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CN-115029466-B - Application of SNP molecular marker related to rice bacterial leaf blight resistance and primer composition thereof

CN115029466BCN 115029466 BCN115029466 BCN 115029466BCN-115029466-B

Abstract

The invention discloses an application of SNP molecular markers related to identification or auxiliary identification of rice bacterial leaf blight resistance and a primer composition thereof. The method comprises the steps of detecting polymorphism or genotype (allele) of SNP locus in rice genome to be detected, and identifying or assisting in identifying bacterial leaf blight resistance of rice according to the genotype, wherein the SNP locus is a locus on chromosome 5 of rice, the nucleotide type of the SNP locus is A or G, and the SNP locus is nucleotide at position 30 of sequence 4 in a sequence table. The method can be used for predicting the resistance of rice to bacterial leaf blight and carrying out rice breeding. The substances for detecting the SNP locus polymorphism and the genotype can be combined with other substances (such as substances for detecting single nucleotide polymorphism or genotype of other molecular markers related to rice anti-white leaf blight) to prepare and identify rice anti-white leaf blight variety products.

Inventors

  • ZHOU YONGLI
  • LI JIANMIN

Assignees

  • 中国农业科学院作物科学研究所

Dates

Publication Date
20260508
Application Date
20220414

Claims (7)

  1. 1. The application of the substance for detecting the polymorphism or genotype of SNP locus in rice genome, (1) Identifying or assisting in identifying bacterial leaf blight resistance of rice; (2) Screening or breeding single plants or lines or varieties of rice with bacterial leaf blight resistance; (3) Screening or breeding single plants or strains or varieties of rice with bacterial leaf blight; (4) Preparing a product for identifying or assisting in identifying rice bacterial leaf blight resistance; (5) Preparing a product for screening or breeding single plants or lines or varieties of rice with bacterial leaf blight resistance; (6) Preparing a product for screening or breeding single plants or lines or varieties of rice with bacterial leaf blight; the SNP locus is a locus on a rice chromosome 5, the nucleotide type of the SNP locus is A or G, and the SNP locus is the 30 th nucleotide of a sequence 4 in a sequence table.
  2. 2. The method according to claim 1, wherein the substance is D1), D2) or D3): D1 The substance is a primer composition for amplifying rice genome DNA fragments including the SNP locus; d2 The substance is a PCR reagent containing the primer composition of D1); d3 The substance is a kit containing the primer composition of D1) or the PCR reagent of D2).
  3. 3. The method according to claim 2, wherein the primer composition comprises primer A, primer B and primer C; the primer A is a single-stranded DNA molecule with a nucleotide sequence of a sequence 1 in a sequence table or a single-stranded DNA with a nucleotide sequence of 22 th-40 th positions of the sequence 1 in the sequence table; The primer B is a single-stranded DNA molecule with a nucleotide sequence of sequence 2 in a sequence table or a single-stranded DNA with a nucleotide sequence of 22 th-40 th positions of sequence 2 in the sequence table; the nucleotide sequence of the primer C is a single-stranded DNA molecule of a sequence 3 in a sequence table.
  4. 4. The method for identifying or assisting in identifying the bacterial leaf blight resistance of the rice is characterized by comprising the steps of detecting the genotype of SNP loci in a genome of the rice to be detected, identifying or assisting in identifying the bacterial leaf blight resistance of the rice according to the genotype, wherein the SNP loci are loci on chromosome 5 of the rice, the nucleotide type of the SNP loci is A or G, the 30 th nucleotide of a sequence 4 in a sequence table, the genotype of the SNP loci is AA, AG or GG, the GG is homozygous for the SNP loci to G, the AA is homozygous for the SNP loci to A, and the AG is heterozygous for the SNP loci to A and G; The identification or auxiliary identification of the bacterial leaf blight resistance of the rice is realized by any one of the following modes: 1) The rice to be detected with the genotype of AA or AG of the SNP locus is or is candidate to be rice resisting bacterial leaf blight, 2) The rice to be detected with the genotype GG of the SNP locus is or is candidate to be rice with bacterial leaf blight; 3) The bacterial leaf blight resistance of the rice to be detected with the genotype of the SNP locus being AA or AG is higher than that of the rice to be detected with the genotype of the SNP locus being GG, and the bacterial leaf blight resistance of the rice to be detected with the genotype of the SNP locus being AA is higher than that of the rice to be detected with the genotype of the SNP locus being AG.
  5. 5. Use of the method of claim 4 in rice breeding.
  6. 6. The rice breeding method is characterized in that the method is M1 or M2: m1, the method comprises detecting genotype of the SNP locus in claim 1 in a rice genome, selecting rice with genotype of the SNP locus of AA or AG as a parent for breeding, wherein AA is homozygous type of the SNP locus of A, AG is heterozygous type of the SNP locus of A and G, and the aim of breeding is to breed rice with bacterial leaf blight resistance; M2, the method comprises detecting the genotype of the SNP locus in claim 1 in a rice genome, selecting rice with the genotype of the SNP locus as a parent for breeding, wherein GG is homozygous with the SNP locus as G, and the purpose of breeding by the method is to breed rice with bacterial leaf blight.
  7. 7. The application of the DNA molecule with the nucleotide sequence of the sequence 4 in the sequence table in any one of the following, (1) Identifying or assisting in identifying bacterial leaf blight resistance of rice; (2) Screening or breeding single plants or lines or varieties of rice with bacterial leaf blight resistance; (3) Screening or breeding single plants or strains or varieties of rice with bacterial leaf blight; (4) Preparing a product for identifying or assisting in identifying rice bacterial leaf blight resistance; (5) Preparing a product for screening or breeding single plants or lines or varieties of rice with bacterial leaf blight resistance; (6) And (3) preparing a product for screening or breeding single plants or lines or varieties of rice with bacterial leaf blight.

