced by one order of magnitude, and the continuity of gapless sequences is improved by several times.

The invention relates to the technical field of genetic breeding, in particular to application of a haplotype molecular marker related to mutton sheep weight traits. The haplotype molecular marker is a nucleotide sequence as shown in SEQ ID NO.1 and a nucleotide sequence as shown in SEQ ID NO.3; the nucleotide at the 101bp site of the SEQ ID NO. 1 is C or G; the nucleotide at the 101bp site of the SEQ ID NO.3 is C or G, and the nucleotide at the 101bp site of the SEQ ID NO.3 is C or G; the application refers to any one of the following (1) and (2); (1) identifying the weight of the mutton sheep; (2) increasing the weight of the offspring of the mutton sheep. The haplotype molecular marker provided by the invention can be used for early identification and auxiliary seed selection of weight traits of meat sheep, and the weight level of offspring can be effectively improved by screening individuals of which haplotypes are combined into GGGG as parents.

The invention belongs to the technical field of biological detection, and relates to a target area amplification method suitable for long-read-long three-generation sequencing, which comprises the following steps: designing at least one pair of amplification primers, and enabling the amplification primers to cover a target area; if the length of the target area is less than or equal to 20kb, designing a pair of amplification primers; if the length of the target area is larger than 20 kb, multiple pairs of amplification primers are designed, the adjacent amplification primers have overlapped areas, the multiple pairs of amplification primers are divided into two groups, and the coverage areas of the amplification primers in each group are not overlapped; performing long fragment amplification on the gDNA of the detection sample by adopting the amplification primer to obtain a to-be-detected product; carrying out library building and third-generation sequencing on the to-be-detected product; and carrying out single-gene genetic disease detection and / or haplotype analysis to obtain single-gene genetic disease information and / or haplotype information of the target gene. According to the method disclosed by the invention, the sequencing cost and the analysis time are remarkably reduced, and the method has relatively high detection accuracy.

The invention provides an InDel molecular marker sequence related to wheat drought resistance as well as a detection method and application thereof, and belongs to the technical field of molecular markers. The invention provides a polymorphic site for forming different drought resistance of wheat, the polymorphic site only has two haplotypes: a sequence of a 724bp long fragment as shown in SEQ ID No.2 is inserted between the fragments 245-246bp as shown in SEQ ID No.1, and the haplotype is homozygous as a haplotype A; the drought resistance of to-be-detected wheat which is not inserted with the 724bp long fragment sequence shown at the site, is haplotype B homozygous and is determined to be haplotype A homozygous is higher than that of a variety determined to be haplotype B homozygous, so that the drought resistance of the to-be-detected wheat is determined to be haplotype A homozygous by detecting the condition of the polymorphic site when the wheat is subjected to molecular marker-assisted selective breeding, and the drought resistance of the to-be-detected wheat is determined to be haplotype A homozygous. The wheat with relatively high drought resistance can be found.

The invention discloses application of a SmCYP82D47 gene in improvement of eggplant bacterial wilt resistance, and belongs to the technical field of molecular biology. 1, and the nucleotide sequence of the gene is as shown in SEQ ID NO. 2. On the basis of positioning an eggplant bacterial wilt resistance linkage site by GWAS, the eggplant bacterial wilt resistance candidate gene SmCYP82D47 is screened through bioinformatics analysis such as gene sequence analysis and haplotype analysis; the tissue expression specificity, hormone response expression characteristics and the like of candidate genes are analyzed; by silencing candidate genes in a resistant material S027 and overexpressing the candidate genes in a susceptible material S054, the disease resistance conditions of a silent plant and a wild type plant as well as the wild type plant and an overexpressed plant are observed, so that the accuracy of a positioning result can be verified, and the effect of the candidate genes in regulating and controlling the bacterial wilt resistance of the eggplant is determined; important theoretical basis and technical means can be provided for eggplant disease-resistant molecular breeding.

The application discloses PRR30 gene SNP and a haplotype combination thereof in identifying bull semen quality, and belongs to the technical field of molecular genetics. Eight SNP sites are identified, wherein SNP7: g.794 C>A or SNP8: g.2247 G>T can be used for identifying the high and low of bull semen collection amount, SNP2: g.-2151 C>T can be used for identifying the high and low of bull sperm abnormality rate, and the haplotype combination of SNP1-SNP8 is that the bull with H1H11 has higher semen collection amount and lower sperm abnormality rate, and can be further used for identifying bull semen quality, thereby helping staff to evaluate bull breeding performance in an early stage, to carry out superior gene bull screening, to promote the cultivation of superior bull, to shorten the screening period and to improve the breeding efficiency.

