716 results about "Haplotype" patented technology

The invention belongs to the technical field of allele typing, and discloses a gene haplotype typing method and device based on sequencing data and a medium, and the method comprises the following steps: obtaining to-be-detected gene sequencing data from a to-be-detected sample; splitting the sequencing data into genes according to a reference sequence, and performing variation information detection and variation information filtering; after sequence splitting is carried out on the basis of the sequence obtained after variation information filtering, the haplotype sequence obtained after sequence splitting is corrected, and a to-be-detected gene haplotype typing result of the to-be-detected sample is obtained. According to the method, complex calculation is simplified by adopting a mode of firstly splitting sequences into genes, the method does not completely depend on sequence comparison results, and similar typing is finally evaluated by adopting a mode of combining comparison with backtracking variation information scoring, so that typing difference information can be effectively refined, and interference of sequencing data noise on the results is reduced; and a haplotype result is verified for multiple times by adopting a primary typing and correction mode, so that the result accuracy is higher.

The invention provides application of a Pto-C3H35 gene haplotype in evaluation of poplar lignin content, and belongs to the technical field of molecular markers. According to the invention, the haplotype of the Pto-C3H35 gene is determined according to the nucleotides of SNP1, InDel1, InDel2, InDel3 and SNP2. The invention provides a primer group and a kit for determining the gene haplotype as well as a method for determining the gene haplotype, the lignin content of the poplar can be accurately judged by determining the genotype combination of the five sites, and superior plants with low lignin content are accurately and efficiently screened in the early growth stage of the poplar; the method is applied to new variety breeding of industrial poplar artificial forests, and effectively shortens the breeding period.

The invention discloses a rice nitrogen response regulation and control network analysis and breeding target identification system and method based on multi-omics data. According to the system, organic combination of regulation and control network construction based on single or multiple varieties of materials, key transcription factor recognition and accurate positioning of regulation and control areas where transcription factors play roles is achieved through an expression-chromatin accessibility correlation research method, and cis-trans effect distinguishing of the regulation and control areas is achieved through a deep learning model. The method comprises the following steps: carrying out nitrogen starvation pretreatment on rice, then carrying out nitrogen resupply, collecting a root sample, and carrying out ATAC-seq and RNA-seq sequencing; an eCAAS method is adopted to construct a regulation and control network, and key transcription factors are identified and accurately positioned; the chromatin accessibility difference of different varieties is predicted through a deep learning model, the cis-action effect and the trans-action effect are distinguished, an upstream transcription factor target is provided for genes dominated by the trans-effect, and haplotype and editable regulatory region targets available for direct breeding are provided for genes dominated by the cis-effect.

The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.

The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.

The invention belongs to the technical field of sesbania genetic breeding, and particularly relates to a molecular marker for breeding or auxiliary breeding of stem tumor sesbania and application of the molecular marker in cross breeding and haploid breeding. The molecular marker provided by the invention is a set of InDel molecular markers for detecting the genetic similarity between the sesbania variety and germplasm and the stem tumor sesbania, and is distributed on the first, third, fourth, fifth and sixth chromosomes of the sesbania. The haplotype of the InDel molecular marker has great difference between the stem tumor sesbania and the core germplasm and variety of the sesbania, and is stably inherited. According to the invention, a primer pair for specifically amplifying the molecular marker is developed according to the difference of the molecular marker between stem tumor sesbania and root nodule sesbania, and by utilizing the primer pair provided by the invention, only the sesbania genome DNA needs to be extracted and then PCR amplification and agarose gel electrophoresis are carried out; therefore, whether the heredity source of sesbania is stem tumor sesbania can be rapidly and accurately identified or identified in an auxiliary manner.

The invention discloses a KASP molecular marker for detecting wheat grain length and thousand grain weight character genes and application, and belongs to the technical field of biology. The primer group for detecting the SNP or the character of the KASP molecular marker is a primer group I and / or a primer group II, and specific sequences of the primer group I and the primer group II are given; meanwhile, the KASP molecular marker can be applied to the detection and identification of SNP allelic variation and haplotype of the wheat TaARF16-7D gene, and the auxiliary identification of the grain length and thousand grain weight characters of wheat grains or the auxiliary breeding of the molecular marker. The related primer group is developed on the basis of the grain length and thousand grain weight characters of the wheat grains, the SNP loci of the related characters and the excellent haplotypes of the SNP loci can be rapidly and conveniently detected, and the primer group has the advantages of being rapid in identification, high in accuracy and the like and has a good application prospect.

