CN104513866A - Apple stem grooving virus and prunus necrotic ringspot ilarvirus detection specific primers and probes and gene chips - Google Patents
Apple stem grooving virus and prunus necrotic ringspot ilarvirus detection specific primers and probes and gene chips Download PDFInfo
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Abstract
The present invention discloses an apple stem grooving virus and prunus necrotic ringspot ilarvirus detection specific primers and probes and gene chips. The nucleotide sequences of the apple stem grooving virus and prunus necrotic ringspot ilarvirus detection specific primer pair are shown as SEQ ID No.1 and SEQ ID No.2, and the nucleotide sequences of the probe is shown as SEQ ID No.3. The nucleotide sequences of the prunus necrotic ringspot ilarvirus detection specific primer pair are shown as SEQ ID No.4 and SEQ ID No.5, and the nucleotide sequences of the probe is shown as SEQ ID No.6. By combination of RT-PCR (reverse transcription-polymerase chain reaction) detection, the apple stem grooving virus and prunus necrotic ringspot ilarvirus detection gene chips prepared by use of the probes are tested, results show good specificity, strong sensitivity, stable reproducibility, short operation time and simple operation, and the apple stem grooving virus and prunus necrotic ringspot ilarvirus detection gene chips can be widely used in early diagnosis and prevention and control of plant virus disease caused by the apple stem grooving virus and the prunus necrotic ringspot ilarvirus.
Description
Technical field
The gene detecting chip that the present invention relates to the primer of detection plant virus, probe and prepare with them, particularly relate to and detect apple stem grooving virus (Apple stem grooving virus, and Prunus necrotic ring spot virus (Prunus necrotic ringspot virus ASGV), PNRSV) special primer and probe and with the gene chip that they are prepared, belong to the Molecular Detection field of apple stem grooving virus and Prunus necrotic ring spot virus.
Background technology
Apple stem grooving virus (Apple stem grooving virus, ASGV) is that one of general cryptovirus occurs for apple and pears, has reported that the natural host of this virus is except apple and pears, also can endanger fruit tree and the lilies such as cherry, apricot, oranges and tangerines.Prunus necrotic ring spot virus (Prunus necroticringspot virus, PNRSV) is a kind of virus worldwide distributed, and this virus host scope is wide, can infect Prunus and the guls such as Chinese rose, apple such as peach, apricot, cherry.PNRSV is two class Import quarantine harmful organisms of China, is a serious threat to the cultivation of fruit tree in the north.At present, the method detecting this two-strain mainly contains enzyme-linked immunosorbent assay, electron microscopy and RT-PCR.The Methods For Purification process that these technology have in practical application is loaded down with trivial details, length consuming time, and some complex operations are easy to pollute, occur false positive.And the biochip technology grown up in recent years has the advantages such as integrated and high-throughput, and obtain in gene expression analysis, microorganism identification, single nucleotide polymorphism detection etc. and apply widely.Gene chip solidifies in support surface by the nucleic acid fragment of a large amount of known array by the arrangement mode designed, and makes chip.Detect sample after fluorescent marker pcr amplification, fully hybridize with probe, scan after wash-out, show results of hybridization with image.This technology is in human body, animals and plants virus, and there is application transgenic plant detection aspect.
Summary of the invention
An object of the present invention is to provide a pair Auele Specific Primer for detecting apple stem grooving virus and a probe;
Two of object of the present invention is the gene chips becoming to detect apple stem grooving virus by a pair Auele Specific Primer being used for detecting apple stem grooving virus and a probe preparation;
Three of object of the present invention is to provide a pair Auele Specific Primer for detecting Prunus necrotic ring spot virus and a probe;
Four of object of the present invention is the gene chips becoming to detect apple stem grooving virus by a pair Auele Specific Primer being used for detecting Prunus necrotic ring spot virus and a probe preparation;
Above-mentioned purpose of the present invention is achieved through the following technical solutions:
The invention provides a pair Auele Specific Primer for detecting apple stem grooving virus and a probe; Wherein, the nucleotide sequence of a pair described Auele Specific Primer is respectively shown in SEQ ID No.1 and SEQ IDNo.2, and the nucleotides sequence of described probe is classified as shown in SEQ ID No.3.
Can adopt the usual manner of this area, the probe preparation of the detection apple stem grooving virus described in application becomes to detect the biochip of apple stem grooving virus, such as: gene chip, organization chip or cell chip etc.; As the present invention, be preferably gene chip.Gene chip is the large batch of nucleic acid probe of arrangement (also claiming DNA chip or DNA microarray) orderly according to the position high-density designed in advance on carrier (nylon membrane, sheet glass or silicon chip etc.), forms high-density dot matrix.
