CN108546778A - A kind of SNP marker and its application for detecting anti-cucumber powdery mildew character - Google Patents

A kind of SNP marker and its application for detecting anti-cucumber powdery mildew character Download PDF

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CN108546778A
CN108546778A CN201810798871.0A CN201810798871A CN108546778A CN 108546778 A CN108546778 A CN 108546778A CN 201810798871 A CN201810798871 A CN 201810798871A CN 108546778 A CN108546778 A CN 108546778A
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cucumber
mildew
snp marker
powdery mildew
primer
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CN108546778B (en
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张红梅
金海军
丁小涛
余纪柱
翟文
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Shanghai Academy of Agricultural Sciences
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Abstract

The invention discloses a kind of SNP marker and its applications for detecting anti-cucumber powdery mildew character.The SNP marker is located at cucumber rice chromosome, associated region is in the segment of NCBI numbers NC_026660.1, initial position 22.3Mb, final position 23.1Mb, the sequence of the SNP marker is as shown in SEQ ID NO.1, base r wherein at the sites 51nt is A or G, and it is disease-resistant which is that the cucumber of G shows as, and it is susceptible that base is that the cucumber of A shows as.Present invention application KASP technologies carry out Genotyping to the SNP marker found, can fast and accurately detect resistance of the cucumber to powdery mildew, greatly improve hereditary transformation efficiency.And detection process does not need digestion, electrophoresis and sequencing etc., and it is easy to operation, it is conducive to high-throughput quickly detection, has thoroughly prevented the pollution of the Aerosol Pollution and EB of PCR product to environment, and the harm to human body.

Description

A kind of SNP marker and its application for detecting anti-cucumber powdery mildew character
Technical field
The invention belongs to SNP marker technical fields, and in particular to a kind of for detecting anti-cucumber powdery mildew character SNP marker and its application.
Background technology
Traditional pedigree method selection is the breeding method that breed cucumber men generally use, for many years by breeders A large amount of high-quality, high yield and disease-resistant new breeds of cucumbers are cultivated and have been formulated in effort.However, the tradition in conjunction with phenotypic evaluation is educated The defects of there are phenotype controls to be not allowed for kind pattern, genetic group demand is big, human cost is high, breeding cycle is long, is difficult to realize Large-scale commercial integrates breeding or the improvement of material genetic breeding.Along with the hair of molecular biology and bioinformatics Exhibition, molecular mark selection (Molecular Assisted Selection, MAS) show that huge technology is excellent Gesture realizes hereditary basis and effective combination of Goal Present Situation, and the material (single plant) containing target gene is selected to carry out combo, real Show the accurate improvement of objective trait, can effectively avoid the technical barrier of traditional breeding way.
Single nucleotide acid variation (Single Nucleotide Polymorphism, SNP) is wide on the genome of species General presence, including:The conversion or transversion of single base, single base (segment) are inserted into or the forms such as missing, more for these The SNP marker technology of a new generation is gradually risen in state property site.For the Data mining function SNP marks of control targe character Note, character is associated with genotype, and then realize efficient, accurate breeding.At this stage, it is suitable for the detection means of SNP marker Mainly gel electrophoresis, quantitative fluorescent PCR and competitiveness allele PCR (Kompetitive Allele Specific PCR,KASP).The label that the present invention is developed is suitable for KASP methods and detects SNP site, and this method is applied to divide successively The work such as sub- assistant breeding, the objective trait assignment of genes gene mapping, seed purity and authenticity identification, at low cost, flux is high, experiment The advantages such as safe operation and fluorescence signal acquisition data are accurate.
