33 results about "Linkage disequilibrium" patented technology

The invention discloses a marker screening and model building method for precise evaluation of parent genome breeding values, and belongs to the technical field of molecular breeding and genomics. The method comprises the following steps: acquiring genetic typing data and target character phenotype data of a reference group, and performing digital coding; calculating a secondary allele frequency (MAF) and a linkage imbalance score (LD score) of each marker site; based on the joint screening rule of the MAF and the LD score, screening to obtain a core marker subset with relatively high genetic stability and linkage structure representativeness; and constructing a differentially weighted genome prediction model based on the core marker subset to estimate the genome breeding value of the parent individual. According to the method, allele frequency information and linkage imbalance structure information are jointly utilized, interference of low-frequency or weak linkage sites on the prediction model is reduced, the prediction accuracy of parent breeding values in cross-generation predictor representative types is improved, and the method is suitable for genome prediction and molecular breeding of complex characters.

The invention discloses a tomato breeding prediction and design method based on a bidirectional generation model. The method comprises the following steps: firstly, constructing a tomato genotype and phenotype comprehensive data set, and carrying out feature correlation analysis by utilizing an attention mechanism; and then constructing a bidirectional deep learning model containing a forward prediction and reverse design path. The forward network accurately predicts phenotypes from genotypes by adopting a self-attention mechanism, the reverse network reversely deduces virtual genotypes from target phenotypes through transposition convolution, and cyclic consistency and linkage imbalance constraints are introduced for joint training. According to the method, the problem of nonlinear mapping between genotypes and phenotypes is effectively solved, two-way intercommunication between character prediction and parent design is realized, and the precision breeding efficiency of tomatoes is remarkably improved.

The application discloses a kind of molecular markers of wheat stripe rust SNP homozygous site based on whole genome sequence and application thereof.The application is analyzed to 28 strains of global wheat stripe rust genome sequence, compared with reference genome, and more than a million SNP sites are mined out.Sequence depth screening, linkage disequilibrium analysis and heterozygosity detection, identify 1076 SNP homozygous sites.Further based on the frequency of secondary allele, screening of deletion rate and adjacent simple repeat sequence, finally determine 37 core SNP markers.Through primer design to these SNP sites, and add fluorescent linker, develop KASP-SNP molecular marker, which can be used for accurate genotyping identification of wheat stripe rust population.The molecular marker developed based on global wheat stripe rust whole genome is suitable for wheat stripe rust population research in all regions of the world.Based on the development of molecular marker of homozygous site, polymorphism difference caused by heterozygous site can be effectively excluded, to ensure the accuracy of detection site.The set of KASP-SNP molecular marker has high polymorphism, good repeatability and high detection efficiency, and can be widely applied to genetic research of wheat stripe rust population.

The application discloses a high-throughput genotype intelligent analysis method, which comprises data acquisition and preprocessing, molecular marker identification and prediction of genetic relationship and hybridization advantage; high-throughput genotype data are subjected to standardization treatment, three quality evaluation standards of coverage, transversion / transversion ratio and error rate are established, and batch effect is corrected through a position effect index; then genetic similarity matrix between samples is calculated based on the pretreated data, a label SNP with high centrality is identified as a molecular marker through linkage disequilibrium network analysis; the population genetic relationship is estimated by using the marker, and a phylogenetic tree is constructed, and the hybridization advantage is predicted based on the relationship index of heterozygosity and genetic distance. The application significantly improves the quality of genotype data, optimizes the screening of molecular markers, accurately estimates the population genetic relationship and accurately predicts the hybridization advantage, and provides an efficient bioinformatics solution for modern breeding.

