Set of core SNP markers suitable for constructing variety nucleic acid fingerprint database of Chinese cabbage and applications of core SNP markers

A technology of Chinese cabbage and varieties, applied in the direction of recombinant DNA technology, microbial determination/inspection, DNA/RNA fragments, etc.

Active Publication Date: 2016-07-20
BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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  • Abstract
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  • Application Information

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Problems solved by technology

However, there are no relevant reports on the construction of DNA fingerprint database and variety identification of head cabbage using SNP marker technology in my country.

Method used

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  • Set of core SNP markers suitable for constructing variety nucleic acid fingerprint database of Chinese cabbage and applications of core SNP markers
  • Set of core SNP markers suitable for constructing variety nucleic acid fingerprint database of Chinese cabbage and applications of core SNP markers
  • Set of core SNP markers suitable for constructing variety nucleic acid fingerprint database of Chinese cabbage and applications of core SNP markers

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Embodiment 1

[0529] Example 1, a set of SNP primers suitable for the construction of Chinese cabbage variety nucleic acid fingerprint database

[0530] 1. 96 sets of SNP core primers

[0531] The present invention designs 96 sets of SNP core primers suitable for the construction of Chinese cabbage variety nucleic acid fingerprint database based on 96 SNP sites, and each set of primers consists of 3 primer sequences. The physical positions, differential bases and nucleotide sequences of 96 sets of SNP core primers of the 96 SNP sites are shown in Table 1. 1-96 in Table 1 represent 96 SNP sites, the linkage group represents the chromosome number, the physical position represents the number of digits on the chromosome corresponding to the SNP site, and the difference base represents the base of the SNP site, such as SNP Locus 1 is located at No. 1248141 on chromosome A01, and its base is T or C.

[0532] The physical positions of the above 96 SNP sites were determined based on the alignment...

Embodiment 2

[0541] Embodiment 2, the application of the SNP primer group that is suitable for Chinese cabbage variety nucleic acid fingerprint database construction

[0542] 1. Genomic DNA extraction

[0543] Genomic DNA of 328 Chinese cabbage varieties to be tested in 53 provinces and cities in Table 2 were extracted respectively. The extraction method can be the conventional CTAB method or the method of rapid and high-throughput extraction of plant genomic DNA. The invention adopts conventional CTAB method to extract genome DNA. Specific steps are as follows:

[0544] First, take 4-5 seeds from each material to accelerate germination for 2-3 days, put the small buds with two green cotyledons into a 2mL centrifuge tube individually, add 1 0.4mm steel ball, write the number clearly, put it into the liquid Freeze in nitrogen for 5-10 minutes, and then crush using a tissue grinder. Add 800 μL of CTAB buffer solution preheated at 65°C to each tube, vortex quickly to mix well, and place in...

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Abstract

The invention discloses a set of core SNP markers suitable for constructing a variety nucleic acid fingerprint database of Chinese cabbage and applications of the core SNP markers. The set of core SNP markers is based on the re-sequencing of 10 core resources of the Chinese cabbage, the whole-genome serial variation of the Chinese cabbage is explored, and the set including 96 groups of SNP core primers suitable for constructing the variety nucleic acid fingerprint database of the Chinese cabbage is screened. The 96 groups of SNP core primers have relatively high polymorphic information content, the minimal allele frequency and the relatively low expectation heterozygosity, and can be used for accurately identifying 329 business varieties, and the genetic typing result is stable. The SNP loci and a detection method provided by the invention can be used for the study including the genetic diversity analysis and the construction of the variety nucleic acid fingerprint database of the Chinese cabbage, and can provide technical support for the establishment of a detection system for the specificity, the consistency and the stability of the new varieties, and the protection for the new varieties. Meanwhile, the high-throughput, low-cost and standardized detection system for the variety of the Chinese cabbage can be established.

Description

technical field [0001] The invention belongs to the field of biotechnology, and in particular relates to a set of core SNP markers suitable for the construction of Chinese cabbage variety nucleic acid fingerprint databases and applications thereof. Background technique [0002] my country is the world's largest producer and consumer of vegetables. In 2014, the sown area of ​​vegetables reached 360 million mu, with a total output of 840 million tons and an output value of more than 1.3 trillion yuan. It has surpassed food crops and become my country's largest planting industry. Chinese cabbage (Brassicarapa L. ssp. Pekinensis) is the vegetable crop with the largest planting area in my country, and plays a decisive role in the vegetable basket project in China. At the same time, Chinese cabbage has become a model plant for genetic research because it is a hybrid crop, has a high recombination rate, rich genetic diversity, and a good basis for genomics research. [0003] With ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12N15/11
CPCC12Q1/6895C12Q2600/156
Inventor 于拴仓苏同兵张凤兰余阳俊张德双赵岫云汪维红卢桂香隋光磊
Owner BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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