The invention belongs to the field of molecular marker screening of aquatic animals, and provides a KASP molecular marker for identifying high temperature resistance of procambarus clarkii and application of the KASP molecular marker. According to the procambarus clarkia high-temperature-resistant gene Hsp70-1 and the procambarus clarkia high-temperature-resistant gene Hsp70-2 disclosed by the invention, two SNP (Single Nucleotide Polymorphism) sites of the procambarus clarkia high-temperature-resistant gene Hsp70-1 and the procambarus clarkia high-temperature-resistant gene Hsp70-2 are remarkably related to high-temperature resistance, Hsp70-1-Hap1 haplotypes and Hsp70-2-Hap1 haplotypes are high-temperature-resistant dominant haplotypes, and the application potential of high-temperature-resistant application through combination of the double genes of KSAP markers developed aiming at the loci are good in typing effect, high in specificity, good in stability, convenient to detect, economical and efficient, and can be widely applied to breeding of high-temperature-resistant varieties of the procambarus clarkii. The KASP marker disclosed by the invention can screen out the procambarus clarkii with the SNP haplotype combination with the high-temperature-resistant advantage, and meets the technical requirements of high-temperature-resistant molecule-assisted breeding of the procambarus clarkii.

The application discloses an evaluation method of egg laying performance of Leizhou black duck. The application is aimed at Leizhou black duck, and finds that 5 SNP sites are significantly related to the age of starting laying of Leizhou black duck; 2 SNP sites are extremely significantly related to the body weight of starting laying of Leizhou black duck. It is further found that a haplotype has low starting laying age, high starting laying body weight and high egg laying quantity, so that individuals with low starting laying age, low starting laying body weight and high egg laying quantity can be screened from the advantageous genotypes of the 7 SNP sites, so as to improve the egg laying performance and economic benefits.

Disclosed are methods for trapping and barcoding discrete biological units in a hydrogel. Also disclosed are methods for analyzing gene expression, genotype, haplotype or epigenome in discrete biological units, as well as kits for implementing the methods of the present disclosure.

The invention discloses a molecular marker of a wheat TaREC2-6B gene and application of the molecular marker, and belongs to the technical field of crop seed selection and cultivation. The molecular marker is a KASP marker and is obtained by amplifying a KASP marker primer group (AllleFAM, AllleHEX and Common), after a fluorescence signal is analyzed by a KlusterCaller, haplotypes of the wheat TaREC2-6B gene are divided into TaREC2-6B-HapI and TaREC2-6B-HapII, and the haplotypes of the TaREC2-6B gene are relatively wide in flag leaf width, relatively large in thousand seed weight and relatively large in single plant yield, so that the haplotypes of the TaREC2-6B gene are excellent genotypes of the wheat TaREC2-6B gene. The method has the beneficial effect that a new tool is provided for wheat breeding.

Disclosed is a combination in which, when at least one target gene present at the S locus is amplified by PCR, a tail sequence that does not hybridize to the nucleic acid sequence of the target gene and does not affect the amplification reaction is added to the 5' side of at least one primer so that the S haplotype can be identified based on the size difference of the amplified DNA fragment, and a size difference occurs in the amplified DNA fragment. The haplotype can be identified through a simple method, such as electrophoresis, due to a size difference occurring in the amplified DNA fragment. The present invention makes it possible to provide a method for easily identifying the S haplotype that controls self-incompatibility in plants.

The invention relates to application of an SNP site of a Yanbian cattle FABP2 gene in improving meat quality of Yanbian cattle, and belongs to the technical field of molecular biology. The SNP (Single Nucleotide Polymorphism) sites comprise one or more of a g.5970161 site, a g.5970209 site, a g.5972550 site, a g.5972551 site and a g.5973068 site, and are divided into five types of haplotypes, namely H001, H002, H003, H004 and H005 respectively. The five SNP loci of the Yanbian cattle FABP2 gene can regulate and control meat quality traits, provide reliable markers for molecular breeding of Yanbian cattle, accelerate polymerization and fixation of excellent alleles, realize accurate improvement of high-quality meat traits of Yanbian cattle, further select individuals carrying excellent genotypes for breeding, accelerate fixation and inheritance of excellent traits, and improve the breeding efficiency of Yanbian cattle. The Yanbian cattle variety with better meat quality is bred.

The invention discloses a DVQE-based gene phasing method, device and equipment and a storage medium, which are used for solving the problems that the existing gene phasing method is easy to fall into local optimum and is insufficient in convergence precision when processing large-scale sequencing data. The method comprises the following steps: mapping obtained gene sequencing fragments into nodes of an undirected graph, and taking a difference base number of the gene sequencing fragments on an SNP (Single Nucleotide Polymorphism) site as an edge weight between the nodes; converting a gene phasing problem into a maximum cut problem of an undirected graph; constructing a target function according to the maximum cut problem of the undirected graph, and mapping the target function into a global Hamiltonian of the Isin model based on the constructed target function; decomposing the global Hamiltonian into a plurality of sub-Hamiltonian based on the bearable bit number of the quantum processor; adopting a distributed quantum variational character solicitation solver DVQE to execute parallel solution on each sub Hamiltonian to obtain a global solution; and determining a haplotype source of each sequencing fragment according to the global solution.