The invention provides a genome method and an SNP (Single Nucleotide Polymorphism) marker combination for a pig to adapt to related traits in a high-temperature and high-humidity environment, and belongs to the technical field of genome prediction, the method comprises the following steps: taking a local pig SNP marker combination as a prior fixing effect; standard miscalculation of a p value, a beta value and a beta value based on whole genome association analysis; performing interval dimension reduction based on linkage imbalance; searching an optimal parameter by using a genetic algorithm, and adaptively grouping the SNPs; performing weighted summation on the G matrix; the SNP marker combination is used as a fixed effect, the weighted G matrix is used as a random effect, a genetic evaluation model is configured, and genome prediction is carried out on target characters. According to the method, the large-effect SNP and the minor-effect multi-gene effect which are causally associated with the target prediction character can be accurately captured, redundant information is removed through dimension reduction in the interval, the optimal parameter combination is found through the genetic algorithm, and the calculation speed is greatly increased while the accuracy of genome prediction is improved.

The invention relates to the field of molecular biology, and discloses a haplotype marker for dairy cow milk production butter-fat percentage character breeding and application of the haplotype marker, the haplotype marker is composed of three SNP sites in a strong linkage imbalance state, and the three SNP sites are located in a Block1 haplotype block region of a 10 # chromosome NC037337.1 of a dairy cow ARS-UCD1.2 genome; the three SNP sites are as follows: SNP1: g.59680573 A > C, SNP2: g.59743173 G > C, and SNP3: g.59743414 C > T; the dominant haplotype of the haplotype marker is H2, and the allele combination of the haplotype marker is SNP1-A, SNP2-G and SNP3-C; the homozygous H2H2 of the dominant haplotype H2 is significantly related to the high milk fat percentage character of milk production of dairy cows. The bottleneck of the traditional technology is solved, and the breeding accuracy is remarkably improved; the screening detection technical scheme is stable and reliable and has a wide application range; the milk production quality of groups is improved, and the industrial economic value is enhanced.

The invention discloses a DNA molecular marker related to rice seedling stage cold-tolerant gene haplotype and application of the DNA molecular marker, and belongs to the technical field of functional molecular markers. The rice seedling stage cold-resistant gene OsCTS11 has three main linkage imbalance blocks. Through correlation analysis of low-temperature stress phenotypes and haplotypes, it is determined that Hap4 (GCACA) of LD BLOCK1, Hap3 (GAA) of BLOCK2 and Hap4 (GTTG) of BLOCK3 are dominant haplotypes. The KASP molecular marker developed on the basis of different haplotype SNP sites can be used for analyzing OsCTS11 genotypes in different rice materials, and breeding materials with seedling-stage cold resistance can be screened out through the molecular marker.

To provide simple and efficient means for predicting the risk of side effects in chemotherapy for pancreatic cancer.SOLUTION: The single nucleotide polymorphism of any of (a) to (c): (a) a single nucleotide polymorphism identified by rs1980576 in APCDD1 L gene or a single nucleotide polymorphism in linkage disequilibrium or genetic linkage with the single nucleotide polymorphism; (b) a single nucleotide polymorphism identified by rs2272761 in R3HCC1 gene or a single nucleotide polymorphism in linkage disequilibrium or genetic linkage with the single nucleotide polymorphism; and (c) a single nucleotide polymorphism identified by rs9425343 in EDEM3 gene or a single nucleotide polymorphism in linkage disequilibrium or genetic linkage with the single nucleotide polymorphism, which are present on the genomic DNA in a biological sample taken from a subject, is analyzed, the genotype for the single nucleotide polymorphism is determined, and based on the determined genotype, the prediction of the risk of side effects when chemotherapy for pancreatic cancer is performed is assisted.SELECTED DRAWING: None

The invention belongs to the field of molecular breeding of aquatic animals, and particularly relates to a fish genome selective breeding method based on machine learning, which comprises the following steps: acquiring genome sequencing data and target character phenotype data of a target fish individual; carrying out whole genome association analysis to screen out candidate variation sites significantly related to characters; dimensionality reduction is performed on the candidate sites through linkage imbalance analysis, and representative sites are selected to form a feature set; screening the model by using the feature set as an input feature; training the model through the test set to obtain a genome prediction model; and finally, carrying out genome breeding value prediction on individuals with unknown phenotypes by utilizing the trained genome prediction model, and carrying out breeding selection according to a prediction result. According to the method, the prediction accuracy and breeding selection efficiency of complex characters such as fish disease resistance are remarkably improved, and the method has important application value.

