CN110358855B - SNP (Single nucleotide polymorphism) marker 5-156 of pepper phytophthora disease resistance gene as well as specific primer and application thereof - Google Patents

SNP (Single nucleotide polymorphism) marker 5-156 of pepper phytophthora disease resistance gene as well as specific primer and application thereof Download PDF

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CN110358855B
CN110358855B CN201910627068.5A CN201910627068A CN110358855B CN 110358855 B CN110358855 B CN 110358855B CN 201910627068 A CN201910627068 A CN 201910627068A CN 110358855 B CN110358855 B CN 110358855B
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张正海
曹亚从
于海龙
王立浩
张宝玺
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Abstract

The invention belongs to the technical field of agricultural biology, and particularly relates to a pepper phytophthora disease resistance gene SNP marker 5-156, and a specific primer and application thereof. The invention determines the SNP locus related to the resistance shape of the pepper phytophthora blight in the pepper genome, and by applying the SNP locus, the pepper phytophthora blight resistance gene can be judged only by detecting the DNA of a pepper plant in the seedling stage, so that the SNP locus can be widely applied to molecular marker assisted breeding.

Description

SNP (Single nucleotide polymorphism) marker 5-156 of pepper phytophthora blight resistance gene as well as specific primer and application thereof
Technical Field
The invention belongs to the technical field of agricultural biology, and particularly relates to a pepper phytophthora blight resistance gene SNP marker 5-156, and a specific primer and application thereof.
Background
The Phytophthora capsici is one of main diseases affecting pepper production, and is caused by Phytophthora capsici Leonian (Phytophthora capsici Leonian), and after the pepper is infected by the Phytophthora capsici, symptoms such as root system necrosis, stem, leaf and fruit decay and the like can occur, so that serious loss is caused. The introduction of epidemic disease resistance genes through hybridization is a main means for cultivating pepper disease-resistant varieties, and the method has the difficulty that pepper materials have various genetic rules of resistance to epidemic diseases, the genetic rules are mainly controlled by 2 or more than 2 polygenes, a single dominant gene and a single dominant gene plus modifier gene control model, and the resistance genes have the characteristics of microspecies specificity and harm symptom specificity.
Molecular marker assisted breeding selects germplasm resources based on genotypes, avoids or reduces errors of phenotype selection, can greatly shorten breeding process, and is an important means for improving accuracy and efficiency of transformation. The prior art discloses a plurality of molecular markers for pepper phytophthora blight resistance, however, the molecular markers also have the problems of inconsistent genotype and phenotype and the like, and the application of the molecular markers in material screening and molecular marker-assisted breeding is influenced. The molecular markers which are more closely linked with related genes, higher in suitability and more efficient in detection are developed aiming at different resistant materials, and the molecular markers are beneficial to selection and variety breeding of the hot pepper epidemic disease resistant materials.
Disclosure of Invention
The invention aims to provide a pepper phytophthora blight resistance gene SNP marker 5-156.
Another object of the present invention is to provide KASP-specific primers for the SNP markers.
Still another object of the present invention is to provide the use of the SNP markers and primers.
Still another object of the present invention is to provide a method for identifying pepper resistant to phytophthora blight.
Still another object of the present invention is to provide a detection kit for identifying pepper resistant to epidemic diseases.
According to the specific embodiment of the invention, the SNP marker 5-156 of the hot pepper phytophthora blight resistance gene has a nucleotide sequence shown as SEQ ID No.1, wherein the 24 th base of the sequence shown as SEQ ID No.1 is represented by W, and W represents T or A.
SEQ ID No.1:
ATGAATTGCAACTTTTTTCTCCAWGGAAGAACAAATCACCTCCAAA
According to the KASP specific primer of the SNP marker 5-156 of the hot pepper phytophthora blight resistance gene, the sequence of the primer 5-156 is as follows:
the primer A1: 5'-ATGAATTGCAACTTTTTTCTCCAT-3' is used as a primer,
the primer A2: 5'-ATGAATTGCAACTTTTTTCTCCAA-3' is used as a primer,
and the rear primer C: 5'-TTTGGAGGTGATTTGTTCTTCC-3'.
According to the KASP specific primer of the embodiment of the invention, the 5 ' ends of the pre-primers A1 and A2 are added with fluorescent labels, wherein the 5 ' end of the pre-primer A1 is added with a FAM fluorescent label sequence, and the 5 ' end of the pre-primer A2 is added with a HEX fluorescent label sequence.
According to the KASP specific primer of the embodiment of the invention, the FAM fluorescent tag sequence is 5'-GAAGGTGACCAAGTTCATGCT-3', and the HEX fluorescent tag sequence is 5'-GAAGGTCGGAGTCAACGGATT-3'.
The invention provides application of a pepper phytophthora blight resistance gene SNP marker, in particular application in pepper molecular marker assisted breeding.
