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SNP molecular marker combination for maize 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 small quantity, inability to meet large-scale commercial breeding, cumbersome operation process, etc., and achieve reduction Labor cost, accurate and reliable genotyping data, good genetic stability and repeatability

Active Publication Date: 2017-08-25
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 combination for maize genotyping and application thereof
  • SNP molecular marker combination for maize genotyping and application thereof
  • SNP molecular marker combination for maize genotyping and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0030] Embodiment 1 is used for the development of the SNP molecular marker combination of maize genotyping

[0031] Whole genome sequencing of 276 maize cultivars was performed using exome sequencing technology. At the same time, the genome sequencing data of 206 maize varieties were sequenced using restriction endonuclease-associated site sequencing technology, and a total of 397 maize materials were sequenced. Combining the resequencing data of other maize varieties in the public database (including the SNP information of 540 maize materials of Professor Yan Jianbing of Huazhong Agricultural University and the SNP information of 503 materials of Hirsch et al. (2014)), the maize B73 genome AGPv3 was used as the reference sequence , analyzed and identified SNP loci, and selected representative, 397 maize materials with a total of 64656 unique SNP markers. Follow the steps below to identify and screen core SNPs.

[0032] 1. Alignment of sequencing reads and maize B73 referen...

Embodiment 2

[0067] Embodiment 2 utilizes KASP technology to detect the method for maize genotype

[0068] According to the core SNP sequence obtained in Example 1, the maize genotype was detected in combination with KASP technology. The specific method is as follows:

[0069] 1. Design KASP primers according to the 50 bp nucleotide sequences flanking each of the 448 SNP sites;

[0070] 2. Select representative corn materials, extract genomic DNA, perform PCR reaction, and verify the availability of KASP primers according to the results of PCR reaction;

[0071] 3. Use the verified KASP primers and SNP high-throughput typing equipment to perform genotyping of the maize material to be tested, so as to identify the genotype of the maize to be tested.

[0072] The sequences of some primers used are listed in Table 2.

[0073] Table 2 partial primer sequence (5'-3')

[0074]

[0075] Step 3 is as follows:

[0076] (1) extracting the genomic DNA of the corn sample to be tested;

[0077...

Embodiment 344

[0083] Example 3 PCA analysis of 448 SNP markers

[0084] For the PCA analysis results of 448 SNP markers, see Image 6 , the paternal group and the maternal group can be clearly divided, which is consistent with the clustering and group structure analysis results.

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Abstract

The invention provides an SNP molecular marker combination for maize genotyping. The SNP molecular marker combination comprises 448 SNP markers, wherein the numbers of the SNP markers are ZmSNP001-ZmSNP448, and nucleotide sequences thereof are as shown in SEQ ID NO:1-448 separately. Molecular marker fingerprint analysis of maize variety resources, genotype identification of offspring of hybrid population, variety authentication, analysis and screening of genetic backgrounds of breeding materials, and correlation analysis of agronomic characters can be carried out by using the SNP molecular marker combination, and the SNP molecular marker combination has wide application prospects.

Description

technical field [0001] The invention relates to the fields of genomics, molecular biology, bioinformatics and molecular plant breeding, in particular to a combination of SNP molecular markers for maize genotyping and its application. Background technique [0002] Whole exome sequencing (WES) and restriction endonuclease-associated site sequencing (RADseq) are more cost-effective genome sequencing methods for SNP discovery in species with complex genomes. [0003] Molecular marker technologies are important tools in molecular breeding. Traditional molecular marker technologies, such as RFLP (Restriction Fragment Length Polymorphism, restriction fragment length polymorphism) and SSR (Simple Sequence Repeat, simple sequence repeat) technology have played an important role in functional genomics research. However, the traditional molecular marker technology has many limitations, such as low throughput, small quantity, cumbersome operation process, and cannot meet the needs of l...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C12N15/11
CPCC12Q1/6895C12Q2600/156
Inventor 邹继军阮详经卢东林刘海波王冰冰刘法新
Owner YUAN LONGPING HIGH TECH AGRI CO LTD
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