The invention discloses a receptor-like protein kinase gene containing a Malectin-like structural domain and associated with the heat resistance character of cotton, and belongs to the field of biotechnology application. The invention provides a cDNA (complementary deoxyribonucleic acid) sequence (SEQ ID NO.1) and a genomic sequence (SEQ ID NO.2) of the gene in allotetraploid upland cotton, 456 upland cotton varieties can be divided into two haplotype promoters according to a heat-resistant character GWAS associated site A11: 20036111, the sequence of a CC heat-labile haplotype promoter is shown as SEQ ID NO.3, and the sequence of a TT heat-resistant haplotype promoter is shown as SEQ ID NO.4. The invention also provides a method for preparing the promoter. The gene provided by the invention is obtained by cotton variety re-sequencing and whole genome association analysis, and is significantly associated with the heat-resistant character of cotton, and two promoter haplotypes of the gene are utilized to distinguish heat-resistant and non-heat-resistant haplotypes. The gene has important research value and application prospect in improvement of the heat-resistant character of cotton and cultivation of new heat-resistant varieties of cotton.

The invention discloses haplotype molecular markers related to wheat drought resistance, primers, a kit and application of the haplotype molecular markers, and aims to solve the technical problem that molecular markers capable of identifying excellent haplotypes of TaXTH-2B gene promoters are lacked at present. It is confirmed that the TaXTH-2B gene promoter has two haplotypes, and the Hap II haplotype is an excellent haplotype endowing wheat with a high drought resistance index and has high promoter activity; meanwhile, the invention develops molecular marker primers for distinguishing the two haplotypes, and the molecular marker primers have wide application prospects in the aspects of identifying and screening bred wheat varieties or breeding intermediate generation materials, assisting in selecting wheat materials with high drought resistance indexes and the like.

The invention belongs to the field of molecular biology, and discloses acquisition of a waterlogging-resistant major QTL qWT1.1 in a corn seedling stage and development and application of a molecular marker primer of the waterlogging-resistant major QTL qWT1.1. The invention provides a major QTL qWT1.1 for controlling the waterlogging survival rate in the corn seedling stage, the major QTL qWT1.1 is located at the fifth version physical position of a reference genome in the first staining of the corn, the fifth version physical position of the reference genome is Chr1: 25904794-27039204, the major QTL site is used for controlling waterlogging-resistant phenotypic variation, an excellent haplotype SNP marker closely linked with the major QTL site is located at the 27039148th basic group of a first chromosome of a reference genome of the corn B73, and the excellent haplotype SNP marker is located at the 27039148th basic group of a second chromosome of the reference genome of the corn B73. The explained waterlogging survival rate phenotypic contribution rate is 10.03%, the PARMS marker designed by the SNP is used for detecting a corn inbred line group, the operation is simple and convenient, the typing is clear, the good selection effect on characters such as root length, root number, plant height, branch number and yield under the stress of corn waterlogging is realized, and the application prospect is wide. The molecular marker can be used for molecular marker-assisted selective breeding of the waterlogging resistance character in the corn seedling stage.

The invention provides a method for jointly evaluating the cellulose content and the lignin content of poplar wood based on a Pto-CDPK4 haplotype and application of the method, and belongs to the technical field of forest molecular breeding. According to the method disclosed by the invention, genotypes of mutation sites at the 248th site, the 255th site, the 297th site, the 363th site and the 367th site of a Pto-CDPK4 promoter region are detected, and according to a haplotype combination of the five sites, the cellulose and lignin contents of the poplar wood are accurately predicted and jointly evaluated; therefore, excellent individuals with high cellulose content and low lignin content in the wood can be accurately and efficiently screened in the early growth stage of the poplar, the breeding period can be remarkably shortened, and the breeding efficiency can be improved.

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 discloses a virus co-infection detection method and system based on penalty regression and sequencing physical linkage. The method comprises the following steps: collecting virus sequences and corresponding pedigree information thereof; counting and screening high-frequency variation to obtain representative variation of the pedigree; constructing a virus pedigree site variation map as a reference map of a reconstruction model by using representative variation of the pedigree; establishing an index for the reference genome, and comparing a to-be-reconstructed virus sequencing sample with the reference genome by using BWA; converting the compared sequencing sample into a BAM file in a binary format; performing variation detection on the virus sequencing samples after comparison to obtain single nucleotide polymorphism (SNP) and insertion / deletion (INDEL) and frequency information thereof; finally, constructing a regression equation according to the SNP and INDEL of the sample as well as the frequency and the reference map of the sample; and performing regression by using a square error loss function in combination with L0 regularization and L1 regularization, and finally obtaining the spectrum haplotype corresponding to the sample and the frequency thereof.

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.

