SNP locus primer combination for identifying pinus bungeana germplasm resources and application

A technique of white bark pine and locus, which is applied in the field of identification of white bark pine germplasm resources

Active Publication Date: 2021-01-15
INST OF FORESTRY CHINESE ACAD OF FORESTRY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, there is still no report on the use of SNP

Method used

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  • SNP locus primer combination for identifying pinus bungeana germplasm resources and application
  • SNP locus primer combination for identifying pinus bungeana germplasm resources and application
  • SNP locus primer combination for identifying pinus bungeana germplasm resources and application

Examples

Experimental program
Comparison scheme
Effect test

preparation example Construction

[0148] The preparation method of the above kit includes packaging each primer in any one of the above primer sets separately.

[0149] In the fourth aspect, the present invention provides the above-mentioned DNA fingerprint database of Pine bark germplasm resources based on core SNP markers. The DNA fingerprint database includes: the genotypes of the standard Pine bark germplasm resources at the above 36 SNP sites.

[0150] The above-mentioned standard pine germplasm resources are selected from the following 137 pine germplasm resources:

[0151] Jingxi No. 1, Jingxi No. 11, Jingxi No. 12, Jingxi No. 13, Jingxi No. 14, Jingxi No. 15, Jingxi No. 2, Jingxi No. 3, Jingxi No. 4, Jingxi No. 5, Jingxi No. 6, Jingxi No. 7, Jingxi No. 8, Jingxi No. 9, Penxian, Ruiwang, Nine Trees, Ganjing No. 1, Ganjing No. 10, Ganjing No. 11, Ganjing No. 12, Ganjing No. 13, Ganjing No. 14, Ganjing No. 15, Ganjing No. 2, Ganjing No. 3, Ganjing No. 4, Ganjing No. 5, Ganjing No. 6, Ganjing No. 7, Ganji...

Embodiment 1

[0169] Acquisition of Loci and Primer Combinations for Identification of Pine Pine Germplasm Resources

[0170] 1. Discovery of 36 core SNP sites

[0171] The present invention uses an Illumina sequencer, based on the SLAF sequencing (Specific-Locus Amplified Fragment Sequencing) data of 150 pine germplasm resources, and finally obtains 36 SNP sites. These 150 germplasm resources of Pine bark are from different provinces in China, with high genetic diversity and extremely representative genetics.

[0172] SNP site screening criteria are as follows: (1) SLAF sequencing, based on the no-reference genome method, obtained 20,911 SNPs, removed SNP sites with MAF0.3, and heterozygosity rate greater than 0.3, and obtained 7,795 SNPs. (2) Extract the flanking sequence, remove the SNP located within 20bp of the head and tail of the two reads, and intercept 20-40bp from the upstream and downstream according to the actual situation, and obtain 3,843 SNPs. (3) Design Kaspar platform pri...

Embodiment 2

[0190] This example is a test of the effectiveness of the SNP primer combination developed in Example 1, and also the construction of a DNA fingerprint database of Pine bark germplasm resources based on the above-mentioned 36 core SNP markers.

[0191] The 137 pine germplasm resources for testing in the present embodiment are common excellent germplasm resources, and the specific circumstances are as follows in Table 3:

[0192] Table 3: Sources of Germplasm Resources

[0193]

[0194]

[0195] 1. Obtaining the genomic DNA of the tested Pine bark germplasm resources

[0196] Genomic DNA of 137 coniferous needles of pine germplasm resources tested was extracted by CTAB method, and genomic DNA of pine germplasm resources tested was obtained.

[0197] The operation of the above CTAB method is as follows:

[0198] (1) The needles of the above-mentioned 137 pine germplasm resources at the mature stage were harvested, and placed in a freeze dryer (CoolSafe 55-4) for dehydrat...

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Abstract

The invention belongs to the field of molecular markers and detection thereof, and particularly relates to a core SNP locus and primer combination for identifying the authenticity of pinus bungeana germplasm, a DNA fingerprint database based on SNP loci, a database construction method, a method for identifying the authenticity of the pinus bungeana germplasm based on the SNP loci and application.The SNP loci are selected from any one to 36 of the first SNP locus to the thirty-sixth SNP locus. The DNA fingerprint database for identifying the authenticity of the pinus bungeana germplasm based on high-throughput sequencing is established and can be used for carrying out early identification on the pinus bungeana germplasm in tissues or organs such as seeds, seedlings and leaves, and technical support is provided for pinus bungeana germplasm resource protection. The method not only can be used for identifying unknown pinus bungeana germplasm, but also can be used for identifying the authenticity of known pinus bungeana germplasm. The method has the advantages of high flux, accuracy, low cost, simplicity in operation, manpower and material resource saving and the like, and has very wide application prospects.

Description

technical field [0001] The invention belongs to the field of molecular markers and detection thereof, and specifically relates to a core SNP site for identifying germplasm resources of Pinus chinensis, a combination of primers, a DNA fingerprint database based on the SNP site, a database construction method, and a germplasm of Pinus chinensis based on the SNP site Identification methods and applications of resources. Background technique [0002] White bark pine, Latin scientific name Pinus bungeana Zucc.ex Endl, also known as white bone pine, three-needle pine, ginkgo pine, tiger bark pine, and dragon pine, is a unique native tree species in my country with a long history of cultivation. It belongs to the middle conifer species of the genus Pinus, and is naturally distributed in Shanxi, Shaanxi, Gansu, Henan, Sichuan, Hubei and other places. White bark pine has high ecological value and economic value. It has strong cold resistance, drought resistance and barren resistanc...

Claims

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Application Information

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IPC IPC(8): C12N15/11C12Q1/6895C12Q1/6869C12Q1/6858
CPCC12Q1/6895C12Q1/6869C12Q1/6858C12Q2600/13C12Q2600/156C12Q2535/122C12Q2531/113
Inventor 李斌郑勇奇林富荣郭文英黄平
Owner INST OF FORESTRY CHINESE ACAD OF FORESTRY
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