Powdery mildew (Powdery mildew, PM) is commonly called as white hair, is a kind of worldwide disease occurred extensively.Pathogen master To be propagated by air-flow, have the characteristics that short incubation period, infect again it is frequent, popular strong.Northern germ is with cleistothecium with invalid Body stays in overwintering on ground or greenhouse, vinyl house melon crop.Southern germ is overwintering on host with mycelia or conidium Or more summer, become next year primary source of infection.In China, spring protecting field and summer and autumn open country cucumber are every year all caused by the generation of powdery mildew A large amount of losses, powdery mildew can fall ill in entire cucumber breeding time, and main harm blade is serious to endanger vines, especially in life Long middle and later periods morbidity is serious, so that plant is uprooted plants after their edible portions have been harvested ahead of time, causes Severe Reduction.In the Protectorate cultivation of Shanghai and southern area, The harm of both diseases is increasingly severe.Under the moist planting environment of long-term wet weather, field improper ventilation, illumination is insufficient, plant Growing way is weak, humidity increases a large amount of generations for being conducive to cause of disease powdery mildew.At present production on mainly with the method for medical treatment come The generation of controlling disease, but environment is polluted, pesticide residue influences fruit quality, jeopardizes food security, while increasing farmer Cost.Long-term dispenser can generate resistance to the biological strain of pathogen again, to increase difficulty of prevention and cure, therefore, only cultivate anti- The cucumber variety of powdery mildew could fundamentally solve the problems, such as cucumber No-harmful apple orchard.In breeding process carry out field and Indoor identification is time-consuming and laborious, and therefore, exploitation is suitable for seedling stage high throughput identification cucumber plant and mildew-resistance character close linkage SNP marker, contribute to the resistance for quickly and efficiently detecting cucumber to powdery mildew, contribute on a large scale be commercialized point Sub- breeding, has a good application prospect and economic value.
Invention content
It is an object of the present invention to provide a kind of SNP marker and its applications for detecting anti-cucumber powdery mildew character.
The present invention is that technical solution used by above-mentioned purpose is as follows:
A kind of SNP marker for detecting anti-cucumber powdery mildew character, the SNP marker are located at cucumber the 4th Number chromosome, associated region are named as qCSSL-04, initial position 22.3Mb in the segment of NCBI numbers NC_026660.1, Final position 23.1Mb, the sequence of the SNP marker is as shown in SEQ ID NO.1, wherein the base r at the sites 51nt For A or G, it is disease-resistant which is that the cucumber of G shows as, and it is susceptible that base is that the cucumber of A shows as.
The SNP marker CS_K_040108, sequence are as follows:taactccaactactctcttttcagttcttt Tcatttcccaaacactaccartctcatctgtcaaacaaattgggcatataatgagt attgacagtagagta, wherein Base r at the sites 51nt is A or G.The present invention confirms through population experiment, the property of above-mentioned molecular labeling and anti-cucumber powdery mildew Shape is closely related, in 2 detected parent and its F2 groups, alkali of the parent material SL02 in CS_K_040108 test sites Fundamental mode is G:G, shows as disease-resistant, and the base types of XL01 test sites is then A:A shows as susceptible, 215 F2 groups single plants In, there are 4 single plants to detect G:G has 17 single plants to detect A:A is shown as homozygous;There are 158 single plants to detect A: G is shown to be heterozygous.
The present invention also provides the specific primer sets for detecting the SNP marker, including:
(1) two special primer CS_K_040108X and CS_K_040108Y:The sequence of CS_K_040108X such as SEQ ID Shown in NO.2, the sequence of CS_K_040108Y is as shown in SEQ ID NO.3;
(2) universal primer CS_K_040108C:Its sequence is as shown in SEQ ID NO.4.
The nucleotide sequence and universal primer sequence of two specific primers are shown in Table 1.
1 labeled primer sequence table of table
The present invention also provides application of the specific primer sets in detecting cucumber variety mildew-resistance character.Tool Body includes the following steps:
(1) Cucumber germplasm DNA to be measured is extracted;
(2) using Cucumber germplasm DNA as template, KASP reaction detections are carried out using the specific primer sets, two The 5 '-ends of specific primer CS_K_040108X and CS_K_040108Y are separately connected FAM-tail:5’- Gaaggtgaccaagttcatgct-3 ' (shown in SEQ ID NO.5) and VIC-tail:5’-gaaggtcggagtcaacggatt- 3 ' (shown in SEQ ID NO.6) universal fluorescent sequence labels;
(3) it when detecting anti-cucumber powdery mildew character, is answered if only detecting the connected fluorescence sequence pairs of primer CS_K_040108Y Fluorescence signal, then cucumber to be measured show as mildew-resistance;If only detecting the connected fluorescence sequence pairs of primer CS_K_040108X The fluorescence signal answered then judges that cucumber to be measured is not disease-resistant material;Judge that cucumber is white to resist if being detected simultaneously by the two fluorescence The heterozygous of powder disease.The degree of correlation of label and powdery mildew disease-resistant carries out test and verifies as extremely significantly (p<0.05)
Preferably, when carrying out breed cucumber, selection detects that the connected fluorescence sequences of primer CS_K_040108Y are corresponding The cucumber sample of fluorescence signal carries out breeding.