After DNA with described primer amplified sample, hybridized with the probe molecule on chip under the same conditions by molecular hybridization, adopt the methods such as isotope method, chemiluminescence or chemoluminescence method to show reaction result, corresponding method can also be adopted to carry out quantitatively.
Specific to the present invention, the probe shown in SEQ ID No.3 can be adopted original position point sample method or directly the mode such as point sample method by probe according to the orderly arrangement of the position high-density designed in advance or point sample on nylon membrane carrier, obtain gene chip; From plant sample to be detected, extract RNA uses the Auele Specific Primer shown in SEQ ID No.1 and SEQ ID No.2 (the Auele Specific Primer Cy3 wherein shown in SEQ ID No.2 marks) to carry out pcr amplification again after reverse transcription, probe molecule on amplified production and chip is carried out molecular hybridization, whether contains apple stem grooving virus according in fluorescent signal judgement sample.
Present invention also offers a pair Auele Specific Primer for detecting Prunus necrotic ring spot virus and a probe; Wherein, the nucleotide sequence of a pair described Auele Specific Primer is respectively shown in SEQ ID No.4 and SEQ ID No.5, and the nucleotides sequence of described probe is classified as shown in SEQ ID No.6.
Same, can adopt the usual manner of this area, the probe preparation of the detection apple stem grooving virus described in application becomes to detect the biochip of Prunus necrotic ring spot virus, such as: gene chip, organization chip or cell chip etc.; As the present invention, be preferably gene chip.Specific to the present invention, the probe shown in SEQ ID No.6 can be adopted original position point sample method or directly the mode such as point sample method by probe according to the orderly arrangement of the position high-density designed in advance or point sample on nylon membrane carrier, obtain gene chip; From plant sample to be detected, extract RNA uses the Auele Specific Primer shown in SEQ ID No.4 and SEQ ID No.5 (the Auele Specific Primer Cy3 wherein shown in SEQ ID No.5 marks) to carry out pcr amplification again after reverse transcription, probe molecule on amplified production and chip is carried out molecular hybridization, whether contains Prunus necrotic ring spot virus according in fluorescent signal judgement sample.
For the preparation of the method for gene chip and the method for genechip detection apple stem grooving virus prepared by adopting, known by those skilled in the art.
The present invention is prepared into gene chip with the oligonucleotide shown in SEQ ID No.3 and SEQ ID No.6 respectively, marks antisense primer, asymmetric PCR amplified production and oligonucleotide probe hybridization with Cy3, scans and carries out interpretation of result.Test-results shows, repeatedly hybridizes, PNRSV and ASGV all produces stronger positive signal, and 10 kinds of equal no signals of negative viral produce.It can reach 10 to the detection sensitivity of plasmid
3copy number.Prove that biochip technology has good stability, specificity and highly sensitive.
The present invention detects in conjunction with RT-PCR, the genechip detection of ASGV and PNRSV two-strain is explored, result shows that this technology specificity is good, susceptibility is strong, circulation ratio is stable, the operating time is short, simple, the early diagnosis of the viroses of plant that apple stem grooving virus and Prunus necrotic ring spot virus cause, control can be widely used in.The present invention is fruit tree virus early monitoring, carrying out smoothly of work such as group training detoxification, Anti-virus Disease Breeding etc. provides practicable technical backstopping.
Accompanying drawing explanation
The RT-PCR detected result of Figure 1A SGV and PNRSV; 1. infect the leaf of Falsesour cherry of PNRSV, 3. infect the Folium Mali pumilae of ASGV, 2,4. contrast leaf.
The results of hybridization of Fig. 2 chip detection PNRSV and ASGV; 1.PNRSV; 2.ASGV; 3. the signal on the left side is PNRSV, and right side singal is ASGV; 4.negative samples; 5. blank.
The sensitivity test results of hybridization of Fig. 3 chip detection PNRSV and ASGV; 1,2,3,4 represent that plasmid template is 10 respectively
5, 10
4, 10
3, 10
2pNRSV and ASGV of copy; 5 is negative control.
Embodiment
Further describe the present invention below in conjunction with specific embodiment, advantage and disadvantage of the present invention will be more clear along with description.But these embodiments are only exemplary, do not form any restriction to scope of the present invention.It will be understood by those skilled in the art that and can modify to the details of technical solution of the present invention and form or replace down without departing from the spirit and scope of the present invention, but these amendments and replacement all fall within the scope of protection of the present invention.