The invention discloses application of a diplotype of a high-association SNP (Single Nucleotide Polymorphism) site of a rudon septentrionalis body in breeding, and belongs to the technical field of aquatic breeding. The method comprises the following steps: analyzing early-stage sequencing data of a W group and an M group of navodon septentrionalis to identify two linkage imbalance SNP sites at 269 and 469 positions of an MYF6 gene with relatively high genetic diversity, totally detecting three haplotypes in the W group and the M group, and randomly forming five diplotypes by the three haplotypes, compared with other four diplotypes, the homozygous diplotype V (G269G269C469C46969) has remarkable advantages in the aspects of average body height and MYF6 gene expression, can be used as a molecular marker related to the body height, and is applied to molecule-assisted breeding of a new fast-growing strain of the navodon septentrionalis so as to improve the yield of a fast-growing improved variety of the navodon septentrionalis.

The application relates to a method for screening functional sites based on sequencing data, and the specific steps are as follows: 1. obtaining SNP sites of all samples through genome sequencing, randomly selecting a plurality of samples as a discovery population, and extracting biological prior information; 2. demarcating important regions of the genome according to the biological prior information obtained in step 1; 3. performing frame linkage disequilibrium filtering on the whole genome, reducing the threshold of LD filtering in the important regions or not performing filtering, and improving the marker density of the important regions, and finally screening a trait-specific marker set. Before performing breeding value estimation, the selective linkage disequilibrium site screening can increase the signal-to-noise ratio of the site, improve the prediction accuracy, and further reduce the consumption of computing resources and time, and improve the breeding efficiency.

The application belongs to the field of animal and plant breeding prediction, and discloses a fast and accurate genomic prediction method based on a genetic force model, which calculates the minor allele frequency and linkage disequilibrium score of a marker; obtains an optimal SNP genetic force model through a SNP genetic force model; selects an optimal number of layers; obtains layer genotype data formed by the genotype data of all individuals in a corresponding layer of a to-be-predicted data set; calculates the estimated genetic force of each layer of SNPs based on the optimal SNP genetic force model, and assigns the estimated genetic force to a corresponding diagonal weight matrix of the layer; calculates the kinship matrix between individuals in the corresponding layer genotype data of each layer; fits a multi-random mixed model to obtain the genomic estimated breeding value of each phenotype of all individuals in the to-be-tested data set. The application is based on a linear model framework, has low calculation complexity, and the key steps can be processed in parallel, so the calculation speed is fast; the application constructs a trait-specific SNP genetic force model, optimizes the model representation of the genetic structure of a complex trait, and thus improves the prediction performance.

The application discloses a method for fine positioning of anti-sporozoan genes of Carassius auratus based on linkage disequilibrium analysis, relates to the technical field of fine positioning of fish genes, and comprises the following steps: collecting whole blood samples of a Carassius auratus population, extracting genomic nucleic acid sequences, constructing a whole genome marker site set with a preset marker density gradient, dividing haplotype blocks to generate an initial haplotype data set, obtaining a population linkage disequilibrium distribution map through sliding window comparison, selecting a region with a decay rate lower than a standard value as a candidate correlation section and extracting a genotype coding sequence, matching and calculating correlation strength values with sporozoan infection survival phenotype data, reconstructing haplotype phase information of the candidate section and iteratively calculating until the threshold is met if the preset threshold is not reached. The method is suitable for genetic structure differences of genomes, optimizes correlation determination processes, and improves the accuracy of anti-sporozoan gene positioning and the reliability of section screening.