The fluorescence sequence can be fluorescence sequence commonly used in the art, the big fluorescence of preferably two fluorescence color difference Sequence.In a specific implementation mode in the present invention, selection is connected to Liang Tiaote using FAM and VIC fluorescence sequences It is anisotropic because 5 ' end.
Preferably, the PCR conditions in the step (2) in KASP detections are:94℃15min;95 DEG C of 20sec, 65-56 DEG C 60sec, each cycle annealing elongating temperature reduce by 0.8 DEG C, totally 10 cycles;94 DEG C of 20sec, 57 DEG C of 60sec, totally 26 are followed Ring.
The present invention also provides the method that the specific primer sets are used to detect the SNP marker, the party Method is:
KASP detections are carried out to the genomic DNA of cucumber to be detected using the specific primer sets, in primer CS_K_ The 5 '-ends of 040108X and primer CS_K_040108Y are separately connected different universal fluorescent sequence labels;If only detecting primer The corresponding fluorescence signal of the connected fluorescence sequences of CS_K_040108Y, then cucumber to be measured be mildew-resistance material, genotype G, If only detecting the fluorescence signal of the connected fluorescence sequences of primer CS_K_040108X, judge cucumber to be measured for not mildew-resistance Material, genotype A;If being detected simultaneously by two kinds of fluorescence, cucumber sample is judged to carry the heterozygosis of mildew-resistance character The degree of correlation of type, label and powdery mildew disease-resistant carries out test and verifies as extremely significantly (p<0.05).
The present invention also provides the kits for including the specific primer sets.
The present invention also provides application of the kit in Cucumber Germplasm improvement.
The present invention also provides application of the kit in cultivating powdery mildew resisting green cucumber.
The detection method of the substantially molecular labeling of above application.Wherein, ability can be used with system in PCR response procedures Domain routine techniques, the present invention are not construed as limiting this separately.
Compared with prior art, beneficial effects of the present invention are:
(1) screening of SNP site and the group of structure are related, related with genetic effect value.If position in screening process Point unobvious, then need to rebuild population material and be screened again.Inventor passes through many experiments Exploring Analysis, structure The suitable population material of acquisition is built, then further build anti-susceptible gene pool progress genome resurveys sequence, then carries out BSA and determine Position analysis, it is final to obtain the SNP marker that can be used for detecting anti-cucumber powdery mildew character.
(2) detection of the above-mentioned SNP marker in breed cucumber is provided, using the molecular labeling and detection method, The molecular labeling of selection and mildew-resistance close linkage, can be used for identification and the assisted selection of anti-cucumber powdery mildew, right The molecular breeding of mildew-resistance is promoted to be of great significance.
(3) present invention carries out Genotyping using KASP technologies to the SNP marker found, can quickly, accurately Detection cucumber to the resistance of powdery mildew, greatly improve hereditary transformation efficiency.And detection process does not need digestion, electrophoresis and sequencing Deng, it is easy to operation, it is conducive to high-throughput quickly detection, has thoroughly prevented the pollution of the Aerosol Pollution and EB of PCR product to environment, And the harm to human body.
Description of the drawings
Fig. 1 is that application BSA-seq methods of the embodiment of the present invention position mildew-resistance QTLs's on cucumber rice chromosome Schematic diagram, wherein black horizontal line represent positioning section.
Fig. 2 is the Genotyping test chart of the invention with the SNP marker of anti-cucumber powdery mildew close linkage in group;Its Middle G:G is disease-resistant homozygous genotype, A:A is susceptible homozygous genotype, A:G is heterozygous, and NTC is no template control.
Specific implementation mode
Technical scheme of the present invention is described in detail with reference to embodiment.Tested point experiment in following embodiments Method is conventional method unless otherwise specified.The materials, reagents and the like used in the following examples, unless otherwise instructed, It obtains from commercial channels.The LGC SNPline Genotypings platforms used in embodiment are purchased from English with its matched reagent consumptive material LGC companies of state.
