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Auxiliary screening method for indica rice and japonica rice, and special-purpose primer for the same

A technology for indica and japonica rice, which is applied in biochemical equipment and methods, microbial determination/inspection, DNA/RNA fragments, etc., can solve problems such as difficult to study the degree of indica-japonica differentiation in rice, indica-japonica differentiation is not obvious, intermediate, slow, etc. , to achieve the effect of speeding up breeding, low cost and simple operation

Inactive Publication Date: 2008-07-09
CHINA AGRI UNIV
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AI Technical Summary

Problems solved by technology

However, the indica-japonica differentiation of rice is a slow evolutionary process. There are typical indica or japonica varieties in many rice landraces, but there are also intermediate types with indistinct indica-japonica differentiation. It is difficult to use traditional methods for these types It is more difficult to study the degree of indica-japonica differentiation in rice

Method used

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  • Auxiliary screening method for indica rice and japonica rice, and special-purpose primer for the same
  • Auxiliary screening method for indica rice and japonica rice, and special-purpose primer for the same

Examples

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Comparison scheme
Effect test

Embodiment 1

[0020] Example 1. Discovery of different expression patterns of gene LOC_Os11g27730 in indica and japonica rice

[0021] Firstly, the microarray data of indica and japonica rice at different developmental stages and different tissue parts were mined and analyzed. The results showed that the expression level of gene LOC_Os11g27730 was very low or even not expressed in indica rice, while the expression level in japonica rice was extremely high. According to previous research results, the main reason for the difference in gene expression may be the insertion / deletion (InDel) of the base sequence or the regulation of other genes.

Embodiment 2

[0022] Embodiment 2, be used for the design of the primer of auxiliary screening indica rice and japonica rice

[0023] Using the method of comparative genomics, the nucleotide sequence alignment (Blast) analysis of the genome sequence of the gene LOC_Os11g27730 in the indica rice variety 93-11 and the japonica rice variety Nipponbare was first carried out, and it was found that the gene was indeed deleted in 93-11 (figure 1).

[0024] In order to further verify whether there is a genome-level difference between 93-11 and Nipponbare, according to the Nipponbare sequence, primers MVRT1D were designed in the region where the two had genome differences: MVRT1DF (sequence shown in sequence 1 in the sequence table) and MVRT1DR (sequence shown in Sequence 2 in the sequence listing), and the genomic DNA of Nipponbare and 93-11 were used as templates for PCR verification. The reaction system of PCR amplification is: rice genomic DNA template 20ng, Taq Plus DNA polymerase 0.5U, 2.0μl ...

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Abstract

The invention discloses a process of auxiliary screening hsien rice and japonica rice. The process for auxiliary screening hsien rice and japonica rice which is provided by the invention is used to detect whether rice losses ribonucleotide sequence of 122836-124566 from 5' end in AC132003, the detected rice is candidate hsien rice if lost, or the detected rice is candidate japonica rice if not lost. The process for auxiliary screening rice subspecies which is provided by the invention can be used to evaluate hsien rice and japonica rice breeds or local breed in early period, to find out genetic differentiation of hsien rice and japonica rice, and plays important guiding roles for using heterosis of hsien rice and japonica rice and cultivating high-yield and high grade hybridization rice, thereby optimizing hybridized combination, accelerating breeding speed, reducing breeding cost, and having the advantages of simple operation, low cost and short cycle, which is suitable to be popularized and applied, and provides a fast choose method for the evaluation of rice subspecies germplasm.

Description

technical field [0001] The invention relates to a method for assisting in screening indica rice and japonica rice and special primers thereof. Background technique [0002] Cultivated rice is one of the most important food crops in the world. During its domestication history of more than 11,500 years, in order to adapt to different agro-ecological environments, cultivated rice has formed rich genetic diversity and obvious genetic differentiation, resulting in indica rice (Morishima H, Oka HI. Phylogenetic differentiation of cultivated rice. XXII. Numerableevaluation of the Indica-Japonica differentiation. Japanese Journal of Breeding, 1981, 31: 402-413; Glaszmann J C. Isozymes and classification of Asian rice varieties. Theoretical and Applied Genetics, 1987, 74: 21-30; Wang Z Y, Tanksley S D. Restriction fragment length polymorphism in Oryza sativa L. Genome, 1989, 32: 1113-1118; Blair M W, Panaud O, McCouch S R. Inter-simple sequence repeat (ISSR) amplification for analys...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C12N15/11
Inventor 苏震刘凤霞徐文英谭禄宾邸超张振海孙传清薛勇彪
Owner CHINA AGRI UNIV
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