The invention relates to the field of corn molecular marker assisted breeding, and particularly discloses an application of a Zm00001eb023590 gene in ear thickness corn breeding, the invention provides a corn ear thickness molecular marker, the sequence of the molecular marker is shown as SEQ ID NO: 1, GWA analysis and genetic linkage analysis are utilized to jointly locate to a chromosome 1 and excavate to a functional gene Zm00001eb023590 for regulating and controlling ear thickness, and the functional gene Zm00001eb023590 for regulating and controlling ear thickness is obtained. According to the present invention, the corn ear thickness character genetic gene is enriched, the representative molecular marker site in the gene is screened by carrying out haplotype analysis on the gene, the redundancy detection cost in molecular breeding is reduced, and the integrity of the genetic information is retained;

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 discloses a corn flowering period regulation gene Zm00001d032922 as well as an encoding protein, a molecular marker and application of the corn flowering period regulation gene Zm00001d032922. According to the application, a key gene Zm00001d032922 which affects differentiation from apical meristem to tassel is cloned by utilizing a reproductive defect natural mutant id1 found in a corn field breeding line selection process, and the gene encodes a C2H2 type zinc finger protein transcription factor; the Zm00001d032922 gene is used for regulating and controlling the flowering period of the corn, and has an important value for improving the growth period of the corn; the identification of the excellent haplotype of the Zm00001d032922 provides technical support and excellent germplasm resources for the utilization of the gene. By utilizing the gene and the molecular marker disclosed by the invention, the creation of high-yield or high-quality breeding materials of corn can be facilitated, the breeding period of new crop varieties can be shortened, the breeding cost can be reduced, and the breeding efficiency can be improved.

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.

The invention discloses a kit for detecting micro-haplotype and STR gene loci of normal, Y and X chromosomes based on a next-generation sequencing technology and a primer combination of the kit. The primer combination provided by the invention consists of 738 types of primers which are sequentially shown as SEQ ID NO: 1 to SEQ ID NO: 738. According to the invention, a multi-genetic marker composite detection system containing autosomal STR gene loci, X-STR gene loci, Y-STR gene loci and micro-haplotype gene loci is constructed, and 378 gene loci, namely 55 autosomal STR gene loci, 96 Y-chromosome STR gene loci, 30 X-STR gene loci, 196 micro-haplotype gene loci and 1 gender determination gene locus, can be detected at a time. The method can support forensic medicine applications such as individual identification, paternity test, fine checking of male families, mixed DNA splitting, complex genetic relationship analysis and micro-degradation sample inspection, and provides powerful evidences for practical applications such as case reconnaissance.

The invention discloses a molecular marker related to the oil content of brassica napus and application of the molecular marker, and belongs to the technical field of molecular marker assisted breeding. A transcription factor BnaA09.MYB52 for coding an MYB structural domain is proved to be capable of influencing the oil content of cabbage type rape seeds, molecular markers corresponding to different haplotypes of the gene and primers of the molecular markers are designed by utilizing re-sequencing data, and the DNA molecular markers can be used for distinguishing the functional haplotypes of the gene of a cabbage type rape strain to be detected; the gene molecular marker can be used for detecting and predicting the oil content of the brassica napus, can also be used for molecular marker-assisted selective breeding of the high-oil-content brassica napus, can effectively accelerate the process of high-oil-content breeding of the brassica napus, is suitable for large-scale popularization and application, and has a wide application prospect.

The invention discloses a method capable of improving CCS-based single-molecule 5mC methylation detection accuracy. The method comprises the following steps: acquiring a native data set and a processed data set, and constructing a training data set and a test data set; constructing a single-molecule CpG methylation recognition module based on a graph convolution deep neural network, and performing training by using training data of different background base lengths; testing the background base length and the model performance, selecting a proper base length and training a corresponding model; and performing single-molecule 5mC methylation detection by using the trained single-molecule CpG methylation recognition module based on the graph convolution deep neural network. The whole genome methylation frequency quantitative result of the read counting mode has superior performance in all test data sets including different data sources, sequencing library lengths or sequencing depths. In addition, through high CpG methylation recognition, complex single-molecule CpG methylation modes, including methylation modes of haplotypes and repeated regions, can be found.

The invention relates to the technical field of functional molecular markers, in particular to a DNA molecular marker related to rice cold-tolerant gene haplotype and application of the DNA molecular marker. The haplotype of the rice cold-resistant gene COLD1 is composed of SNP145938700 and SNP145938916, and the haplotype of the rice cold-resistant gene COLD1 is composed of When corresponding basic groups of the two SNPs are detected to be AG, the two SNPs are favorable haplotypes (Hap2) of the COLD1 gene, and the cold resistance in the bud stage is high. The molecular marker provided by the invention can be used for haplotype analysis of COLD1 genes with the cold resistance in the bud stage of different rice materials, breeding materials with the cold resistance in the bud stage are screened through the molecular marker, and compared with traditional phenotype screening, time and labor are saved, efficiency is high, and cost is saved; the method can be applied to molecular breeding, and the breeding efficiency is improved.

