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SNP (Single Nucleotide Polymorphism) marker for cloud black goats and application of SNP marker in identification of varieties of cloud black goats

A black goat and identification cloud technology, which is applied in the direction of recombinant DNA technology, microbial measurement/inspection, DNA/RNA fragments, etc., can solve the problems of time-consuming, and the accuracy of results needs to be improved.

Active Publication Date: 2022-07-22
YUNNAN ANIMAL SCI & VETERINARY INST
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, there is no report on the SNP sites used to identify the Yunshang black goat breed. In the prior art, most of the application methods for identifying sheep breeds using SNP sites are identified by site combination or site matching. , takes a long time and the accuracy of the results needs to be improved

Method used

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  • SNP (Single Nucleotide Polymorphism) marker for cloud black goats and application of SNP marker in identification of varieties of cloud black goats
  • SNP (Single Nucleotide Polymorphism) marker for cloud black goats and application of SNP marker in identification of varieties of cloud black goats
  • SNP (Single Nucleotide Polymorphism) marker for cloud black goats and application of SNP marker in identification of varieties of cloud black goats

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0056] Example 1 First screening of cloud-shang black goat differential SNP sites

[0057] For 4 breeds (Yunshang black goat, hybrid sheep F2 generation, Yunling black goat and Chuanzhong black goat), a total of 160 sample data, including 31768735 loci. In order to obtain high-quality differential loci between varieties, the samples and loci are first filtered, and then the differential loci are screened on this basis. The specific flowchart is as follows figure 1 .

[0058] GWAS analysis and Fst analysis were performed on the 110 samples retained after filtering and the remaining loci after quality control, so as to screen the differential loci among varieties. In this project, there are 4 breeds, so in gwas analysis and Fst analysis, we divide the samples into 2 groups (for example, YSH.vs.Other, YSH: black goat on the cloud), and obtain significant difference sites respectively. Based on the results of GWAS and Fst, the TOP 23 SNP sites with significant differences betwee...

Embodiment 2

[0091] Example 2 Second screening of cloud black goat differential SNP sites

[0092] Considering the identification accuracy rate and the distribution of loci in the whole genome, the second selection is carried out according to the analysis results of the resequencing data. The screening principle is to select loci with large differences between varieties, and try to ensure that the loci are evenly distributed in the whole genome. Distribution, the newly selected 26 loci are distributed on 12 chromosomes such as 3, 4, 5, etc. The detailed information of the loci is shown in the table below.

[0093] Table 3 26 SNP sites for the second screening

[0094]

[0095]

[0096] Library building and blind testing:

[0097] The genotyping of 26 loci of 384 samples of 4 varieties was detected by mass spectrometry, and the blindly tested samples were identified after the completion of the library construction. For the specific statistical results, see figure 2 .

[0098] Depe...

Embodiment 3

[0100] Example 3 Construction of a reference group data model for identifying cloud black goats and non-cloud black goats

[0101] Collected 1013 cloud black goats (Shuangbai County Yunnan Xianghong Agriculture and Animal Husbandry Co., Ltd., self-employed households in Shiyang Town, Dayao County, etc.) and 1291 non-cloud black goats (Shuangbai County Ainishan Haizidi Village, Dayao County, etc.) County Sanchahe Township, Sichuan Ziyang City Lezhi County Chuanzong Sheep Industry Company, etc.) blood or ear tissue genomic DNA, and then Sequenom test. Among them, the specific operation steps of Sequenom detection are as follows:

[0102] 1. Primer Design

[0103] Use Genotyping Tools and MassARRAY Assay Design software of Sequenom company to design PCR amplification primers and single-base extension primers of the SNP site to be tested, and hand them over to the bio-company for synthesis. The primer information for each SNP is shown in the sequence 1-79 in Table 4:

[0104] T...

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Abstract

The invention relates to an on-cloud black goat SNP marker and application thereof in identification of on-cloud black goat breeds, the on-cloud black goat SNP marker comprises 26 sites, typing results of the 26 SNP sites in a to-be-detected goat genome are detected, the typing results of the 26 SNP sites are substituted into a model constructed by reference group data, and the typing results of the 26 SNP sites in the to-be-detected goat genome are compared with the typing results of the 26 SNP sites in the to-be-detected goat genome. The probability values of "yes" and "NOT" corresponding to the typing result of each SNP locus are calculated, the probability values of the 26 SNP loci are summed to obtain the sum identification probability value of "yes" and "NOT", and if the sum identification probability value of "yes" is greater than the sum identification probability value of "NOT", the goat to be detected is identified as a cloud black goat. The reference group data model for identifying the variety of the cloud black goats is provided for the first time, the identification accuracy of the cloud black goats reaches up to 89.58% by adopting the 26 SNP loci and the identification technology provided by the invention, and powerful technical support is provided for identification, breed conservation and genetic breeding of the cloud black goats in the future.

Description

technical field [0001] The invention relates to the technical field of animal breed identification, in particular to a Yunshang black goat SNP marker and its application in identifying the Yunshang black goat breed. [0002] technical background [0003] Yunshang black goat is a local goat developed by the Yunnan Academy of Animal Husbandry and Veterinary Sciences in conjunction with the Yunnan Provincial Sheep Breeding and Promotion Center and related breeding programs to address the shortcomings of local goats, such as slow growth rate, low meat production, low lambing rate, poor lactation performance, and unsuitability for large-scale breeding. The company, with Nubi goat as male parent and Yunling black goat as female parent, is a new breed of black goat for meat that has been systematically bred for 22 years and 5 generations. Yunshang black goat has excellent characteristics such as full black coat, fast growth and development, perennial estrus, high fecundity, good mea...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6888C12Q1/6872C12N15/11G16B20/40G16B25/20G16B30/00G16B40/10G16B40/20
CPCC12Q1/6888C12Q1/6872G16B40/10G16B40/20G16B30/00G16B25/20G16B20/40C12Q2600/156C12Q2600/16C12Q2537/143C12Q2531/113
Inventor 洪琼花欧阳依娜邵庆勇兰蓉江炎庭李卫娟朱兰
Owner YUNNAN ANIMAL SCI & VETERINARY INST
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