The exploitation of embodiment 1 and the SNP marker of the anti-cucumber powdery mildew linkage of characters
Identify that the cucumber self-mating system SL02 of the mildew-resistance of acquisition is female parent using interior, susceptible self-mating system XL01 is father This, obtains 215 single plants of F2 segregating populations by hybridizing, being selfed, is identified by indoors artificial, according to plant leaf powdery mildew disease Spot number, by plant morbidity grade be divided into 0 grade (not falling ill), 1 grade, 3 grades and 5 grades.The morbidity feelings of 215 single plants of F2 groups Condition is:0 grade 40 plants, 1 grade 93 plants, 3 grades 65 plants and 5 grades 17 plants, by 17 that F2 groups morbidity grade is 0 grade (non-disease plant) Single plant builds extreme disease-resistant gene pond R-pool, and 17 single plants of morbidity class 5 grade build susceptible gene pool S-pool and carry out base Because of the sequence of resurveying of group, then carries out BSA and positioning analysis is sequenced, navigate to the region of rice chromosome region 22.3M-23.1M. Referring to Fig. 1, which is the schematic diagram for positioning mildew-resistance QTLs on cucumber rice chromosome using BSA-seq methods, wherein QCSSL-04 black horizontal lines represent positioning section.
Design of primers is carried out according to sequence at the 23159853rd bit base of parent's polymorphic SNP site in this target area. The primer for detecting above-mentioned SNP marker that the present invention designs is combined as:(1) two specific primer:
CS_K_040108X:
gaaggtgaccaagttcatgcttttcatttcccaaacactaccag;
CS_K_040108Y:
gaaggtcggagtcaacggattttcatttcccaaacactaccaa。
(2) universal primers
CS_K_040108C:tgcccaatttgtttgacaga.
It is separately connected FAM-tail at two specific primer 5 '-ends:5 '-gaaggtgaccaagttcatgct-3 ' and VIC-tail:5 '-gaaggtcggagtcaacggatt-3 ' universal fluorescent sequence labels;KASP reactions are carried out to cucumber to be measured Detection.
The detection of the KASP reactions for the SNP marker that embodiment 2 is developed
1, be directed to molecular labeling design primer of the present invention, using KASP reactions can be high-throughput to the anti-white powder of cucumber Characteristic of disease shape is detected, and is combined using the primer that embodiment 1 designs.
2, using CTAB methods are simplified, genomic DNA is extracted from cucumber leaves.
(1) it takes the fresh sample of appropriate cucumber leaves or freezes sample, be put into 2ml centrifuge tubes, two steel balls be added, in tissue grinder instrument On grind;
(2) 750 μ L CTAB solution are added, shake homogenate, 65 DEG C of concussion warm bath 0.5-1h;
(3) it is cooled to room temperature, 750 μ L chloroforms is added in draught cupboard:Isoamyl alcohol you (24:1) 3-4 mixing of electric knife;
(4) 12000rmp centrifuges 10min, takes in supernatant 500 μ L to new 1.5mL centrifuge tubes;
(5) isometric aqueous isopropanol is added gently to shake, precipitated 1 hour in -20 DEG C or more, 12000rmp centrifugations 3min abandons supernatant;
(6) 70% ethyl alcohol of 1mL is added, flicks precipitation, 1000rmp centrifuges 3min, abandons supernatant;
(7) 300mL H are added2O, dissolving are spare.
3, KASP reaction tests:
KASP reaction tests carry out on LCG SNPline genetic analysis platforms.1.0- is added in microwell plate reaction plate The 20ng/ μ L DNA samples of 1.5 μ L, are added KASP reaction mixtures after drying, reaction system is shown in Table 2.PCR amplification is in water-bath heat It is completed in circulating instrument, reaction condition is:94℃15min;95 DEG C of 20sec, 65-56 DEG C of 60sec, each cycle annealing elongating temperature 0.8 DEG C is reduced, totally 10 cycles;94 DEG C of 20sec, 57 DEG C of 60sec, totally 26 recycle;Scanner is utilized after the completion of reaction Pherastar carries out fluorescence data reading to KASP reaction products, and the result of fluorescent scanning can be converted to figure automatically.As a result join Fig. 2 is seen, for Genotyping test chart of the SNP marker with anti-cucumber powdery mildew close linkage in group;Wherein G:G is disease-resistant Homozygous genotype, A:A is susceptible homozygous genotype, A:G is heterozygous, and NTC is no template control.Fig. 2 results show parting effect Fruit is good.
