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Chicken low-density SNP liquid phase chip based on targeted capture sequencing and application thereof

A liquid-phase chip and low-density technology, which is applied in the field of chicken low-density SNP liquid-phase chip, can solve the problems of no gene chip and achieve good flexibility, low typing cost, and high cost performance

Active Publication Date: 2022-05-13
JIANGSU INST OF POULTRY SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, the economic traits related to slaughter breeds such as chicken carcass appearance are still dominated by conventional selection, the research and application of related molecular markers need to be improved, and there is no gene chip suitable for slaughter breed selection

Method used

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  • Chicken low-density SNP liquid phase chip based on targeted capture sequencing and application thereof
  • Chicken low-density SNP liquid phase chip based on targeted capture sequencing and application thereof
  • Chicken low-density SNP liquid phase chip based on targeted capture sequencing and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0057] Embodiment 1 Design and preparation of chicken low-density SNP liquid chip

[0058] 1. Establishment of local chicken SNP background database

[0059]The present invention utilizes the whole genome resequencing data of 475 individuals of 33 local chicken breeds in China, and obtains highly credible SNP sites through data analysis for subsequent screening.

[0060] Blood samples of local chicken breeds were obtained from the Poultry Genetic Material Bank of Jiangsu Poultry Research Institute. Firstly, the whole genome of 475 local chickens (Table 2) was resequenced using the HiseqX-ten sequencer (Illumina), and the average genome coverage of each sample was above 10×. After preliminary quality control of the off-machine data, the sequencing data was compared to the chicken reference genome (GRCg6a) by BWA software (Li and Durbin, 2010), and the SNP mutation identification was performed using the Haplotype caller module of the GATK4 software. A total of 17,464,141 high-...

Embodiment 2

[0079] Example 2 Application method of chicken low-density SNP liquid chip in chicken DNA sample detection

[0080] 1. Extraction of chicken genomic DNA samples: blood was collected from chicken wing veins, and DNA was extracted using the phenol-chloroform method.

[0081] 2. DNA sample quality detection: Agilent 2100 bioanalyzer (Agilent) was used to measure the DNA concentration, and 1% agarose gel electrophoresis was used to detect the integrity of the DNA. Qualified samples were stored in a 4°C refrigerator for later use.

[0082] 3. Liquid phase chip detection: operate according to the standard procedure of liquid phase chip detection (http: / / www.molbreeding.com / index.php / Technology / GenoBaits.html).

[0083] 4. Data analysis: The obtained raw data was quality controlled using fastp software (Chen et al., 2018), and then the sequencing data was compared to the chicken reference genome GRCg6a using BWA software (Li and Durbin, 2010), using GATK4 software The standard proc...

Embodiment 3

[0084] Example 3 Application of chicken low-density SNP liquid-phase chip in the detection of genetic diversity of local chicken breeds

[0085] The present invention uses the chicken liquid chip prepared in Example 1 to perform genotyping of 8 local chicken breeds (see Example 2 for the specific operation method). Specific local chicken breeds include Jinhu Wufeng chicken (JH), Langshan chicken (LS), Langya chicken (LY), Wenshang reed chicken (WS), silky silkie (SK), bantam (AJ) ), Dongxiang Green-shell Chicken (DX), Gushi Chicken (GS). The samples were all from the National Gene Bank of Local Chicken Breeds of the Jiangsu Institute of Poultry Science, with 10 chickens for each breed. Among the tested varieties, the detection rate of the target SNP loci was above 98%, the loci with MAF>0.05 exceeded 91% of all the target loci, and the average MAF within the variety was between 0.34 and 0.41. In addition to the target SNP, 14,895 sites around the target SNP were detected. Af...

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Abstract

The invention discloses a chicken low-density SNP liquid phase chip based on targeted capture sequencing and application of the chicken low-density SNP liquid phase chip, the chip contains 5912 SNP loci, 2582 SNP loci obviously associated with economic traits of slaughter type chicken breeds are derived from whole genome re-sequencing data of 33 representative local chicken breeds in China and related researches, and the SNP loci have the advantages that the SNP loci are high in specificity and high in specificity; the method is suitable for resource evaluation and genetic identification of local chicken varieties and application to economic character genetic improvement of slaughter type broiler chicken varieties. Meanwhile, according to the chicken low-density liquid-phase chip, the target SNP sites can be adjusted by directly increasing or decreasing the probes, and compared with a solid-phase chip, the chicken low-density liquid-phase chip has better flexibility.

Description

technical field [0001] The application belongs to the field of gene chip technology, and relates to a chicken low-density SNP liquid chip based on targeted capture sequencing and its application. Background technique [0002] Single nucleotide polymorphism (Single Nucleotide Polymorphism, SNP), as the latest generation of molecular markers, has been widely used in medical diagnosis, agricultural breeding and other fields due to its advantages of large number, wide distribution, rich polymorphism and easy detection. . With the rapid development of molecular biology and related disciplines, genome sequencing of more and more species has been completed one after another, and high-throughput SNP detection technology has emerged to meet the growing demand for genome-level SNP detection. [0003] At present, high-throughput SNP detection technology mainly adopts two strategies: solid-phase chip and sequencing. Solid-phase chips are based on the complementary hybridization of pro...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6888C12Q1/6837C12N15/11
CPCC12Q1/6888C12Q1/6837C12Q2600/156C12Q2600/124
Inventor 刘一帆束婧婷章明邹剑敏屠云洁单艳菊姬改革巨晓军盛中伟贾晓旭周成浩李云雷
Owner JIANGSU INST OF POULTRY SCI
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