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Larimichthys crocea genome breeding chip and application

A large yellow croaker and genome technology, applied in the fields of molecular biology and genome breeding, bioinformatics, and genomics, can solve the problems that restrict the healthy and sustainable development of the large yellow croaker farming industry, the decline of genetic diversity of the cultured population, and the lack of germplasm resources and other issues, to achieve the effects of reduced sequencing costs, improved sequencing throughput, and simple data analysis

Inactive Publication Date: 2021-02-26
XIAMEN UNIV +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the extensive and rapid development of the large yellow croaker farming industry has also accumulated a large number of bottlenecks that restrict the healthy development of the industry, such as: wild large yellow croaker resources are depleting day by day, germplasm resources are scarce, genetic diversity of cultured populations is rapidly declining, and germplasm degradation is serious. Restricting the healthy and sustainable development of large yellow croaker farming industry

Method used

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  • Larimichthys crocea genome breeding chip and application
  • Larimichthys crocea genome breeding chip and application
  • Larimichthys crocea genome breeding chip and application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0042] Example 1 Preparation method of "Ningxin No. 1" large yellow croaker genome breeding chip

[0043] 1. Using Illumina sequencing technology, the whole genome of 82 large yellow croakers from 5 groups was resequenced. The total sequencing volume was 650.5G, and the average sequencing depth of each sample was 11.33X (Table 1). After aligning the sequencing data to the high-quality large yellow croaker reference genome sequence ([19] Chen B H, Zhou Z X, Ke Q Z, Wu Y D, Bai H Q, Pu F, XuP. The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies [J]. Scientific Data, 2019, 6), follow the steps below to identify and screen SNPs.

[0044] Table 1 The amount of sequencing and the number of SNPs in the population

[0045]

[0046] 2. Screen out 9,335,807 high-quality SNP sites from all large yellow croaker sequencing data. High-quality SNP sites are based on the following principles: the SNP sequence is located in a specific seq...

Embodiment 2

[0051] Example 2 Application of "Ningxin No. 1" large yellow croaker genome breeding chip in the detection of large yellow croaker DNA samples

[0052] (1) Genomic DNA extraction from large yellow croaker: Genomic DNA was extracted from large yellow croaker muscles, fin rays, blood and other tissues using the phenol-chloroform method or a DNA extraction kit (DNeasy 96 Blood and Tissue Kit, Qiagen, China) according to the detection requirements.

[0053] (2) DNA sample quality detection: detect with the agarose gel electrophoresis that mass fraction is 1-1.5% (W / W), judge electrophoresis result with gel imaging system (GelDocXRSystem, U.S. Bio-Rad company), guarantee genome DNA integrity is good, and the length of the genomic DNA fragment is greater than 10kb; measure the concentration of genomic DNA with a micro-volume ultraviolet spectrophotometer (Q5000, Quawell, USA) or a similar nucleic acid and protein analyzer, and adjust the DNA concentration to a working concentration o...

Embodiment 3

[0056] Example 3 Application of "Ningxin No. 1" large yellow croaker genome breeding chip in genetic background analysis of large yellow croaker breeding materials

[0057] In order to verify the application of the "Ningxin No. 1" large yellow croaker genome breeding chip in the genetic background analysis of large yellow croaker breeding materials, the present invention was used to analyze samples from Zhoushan (12), Fuding (12), Xiamen (6), The samples of wild large yellow croaker from four locations in Zhanjiang (9) and 27 cultured large yellow croakers from Ningde City Fufa Aquatic Products Co., Ltd. were detected. The detection method refers to Example 2, and the results show that the typing success rate in all groups is average. Above 95% ( figure 2 ). After removing sites with a typing success rate of less than 90% and a minimum allele frequency of less than 2%, the genotype information of 514,726 high-quality SNP sites was obtained. Based on this, the principal comp...

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Abstract

The invention discloses a larimichthys crocea genome breeding chip and application, and relates to the technical field of genomics, bioinformatics, molecular biology and genome breeding. The larimichthys crocea whole-genome breeding chip is named as Ningxin No.1 and is manufactured on the basis of an Affymetrix gene chip technology of Thermofisher Company. Each chip can simultaneously detect 96 samples and contains 591,765 high-quality SNP (single-nucleotide polymorphism) sites, and the SNP sites have nucleotide sequences shown as SEQ ID NO. 1 to SEQ ID NO.591765. The chip can be applied to detecting DNA samples of larimichthys crocea, genetic background analysis can be carried out on larimichthys crocea breeding materials, genotype identification can be carried out on closely-related species of larimichthys, and correlation analysis is carried out on economic traits of the larimichthys crocea. The method has the advantages of high throughput, good repeatability, simple data analysis,low cost of single labeled data and a wide application prospect.

Description

technical field [0001] The invention relates to the technical fields of genomics, bioinformatics, molecular biology and genome breeding, in particular to a large yellow croaker genome breeding chip and its application. Background technique [0002] In recent years, DNA sequencing technology has made breakthroughs. The development of high-throughput DNA sequencing technology has greatly improved genome sequencing efficiency, greatly reduced sequencing time and cost, and brought great convenience to functional genome research. [0003] In terms of aquatic animals, researchers used high-throughput sequencing technology to genotype large yellow croakers for the first time in 2016, and obtained 69,800 single nucleotide polymorphisms through simplified genome sequencing of 500 offspring of group breeding Sex markers (Single Nucleotide Polymorphims, SNPs) were used in Genome-wide Association Studies (GWAS), and finally got the combination of Eicosapentaenoic Acid (EPA) and Docosahe...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6888C40B40/06C40B50/00
CPCC12Q1/6888C40B40/06C40B50/00C12Q2600/156C12Q2600/124
Inventor 徐鹏陈葆华郑炜豪柯巧珍潘滢
Owner XIAMEN UNIV
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