The application relates to the field of homologous tetraploid organisms, in particular to a combined determination method of homologous tetraploid double-reduction parameters and HWD coefficients. The method comprises the following steps: constructing a homologous tetraploid natural population double-reduction and linkage disequilibrium combined model; constructing a combined calculation model; inputting actual values of double-marker offspring zygote frequencies into the combined calculation model to determine estimated values of double-marker direct parent gamete frequencies; calculating estimated values of single-marker direct parent gamete frequencies according to the estimated values of the double-marker direct parent gamete frequencies; inputting the estimated values of the single-marker direct parent gamete frequencies into a single-marker direct parent gamete frequency calculation model to obtain a nonlinear equation; and determining the measured values of the double-reduction parameters and the Hardy-Weinberg disequilibrium coefficients according to the nonlinear equation. The application simultaneously completes the determination of double-reduction frequency estimation, Hardy-Weinberg disequilibrium and linkage disequilibrium between markers by constructing a combined model, and improves the precision of parameter estimation.

The invention relates to the technical field of molecular identification of pig varieties, and discloses an SNP molecular marker combination for identification of Huoshou black pigs, the combination is composed of the following 27 SNP sites, and the physical position and allele information of each SNP site are determined based on a pig reference genome Sscrofa11.1: rs3473390918 located at 229783932bp of a chromosome 1, the allele of which is C / T; the rs690957272 is located at the 230954563bp position of the chromosome 1, and the allele of the rs690957272 is T / C; and the rs337901794 is located at the 231278598bp position of the chromosome 1, and the allele of the rs337901794 is T / A. According to the invention, through whole genome re-sequencing and population genetics analysis (FST screening), in combination with partial least squares regression importance evaluation, PLS-DA modeling, cross validation and linkage imbalance redundancy elimination, 27 Houshou black pig specific SNP loci are finally optimized.

This invention discloses a negative regulatory gene for cold tolerance in rice seedlings. OsDMY01 Haplotypes and KASP molecular markers and their applications. Genes OsDMY01 The nucleotide sequence is shown in SEQ ID NO.1. Knocking out this gene using gene editing technology significantly improved the survival rate of rice seedlings under low-temperature stress, while overexpression of this gene reduced cold tolerance, indicating that... OsDMY01 It is a negative regulator of cold tolerance in rice seedlings. OsDMY01 Two linkage disequilibrium blocks (LD BLOCK1 and LD BLOCK2) were identified in the regulatory and exon regions of the gene, each containing the favorable haplotype Hap2, which was significantly associated with cold tolerance at the seedling stage. Corresponding KASP molecular markers were developed for the favorable haplotypes, which can be used for efficient and precise screening and creation of cold-tolerant rice germplasm, providing important genetic resources and molecular tools for molecular breeding of cold-tolerant rice.

The invention discloses a basic group editing and monitoring system for gene linkage imbalance. The basic group editing and monitoring system comprises guide RNA (Ribonucleic Acid) designed for molecular targets obtained by screening transcription factor mediated gene linkage imbalance, a magnetic navigation-lipidosome nano-particle carrier and a reagent used by a space group imaging technology. According to the invention, magnetic navigation is combined with ferric oxide magnetic nanoparticles-lipid nanoparticles, so that the beneficial effects of improving editing targeting and efficiency and achieving accurate delivery are achieved; according to the method, multiple sites of the gene are edited at the same time, and overall intervention is carried out on the multiple sites of the gene linkage imbalance; the imaging system introduced by the invention can realize monitoring and spatial characterization of linkage imbalance, and is helpful for analyzing an immune mechanism.