Embodiment
1 test materials and method
1.1 test materials
The Apple Leaves positive that apple stem grooving virus ASGV infects is provided by Institute of quarantine of animals and plants, Chinese Academy of Inspection and.The sweet cherry leaves that PNRSV infects provided by Hebei Prov. Academy of Agricultural &. Forest Sciences's Changli fruit tree research.Negative sample is cucumber green mottle mosaic virus (CGMMV), potato mop-top virus (PMTV), potato yellow dwarf virus (PYDV), broad bean wilt virus (BBWV), Maize rough dwarf virus (MRDV), rice stripe virus (RSV), Pepper mild mottle virus (PMMoV), Dasheen mosaic virus (DsMV), Tomato mosaic virus (ToMV), rose of Sharon chlorisis ring spot virus (HCRSV), by Plant Protection institute, Chinese Academy of Agricultral Sciences, China Agricultural University, Zhejiang Agriculture research institute, Tanghai County, Hebei Province plant protection unit provides.
1.2 test method
(1) Design and synthesis of primer and probe.According to ASGV and PNRSVCP gene conserved sequence, with Primer software design special primer, expanding fragment length is respectively 414bp and 340bp.Simultaneously according to the probe sequence of ASGV and PNRSV CP gene and each gene of negative control rat gene DNASIS software design, compare through GenBank sequence homology, obtain the sequence oligonucleotide probe of ASGV and PNRSV CP gene specific.
ASGV sense primer: 5 '-AAAACCTTTGCTGCCACTTC-3 '
ASGV antisense primer: 5 '-TTTCACACGACTCCTAACCC-3 '
ASGV probe: 5 '-CCAGGCAGAACTCTTTGAACGAATGTACG-3 '.
PNRSV sense primer: 5 '-AACAGAGGGCTGCGAATAAC-3 '
PNRSV antisense primer: 5 '-AATCTAAATCGGAAGGAGGG-3 '
PNRSV probe: 5 '-TCGAATGGTTGGATTGGGATGGTGGAGGACTATAAGGTGG-3 '.
(2) plant total serum IgE extraction, RT-PCR amplification and plasmid construction.
The extraction of plant total serum IgE is see " molecular cloning " third edition.Reverse transcription is carried out according to Promega Reverse Transcription box specification sheets; Then get above-mentioned reverse transcription product, add PCR damping fluid (dNTPs200 μM, Mg
2+1.5 μm of ol/L), each 0.5 μM of positive antisense primer, Taq enzyme 1U, H
2o complements to 20 μ L; Response procedures is: 94 DEG C, 5min; 94 DEG C, 30s; 57 DEG C, 30s; 72 DEG C, 30s; 30 circulations, 4 DEG C of preservations.Get amplified production 2.0% agarose gel electrophoresis after RT-PCR terminates to detect.Fluorescent mark RT-PCR reaction system and amplification condition the same, sense primer concentration is 0.1 μm of ol/L, and antisense primer is Cy3 labeled primer concentration is 1.0 μm of ol/L.
Carry out RT-PCR amplification respectively, purifying DNA fragment with the sick leaf total serum IgE that above-mentioned special primer pair PNRSV and ASGV infects, pGEM-T carrier connects, Transformed E .coli DH5 α, extracts plasmid, order-checking.
(3) hybridization and scanning.By two kinds of fluorescent mark amplified productions, 94 DEG C of thermally denatures, then ice bath immediately; Respectively get PCR primer and hybridization solution fully mixes, add chip reaction zone, 42 DEG C of hybridization; After hybridization terminates, take out chip successively in A (1 × SSC, 0.2%SDS), each rinsing in the washing lotion of B (0.2 × SSC), C (0.1 × SSC), room temperature dries rear GenePix4000B scanner scanning.
(4) chip specific test, sensitivity test and replica test.
ASGV with PNRSV probe is repeated respectively on slide become row 4 times.PNRSV and ASGV is carried out RT-PCR respectively, and carries out double PCR with PNRSV and ASGV plasmid, and set 10 kinds of negative viral as negative control and water be blank, product checks its specificity with probe hybridization respectively.Two are become to arrange 8 times PNRSV with ASGV probe each repetition on slide.10 are become by 10 times of gradient dilutions after ASGV with PNRSV plasmid is quantitative
5~ 10
2copy/μ L, each extent of dilution respectively gets 1 μ L as template fluorescent mark PCR, and amplified production and probe hybridization check sensitivity.ASGV with PNRSV probe is repeated respectively on slide become row 4 times.With the RNA of ASGV and PNRSV for template, carry out repeated detection continuously.For the stability of chip between inspection different batches, the chip utilizing the same RT-PCR product of ASGV and PNRSV to prepare in different batches carries out hybridization assays repeatability.