The SNP marker pcr amplification reaction system of 2 mildew-resistance of table
Embodiment 3:F2 segregating populations Disease Resistance Identification and molecular labeling and phenotype correlation analysis
Phenotype verification is carried out to the label in the present invention, is as follows:
1, with suspension spore liquid (concentration 1 × 104~1 × 106A/ml) in 25 DEG C of daytime/20 DEG C nights of temperature, humidity It is inoculated with Leaf of Cucumber Seedling under 80% environment, is object by the 2nd and the 3rd true leaf of cucumber seedling, according to scab face on blade Long-pending size is investigated, is evaluated the morbidity light and heavy degree of powdery mildew of cucumber to each single plant incidence:
0 grade-do not fall ill, highly resistance;
1 grade-scab accounts for blade area about 30%;
3 grades-scab accounts for blade area about 70%;
5 grades-scab accounts for blade area about 100%.
2, according to the disease index (DSI) of the morbidity rating calculation parent of investigation.It is parent and F2 groups referring to table 3 Incidence.Using the cucumber self-mating system SL02 (DSI=5.0) of the mildew-resistance of indoor acquisition, easy susceptible self-mating system XL01 (DSI=96.8).215 single plants of F2 segregating populations are obtained by hybridization of female parent, selfing of SL02.215 single plants of F2 groups Incidence is:0 grade 40 plants, 1 grade 93 plants, 3 grades 65 plants and 5 grades 17 plants.
The incidence of 3 parent of table and F2 groups is identified
3, the F2 hybridized with the susceptible material XL01 of receptor with reference to the method in embodiment 2, detection donor resistance parent SL02 The phenotypic results such as table 4 of the anti-sense powdery mildew of segregating population single plant.F2 segregating populations single plant phenotypic evaluation result and Genotyping knot Fruit height correspond to, in F2 groups with the homozygous genotype G of disease-resistant parent SL02:G it is consistent have 8 plants 0 grade, 12 plants 1 grade, 9 plant 3 Grade, 1 plant 5 grades, with Susceptible parent XL01 homozygous genotypes A:A it is consistent have 7 plants 0 grade, 31 plants 1 grade, 22 plants 3 grades, 12 plants 5 grades, A:G base types are totally 114 plants of heterozygous plant.
4, the genotype to F2 groups and phenotype relevance verification result carry out t-test analyses, and result is p=0.029 (p <0.05), display CS_K_040108 labels are closely related with powdery mildew of cucumber disease resistance.
Table 4 CS_K_040108 labels are in F2 segregating population testing results
The present invention relates to the SNP marker of anti-cucumber powdery mildew material, which is located at No. 4 dyeing of cucumber Body, associated region is in the segment of NCBI numbers NC_026660.1, initial position 22.3Mb, final position 23.1Mb, according to for Sequence end base design SNP marker is changed, which is A/G.The present invention provides for detecting the SNP The specific primer sets and detection method in site, the specific primer sets difference are as shown in table 1.SNP points of the present invention Son label can be used for the prediction of anti-cucumber powdery mildew, can be used for screening and identifies whether nature genetic stocks has mildew-resistance Character.Detection method provided by the invention is accurate and reliable, easy to operate, suitable for answering for high-throughput commercialization molecular breeding With providing scientific basis for the selection and breeding or improvement of anti-cucumber powdery mildew kind.
The part preferred embodiment of the present invention is above are only, the present invention is not limited in the content of embodiment.For ability For technical staff in domain, can there is various change and change in the conception range of technical solution of the present invention, made by appoint What changes and change, within the scope of the present invention.
