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SNP molecular marker for rice genotyping and application thereof

A molecular marker and genotyping technology, applied in the fields of bioinformatics and molecular plant breeding, molecular biology, and genomics, can solve the problems of cumbersome operation process, small quantity, and low throughput, and achieve broad application prospects and scope Wide, simple effect of data analysis

Active Publication Date: 2018-12-14
YUAN LONGPING HIGH TECH AGRI CO LTD +1
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, traditional molecular marker technology has many limitations, such as low throughput, small quantity, cumbersome operation process, and cannot meet the needs of large-scale commercial breeding

Method used

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  • SNP molecular marker for rice genotyping and application thereof
  • SNP molecular marker for rice genotyping and application thereof
  • SNP molecular marker for rice genotyping and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0038] Example 1 The development process of rice 1200SNP molecular marker

[0039] 3,444,971 SNPs obtained based on the sequencing data of 3000 rice cultivars (http: / / snp-seek.irri.org / index.zul). First, use the Nipponbare repeat region annotation file to delete the SNPs located in the repeat region among the SNPs obtained by resequencing. Then set to filter out the SNP sites with MAF>0.4 in the remaining sites. Set SNP search points at every 15kb site on the genome, and extract all SNPs within the length range of 3kb before and after the search point. Considering the impact of mutations on gene function, use annotation software such as snpEff and VARANNO to analyze the impact of mutations on gene function, and then select according to the degree of impact on gene function, and prioritize SNPs (non-synonymous mutation>promoter region>UTR region >Synonymous mutations>Intron region) are sorted from high to low, and the SNP with the highest priority is selected as the search po...

Embodiment 2

[0040] Embodiment 2 utilizes KASP technology to detect the method for rice genotype

[0041] According to the core SNP markers obtained in Example 1, the detection of rice genotypes was performed in combination with KASP technology. The specific method is as follows:

[0042] 1. Design KASP primers respectively according to the 50 bp nucleotide sequences flanking each of the 1200 SNP sites (Table 2);

[0043] 2. Select representative rice materials, extract genomic DNA, perform PCR reaction, and verify the availability of KASP primers according to the results of PCR reaction;

[0044] 3. Use the verified KASP primers and SNP high-throughput typing equipment to perform genotyping of the rice materials to be tested, so as to identify the genotype of the rice to be tested.

[0045] Step 3 is as follows:

[0046] (1) extracting the genomic DNA of the rice sample to be tested;

[0047] (2) Use the IntelliQube SNP detection system produced by LGC to carry out high-throughput ali...

Embodiment 3

[0067] Example 3 Application of 1200 SNP markers in rice in gene fingerprint analysis of rice germplasm resources

[0068] The present invention uses 1200 SNP markers to analyze 143 rice germplasm resources (numbered LPR001-LPR143, all from Yuan Longping Agricultural High-Tech Co., Ltd., see Table 4). Detect with reference to the method of embodiment 2. KASP technology was used to detect genotypes, and cluster analysis was performed on these 143 varieties, which can be divided into three categories: indica, japonica and intermediate types ( image 3 ), which is in good agreement with the classification according to the phenotype. The results show that the 1200 SNP markers used for rice genotyping in the present invention are very suitable for establishing a gene fingerprint database of rice varieties, which is convenient for comparing the genetic relationship between different varieties and speeding up the breeding process.

[0069] Table 4 List of 143 germplasm resources us...

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Abstract

The invention provides an SNP molecular marker for rice genotyping and application thereof. The molecular marker is selected from at least one of 1200 SNP markers, and their information is shown in Table 1. The SNP molecular marker and the combination thereof can be used for carrying out molecular marker fingerprint analysis on rice germplasm resources, carrying out genotype identification on offspring of rice hybrid populations, identifying authenticity of rice varieties, analyzing and screening genetic backgrounds of rice breeding materials, and carrying out correlation analysis on agronomictraits, thus having a wide application prospect.

Description

technical field [0001] The invention relates to the fields of genomics, molecular biology, bioinformatics and molecular plant breeding, in particular to SNP molecular markers for rice genotyping and applications thereof. Background technique [0002] Rice is one of the most important food crops in my country and plays a pivotal role in ensuring national food security. The source of food production lies in the breeding of fine varieties, while traditional breed selection depends on the phenotype of the plant, and the cultivation of a fine variety often takes as long as a period of more than ten years. In order to improve the efficiency of selection, breeders are constantly exploring the use of molecular marker technologies (Molecular marker technologies) for breeding selection in practice. [0003] Molecular marker technology is an important tool in molecular breeding. Traditional molecular marker technologies, such as RFLP (Restriction Fragment Length Polymorphism, restric...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12N15/11C40B40/06
CPCC12Q1/6895C12Q2600/13C12Q2600/156C40B40/06
Inventor 曾冬冬邹继军卢东林林海艳王凯张嘉楠杨远柱
Owner YUAN LONGPING HIGH TECH AGRI CO LTD
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