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SNP marker combination for germplasm resource and variety identification of rice and application of SNP marker combination

A variety identification and labeling technology, applied in the fields of bioinformatics and plant genetics and breeding, can solve the problems of inflexible use, many restrictive factors, high price, etc., and achieve the effect of saving detection cost, high detection efficiency and good repeatability

Active Publication Date: 2019-12-03
INST OF CROP SCI CHINESE ACAD OF AGRI SCI +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The traditional gene chips (6K, 50K, 56K, 60K, etc.) produced by Illumina and Affymetrix have many limiting factors in use. They are not only expensive, require special equipment, but also are inflexible in use and have certain restrictions on the number of samples.
Resequencing technology is limited by the depth of sequencing, and cannot accurately and efficiently identify certain specific SNP sites, and the cost is also high. The above two technologies are difficult to meet the requirements for efficient, fast and low-cost identification of rice germplasm resources and varieties

Method used

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  • SNP marker combination for germplasm resource and variety identification of rice and application of SNP marker combination
  • SNP marker combination for germplasm resource and variety identification of rice and application of SNP marker combination
  • SNP marker combination for germplasm resource and variety identification of rice and application of SNP marker combination

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0050] Example 1 The acquisition of rice germplasm resources core and extended SNP site combination

[0051] 1. SNP data of 3000 rice core germplasm resources

[0052] 3,000 accessions of rice (from 89 countries and regions around the world) represent the core germplasm of about 95% diversity of 780,000 accessions of rice germplasm in the world. Through preliminary research, a total of 32M high-quality SNPs were detected in 3,000 accessions of rice germplasm resources and InDels, for a more detailed and accurate description and division of the structure and differentiation of Asian cultivated rice populations. The present inventor downloaded all SNP variation information (3K RG 32mioSNPs) of 3000 resequencing data from http: / / snp-seek.irri.org website to perform omnidirectional and multi-angle dimensionality reduction processing.

[0053] 2. Dimensionality reduction processing and preliminary screening of genome-wide marker loci

[0054] In order to ensure the versatility an...

Embodiment 2

[0071] Example 2 Application of Core and Extended SNP Site Combinations in Identifying Rice Varieties

[0072] In order to verify the distinguishing ability of core loci and extended loci, 432 japonica rice varieties from Northeast China were selected as test materials, and 70 core loci and 200 extended loci (70 core loci included in the 200 extension loci) genotype information. The calculated ability of the core loci to distinguish 432 similar varieties was 96.52%, and the ability of the extended loci to distinguish 432 similar varieties was 97.91%. The undifferentiated samples of the extended loci were unable to distinguish due to the lack of information on the loci.

[0073] The 432 accessions of japonica rice come from popularized varieties bred over the years in Northeast China. The diversity of japonica rice varieties in Northeast China is the lowest among all regional japonica rice varieties. The polymorphic information content (PIC) of japonica rice varieties in Jilin,...

Embodiment 3

[0074] The primer development of embodiment 3 core site and extended site

[0075] In order to make better use of core sites and extended sites to detect samples, multiple PCR primers for all 200 core and extended sites were designed (Table 2 and Table 4), and the specific detection methods are as follows:

[0076] 1. Construction of Multiplex PCR Sequencing Library

[0077] Add 20ng of extracted rice leaf DNA, 10μL of GenoPlexs 3×T PCRMaster Mix (multiple PCR library construction kit from Shijiazhuang Boruidi Biotechnology Co., Ltd.)] and 8μL of primer mixture (each primer concentration ABI 9700 PCR instrument was used for amplification, the amplification program was: 95°C pre-denaturation for 5 minutes; 95°C denaturation for 30 seconds, 60°C annealing for 4 minutes, a total of 20 cycles; 72°C extension for 5 minutes.

[0078] Add 15 μL of Beckmen AMPure XP Beads to the first round of PCR product, pipette up and down evenly, place the 0.2mL PCR tube on the magnetic stand unt...

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Abstract

The invention provides an SNP marker combination for germplasm resource and variety identification of rice and an application of the SNP marker combination. According to the SNP marker combination disclosed by the invention, rice germplasm resources are used as a research target, bioinformatics and a high-flux genotyping means are in comprehensive utilization, excellent marker sites of a completegenome are subjected to omnidirectional multi-angle dimension reduction treatment, and a set of core sites (70 core SNPs) and expansion sites (130 expansion SNPs) is formed, and the site combination is high in detection accuracy, good in repeatability, high in detection efficiency and high in operability. A strong technical support is provided for germplasm resource and variety identity identification, purity identification and variety right confirmation.

Description

technical field [0001] The invention relates to the technical fields of bioinformatics and plant genetic breeding, in particular to a combination of SNP markers for identification of rice germplasm resources and varieties and applications thereof. Background technique [0002] Rice is one of the most important food crops in my country, and the breeding of fine varieties is the source of ensuring food production. Rice germplasm resources are the material basis for new rice variety breeding, biotechnology research and agricultural production. China has abundant rice germplasm resources, but its breeding utilization rate is not high. One of the reasons is that traditional methods cannot accurately identify and evaluate them. Moreover, with the rapid development of my country's rice breeding and seed industry, as well as the continuous introduction of foreign germplasm resources, the number of rice varieties and germplasm resources has increased sharply, which has brought chall...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12N15/11
CPCC12Q1/6895C12Q2600/16C12Q2600/156
Inventor 徐建龙王文生朱亚军陈凯申聪聪赵秀琴
Owner INST OF CROP SCI CHINESE ACAD OF AGRI SCI
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