7 results about "Haplotype block" patented technology

The invention discloses a molecular marker related to correction day age of 100 kg weight of a pig and application of the molecular marker, and belongs to the technical field of molecular genetics. According to the invention, for the first time, two SNP loci obviously associated with the weight correction age of a pig reaching 100 kg are identified in a CDS region of a GREB1 gene, and the two SNP loci show complete linkage imbalance and form a conservative haplotype block. The two mutation sites are significantly related to the corrected day age (Plt; 0.001) of the 100 kg weight of the pig, and the corrected day age of the GA genotype is significantly shorter than the corrected day age of the GG genotype and the AA genotype. Detection of the molecular marker associated with the correction day age reaching 100 kg is beneficial to breeding of meat varieties / lines with high growth speed, and has important significance for breeding of pig varieties.

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 haplotype molecular marker related to cotton fiber strength and application of a detection primer of the haplotype molecular marker, and relates to the technical field of plant molecular biology and genetic breeding. The haplotype molecular marker is located in 112, 985, 431-112, 990 and 059bp regions of A06 chromosome of a cotton reference genome, a haplotype block is formed by nine closely linked SNP (Single Nucleotide Polymorphism) sites, the incidence relation between three haplotypes Hap1, Hap2 and Hap3 in the block and fiber strength is defined, and a new molecular target is provided for cotton fiber quality breeding. Compared with a single SNP marker, the haplotype molecular marker provided by the invention has higher stability and phenotype prediction accuracy under a complex genetic background. Genetic typing can be carried out in the cotton seedling stage based on the marker, fiber maturation does not need to be waited, the breeding period is greatly shortened, and the field screening cost is reduced.

The 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.

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.

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.

This invention discloses a whole-genome haplotype typing method for long-read sequencing data. Specifically, it relates to a whole-genome haplotype typing method for long-read sequencing data. This invention addresses the technical challenge of existing methods requiring complete sequencing before typing, resulting in long analysis cycles and inability to meet rapid response requirements. It also overcomes the shortcomings of existing methods in terms of computational efficiency, noise resistance, and continuity. The process is as follows: 1. Determine the alleles supported by the read; 2. Obtain the final haplotype blocks; 3. Process the haplotype blocks sequentially to obtain a ligation queue, and determine the haplotype blocks based on the ligation queue; in adjacent haplotype block pairs, the preceding block is denoted as Block A, and the following block as Block B; determine whether Block A and Block B should be ligated; continue until all haplotype blocks are ligated, and output the typing results.