Sequence table
<110>Academy of Agricultural Sciences, Shanghai City
<120>A kind of SNP marker and its application for detecting anti-cucumber powdery mildew character
<160> 6
<170> SIPOSequenceListing 1.0
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<211> 101
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<213>Cucumber (Cucumis sativus)
<400> 2
taactccaac tactctcttt tcagttcttt tcatttccca aacactacca rtctcatctg 60
tcaaacaaat tgggcatata atgagtattg acagtagagt a 101
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gaaggtgacc aagttcatgc ttttcatttc ccaaacacta ccag 44
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gaaggtcgga gtcaacggat tttcatttcc caaacactac caa 43
<210> 4
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<212> DNA
<213>Artificial sequence (Artificial Sequence)
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tgcccaattt gtttgacaga 20
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<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 5
gaaggtgacc aagttcatgc t 21
<210> 6
<211> 21
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 6
gaaggtcgga gtcaacggat t 21

Claims (10)

1. a kind of SNP marker for detecting anti-cucumber powdery mildew character, it is characterised in that:The SNP marker position In cucumber rice chromosome, associated region is in the segment of NCBI numbers NC_026660.1, initial position 22.3Mb, stop bit Set 23.1Mb, the sequence of the SNP marker as shown in SEQ ID NO.1, wherein base r at the sites 51nt be A or G, the site base be G cucumber show as it is disease-resistant, base be A cucumber show as it is susceptible.
2. requiring the specific primer sets of the SNP marker described in 1 for test right, which is characterized in that including:
(1) two special primer CS_K_040108X and CS_K_040108Y:The sequence of primer CS_K_040108X such as SEQ ID Shown in NO.2, the sequence of primer CS_K_040108Y is as shown in SEQ ID NO.3;
(2) universal primer CS_K_040108C:Its sequence is as shown in SEQ ID NO.4.
3. application of the specific primer sets in detecting cucumber variety mildew-resistance character described in claim 2.
4. application of the specific primer sets according to claim 3 in detecting cucumber variety mildew-resistance character, It is characterized in that, includes the following steps:
(1) Cucumber germplasm DNA to be measured is extracted;
(2) using Cucumber germplasm DNA as template, KASP reaction inspections are carried out using the specific primer sets described in claim 2 It surveys, FAM-tail is separately connected at the 5 '-ends of two specific primers CS_K_040108X and CS_K_040108Y:5’- GAAGGTGACCAAGTTCATGCT-3 ' and VIC-tail:5 '-GAAGGTCGGAGTCAACGGATT-3 ' universal fluorescent label sequences Row;
(3) when detecting anti-cucumber powdery mildew character, if it is corresponding glimmering to only detect the connected fluorescence sequences of primer CS_K_040108Y Optical signal, then cucumber to be measured show as mildew-resistance;If it is corresponding to only detect the connected fluorescence sequences of primer CS_K_040108X Fluorescence signal then judges that cucumber to be measured is not disease-resistant material;Judge cucumber for mildew-resistance if being detected simultaneously by the two fluorescence Heterozygous.
5. application of the specific primer sets according to claim 4 in detecting cucumber variety mildew-resistance character, It is characterized in that:Selection detects that the cucumber sample of the corresponding fluorescence signal of the connected fluorescence sequences of primer CS_K_040108Y is educated Kind.
6. application of the specific primer sets according to claim 4 in detecting cucumber variety mildew-resistance character, It is characterized in that, the PCR conditions in step (2) in KASP detections are:94℃15min;95 DEG C of 20sec, 65-56 DEG C of 60sec, each Cycle annealing elongating temperature reduces by 0.8 DEG C, totally 10 cycles;94 DEG C of 20sec, 57 DEG C of 60sec, totally 26 recycle.
7. the method that the specific primer sets described in claim 2 are used to detect the SNP marker, this method are:
KASP detections are carried out to the genomic DNA of cucumber to be detected using the specific primer sets described in claim 2, are being drawn The 5 '-ends of object CS_K_040108X and primer CS_K_040108Y are separately connected different universal fluorescent sequence labels;If only examining The corresponding fluorescence signal of the connected fluorescence sequences of primer CS_K_040108Y is measured, then cucumber to be measured is mildew-resistance material, base Because type is G, if only detecting the fluorescence signal of the connected fluorescence sequences of primer CS_K_040108X, judge that cucumber to be measured is not resist The material of powdery mildew, genotype A;If being detected simultaneously by two kinds of fluorescence, cucumber sample is judged to carry resistance to powdery mildew The heterozygous of shape.
8. including the kit of the specific primer sets described in claim 2.
9. application of the kit according to any one of claims 8 in Cucumber Germplasm improvement.
10. application of the kit according to any one of claims 8 in cultivating powdery mildew resisting green cucumber.
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