The invention discloses an application of a diplotype of a body length associated SNP (Single Nucleotide Polymorphism) site of modestus septentrionalis in breeding, and belongs to the technical field of aquatic breeding. The method comprises the following steps: analyzing early-stage sequencing data of a W group and an M group of navodon septentrionalis to identify two linkage imbalance SNP sites at 268 and 532 positions of an IGFBP2 gene with higher genetic diversity, totally detecting three haplotypes in the W group and the M group, randomly forming five diplotypes by the three haplotypes, compared with other four diplotypes, the homozygous diplotype V (A268A268C532C532) has remarkable advantages in the aspects of average body length and IGFBP2 gene expression, can be used as a molecular marker related to the body length, and is applied to molecule-assisted breeding of a new fast-growing strain of the navodon septentrionalis so as to improve the yield of a fast-growing improved variety of the navodon septentrionalis.

The invention provides a multisystem disease analysis method based on gastrin plasma proteomics, which comprises the following steps of: A, analyzing a large number of adult individuals subjected to baseline evaluation by using queue research data of a biological sample library, and measuring a plurality of plasma proteins; b, analyzing a standardized protein expression (NPX) value of gastrin (GAST) by adopting a multivariable Cox proportional risk model, and correcting by using Bonferroni so as to reduce a false positive result; and C, exploring the correlation between the GAST-PRS and the disease phenotype by adopting full phenotype correlation analysis (PheWAS) based on polygene risk score (PRS), and further analyzing the genetic correlation between the GAST and the disease by using linkage imbalance score regression (LDSC). According to the method, the GAST can be redefined as a cross-system risk regulation factor, and the method is of great significance to layering of patients with shared pathway imbalance. The GAST has multi-system correlation with morbidity and mortality in the outcome of 168 diseases, and challenges the classical normal form of the gastrointestinal specific function of the GAST. These findings establish the location of GAST as a multi-system risk indicator.

The invention discloses an application of a diplotype of a body weight associated SNP (Single Nucleotide Polymorphism) site of navodon septentrionalis in breeding, and belongs to the technical field of aquatic breeding. The method comprises the following steps: analyzing early-stage sequencing data of a W group and an M group of navodon septentrionalis to identify two linkage imbalance SNP sites at 521 and 823 positions of EGFR genes with relatively high genetic diversity, totally detecting three haplotypes in the W group and the M group, randomly forming five diplotypes by the three haplotypes, compared with other four diplotypes, the homozygous diplotype V (G521G521G823G823) has remarkable advantages in average weight and relative expression of EGFR genes, can be used as a weight-related molecular marker, and is applied to molecule-assisted breeding of a new fast-growing strain of the modestus septentrionalis so as to improve the yield of a fast-growing improved variety of the modestus septentrionalis.

A method for evaluating fetal DNA concentration (cffDNA) in maternal blood during pregnancy through polymorphic locus linkage block, comprising: obtaining low-depth WGS sequencing data of the sample; obtaining a mapping relationship between the locus and the linkage polymorphism; and calculating the concentration according to the low-depth WGS sequencing data and the mapping relationship between the locus and the linkage polymorphism and taking a plurality of loci constituting the linkage polymorphism as a unit. Wherein, the mapping relationship between the locus and the linkage polymorphism can be obtained by processing public genome WGS data, processing public linkage polymorphism block data or processing a large amount of high-depth WGS measured data. The present application is based on low-depth WGS data, and the heterozygosity of the linkage SNP block can be used to calculate the cffDNA concentration in the maternal blood during pregnancy, which is not affected by the fetal gender in the actual application of NIPT, does not require the father's sample and does not require additional experiments, has high stability, high performance and low cost.

This application discloses a method for identifying SNP molecular markers significantly associated with potato starch content, belonging to the field of SNP molecular marker technology. Based on high-quality SNP sets and starch content phenotypic data, this application employs a mixed linear model for genome-wide association analysis, effectively controlling population structure and phylogenetic relationships, and significantly reducing the false positive rate. By constructing haplotype blocks and introducing an effect accumulation assessment algorithm, it overcomes the limitations of traditional single SNP analysis, detecting the synergistic effect of allele combinations, and the selected haplotype blocks have higher phenotypic explanatory power. Representative SNPs are screened using linkage disequilibrium analysis, and the introduction of independent validation populations ensures the stability and cross-population applicability of the molecular markers. Finally, SNP molecular markers significantly associated with potato starch content are obtained, which can be directly used for early screening of high-starch germplasm and marker-assisted breeding, significantly shortening the breeding cycle and improving selection efficiency.

