Method for evaluating inheritance effect of SNP (Single Nucleotide Polymorphism) sites to traits and application thereof

An evaluation method and a technology of genetic effects, applied in the field of evaluation of genetic effects of SNP sites on traits, can solve problems such as no substantial progress, and achieve the effects of eliminating experiments, fast analysis speed, and high accuracy

Inactive Publication Date: 2013-06-12
ANHUI AGRICULTURAL UNIVERSITY
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  • Summary
  • Abstract
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  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The genetic basis of the phenotypic variation of a trait is the result of the joint action of many SNP loci that affect the

Method used

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  • Method for evaluating inheritance effect of SNP (Single Nucleotide Polymorphism) sites to traits and application thereof
  • Method for evaluating inheritance effect of SNP (Single Nucleotide Polymorphism) sites to traits and application thereof
  • Method for evaluating inheritance effect of SNP (Single Nucleotide Polymorphism) sites to traits and application thereof

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Experimental program
Comparison scheme
Effect test

Embodiment

[0026] 1. Determination of target traits and detection of SNPs

[0027] Genomic DNA was extracted from Landrace pigs (24 heads), Large White pigs (86 heads), Red Duroc pigs (33 heads) and White Duroc pigs (11 heads). In this example, the trait of pig daily gain is determined as the target trait, and the average daily gain (DGW) from birth to 100 kg is detected.

[0028] Taking the three SNP sites of a target fragment in the 5' regulatory region of the THRSP gene as an example, the linkage sequence is SNP1-SNP2-SNP3. The genotype of the SNP site of the individual is counted.

[0029] 2. Establish a linear model for genotype effect analysis and estimate the genotype effect

[0030] the y ijklt =μ+b i +g 1j +g 2k +g 3t +e ijklt ,

[0031] ∑n i b i =0,∑n 1j g 1j =0,∑n 2k g 2k =0 and ∑n 3t g 3t =0.

[0032] Here, y ijklt is the measured value of the trait, μ is the population mean, b i is the i-th variety effect, g 1j is the genotype effect of the first SNP1 locu...

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Abstract

The invention relates to a method for evaluating the inheritance effect of SNP (Single Nucleotide Polymorphism) sites to traits. The method comprises the following steps of: (1) obtaining gene fragments related to traits to be analyzed, and determining SNP sites related to the traits and genotypes of the SNP sites; and (2) analyzing the relevance between the SNP sites and the traits, wherein the specific calculation method is as follows: when the number of the SNP sites is one, the relevance between the SNP site and the traits is the direct influence of the SNP site, and when the number of the SNP sites is more than two, the relevance between the i-th SNP site and the traits is the sum of the direct influence and all indirect influence of the i-th SNP site. The method has the advantages that the problem in the prior art that blanks exist in the screening and evaluating of the inheritance effect of the SNP sites to the traits is solved; the method is simple, convenient and feasible, is high in accuracy and high in analyzing speed, so that many complicated tests are not needed; and the method is time-saving and labor-saving.

Description

technical field [0001] The invention relates to the field of molecular biology, in particular to a method and application for evaluating the genetic effect of SNP sites on traits. Background technique [0002] Since the 1990s, with the development of molecular biology techniques, a large number of single nucleotide polymorphisms (SNPs) have been obtained from animal and plant genes. Auxiliary selection serves for the variety improvement and genetic manipulation of animals and plants, and improves the efficiency of breeding. Judging from the current research results, this transformation has great practical value, and the methods surrounding SNPs detection have been constantly updated. However, when tens of millions of SNP loci are presented in front of people, how to evaluate the genetic effects of the loci and whether they have a large enough genetic effect in the practice of animal and plant breeding will directly affect the biology of these SNP loci. Scientific significa...

Claims

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Application Information

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IPC IPC(8): C12Q1/68G06F19/24
Inventor 陈宏权陈华
Owner ANHUI AGRICULTURAL UNIVERSITY
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