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 provides a male specific DNA (deoxyribonucleic acid) molecular marker for identifying sex of salix tamariski and a detection primer of the male specific DNA molecular marker. According to the invention, the salix tamariski is identified as a male alien ligand (XX / XY) by utilizing a high-quality haplotype genome and re-sequencing data of the salix tamariski and using methods such as CQ and Fst, the sex chromosome of the salix tamariski is positioned in the No.15, the Y sex linkage region is 5.83-7.16 Mb, and four Y specific gene sequences are finally identified as the male specific DNA molecular marker of the salix tamariski through blastp comparative analysis. Primers are designed for the male specific DNA molecular marker, and PCR amplification is carried out, so that the male and female plants of the salix tamariski can be rapidly identified. The method can be used for rapidly identifying male and female plants of the salix triangularis in the seedling stage, saves cost for screening target sex in the breeding period, provides convenience, and has wide application prospects in production practice of sex identification of salix.

The invention belongs to the field of molecular biology, and discloses acquisition of corn kernel protein major QTL qHP5 and development and application of molecular marker primers of the corn kernel protein major QTL qHP5. The major QTL qHP5 for controlling the corn kernel protein is located at the fifth chromosome of the corn, the major QTL locus for controlling the variation of the corn kernel protein is an excellent haplotype SNP marker which is closely linked with the major QTL locus and is located at the 166392631th basic group of the fifth chromosome of a corn B73 reference genome, the explained phenotype contribution rate of the corn kernel protein is 9.8%, and the explained phenotype contribution rate of the corn kernel protein is 9.8%. The PARMS marker designed by using the SNP is used for detecting a corn inbred line group, is simple and convenient to operate and clear in typing, has a good selection effect on yield traits and growth period traits such as corn ear weight, hundred-grain weight, single-ear grain weight, row number of ears, row number of grains and the like, and can be used for molecular marker-assisted selection breeding of the corn kernel protein content.

Described herein are methods of inhibiting an allele that contains a mutation in a cell (e.g., treating a subject with an allele that contains a mutation). The method includes delivering to the cell an antisense oligonucleotide that targets a variant allele that is in cis with the mutation (e.g., the mutation is a gain of function mutation or a dominant negative mutation), wherein the cell or subject is heterozygous for the target variant, and the antisense molecule is effective at knocking down expression the target variant allele (e.g., effective at preventing, treating, or ameliorating at least one symptom associated with the mutation). Also described herein are methods of haplotyping a cell or subject, and antisense oligonucleotides that target mutant superoxide dismutase 1 (SOD1) and other genes.

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 application of a Glyma. 08g106300 gene in identifying saline-alkaline tolerance of soybeans, and relates to the technical field of biology. A FramCPU model is adopted to carry out GWAS analysis on 899 parts of soybean germplasm materials, the Glyma. 08g106300 gene related to the saline-alkaline tolerance of soybeans is obtained through screening, haplotype analysis and yeast transgene verification experiments prove that the mutation type of the Glyma. 08g106300 gene can really influence the saline-alkaline tolerance of the soybeans, and Hap1 haplotype soybean plants have higher saline-alkaline tolerance. The invention proves that the Glyma. 08g106300 gene is related to saline-alkaline tolerance of soybeans and can be used for identifying the saline-alkaline tolerance of the soybeans, so that a technical support is provided for breeding saline-alkaline tolerance varieties of the soybeans.

The invention provides a method for identifying a structure variation linked haplotype, and particularly relates to a method for identifying an embryo structure variation linked haplotype. The method is independent of family information and is particularly suitable for identifying whether an embryo lacking family information carries a chromosomal structural variation in pre-transplantation screening and / or pre-natal screening, thereby implementing variation blocking. The invention also provides a detection product for implementing the method.

The invention relates to the technical field of functional molecular markers, in particular to a DNA (deoxyribonucleic acid) molecular marker related to rice germination stage flooding-resistant seedling gene haplotype. The haplotype of the waterflooding-resistant seedling-forming gene OsTPP7 in the bud stage of the rice consists of SNP282722617, SNP282723164, SNP282723639, SNP282723858 and SNP282727202, and the haplotype of the waterflooding-resistant seedling-forming gene OsTPP7 in the bud stage of the rice consists of SNP282722617 When a corresponding basic group of the five SNPs is ACGCA, the five SNPs are favorable haplotype (Hap7) of the OsTPP7 gene, and the flooding resistance in the bud stage is high. The molecular marker provided by the invention can be used for haplotype analysis of the OsTPP7 gene with the flooding-resistant seedling-forming ability in the bud stage of different rice materials, breeding materials with the flooding-resistant ability in the bud stage of the rice are screened through the molecular marker, and compared with traditional phenotype screening, time and labor are saved, efficiency is high, and cost is saved; the method can be applied to molecular breeding, and the breeding efficiency is improved.