The method for identifying the pepper with the phytophthora blight comprises the following steps of applying SNP (single nucleotide polymorphism) markers 5-156 related to pepper phytophthora blight resistance genes to identify the phytophthora blight resistance of pepper materials to be detected:
when the disease resistance phenotype of the pepper is 'susceptible', the SNP locus is A: A genotype, namely homozygote of A at the 24 th site of the nucleotide sequence shown in SEQ ID No. 1;
when the disease resistance phenotype of the pepper is disease resistance, the SNP locus is T, namely T genotype, namely the 24 th position of the nucleotide sequence shown by SEQ ID No.1 is homozygote of T; or the SNP locus is an A: T genotype, namely the 24 th site of the nucleotide sequence shown in SEQ ID No.1 is a heterozygous type of A and T.
The method for identifying pepper resistant to phytophthora diseases according to the embodiment of the present invention comprises the step of performing PCR detection using the KASP-specific primer.
According to the specific embodiment of the invention, the detection kit for identifying the pepper with the phytophthora blight contains the KASP specific primer.
The kit also comprises a fluorescent probe A, a fluorescent probe B, a quenching probe A and a quenching probe B.
The nucleotide sequence of the fluorescent probe A is a front primer A1 of the primer 5-156, and the 5' end of the fluorescent probe A is connected with a fluorescent group A; the nucleotide sequence of the quenching probe A is a reverse complementary sequence of the A1 sequence, and the 3' end of the quenching probe A is connected with a quenching group;
the nucleotide sequence of the fluorescent probe B is a front primer A2 of a primer of 5-156, and the 5' end is connected with a fluorescent group B; the nucleotide sequence of the quenching probe B is a reverse complementary sequence of the A2 sequence, and the 3' terminal of the quenching probe B is connected with a quenching group.
In the invention, the fluorophore A is a FAM fluorescent label sequence; the fluorescent group B is specifically a HEX fluorescent label sequence; the quenching group is specifically Q.
The invention has the beneficial effects that:
the SNP molecular marker can judge the pepper phytophthora blight resistance gene only by detecting the DNA of pepper plants in the seedling stage without artificially inoculating and identifying the pepper phytophthora blight resistance, and can be widely applied to molecular marker assisted breeding. The SNP molecular marker of the invention can be used for large-scale detection by using KASP genotyping technology, thus improving the efficiency and shortening the identification time.
Drawings
FIG. 1 shows the amplification results of KASP markers 5-156 in hybrid combinations, blue spots as individuals of the same genotype as the pepper phytophthora resistant parent (T: T genotype), green spots as pepper phytophthora susceptible material (A: A genotype), and red spots as heterozygous individuals (A: T genotype);
FIG. 2 shows the amplification results of KASP markers 5-156 in 44 pepper material, blue dots are individuals of the same genotype as the pepper phytophthora disease resistant parent (T: T genotype) and green dots are pepper phytophthora disease susceptible material (A: A genotype).
Detailed Description
Example 1 acquisition of SNP sites related to Phytophthora capsici resistance Gene and determination of the corresponding KASP primer
1. Test materials
The test materials are 77013, IVF2014032 and H3, disease-resistant materials CM334, perennial, 0601M and RP4 and F1 thereof.
2. Phenotypic identification
The resistance identification of each pepper material and the F1 phenotype thereof adopts an artificial inoculation identification method, each material is repeated for 3 times, 10 plants are repeated, and the resistance identification method is characterized in that according to the agricultural industry standard of the people's republic of China, part 1 of the pepper disease resistance identification technical regulation: the identification technical specification (NYT 2060.1-2011) of pepper phytophthora blight resistance.
The results show that the disease indexes of 77013, IVF2014032 and H3 are 80.00, 80.48 and 75.38 and are more than 70 respectively, and the disease indexes belong to susceptible materials; the disease indexes of CM334, perennial, 0601M and RP4 are respectively 18.09, 48.11, 39.26 and 3.33, and are less than 70, and the disease-resistant material belongs to a disease-resistant material.
3. Acquisition of SNP sites related to pepper phytophthora blight resistance gene and determination of corresponding KASP primer
(1) Genome re-sequencing and molecular marker design
Re-sequencing the genomes of the susceptible material 77013 and the disease-resistant material 0601M, determining SNP sites in the sample by taking the disease-resistant material CM334 as a reference genome, and designing KASP primers.
Each pair of KASP molecular markers contains 3 primer sequences: a1, A2 and C.
Wherein, A1 and A2 are only the differences of the SNP sites at the ends, and different fluorescent tag sequences are respectively added at the 5' ends of A1 and A2.
FAM fluorescent tag sequence: 5'-GAAGGTGACCAAGTTCATGCT-3', respectively;
