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A set of core SNP markers suitable for the construction of non-heading cabbage variety nucleic acid fingerprint database and its application

A technology of head cabbage and varieties, applied in the direction of recombinant DNA technology, microbial measurement/testing, DNA/RNA fragments, etc.

Active Publication Date: 2019-03-08
BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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  • Summary
  • Abstract
  • Description
  • Claims
  • 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 non-heading Chinese cabbage using SNP marker technology in my country.

Method used

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  • A set of core SNP markers suitable for the construction of non-heading cabbage variety nucleic acid fingerprint database and its application
  • A set of core SNP markers suitable for the construction of non-heading cabbage variety nucleic acid fingerprint database and its application
  • A set of core SNP markers suitable for the construction of non-heading cabbage variety nucleic acid fingerprint database and its application

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Embodiment 1

[0358] Example 1, a set of SNP primers suitable for the construction of non-heading Chinese cabbage variety nucleic acid fingerprint database

[0359] 1. 62 sets of SNP core primers

[0360] The present invention designs 62 sets of SNP core primers suitable for constructing the nucleic acid fingerprint database of non-heading cabbage varieties based on 62 SNP sites, and each set of primers consists of 3 primer sequences. The physical positions, differential bases and nucleotide sequences of the 62 sets of SNP core primers of the 62 SNP sites are shown in Table 1. 1-62 in Table 1 represent 62 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 Site 1 is located at position 4878711 on chromosome A01, and its base is T or C.

[0361] The physical positions of the above-mentioned 62 SNP sites ar...

Embodiment 2

[0369] Embodiment 2, the application of the SNP primer group that is suitable for non-heading Chinese cabbage variety nucleic acid fingerprint database construction

[0370] 1. Genomic DNA extraction

[0371] Genomic DNA of 124 non-heading 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:

[0372] 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 t...

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Abstract

The invention discloses a core SNP (single nucleotide polymorphism) marker system suitable for building a variety nucleic acid fingerprint database of non-heading Chinese cabbage and its application. Based on re-sequencing of 10 Chinese cabbage core resources, sequence variation of a whole genome of Chinese cabbage is explored, and a system of 62 groups of SNP core primers suitable for building a variety nucleic acid fingerprint database of non-heading Chinese cabbage is screened out. The 62 groups of SNP core primers have higher polymorphism information quantity, minimum allele frequency and lower expected heterozygosity and can accurately identify 124 commercial varieties, with stable genotyping results. The SNP sites and detection method provided by the invention are applicable to the research on genetic diversity of non-heading Chinese cabbage, building of a variety nucleic acid fingerprint base and the like, and technical support is provided for the building of a detection system for specificity, uniformity and stability of new varieties and for the protection of new varieties; meanwhile, a high-throughput, low-cost and standard detection system for non-heading Chinese cabbage varieties 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 constructing a nucleic acid fingerprint database of non-heading Chinese cabbage varieties and an application thereof. Background technique [0002] Non-heading cabbage, commonly known as green cabbage, Chinese cabbage, or rapeseed, originated in China and has gradually become a worldwide vegetable crop. Chinese cabbage likes to be cold and cold, and is more resistant to low and high temperatures. It can be planted and marketed all year round, and occupies an extremely important position in the annual supply of vegetables. In recent years, with the expansion of non-heading cabbage planting area year by year, the number of varieties has also increased dramatically. The frequent use of a small number of backbone inbred lines makes the genetic basis of new varieties increasingly narrow, the similarity between varieties is high, and ther...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6895C12N15/11
CPCC12Q1/6895C12Q2600/13C12Q2600/156
Inventor 于拴仓苏同兵陈娟张凤兰汪维红余阳俊张德双赵岫云
Owner BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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