Description

Application of SNP molecular marker related to rice bacterial leaf blight resistance and primer composition thereof Technical Field The invention belongs to the technical field of gene biology, and particularly relates to application of SNP molecular markers related to bacterial leaf blight resistance of rice and a primer composition thereof. Background Bacterial leaf blight of rice caused by Xanthomonas oryzae pv. Oryzae (Xoo) is an important bacterial disease in global rice farming. For a long time, breeding and planting disease-resistant varieties play an important role in preventing and controlling bacterial leaf blight. The development of molecular markers for detecting bacterial leaf blight resistance of rice has important application value in screening bacterial leaf blight-resistant rice germplasm resources and rapidly identifying bacterial leaf blight-resistant plants in the breeding process. KASP (Kompetitive Allele-SPECIFIC PCR, competitive allele-specific PCR) specifically recognizes gene loci through fluorescent probes to achieve genotyping effect, and can be used for detecting SNP loci and InDel loci. Compared with SSR, RFLP, inDel and other molecular markers, the KASP marker has the characteristics of quick detection, low cost, easy large-scale application and the like. KASP marking does not need to be typed according to the size of DNA fragments, can get rid of the defects of relatively complicated steps and low flux of the traditional gel electrophoresis detection method, and is suitable for a high flux molecular detection platform. Therefore, the identification of the functional SNP locus related to the bacterial leaf blight resistance of rice, and the development of the bacterial leaf blight resistance KASP molecular marker of rice suitable for a high-flux molecular detection platform have important application value for improving the breeding efficiency and the breeding level of rice in China. Disclosure of Invention The invention aims to solve the problem of how to identify or assist in identifying rice bacterial leaf blight resistance. In order to solve the technical problems, the invention firstly provides the application of a substance for detecting the polymorphism or genotype of SNP in rice genome in any one of the following, (1) Identifying or assisting in identifying bacterial leaf blight resistance of rice; (2) Screening or breeding single plants or lines or varieties of rice with bacterial leaf blight resistance; (3) Screening or breeding single plants or strains or varieties of rice with bacterial leaf blight; (4) Breeding rice; (5) Preparing a product for identifying or assisting in identifying rice bacterial leaf blight resistance; (6) Preparing a product for screening or breeding single plants or lines or varieties of rice with bacterial leaf blight resistance; (7) Preparing a product for screening or breeding single plants or lines or varieties of rice with bacterial leaf blight; (8) Preparing a rice breeding product; the SNP locus is a locus on a rice chromosome 5, the nucleotide type of the SNP locus is A or G, and the SNP locus is the 30 th nucleotide of a sequence 4 in a sequence table. The Japanese sunny genome sequence is taken as a reference genome, and the SNP locus is 15471465bp of a rice No. 5 chromosome (specifically, the 30 th locus of a sequence 4 in a sequence table). The invention also provides a method for identifying or assisting in identifying bacterial leaf blight resistance of rice, which comprises detecting genotypes of SNP loci in rice genomes to be detected, identifying or assisting in identifying bacterial leaf blight resistance of rice according to the genotypes, wherein the genotypes are AA, AG or GG, the GG is homozygous with the SNP loci being G, the AA is homozygous with the SNP loci being A, and the AG is heterozygous with the SNP loci being A and G. Alternatively, according to the above method, the identifying or assisting in identifying bacterial leaf blight resistance of rice is any one of the following ways: (1) The rice to be detected with the genotype of AA or AG of the SNP locus is or is candidate to be rice resisting bacterial leaf blight, (2) The rice to be detected with the genotype GG of the SNP locus is or is candidate to be rice with bacterial leaf blight; (3) The bacterial leaf blight resistance of the rice to be detected with the genotype of the SNP locus being AA or AG is higher than that of the rice to be detected with the genotype of the SNP locus being GG. As an embodiment, the method for identifying or assisting in identifying bacterial leaf blight resistance of rice may comprise the steps of: (1) Taking genome DNA of rice to be detected as a template, and adopting a primer composition to carry out KASP, wherein the primer composition consists of a primer A, a primer B and a primer C; the primer A is a single-stranded DNA molecule with a nucleotide sequence of a sequence 1 in a sequence table or a single-stranded DNA with a