Sika deer whole genome SNP molecular marker combination, SNP chip and application

A molecular marker and genome-wide technology, applied in DNA/RNA fragments, recombinant DNA technology, microbial measurement/inspection, etc., can solve problems that are difficult to meet the needs of sika deer population typing and provenance identification, and achieve maximum utilization value, The effect of a large amount of useful information and rich variations

Active Publication Date: 2022-04-08
INST OF SPECIAL ANIMAL & PLANT SCI OF CAAS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, CN112210611A patent discloses 4 molecular markers for identifying the Hokkaido subspecies of sika deer, and CN107447020B patent discloses 24 molecular markers for identifying sika deer individuals. Although these existing patents can be used to identify sika deer individuals to a certain extent, they only 28 loci are difficult to meet the needs of typing and provenance identification of sika deer population

Method used

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  • Sika deer whole genome SNP molecular marker combination, SNP chip and application
  • Sika deer whole genome SNP molecular marker combination, SNP chip and application
  • Sika deer whole genome SNP molecular marker combination, SNP chip and application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0157] This example provides a method for the development and screening of sika deer 40KSNP molecular marker combinations.

[0158] (1) Data selection was performed on 178 GWAS loci, resequencing data of 50 sika deer samples and locus data of 9 male deer samples.

[0159] 178 GWAS loci were retained; 155,280 loci were screened out from the resequencing data of 50 sika deer samples according to NA<10%, heterozygosity rate<15%, and MAF≥0.1; 155,280 loci were combined with 9 male deer samples The intersection of the loci, and in the intersection screening, the MAF is the highest in the male deer, and only one sample is allowed to be NA at most, a total of 60K background loci.

[0160] (2) Carry out site evaluation.

[0161] Through the above selection process, we finally obtained 178 GWAS sites and 60K background sites, a total of 60,178 sites for subsequent probe design evaluation.

[0162] Designed probes and coverage reference figure 1 As shown, the probe design section cov...

experiment example 1

[0166] The 12 Northeast deer samples were detected, and the specific methods were: library construction, hybrid capture, library quality inspection and sequencing analysis.

[0167] 1. Build the library.

[0168] DNA library construction was carried out according to the method of GenoBaits library construction kit.

[0169] 2. Library hybrid capture

[0170] The genotype of the target sample at the 40K SNP site was determined by liquid gene chip.

[0171] (1) DNA hybridization:

[0172] Take 500 ng of the sample genomic DNA sequencing library that has been constructed, add 5 μL GenoBaits Block I and 2 μL GenoBaits Block II, place it on the Eppendorf Concentrator plus (Eppendorf Company) vacuum concentrator, and evaporate to dryness at a temperature ≤ 70 ° C to dry powder. Add 8.5 μL GenoBaits 2×Hyb Buffer, 2.7 μL GenoBaits Hyb Buffer Enhancer, 2.8 μL Nuclease-Free Water to the dry powder tube, pipette to mix, place on ABI 9700 PCR instrument at 95°C for 10 minutes, then tak...

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PUM

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Abstract

The invention discloses a sika deer whole genome SNP molecular marker combination, an SNP chip and application, and relates to the technical field of molecular marker development. Comprising 43316 SNP molecular markers. According to the SNP molecular marker combination, when the sika deer sample data volume is 1.5 Gb, the site detection rate is 95% or above, and it is indicated that the SNP molecular marker combination is large in useful information amount and has high utilization value. In addition, the SNP molecular marker combination developed by the invention is uniformly distributed on 33 chromosomes of a sika deer whole genome, so that the accuracy of related research application can be improved.

Description

technical field [0001] The invention relates to the technical field of molecular marker development, in particular to a sika deer genome-wide SNP molecular marker combination, a SNP chip and its application. Background technique [0002] Single nucleotide polymorphism (SNP) refers to: DNA sequence polymorphism caused by a single nucleotide variation at the genome level. SNP markers have the advantages of high accuracy, rich variation, and simple operation, and are widely used in animal individual identification and provenance identification. At present, CN112210611A patent discloses 4 molecular markers for identifying the Hokkaido subspecies of sika deer, and CN107447020B patent discloses 24 molecular markers for identifying sika deer individuals. Although these existing patents can be used to identify sika deer individuals to a certain extent, they only The 28 loci are difficult to meet the needs of typing and provenance identification of the sika deer population. [0003...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6888C12N15/11
CPCY02P60/87
Inventor 王桂武杨福合郑军军刘琳玲张禾垟周雅李浩东
Owner INST OF SPECIAL ANIMAL & PLANT SCI OF CAAS
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