The application belongs to the technical field of forensic medicine, and particularly relates to a multiple SNP combined microhaplotype amplification system and construction method, product and application based on one-step library construction. The application is based on RC-PCR technology, and constructs a one-step library construction composite amplification system. The amplification system comprises RC-Primer with a sequence as shown in SEQ ID No. 1-SEQ ID No. 210, I5-Primer with a sequence as shown in SEQ ID No. 211-SEQ ID No. 214, and I7-Primer with a sequence as shown in SEQ ID No. 215-SEQ ID No. 222. The method provided by the application realizes one-time PCR reaction, simultaneously completes targeted amplification and library construction, greatly shortens experimental time and simplifies experimental steps, and the advantage is more significant when a large number of samples are simultaneously detected.

This invention relates to a method for structural variant (SV) identification and genotyping in long-read family pedigree samples. The invention pertains to the field of vegetative variant (SV) detection in families, specifically focusing on methods for identifying and genotyping structural variants. The aim of this invention is to address the problems of existing family-based SV detection methods, which heavily rely on high-coverage sequencing, resulting in insufficient utilization of genetic characteristics and inaccurate SV detection and genotyping, as well as the high cost of sequencing multiple samples. This invention uses individual sequencing data from all family members as input, extracts variant features from each member, performs cluster analysis on the family feature set, assigns features to their respective members, and then uses three family feature signal correction methods to correct detection errors. Finally, SVs are located and anchored using Mendelian inheritance laws, and haplotype genotyping of SVs is completed using linkage information from long-read sequencing fragments.

The invention relates to a full-length sequence amplification primer, an amplification method and a three-generation sequencing method of an HLA-I antigen gene, and belongs to the field of gene detection. The HLA-I antigen gene is subjected to PCR (Polymerase Chain Reaction) amplification by using 8 pairs of characteristic amplification primers. And each gene can be subjected to high-yield specific amplification on a full-length sequence containing complete intron and exon regions only through one round of amplification and enrichment, and 7.8 Kb long-fragment genes can be captured once at most. The experimental deviation caused by simultaneous amplification of a single gene by using a plurality of pairs of segmented primers and the indirect error caused by gene splicing are effectively avoided. The method comprises the following steps: carrying out quality inspection and purification on amplicon PCR (Polymerase Chain Reaction) products, mixing samples, constructing an HLA-I type antigen gene library, carrying out accurate and complete sequencing on the full-length sequence of the HLA-I type antigen gene by adopting a three-generation PacBio Sequel II platform, and ensuring that the Hifi reads base accuracy can reach 99% or above. The reading of HLA-I type antigen gene full-length sequence variation information and the haplotype analysis at a high resolution level can be realized.

The invention belongs to the technical field of molecular markers, and particularly relates to application of a chloride channel protein coding gene GmSALT9 in identification of soybean salt tolerance. The nucleotide sequence of the chloride ion channel protein coding gene GmSALT9 disclosed by the invention is as shown in SEQ ID NO. 1. According to the scheme, the salt tolerance of the soybean can be judged according to the promoter haplotype of the chloride ion channel protein encoding gene GmSALT9; when the promoter haplotype of the GmSALT9 is a TT type, it is prompted that the salt tolerance of the tested soybeans is high; when the promoter haplotype of the GmSALT9 is an AA type, it is prompted that the detected soybean is sensitive to salt. The invention provides remarkable relevance between the chloride ion channel protein coding gene GmSALT9 and the salt-tolerant character of the soybean, and the chloride ion channel protein coding gene GmSALT9 has important research value and application prospect in improvement of the salt-tolerant character of the soybean and cultivation of a new salt-tolerant soybean variety.

The application discloses a SNP site, a CAPS molecular marker and application which are closely linked to a wheat salt stress post-maximum relative root length character, and belongs to the technical field of wheat genetic molecular breeding.The SNP site is at least one of the 274th, 689th, 725th, 767th, 811th and 1038th SNP sites of a TaHSFA2-2A gene sequence.The six SNPs exist in two haplotypes, namely haplotype Hap-2A-1 and haplotype Hap-2A-2, and the two haplotypes of the six SNPs are linked.Through correlation analysis and natural population verification, the maximum relative root length of wheat germination stage salt stress of Hap-2A-2 is significantly greater than that of Hap-2A-1.Therefore, the application has important application value in predicting the maximum relative root length of wheat salt stress or in preparing a reagent for predicting the maximum relative root length of wheat salt stress.

This invention discloses a haplotype SNP molecular marker for identifying wheat grain starch content in the TaMYB44-4D gene and its application. Specifically, the SNP is T or C at position 1557bp of the sequence in SEQ ID NO.1. Based on this SNP, primers for detecting this haplotype SNP molecular marker have also been developed, and a kit containing these primers has been prepared. By PCR and polyacrylamide gel electrophoresis, the SNP and genotype can be accurately identified, thereby distinguishing between superior haplotypes (high starch content) and non-superior haplotypes (low starch content) in wheat.