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Method for designing SNP (single-nucleotide polymorphism) molecular marker with base substitution or insertion deletion

A molecular marker, indel technology, applied in biochemical equipment and methods, microbial determination/inspection, etc., can solve problems such as poor repeatability, low stability, and high price

Inactive Publication Date: 2013-06-12
NORTHWEST A & F UNIV
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Problems solved by technology

[0004] It can be seen from the above methods that the commonly used methods are not stable, have certain limitations, are expensive, and have poor repeatability.

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  • Method for designing SNP (single-nucleotide polymorphism) molecular marker with base substitution or insertion deletion
  • Method for designing SNP (single-nucleotide polymorphism) molecular marker with base substitution or insertion deletion
  • Method for designing SNP (single-nucleotide polymorphism) molecular marker with base substitution or insertion deletion

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Embodiment Construction

[0016] In order to make the object, technical solution and advantages of the present invention clearer, the present invention will be further described in detail below in conjunction with the accompanying drawings and embodiments. It should be understood that the specific embodiments described here are only used to explain the present invention, not to limit the present invention.

[0017] Such as figure 1 It shows the primer design principle of this technology, and there is a substitution of T base and C base at the same gene of two individuals. In this way, the specific primer P1 can be designed by the Allele1 specific site T, and the specific primer P2 can also be designed by the Allele2 specific site C ( figure 1 A). When two pairs of primers were amplified in Genotype1, P1 primers could amplify PCR products normally, but P2 primers could not amplify normally without PCR products ( figure 1 B), the genotype of the gene can be determined as TT; the genotype of Genotype2 ...

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Abstract

The invention discloses a method for designing an SNP (single-nucleotide polymorphism) molecular marker with base substitution or insertion deletion. Since common TaqDNA polymerase needs normal amplification, 5' does not need to be completely paired with the template, and 3' needs complete pairing. Thus, the discovered SNP site can be specifically designed in the 3' position of the primer; the primer designed according to the mutant gene and the wild gene can form 3' terminal mispairing, resulting in incapability of normal amplification; and similarly, the primer designed according to the wild gene and the 3' terminal of the mutant gene generate mispairing, resulting in incapability of normal amplification in the mutant individual genome. By carrying out PCR (polymerase chain reaction) twice and detecting the PCR result by a specific technique, the invention can conveniently determine the genotype of the individual SNP site.

Description

technical field [0001] The invention belongs to the technical field of SNP detection, and in particular relates to a method for designing SNP molecular markers for base substitution or indel. Background technique [0002] Single nucleotide polymorphism (SNP) marking technology belongs to the new generation of marking technology. It is often used to indicate the difference of individual bases at the same allele in different biological individuals. Common single nucleotide polymorphisms include base substitutions and base insertions and deletions. At present, SNP is the most extensive type of variation found in organisms. Even in genes with little sequence difference in different organisms, there are a certain number of SNP sites, so it is an ideal molecular marker in plant genetic research. As an emerging molecular marker, SNP has the following advantages: large number and wide distribution, higher density of SNP than microsatellite markers, and is the most common type of se...

Claims

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Application Information

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IPC IPC(8): C12Q1/68
Inventor 李学军杨子博李立群吴青霞杨林邵慧冉从福
Owner NORTHWEST A & F UNIV
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