Large-scale genetic typing method based on SLAF-seq (Specific-Locus Amplified Fragment Sequencing) technology

A genotyping method and large-scale technology, applied in the field of large-scale sample genotyping, which can solve the problems of low accuracy and low throughput

Active Publication Date: 2013-05-08
BIOMARKER TECH
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  • Abstract
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  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] The purpose of the present invention is to use SLAF-seq technology to reduce genome complexity and perform high-throughput sequencing to conduct research on large-scale samples, solve

Method used

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  • Large-scale genetic typing method based on SLAF-seq (Specific-Locus Amplified Fragment Sequencing) technology
  • Large-scale genetic typing method based on SLAF-seq (Specific-Locus Amplified Fragment Sequencing) technology
  • Large-scale genetic typing method based on SLAF-seq (Specific-Locus Amplified Fragment Sequencing) technology

Examples

Experimental program
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Effect test

Embodiment 1

[0049] Example 1 The large-scale sample genotyping method based on sequencing and SLAFseq technology was applied to the construction of the genetic map of 224 carp F1 populations

[0050] Carp genetic map construction, including the following steps:

[0051] 1. Selection of carp colony (purchased from Heilongjiang Fisheries Research Institute): the colony is F1 colony with 224 strains, 2 parent strains, and 50,000 tags developed.

[0052] 2. As shown in Table 1, the bioinformatics method is used to predict the genome sequence of a similar species of zebrafish, the genome version number is Zv9 published by Ensembl, and the evaluation results of the parameters of the selected optimal solution AluI+MseI, The results showed that the number of enzyme-digested fragments with a specific length of 330-380 was 64,918, which met the needs of tag development, and the ratio of low-copy tags was 94.97%, effectively avoiding highly repetitive sequences; Figure 1A Shown is the evaluation ma...

Embodiment 2

[0077] Example 2 The large-scale sample genotyping method based on sequencing and SLAFseq technology is applied to the construction of haplotype maps and trait association analysis of 512 natural soybean populations

[0078] The soybean haplotype map construction and trait association analysis include the following steps:

[0079]1. Selection of soybean populations: There are 512 germplasm resources of soybean natural populations, and 50,000 SLAF tags are designed.

[0080] 2. If Figure 7 Shown is the evaluation diagram of the effect of avoiding highly repetitive regions of the optimal scheme HaeIII+MseI determined by the bioinformatics simulation of the soybean genome combined with the preliminary experiment. The results show that the digestion fragments of this scheme are evenly distributed on the genome and Effectively reduce the proportion of repetitive sequences in the genome; as shown in Table 6, the genome simplification effect evaluation statistics for this program s...

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Abstract

The invention provides a method for carrying out large-scale gene typing based on an n SLAF-seq (Specific-Locus Amplified Fragment Sequencing) technology. Complexity of the genome is reduced by utilizing the SLAF-seq technology, and genetic typing is carried out on large-scale products. High-throughput sequencing is carried out on the genome, marker-developing, genetic map drawing and whole genome association analyzing are carried out on the samples by utilizing the technology. Compared with the conventional method, the large-scale genetic typing method disclosed by the invention has the advantages that the throughput is greatly improved, and the cost is greatly reduced. The method is mainly applied to marker-developing, genetic map drawing and whole genome association analyzing.

Description

technical field [0001] The present invention provides a large-scale sample genotyping method based on SLAF-seq technology, the core technology of which is to use SLAF-seq technology to reduce genome complexity and perform high-throughput sequencing for marker development, genetic map drawing and genome-wide association analyze. Background technique [0002] With the development of next-generation sequencing technology and bioinformatics with high throughput, low cost, low sequencing error rate, and short sequencing read length, it is possible to develop high-throughput markers for this sequencing technology. SLAF-seq (Specific Length Amplified Fragments sequencing) is a simplified genome deep sequencing technology. On the basis of high-throughput sequencing technology, it uses bioinformatics methods to systematically analyze the reference genome or known BAC sequence of the target species. Based on information such as the GC content of the genome, the status of repetitive s...

Claims

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Application Information

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IPC IPC(8): C12Q1/68
Inventor 郑洪坤
Owner BIOMARKER TECH
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