HEX fluorescent tag sequence 5'-GAAGGTCGGAGTCAACGGATT-3'.
The FAM fluorescent tag sequence and the HEX fluorescent tag sequence are complementary with a sequence with fluorescence in KASP V4.02X Master mix 96/384, Low Rox, and can excite fluorescence after being matched.
C is a reverse complementary sequence.
The KASP-labeled PCR amplification system comprises a DNA template, a primer mixture, a fluorescent probe A, a fluorescent probe B, a quenching probe A, a quenching probe B, high-fidelity Taq enzyme, dNTP and the like. The primer mixture includes primers A1, A2, and C. The sequence of the fluorescent probe A is 5'-GAAGGTGACCAAGTTCATGCT-3', and the 5 ' end is connected with 1 fluorophore FAM; the sequence of the fluorescent probe B is 5'-GAAGGTCGGAGTCAACGGATT-3', and the 5 ' end is connected with 1 fluorophore HEX; the sequence of the quenching probe A is 5'-AGCATGAACTTGGTCACCTTC-3', and the 3 ' terminal is connected with a quenching group Q; the sequence of the quenching probe B is 5'-AATCCGTTGACTCCGACCTTC-3', and the 3 ' terminal is connected with a quenching group Q.
TABLE 1 KASP-tagged nucleotide sequence information
Figure BDA0002125960460000041
(2) Screening for polymorphic SNP markers
The KASP primers are used for carrying out PCR amplification on susceptible materials 77013, IVF2014032 and H3, disease-resistant materials CM334, perennial, 0601M, RP4 and F1 generations thereof.
Reading after the KASP PCR amplification reaction needs to use a Roche 480 fluorescence quantitative instrument for KASP genotyping, reading fluorescence data, and determining the specific genotype of the gene to be detected according to the analysis result as follows: the genotype of the sample showing blue color close to the X axis is the allele linked to the FAM fluorescent tag sequence, the genotype of the sample showing green color close to the Y axis is the allele linked to the HEX fluorescent tag sequence, the genotype of the sample showing red color in the middle is the heterozygote of the two alleles, and the genotype of the sample showing black color in the lower left corner is represented by H2O substituted blank for template.
The KASP primer combination which is consistent with the pepper phytophthora blight resistance phenotype is 5-156, the phenotype and genotype identification results are shown in the table 2 and the figure 1, the molecular marker typing is consistent with the parental phenotype, and the method can be used for SNP molecular marker assisted selection of pepper phytophthora blight resistance materials.
The 5-152, 5-155 and 5-163 markers do not accurately distinguish the resistant parent from its F1, i.e., there is no polymorphism at this SNP between parents, and molecular marker typing of the population cannot be performed.
TABLE 2 molecular markers 5-156 in pepper parents and F1 generation typing
Figure BDA0002125960460000051
The polymorphism of the SNP site is that the 24 th site of the sequence shown in SEQ ID NO.1 is A or T.
When the disease resistance phenotype of the pepper is 'susceptible', the SNP locus is A: A genotype, namely, the 24 th position of the nucleotide sequence shown by SEQ ID No.1 is homozygote of A;
when the disease resistance phenotype of the pepper is disease resistance,
(1) the SNP locus is T genotype, namely the 24 th position of the nucleotide sequence shown in SEQ ID No.1 is homozygote of T; or
(2) The SNP locus is A: G genotype, namely, the 24 th position of the nucleotide sequence shown in SEQ ID No.1 is a heterozygous type of A and T.
Example 2 screening of anti-epidemic Capsici fructus materials from Natural population Using molecular markers 5-156
44 portions of pepper material were selected and subjected to PCR amplification using KASP marker. The results are shown in Table 3 and FIG. 2.
TABLE 3 typing of molecular markers 5-156 in the Natural population of Capsicum
Figure BDA0002125960460000061
Figure BDA0002125960460000071
The result shows that when the phenotype of the tested pepper is disease-resistant, the SNP loci corresponding to the molecular markers 5-156 are T, T genotype respectively; when the phenotype of the tested pepper is 'susceptible', the SNP sites corresponding to the molecular markers 5-156 are A: A respectively. Therefore, the molecular marker 5-156 of the invention can be used for screening the anti-epidemic disease material from the pepper natural population.
Sequence listing
<110> vegetable and flower institute of Chinese academy of agricultural sciences
<120> pepper phytophthora blight resistance gene SNP marker 5-156, and specific primer and application thereof
<160> 4
<170> SIPOSequenceListing 1.0
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<211> 46
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<220>
<221> allele
<222> (24)..(24)
<223> R =T OR A
<400> 1
atgaattgca acttttttct ccawggaaga acaaatcacc tccaaa 46
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<212> DNA
<213> Artificial Sequence (Artificial Sequence)
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atgaattgca acttttttct ccat 24
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<213> Artificial Sequence (Artificial Sequence)
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atgaattgca acttttttct ccaa 24
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<211> 22
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<400> 4
tttggaggtg atttgttctt cc 22

