590 results about "Haplotype" patented technology

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 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 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 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 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 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 discloses a unified coding, storing and calculating method for large-scale genetic variation data. The method comprises the following steps: a genotype coding and memory representation method: coding a genotype from a | b into a unique integer value; the floating length integer coding method is a method for coding an integer from a traditional fixed length byte to a floating byte and is used for recording an index of a sample; storage coding of a genotype sequence: converting the genotype from an integer value sequence into a byte coding sequence which can be directly stored by a computer; a dynamic translation framework of the genotype sequence: quickly loading the byte coding sequence stored in the hard disk in the step (3) into a memory in a low-load manner; and calculating and coding a genotype sequence: converting the genotype from an integer value sequence into 64-bit space coding accelerated calculation according to allele index (x)-ploidy index (y)-sample group (z). The method is of great significance in improving the data processing efficiency and promoting the development of large-queue genetics research and precise medicine.

The invention discloses a haplotype molecular marker Chr19156236840 related to the oil content of peanuts and application of the haplotype molecular marker Chr19156236840, and belongs to the field of molecular marker assisted breeding. The nucleotide sequence of the haplotype molecular marker Chr19156236840 is as shown in SEQ ID NO.1, G / T polymorphism exists at the position of a basic group at the 99th site of the sequence of the haplotype molecular marker Chr19156236840-G, and the haplotype molecular marker Chr19156236840-T comprises two haplotypes, namely Chr19156236840-G and Chr19156236840-T. The oil content of the seeds of the homozygous strain containing the Chr19156236840-G haplotype is obviously higher than that of the seeds of the homozygous strain containing the Chr19156236840-T haplotype. When the haplotype molecular marker is used for detecting peanut germplasm seedling materials, the oil content of the seeds can be accurately and efficiently predicted without waiting for peanut results, and the selection efficiency of peanut breeding is greatly improved.

The invention discloses a TLP1-like gene molecular marker related to cotton verticillium wilt resistance and application of the TLP1-like gene molecular marker, and belongs to the field of biotechnology application. The promoter of the TLP1 protein gene TLP1-like has two haplotypes, the promoter sequence of the haplotype 1 is SEQ ID NO.5, and the genomic sequence of the haplotype 2 is SEQ ID NO.6. The invention also discloses a method for preparing the TLP1 protein gene TLP1-like promoter of the TLP1 protein gene TLP1-like promoter of the TLP1 protein gene. Compared with the haplotype 1, the haplotype 2 has an SV insertion of 2623 bp at a-899 bp position of an ATG upstream promoter region of a TLP1-like gene, so that the expression quantity of the TLP1-like gene is reduced. An InDel functional marker capable of remarkably distinguishing the haplotype 1 and the haplotype 2 is further developed. Compared with the haplotype 1, the haplotype 2 has a remarkable advantage in the aspect of improving the verticillium wilt resistance of the cotton, and the silent haplotype 1 cotton plant TLP1-like remarkably improves the resistance of the cotton to verticillium dahliae. The haplotype 2 has important effects and application prospects in screening cotton disease-resistant materials and cultivating cotton high-resistance varieties.

This disclosure describes methods, non-transitory computer readable media, and systems that implement improved mapping and alignment of nucleotide reads with genomic regions of a reference genome. For instance, the disclosed systems can identify nucleotide reads and candidate population haplotypes within a set of reference spans of a reference genome and generate haplotype set scores for sets of the candidate population haplotypes within the set of reference spans. Based on the haplotype set scores, the disclosed systems can generate a personalized haplotype database comprising a subset of population haplotypes from a population haplotype database and, utilizing the personalized haplotype database, determine one or more personalized alignments of the set of nucleotide reads from the genomic sample.

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 belongs to the technical field of genetic breeding, and particularly relates to a haplotype molecular marker influencing the sheep lumbar muscle thickness character and application, and the haplotype molecular marker comprises two sites CELF4-SNP1-CELF4-SNP2; wherein the position of the gene where CELF4-SNP1 is located is that mutation from G to C occurs at 101bp of a nucleotide sequence as shown in SEQ ID NO.1; the position of the gene where CELF4-SNP2 is located is that mutation from G to C occurs at 101bp of the nucleotide sequence as shown in SEQ ID NO.2. The haplotype molecular marker can be used for identifying the lumbar muscle thickness character of sheep, and the lumbar muscle thickness of offspring is increased by selecting an individual of which the haplotype combination is GGGG as a male parent or a female parent.

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.