This application provides a method, system, and application for identifying potential drug targets, relating to the field of bioinformatics. The method includes: S1, constructing genetic instrumental variables related to a predetermined disease based on a multidimensional dataset, wherein the multidimensional dataset includes: a disease genome dataset, a dataset of druggable genes, and a dataset of plasma protein quantitative trait loci; S2, analyzing the genetic instrumental variables using Mendelian randomization to determine the potential causal relationship between genes and the predetermined disease; S3, validating the potential causal relationship between genes and the predetermined disease using a drug-gene dataset to identify potential drug targets for the predetermined disease. The aforementioned method, by comprehensively integrating disease genome, druggable gene, and protein quantitative trait locus data, effectively eliminates the interference of horizontal pleiotropic effects on the identification of potential drug targets and eliminates the confusion that may be caused by linkage disequilibrium, thereby improving the accuracy and reliability of potential drug target screening.

The invention discloses a Chuzhou crucian carp anti-sporozoan gene fine localization method based on linkage disequilibrium analysis, and relates to the technical field of fish gene fine localization, the Chuzhou crucian carp anti-sporozoan gene fine localization method comprises the following steps: collecting Chuzhou crucian carp population whole blood samples, extracting genome nucleic acid sequences, constructing a whole genome marker site set according to a preset marker density gradient, dividing haplotype blocks to generate an initial haplotype data set, comparing through a sliding window to obtain a population linkage imbalance distribution map, selecting an area of which the attenuation rate is lower than a standard value as a candidate association section, extracting a genotype coding sequence, matching with sporozoan infection survival phenotype data, and calculating an association strength value; and if the preset threshold value is not reached, reconstructing haplotype phase information of the candidate section and carrying out iterative calculation until the threshold value is met. The method adapts to the genetic structure difference of the genome, optimizes the correlation judgment process, and improves the accuracy of anti-sporozoan gene localization and the reliability of section screening.

The invention discloses an SNP (Single Nucleotide Polymorphism) molecular marker related to economic traits of Pinan cattle and application of the SNP molecular marker. Through whole genome re-sequencing (WGRS), whole genome association analysis (GWAS), transcriptome function annotation and linkage imbalance analysis, a key single nucleotide polymorphism (SNP) site rs135687714 (exon region missense mutation) of an APLF gene is identified in Pican-south cattle, and the site and rs137691885 (an intron region, a QTL marker site) disclosed in cattle QTL have medium linkage (R2 = 0.5). Genetic typing and character correlation analysis show that individuals with different genotypes of rs135687714 have significant differences (Plt; 0.01) in 11 growth characters such as body width, hip width, hoof and foot development and the like. The molecular marker constructed based on the APLF gene SNP can be used for pionan cattle germplasm identification and molecular assisted selection (MAS), efficient identification and breeding can be carried out in the early stage of calves, an efficient, simple, convenient and stable technical means is provided for molecular breeding of beef cattle, and the molecular marker has important application value and popularization prospects.

The invention discloses an asthma risk site discovery and multi-gene risk scoring system based on deep learning and multi-character analysis. According to the system, preliminary site screening is carried out through GWAS meta analysis and a multi-character statistical method (condFDR / MTAG), a deep learning model Insight GWAS based on a Transform architecture is innovatively adopted, GWAS statistics, linkage imbalance information and multifunctional genome annotation features are integrated, and high-precision site priority sorting is achieved. A polygene risk score (PRS) constructed on the basis shows excellent prediction performance in an independent verification queue. According to the invention, five novel asthma risk SNP loci including rs11766867, rs17644896 and the like and related genes thereof are identified at the same time, and an important genetic tool and a biomarker are provided for early diagnosis, risk prediction and targeted prevention and treatment of asthma.

