3 results about "Haplotype block" patented technology

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.

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.