Pig-whole-genome low-density SNP chip and manufacturing method and application thereof

A technology of whole genome and production method, applied in the field of gene and molecular breeding, can solve the problems of difficult implementation and high cost of high-density chips, and achieve the effect of reducing costs and improving the breeding process.

Active Publication Date: 2018-04-27
CHINA AGRI UNIV +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0007] The purpose of this application is to provide a low-density SNP chip for the whole genome of pigs, so as to solve the problems of high cost and difficulty in implementing high-density chips in the process of pig breeding and selection

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  • Pig-whole-genome low-density SNP chip and manufacturing method and application thereof
  • Pig-whole-genome low-density SNP chip and manufacturing method and application thereof
  • Pig-whole-genome low-density SNP chip and manufacturing method and application thereof

Examples

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Effect test

Embodiment 1

[0041] Example 1: Production of a low-density SNP chip for the whole pig genome

[0042] The pig whole genome low-density SNP chip of the present invention is referred to as the 9k chip for short. The 9K chip is mainly based on GGP-PorcineHD (68528SNP, developed by geneseek company, referred to as 80K). The degree of linkage disequilibrium between SNP markers has hardly decreased, 0.54 for 80K, and 0.53 for 9K.

[0043] The linkage disequilibrium of SNP markers is the guarantee of the accuracy of genome-wide association analysis and genome selection. The lower the linkage disequilibrium, the lower the accuracy of genome selection will be. At the same time, the allele frequency MAF of the 9K chip has little change with that of the 80K chip. These indicators show that the cost of 9K chips has decreased, but the use effect can still maintain a level close to that of 80K. See Table 1-1 for details.

[0044] Table 1-1 is the comparison of 9K and 80K SNP chip parameters

[0045] ...

Embodiment 2

[0252] Embodiment two: this implementation utilizes the designed 9K chip to estimate the accuracy of the genome breeding value, and compares it with the accuracy of the GGP-PorcineHD (68528SNP, referred to as 80K) chip, including the following steps:

[0253] (1) Obtaining data, the source of data is 27,081 large white pigs born in a pig farm in Beijing between 2007 and 2016. GGP-Porcine HD SNP chip genotype determination was performed on 1,429 sows, and 100 kg for 2 traits Traditional breeding value estimation and corrected phenotype calculations were performed based on age in days and number of piglets born alive. Select 1,429 heads for genotype determination for 9K chip design, and edit the SNP chip data, a total of 8,552 SNPs are used for analysis; select 1,159 of them as a reference group at the age of 100 kg, and the remaining 270 youngest heads as a verification group ; 411 heads were used as a reference group for the number of live litters, and the youngest 210 heads w...

Embodiment 3

[0258] Example 3: Using 9K chip information to identify the genetic relationship between populations

[0259] (1) Obtaining data, the samples come from 1156 American Large White pigs and 878 British Large White pigs from two different pig farms. First, use 26,122 pieces of pedigree information from the American large white and 31,802 pieces from the British large white to construct the A matrix based on the pedigree information, and construct the G matrix and the Kinship matrix based on the chip information with 1,156 American large whites and 878 British large whites from the 9K chip, and calculate the relationship between individuals. kinship relationship between. And use the G array to conduct paternity test on 1156 American large whites to evaluate the accuracy of the pedigree information.

[0260] (2) Use the pedigree information to construct the A array, that is, the molecular relationship matrix (numerator relationship matrix, NRM), and use the 9K chip information to c...

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Abstract

The invention relates to a pig-whole-genome low-density SNP chip. The chip is a DNA sequence which is shown in an SEQ ID NO.1-8846. The pig-whole-genome low-density SNP chip has the advantages that the pig-whole-genome low-density SNP chip is researched and analyzed from an existing 80 k chip, and under the situation that the selection accuracy is not remarkably lowered, unrelated SNP marks are creatively removed, and the number of the SNP marks is lowered to 8846. The pig-whole-genome low-density SNP chip has the innovative significance on pig breeding and selection, so that pig breeding is possibly popularized through the pig-whole-genome low-density SNP chip, and the Chinese pig breeding and selection progress can be greatly accelerated.

Description

technical field [0001] The invention relates to the field of genetic molecular breeding, in particular to a low-density SNP chip of a whole genome of pigs, a method for making a low-density SNP chip of a whole genome of pigs, and an application of a low-density SNP chip of a whole genome of pigs. Background technique [0002] SNP has the characteristics of large number, wide distribution, easy rapid and large-scale screening, and convenient genotyping. Third generation genetic markers. There are two main types of new high-throughput molecular marker technology based on SNP: one is high-throughput molecular marker technology based on sequencing technology; the other is molecular marker technology based on gene chip technology. Although molecular marker technology based on sequencing technology has high throughput and high flexibility, short-segment sequencing relies on the reference genome sequence, and it is difficult to detect and analyze regions located in repetitive sequ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18C40B40/06
CPCC40B40/06G16B20/00
Inventor 丁向东宋海亮张勤唐韶青肖炜云鹏
Owner CHINA AGRI UNIV
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