The invention provides a genomic hierarchical feature screening method and device and electronic equipment, and belongs to the technical field of computers, medicine and breeding, and the method comprises the following steps: carrying out chromosome grouping on genotype information on each SNP site, carrying out missing genotype filling on each chromosome after grouping, and carrying out genotype detection; carrying out chromosome merging on all the filled chromosomes to obtain a primary characteristic gene pool; calculating the deviation between the joint allele frequency between the two SNP sites on the whole chromosome in the primary characteristic gene pool and the expected frequency, calculating a linkage imbalance coefficient based on the deviation, and reserving the SNP sites with the linkage imbalance coefficient smaller than a first set value to obtain a secondary characteristic gene pool; and calculating a Pearson's correlation coefficient between each pair of SNP sites in the secondary characteristic gene pool, and reserving the SNP sites with the Pearson's correlation coefficients smaller than a second set value to obtain a tertiary characteristic gene pool. According to the method, the prediction accuracy of the breeding value is improved through three-stage feature screening.

The invention discloses a coix germplasm resource genetic diversity evaluation method based on big data, which comprises the following steps: acquiring genome sequencing data, high-throughput phenotypic data and geographical environment information of coix germplasm, preprocessing to obtain a ternary coupling matrix, screening core SNPs (Single Nucleotide Polymorphism) through tensor decomposition according to the ternary coupling matrix, and evaluating the genetic diversity of the coix germplasm resource. The method comprises the following steps: constructing a genetic association network based on a linkage imbalance relationship of core SNP, obtaining domestication key gene annotations of coix lacryma-jobi, obtaining causal association path coefficients among characters based on the domestication key gene annotations and an excellent allele combination mode, and endowing different characters with adaptive weights, so as to obtain the adaptive weights of the characteristics of the coix lacryma-jobi; and generating a genetic diversity index according to the excellent allele combination mode and the character adaptive weight, and evaluating the biological diversity. According to the method, the comprehensiveness, the accuracy and the evaluation efficiency of a genetic diversity evaluation result of the germplasm resources are improved by utilizing multi-dimensional data coupling, marker screening and character association analysis.

This application relates to the fields of molecular genetics and biotechnology, particularly to SNP marker sets and their applications for upland cotton variety identification. Through analysis of 10K SNP microarray data from 1205 upland cotton varieties (1194 species), this application identified a core marker set containing 1553 SNP loci. These markers exhibit high polymorphism, low linkage disequilibrium, and uniform chromosome distribution among upland cotton varieties, enabling efficient and accurate identification. This application is the first to determine a genetic distance threshold of 0.3 for identifying the authenticity of upland cotton varieties using this 1553 SNP marker set. This marker set demonstrates strong identification capabilities and high cost-effectiveness, and can be widely applied in areas such as intellectual property protection, breeding, and variety management of upland cotton varieties.

The application belongs to the field of modern agricultural technology, and particularly relates to a gene, haplotype, KASP marker and application for regulating and controlling cold tolerance of rice seedlings OsDMY03 The application can significantly improve the survival rate of rice seedlings under low-temperature stress by knocking out or overexpressing the gene through gene editing technology, which indicates that the gene is a positive regulation factor for cold tolerance of rice seedlings. OsDMY03 In the regulatory region and exon region of the gene, one linkage disequilibrium block (LD BLOCK) is identified, and two favorable haplotypes Hap3 and Hap5 significantly related to cold tolerance of seedlings are screened. OsDMY03 The KASP molecular markers corresponding to the favorable haplotypes are developed, which can be used for efficient and accurate screening and creation of cold-tolerant rice germplasm, and provide important gene resources and molecular tools for rice cold-tolerance molecular breeding, and have important breeding application value.