Rice SNP markers and applications thereof

Abstract

The application discloses a SNP marker and application thereof. The SNP marker is T or C at the 35th base from the 5' end of the nucleotide sequence shown in SEQ ID NO:1, or the SNP marker is A or G at the 46th base from the 5' end of the nucleotide sequence shown in SEQ ID NO:1. The SNP marker is closely related to the rice variety, and can be effectively used for qualitative or quantitative detection of the rice variety.

Claims

1. A method for identifying rice varieties, characterized in that, The method includes: (1) Detect the first SNP molecular marker and the second SNP molecular marker in the rice genome, wherein the SNP site of the first SNP molecular marker is located at position 35 from the 5' end of the nucleotide sequence shown in SEQ ID NO: 1, and the polymorphism is T or C, and the SNP site of the second SNP molecular marker is located at position 46 from the 5' end of the nucleotide sequence shown in SEQ ID NO: 1, and the polymorphism is A or G; (2) Identify rice varieties based on the genotypes of the first SNP molecular marker and the second SNP molecular marker. If the genotype of the first SNP molecular marker is TT and the genotype of the second SNP molecular marker is AA, the variety is identified as Jihong 6. Otherwise, it is identified as non-Jihong 6.

2. The method as described in claim 1, characterized in that, The detection includes performing PCR.

3. The method as described in claim 1, characterized in that, The detection method is quantitative real-time PCR or HRM detection.

4. A method for detecting the content of Jihong No. 6 in a sample, characterized in that, The method includes: (1) The step of amplifying the sequence containing the first SNP molecular marker and the second SNP molecular marker in the rice genome, wherein the SNP site of the first SNP molecular marker is located at position 35 from the 5' end of the nucleotide sequence shown in SEQ ID NO: 1, and the polymorphism is T or C, and the SNP site of the second SNP molecular marker is located at position 46 from the 5' end of the nucleotide sequence shown in SEQ ID NO: 1, and the polymorphism is base A or G; (2) The content of Jihong 6 is determined based on the amplification results of the first SNP molecular marker and the second SNP molecular marker, wherein the amplification results of the first SNP molecular marker genotype being TT and the second SNP molecular marker genotype being AA indicate the content of Jihong 6. The amplification is quantitative real-time PCR. The method further includes using 2 -ΔΔCT The method determines the content of Jihong No. 6; the 2 -ΔΔCT The methods include: Quantitative real-time PCR detects the CT values ​​of probes that identify the first and second SNP molecular markers and the CT value of probes that identify the endogenous reference. The difference between the two values ​​is the sample ΔCT. The sample ΔCT is then subtracted from the control ΔCT to obtain ΔΔCT. The control is either 100% Jihong 6 or 100% non-Jihong 6 sample. The negative of ΔΔCT is then squared to obtain the relative content value, which is used to quantitatively determine the presence of Jihong 6 and non-Jihong 6 in the sample.

5. The uses of reagents for detecting the first SNP molecular marker and the second SNP molecular marker in the rice genome in identifying rice varieties or detecting the content of Jihong 6 in samples, wherein... The SNP site of the first SNP molecular marker is located at position 35 from the 5' end of the nucleotide sequence shown in SEQ ID NO: 1, with a polymorphism of T or C. The SNP site of the second SNP molecular marker is located at position 46 from the 5' end of the nucleotide sequence shown in SEQ ID NO: 1, with a polymorphism of A or G. If the genotype of the first SNP molecular marker is TT and the genotype of the second SNP molecular marker is AA, it is identified as Jihong 6; otherwise, it is identified as non-Jihong 6. The method for detecting the content of Jihong 6 in a sample includes: quantitative real-time PCR detection of the CT value of the probe recognizing the first SNP molecular marker and the second SNP molecular marker and the CT value of the probe recognizing the endogenous reference, subtracting the two to obtain the sample ΔCT, subtracting the sample ΔCT from the control ΔCT to obtain ΔΔCT, wherein the control is a 100% Jihong 6 or 100% non-Jihong 6 sample, and raising the negative number of ΔΔCT to the square to obtain the relative content value, which is used for quantitative determination of Jihong 6 and non-Jihong 6 in the sample.

6. The use of reagents for detecting the first SNP molecular marker and the second SNP molecular marker in the rice genome in the preparation of kits for identifying rice varieties or detecting the content of Jihong 6 in samples, wherein, The SNP site of the first SNP molecular marker is located at position 35 from the 5' end of the nucleotide sequence shown in SEQ ID NO: 1, with a polymorphism of T or C. The SNP site of the second SNP molecular marker is located at position 46 from the 5' end of the nucleotide sequence shown in SEQ ID NO: 1, with a polymorphism of A or G. If the genotype of the first SNP molecular marker is TT and the genotype of the second SNP molecular marker is AA, it is identified as Jihong 6; otherwise, it is identified as non-Jihong 6. The method for detecting the content of Jihong 6 in a sample includes: quantitative real-time PCR detection of the CT value of the probe recognizing the first SNP molecular marker and the second SNP molecular marker and the CT value of the probe recognizing the endogenous reference, subtracting the two to obtain the sample ΔCT, subtracting the sample ΔCT from the control ΔCT to obtain ΔΔCT, wherein the control is a 100% Jihong 6 or 100% non-Jihong 6 sample, and raising the negative number of ΔΔCT to the square to obtain the relative content value, which is used for quantitative determination of Jihong 6 and non-Jihong 6 in the sample.

7. The use according to claim 5 or 6, characterized in that, The reagent contains primers and probes.

Images