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Four SNP site combinations for identifying Tan sheep and non-Tan sheep and application thereof

A non-tan sheep and locus technology, applied in the field of identifying the combination of 4 SNP loci of Tan sheep and non-tan sheep, can solve problems such as Tan sheep brand damage

Active Publication Date: 2019-01-11
BEIJING COMPASS BIOTECHNOLOGY CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the recent emergence of Tan sheep crossed with other sheep breeds and sold as Tan sheep has caused great damage to the Tan sheep brand

Method used

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  • Four SNP site combinations for identifying Tan sheep and non-Tan sheep and application thereof
  • Four SNP site combinations for identifying Tan sheep and non-Tan sheep and application thereof
  • Four SNP site combinations for identifying Tan sheep and non-Tan sheep and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0063] Example 1. Discovery of SNP site combinations for identification of Tan sheep and non-Tan sheep and establishment of detection methods

[0064] 1. Discovery of SNP loci for identification of Tan sheep and non-Tan sheep

[0065] Genomic DNA was extracted from the blood or ear tissues of 50 Tan sheep (from Yanchi County, Ningxia) and 50 Feitan sheep (from Ningxia, Inner Mongolia, etc.). Genomic DNA was resequenced with the Illumina Hiseq X10 instrument, and then analyzed by R software to obtain 25 SNP sites that are different from Tan sheep and non-Tan sheep, and R programming was used to analyze and delete the sites with poor call rate. 模型分析的16个位点如下:10_29432742、14_24803652、14_24807700、14_24812228、15_72453265、15_72476712、19_2161140、20_44865529、25_34435605、2_42344462、2_80645369、3_12248645、6_94503480、6_94540642、7_88811445、7_89505361。

[0066] The physical positions of the 16 SNP sites were determined based on the comparison of the standard sequence of the whole genome of Ta...

Embodiment 2

[0178] Example 2. Blind test-verification of the accuracy of identifying Tan sheep and non-Tan sheep by combining four SNP loci

[0179] Sample: 576 Tan sheep and non-Tan sheep

[0180] Experimental method: use the method for identifying or distinguishing Tan sheep and non-Tan sheep established in Example 1 to detect the genotype of each sample, and obtain the genotyping information of the 4 SNP site combinations of each individual. Compare the identification results with the real results given by experts to test the identification accuracy, false positive rate and false negative rate. Based on the results of the first blind test, the model is optimized by optimizing the training set through machine learning. According to the optimized model, the samples were tested again blindly, and the accuracy rate, false positive rate and false negative rate were evaluated.

[0181] Experimental results: A total of 419 Tan sheep samples and 151 non-Tan sheep samples were identified in t...

Embodiment 3

[0182] Example 3. Blind Test II Verifies the Accuracy Rate of Identification of Tan Sheep and Non-Tan Sheep by Combination of Four SNP Loci

[0183] Sample: 768 Tan sheep and non-Tan sheep

[0184]Experimental method: use blind test-optimized training set to detect the genotype of each sample by using the method of identifying or distinguishing Tan sheep and non-Tan sheep constructed in Example 1 for 768 samples, and obtain 4 kinds of SNP positions of each individual Point combined genotyping information, conduct a second blind test, compare the identification results with the given results, and calculate the identification accuracy rate, false positive rate and false negative rate.

[0185] Experimental results: 679 of the 768 samples were genotyped, and a total of 503 Tan sheep samples and 176 non-Tan sheep samples were identified by the blind test. Compared with the actual species of the given samples, the identification accuracy rate was calculated to be 68.5 %, the false...

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Abstract

The invention discloses four SNP site combinations for identifying Tan sheep and non-Tan sheep and application thereof. The invention provides the application of a substance for detecting the genotypeof the following SNP site combination in the genome of a sheep to be detected in identifying or assisting in identifying whether the sheep to be detected is Tan sheep or non-Tan sheep; Or the use ofa substance for detecting the genotype of a combination of the following SNP loci in the genome of the sheep to be tested in the preparation of a product for identifying or assisting in identifying whether the sheep to be tested are Tan sheep or non-Tan sheep; The invention is to stabilize the quality of Tan sheep, re-establish the brand image of Tan sheep, build Tan sheep into a national well-known brand, explore the unique variation and important trait determination site of Tan sheep by means of re-sequencing, and develop a Tan sheep breed identification chip, so as to provide support for the identification, breeding protection and genetic breeding of Tan sheep in the future.

Description

technical field [0001] The invention belongs to the field of biotechnology, and in particular relates to a combination of four SNP loci for identifying Tan sheep and non-Tan sheep and applications thereof. Background technique [0002] Ningxia Tan sheep is one of the excellent local germplasm resources in my country. The lamb fat of Tan sheep is evenly distributed, the meat is tender and the smell is small, and it is a kind of mutton with better quality among coarse wool sheep. the whole country. The annual output of Tan sheep reaches 6 million heads. It is highly praised by the market for its unique flavor and meat quality. Due to the changes in market demand and the continuous breeding of Tan sheep for meat, Tan sheep are favored by consumers, forming the "Yanchi Tan lamb" "s brand. In 2016, Yanchitan mutton was successfully selected as an ingredient for the G20 summit, which established its high-quality image of safety and health. However, the recent emergence of hybrid...

Claims

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Application Information

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IPC IPC(8): C12Q1/6888
CPCC12Q1/6888C12Q2600/156C12Q2600/16
Inventor 刘继强
Owner BEIJING COMPASS BIOTECHNOLOGY CO LTD
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