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Method for sieving fingerprint spectrum genetic marker

A genetic marker and fingerprint technology, applied in the field of genetic marker screening, can solve problems such as being unsuitable for large data volume, difficult to automate, and single filtering conditions.

Active Publication Date: 2018-05-08
INNER MONGOLIA UNIVERSITY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0010] The present invention provides a new method for efficiently screening genetic markers of fingerprints in order to solve the problems of single filtering conditions, low screening efficiency, difficulty in realizing automation, and unsuitability for large data volumes in traditional screening methods.

Method used

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  • Method for sieving fingerprint spectrum genetic marker
  • Method for sieving fingerprint spectrum genetic marker
  • Method for sieving fingerprint spectrum genetic marker

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0077] This example is used to illustrate how to use MStrat software to screen as few SSR markers as possible to create a fingerprint of peach germplasm resources.

[0078] Step 1: Source data and input files. The data comes from the published paper "Construction of Molecular ID Cards of Main Peach Variety Resources and Their Wild Relatives in China" (Chen Changwen et al., 2011). According to the format requirements in the technical solution of the present invention, the input files are sorted out and imported into MStrat software.

[0079] The second step: Draw the redundancy curve to determine the minimum number of genetic markers. First open the software MStratv4.tcl, then follow the prompts to load three input files in sequence and determine the path and name of the output file. Click 'Options', select 'Nei Indice', and click 'OK' to exit. Then click 'Redundancy', set 'Replicates' to 3, 'Maximum Iteration' to 30, then click 'Step' to set the step value of the abscissa o...

Embodiment 2

[0089] This example is used to illustrate how to use MStrat software to screen as few SNP markers as possible to create a fingerprint of potato germplasm resources.

[0090] Step 1: Source data and input files. The source data is the "Infinium8303Potato Array" gene chip SNP data under the dose model of 221 tetraploid potato samples downloaded from the SolCAP website (http: / / solcap.msu.edu / potato_genotype_data.shtml). In order to ensure the quality of the data used, we performed quality control on the original data, and the filtering conditions were:

[0091] The missing data rate of each SNP site is less than or equal to 0.4, and the minimum allele frequency is greater than or equal to 0.05. Combined with the instructions on the website, the sites with unclear boundary values ​​are removed, and finally 2457 high-quality SNP sites are obtained.

[0092] Digitally convert the filtered SNP data. For the 5 genotypes at each SNP site, they are represented by 0, 1, 2, 3, and 4 in o...

Embodiment 3

[0106] This example is used to illustrate that the 18 SNP combinations obtained in Example 2 (referred to as potato 18SNP) can be used to distinguish and identify different potato varieties.

[0107] In order to verify whether the 18 SNPs of potato can be used for the identification of new potato varieties, we collected 40 potato cultivar resources and carried out the "Infinium 8303 Potato Array" gene chip analysis using the method in Example 2. The genotype data of the 40 potato resources in the potato 18 SNP were extracted, and after inspection, these 40 potato resources could be distinguished in pairs (see Table 3) under the condition of not counting the genetic markers with missing data between any two samples; These 40 potato resources and the 221 potato resources in Example 2 were combined into a set, and the 261 potato germplasm resources in this set could still be passed through the potato 18 SNPs were pairwise differentiated. The above results indicated that the pota...

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Abstract

The invention relates to field of bioinformatics and concretely discloses a method for sieving fingerprint spectrum genetic marker and a new usage of M-strategy. With the application of M-strategy andcombinations of various genetic marker data, a core genetic marker cluster is sieved and a sieved genetic marker is used for establishment of different species fingerprint spectrums; and problems ofgenetic marker sieving standard singularity, poor selection efficiency and automation failure in the prior art can be solved. Genetic diversity information redundancy and complementarities of different genetic markers are considered and high-efficient and quick sieving can be achieved for plenty of genetic markers; genetic marker site diversity information redundancy can be reduced, information waste can be reduced, detection cost can be lowered and sieving efficiency can be enhanced.

Description

technical field [0001] The present invention relates to the field of bioinformatics, in particular to the screening of genetic markers. Background technique [0002] Fingerprint refers to the combination of several genetic markers and their characteristic bands or bands that can distinguish different species or individuals of organisms (including animals, plants, fungi, bacteria, and viruses). This technology has been widely used in the fields of human paternity identification, animal and plant population research, and DUS determination of new crop varieties. Genetic markers for constructing fingerprints include morphological markers (such as plant height, flower color, stem diameter, etc.), cytological markers (such as karyotype), biochemical markers (such as isoenzymes) and DNA markers (such as RFLP, SSR, SNP, etc.) Four categories. DNA markers have become the most widely used genetic markers in fingerprints due to their good repeatability, high stability, rich polymorph...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22
CPCG16B30/00
Inventor 齐建建练群张若芳蒲媛媛
Owner INNER MONGOLIA UNIVERSITY