Claims (4)

1. The method for identifying the pepper with the phytophthora blight resistance is characterized by comprising the step of identifying the phytophthora blight resistance of a pepper material to be detected by using SNP markers 5 to 156 related to pepper phytophthora blight resistance genes, wherein the nucleotide sequence of the SNP markers 5 to 156 is shown as SEQ ID No.1, the 24 th base of the sequence shown as the SEQ ID No.1 is T or A,
when SNP loci corresponding to SNP markers 5-156 related to the pepper phytophthora blight resistance gene are A: A homozygous genotype, the phytophthora blight resistance phenotype of the pepper material to be detected is an infection;
and when the SNP locus corresponding to the SNP marker 5-156 related to the pepper phytophthora blight resistance gene is a T: T homozygous genotype or an A: T heterozygous genotype, the phytophthora blight disease resistance phenotype of the pepper material to be detected is disease resistance.
2. The method for identifying pepper with phytophthora blight resistance according to claim 1, wherein the step of performing fluorescence PCR detection on pepper material to be detected is performed by using KASP specific primers of SNP markers 5-156 related to pepper phytophthora blight resistance genes, wherein the primer sequences are as follows:
the primer A1: 5'-ATGAATTGCAACTTTTTTCTCCAT-3' is used as a primer,
the primer A2: 5'-ATGAATTGCAACTTTTTTCTCCAA-3' is used as a primer,
the rear primer C is 5'-TTTGGAGGTGATTTGTTCTTCC-3', and the primer C is 5'-TTTGGAGGTGATTTGTTCTTCC-3',
wherein, the 5' ends of the front primer A1 and the front primer A2 are added with fluorescent label sequences.
3. The method for identifying pepper resistant to phytophthora disease as claimed in claim 2, wherein the primer A1 has a FAM fluorescent tag sequence at the 5 'end, and the primer A2 has a HEX fluorescent tag sequence at the 5' end.
4. The method for identifying pepper disease resistance as claimed in claim 3, wherein said FAM fluorescent tag sequence is 5'-GAAGGTGACCAAGTTCATGCT-3' and said HEX fluorescent tag sequence is 5'-GAAGGTCGGAGTCAACGGATT-3'.
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