Analysis method of porcine SNP marker loci based on sequencing genotyping technology

A marker locus and genotyping technology, applied in the field of swine SNP marker locus analysis, can solve problems such as difficult varieties or strains, inapplicability, etc., and achieve the advantages of reducing typing costs, improving the quality of sequencing data, and having great application prospects. Effect

Active Publication Date: 2018-08-14
CHINA AGRI UNIV
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  • Abstract
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Problems solved by technology

At present, both Illumina and GeneSeek have launched pig genome-wide SNP chips, among which the PorcineSNP60v2 chip released by Illumina contains 64,232 SNPs, and the PorcineSNP80 chip released by GeneSeek contains 68,528 SNPs. , Large White pig, Duroc pig, Pietrain pig, etc.), many of which are not applicable to local breeds in my country; and once the chip is designed, it is difficult to change the SNP sites contained in it to adapt to different pig breeds or strains

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  • Analysis method of porcine SNP marker loci based on sequencing genotyping technology
  • Analysis method of porcine SNP marker loci based on sequencing genotyping technology
  • Analysis method of porcine SNP marker loci based on sequencing genotyping technology

Examples

Experimental program
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Effect test

Embodiment 1

[0036] Example 1 Prediction of EcoRI-MspI Double Enzyme Cutting Porcine Genome Effect

[0037] This example is used to illustrate the number and size distribution of restriction fragments obtained by EcoRI-MspI double digestion combination. Bioinformatics analysis method was used to simulate the digested pig genome, and the number of double-digested fragments in the range of 100-300bp was counted. The results showed that about 135,495 fragments with a size of 100-300bp could be obtained when EcoRI-MspI double-digested the pig genome Double restriction fragments, which are suitable for simplified genome sequencing library construction are utilized.

Embodiment 2

[0042] Example 2 Simplified Genome Sequencing of Multiple Pig Breeds Using EcoRI-MspI Digestion

[0043] This example is used to illustrate that pig genome can be digested with EcoRI-MspI to obtain SNP information covering the whole genome.

[0044] 1. Experimental materials

[0045] Ear tissue samples of Landrace pigs, Large White pigs, Erhualian pigs, Shawutou pigs, Meishan pigs, and Mi pigs were collected, with 4 pigs for each breed, totaling 24 pig ear tissue samples. Genomic DNA was extracted with DNeasy Blood & Tissue Kit, and the genome concentration was diluted to 50ng / μL for later use.

[0046] 2. Design universal adapters (including oligo1 and oligo2), barcode adapters (including oligo1 and oligo2), and PCR amplification primers (including oligo1 and oligo2) according to the restriction recognition sequences of EcoRI and MspI. There are 24 barcode adapters in total for The 24 samples were differentiated so that they could be sequenced together. Sequences were synt...

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Abstract

A pig SNP marker site analyzing method based on a sequence-based typing technique is provided. The method includes steps of (1) predicting a distribution situation of digested fragments obtained by subjecting a pig genome to double-enzyme digestion using EcoRI and MspI, (2) designing general linkers, bar code linkers and PCR amplification primers according to the digestion recognition sequences of the EcoRI and MspI, (3) constructing a simplified genome sequencing library, (4)performing computer sequencing by utilizing the library constructed in the step (3), and (5) acquiring SNP marker sites according to the sequencing result. The digestion composition used in the method is suitable for all pig varieties. The composition is utilized to simplify genome sequencing, and a number of SNPs acquired can be higher than a number of SNPs on a chip available in the market at present. The method can be used for whole-genome correlation analysis and research and genome selection research, and the typing cost of a single body can be lower than that of a chip popular at present.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a method for analyzing pig SNP marker sites based on sequencing genotyping technology. Background technique [0002] Single nucleotide polymorphisms (Single nucleotide polymorphisms, SNP), as the third-generation molecular markers, have the characteristics of large number, wide distribution, and genetic stability, and are widely used in genetic breeding such as linkage analysis, genome-wide association analysis, and genome selection. field. At present, both Illumina and GeneSeek have launched pig genome-wide SNP chips, among which the PorcineSNP60v2 chip released by Illumina contains 64,232 SNPs, and the PorcineSNP80 chip released by GeneSeek contains 68,528 SNPs. , Large White pig, Duroc pig, Pietrain pig, etc.), many of which are not applicable to local breeds in my country; and once the chip is designed, it is difficult to change the SNP sites contained in it to adapt to Different...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6869
CPCC12Q1/6869C12Q2525/191C12Q2563/143C12Q2521/301
Inventor 胡晓湘谈成李宁黄卓林任江丽
Owner CHINA AGRI UNIV
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