2 test-results
The RT-PCR detected result of 2.1 ASGV and PNRSV
To infect the Apple Leaves of ASGV and PNRSV and cherry total serum IgE for template, RT-PCR, amplified production all has band in agarose gel electrophoresis, basically identical with expection length 414bp and 340bp, and any band (Fig. 1) does not appear in control sample.Record sequence and GenBank sequence homology all reaches more than 90%.This illustrates that the band of amplification is that the amplification of ASGV and PNRSVCP genome specific gets, and RT-PCR system is normal.
2.2 specific test results
Visible according to test-results (Fig. 2), ASGV and PNRSV hybridization produces strong signal respectively.After the double PCR products thereof of ASGV and PNRSV, two-strain all produces strong signal.And 10 kinds of negative controls and all no positive signal of blank produce; Illustrate that this chip has fabulous specificity to detection ASGV and PNRSV.
2.3 sensitivity test results
Visible according to test-results (Fig. 3), along with the reduction of plasmid template amount, hybridization signal also weakens gradually.10
4the fluorescent signal detected during copy is very strong, ASGV and PNRSV can detect; 10
3the fluorescent signal detected during copy is comparatively strong, ASGV and PNRSV also can detect; 10
2during copy, the fluorescent signal of detection is very weak, and detect PNRSV, ASGV does not detect.To detect all genes for standard, the sensitivity of present method can reach 10
3copy.
2.4 replica test results
After hybrid screens, analytical signal value, get the signal averaging that each probe repeats for 4 times, 6 times hybridization data hybridization signal is basically identical, illustrates that the result of chip hybridization detection system is basicly stable.And different batches chip chamber has good repeatability.
Claims (8)
1. for detecting a pair Auele Specific Primer and a probe of apple stem grooving virus (Apple stem grooving virus), it is characterized in that: the nucleotide sequence of a pair described Auele Specific Primer is respectively shown in SEQ ID No.1 and SEQ ID No.2, and the nucleotides sequence of described probe is classified as shown in SEQ ID No.3.
2. a pair Auele Specific Primer according to claim 1 and the application of probe in the reagent of preparation detection apple stem grooving virus.
3. detect a biochip for apple stem grooving virus, it is characterized in that: containing probe according to claim 1.
4. according to biochip according to claim 1, it is characterized in that: it is gene chip.
5. for detecting a pair Auele Specific Primer and a probe of Prunus necrotic ring spot virus (Prunus necrotic ringspotvirus); It is characterized in that: the nucleotide sequence of a pair described Auele Specific Primer is respectively shown in SEQ ID No.4 and SEQ ID No.5, and the nucleotides sequence of described probe is classified as shown in SEQ ID No.6.
6. a pair Auele Specific Primer according to claim 1 and the application of probe in the reagent of preparation detection Prunus necrotic ring spot virus.
7. detect a biochip for Prunus necrotic ring spot virus, it is characterized in that: containing probe according to claim 1.
8. according to biochip according to claim 1, it is characterized in that: it is gene chip.
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Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
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CN108165535A (en) * | 2018-01-29 | 2018-06-15 | 中国农业科学院茶叶研究所 | The complete genome sequence and its detection method of tea tree necrosis ring spot virus |
CN110567951A (en) * | 2019-09-19 | 2019-12-13 | 河南农业大学 | Apple stem groove virus visual detection system based on CRISPR-Cas12a technology and detection method thereof |
CN111411174A (en) * | 2020-04-17 | 2020-07-14 | 鲁东大学 | Method for rapidly detecting prunus necrotic ringspot virus |
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CN1600865A (en) * | 2003-09-23 | 2005-03-30 | 北京金长河科技发展有限公司 | Gene chip for detecting plant virus |
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Cited By (5)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN108165535A (en) * | 2018-01-29 | 2018-06-15 | 中国农业科学院茶叶研究所 | The complete genome sequence and its detection method of tea tree necrosis ring spot virus |
CN108165535B (en) * | 2018-01-29 | 2020-12-01 | 中国农业科学院茶叶研究所 | Complete gene sequence of tea tree necrotic ringspot virus and detection method thereof |
CN110567951A (en) * | 2019-09-19 | 2019-12-13 | 河南农业大学 | Apple stem groove virus visual detection system based on CRISPR-Cas12a technology and detection method thereof |
CN110567951B (en) * | 2019-09-19 | 2020-06-02 | 河南农业大学 | Apple stem groove virus visual detection system based on CRISPR-Cas12a technology and detection method thereof |
CN111411174A (en) * | 2020-04-17 | 2020-07-14 | 鲁东大学 | Method for rapidly detecting prunus necrotic ringspot virus |
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