SNP (simple nucleotide polymorphism) modular marker for rice low cadmium accumulation gene OsHMA3 and application thereof

A technology of molecular markers and low accumulation, applied in the field of molecular biology, can solve the problems of difficult and accurate determination of phenotypic values, few SNP markers, few main effect genes, etc., to achieve accurate prediction of cadmium content in rice grains, easy operation, and application value strong effect

Active Publication Date: 2017-03-08
HUAZHI RICE BIO TECH CO LTD
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  • Abstract
  • Description
  • Claims
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AI Technical Summary

Problems solved by technology

[0004] Since the traits of cadmium content in rice grains are controlled by quantitative traits, and the phenotypic values ​​are not easy to be accurately determined, there are very few main effect genes cloned at present, and there are relatively few SNP markers designed for the main effect genes.
In the prior art, the SNP molecular markers for the trait of rice grain cadmium content are basically designed based on QTL, so such SNP markers are of little value in actual breeding

Method used

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  • SNP (simple nucleotide polymorphism) modular marker for rice low cadmium accumulation gene OsHMA3 and application thereof
  • SNP (simple nucleotide polymorphism) modular marker for rice low cadmium accumulation gene OsHMA3 and application thereof
  • SNP (simple nucleotide polymorphism) modular marker for rice low cadmium accumulation gene OsHMA3 and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0032] Example 1 Development of SNP Molecular Marker of Rice Low Cadmium Accumulation Gene OsHMA3

[0033] According to literature data, the rice OsHMA3 gene was mapped to the physical location on chromosome 7: 7405745-7409553 interval. The gene interval was expanded by 50kb to both sides, and SNP sites were extracted based on 3,000 rice resequencing data from the International Rice Institute, and selected according to the PIC value and whether there were other SNP sites in the 50 bp around the SNP site. The selected SNP sites were designed with primers using BatchPrimer3. For these SNP markers, KASP reaction verification was performed on two gene donor materials of rice varieties Nipponabre and Sasanishiki containing the OsHMA3 gene, two rice varieties of Chokokoku and Habataki that were determined not to have the function of the OsHMA3 gene, and 19 other high-cadmium and low-cadmium materials , to select SNP markers with good co-segregation and amplification effects with th...

Embodiment 2

[0045] Example 2 Application of SNP Molecular Marker of Rice Low Cadmium Accumulation Gene OsHMA3

[0046] 1. Extract the genomic DNA of the rice variety to be tested

[0047] 2. Amplify the nucleotide fragment containing the SNP site

[0048] For the SNP site screened in Example 1, according to the primers of TagSNP-K_070520 (see Table 2), using genomic DNA as a template, amplify the nucleotide fragment where the SNP to be tested is located, as shown in SEQ ID NO.1 Show. The SNP site is located at 22bp of the PCR amplified fragment, where the base polymorphism is A or G.

[0049] KASP response tests were performed on the LGC SNPline genotyping platform. Add 20ng of DNA sample into the microwell reaction plate, add the KASP reaction mixture after drying, the reaction system is shown in Table 5.

[0050] Table 5 Reaction system for KASP detection

[0051] Final concentration Volume (μL) 100UM Primer C 0.42UM 0.0125 100UM Primer X 0.17UM 0.0050...

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Abstract

The invention relates to an SNP (simple nucleotide polymorphism) modular marker for rice low cadmium accumulation gene OsHMA3; a detection site of the marker is at base 7431781 of chromosome 7 of rice. The invention also provides a primer set and method for detecting the SNP marker; the primer set has a sequence shown as in SEQ ID NO. 2-4. The SNP molecular marker and the primer set and method have the advantages that the SNP molecular marker is suitable for predicting the cadmium content of rice kernels before rice not bearing fruits, and suitable for accurate screening, such that breeding of low-cadmium-content varieties of rice is significantly promoted; the detection method is accurate and reliable and is simple to perform; the detection of SNP sites for rice OsHMA3 gene provides scientific basis for the breeding or improvement of low-cadmium-content kernel varieties of rice.

Description

technical field [0001] The invention relates to the technical field of molecular biology, in particular to a SNP molecular marker of rice low cadmium accumulation gene OsHMA3 and a method for detecting rice low cadmium accumulation gene OsHMA3. Background technique [0002] Traditional pedigree breeding is the most common rice breeding method in recent years, and a large number of high-yield and high-quality rice varieties have been born as a result. However, the traditional breeding method of hybridization combined with phenotype often needs to increase the backcross population because of the inaccurate grasp of the phenotype at the macro level, which greatly increases the workload and cost of breeding. Molecular marker-assisted breeding can track target traits on a genetic basis, and select individual plants containing the target gene for crossing (backcrossing). cost. SNP is the abbreviation of single nucleotide polymorphism, which refers to the variation of a single nu...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12N15/11
Inventor 姚文元李继明郑秀婷彭佩贺治洲李卫国肖金华王冰冰
Owner HUAZHI RICE BIO TECH CO LTD
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