CN102242224A - Method for synchronously detecting three kinds of viruses on tobacco through triple one-step method RT-PCR (Reverse Transcription Polymerase Chain Reaction) - Google Patents

Method for synchronously detecting three kinds of viruses on tobacco through triple one-step method RT-PCR (Reverse Transcription Polymerase Chain Reaction) Download PDF

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CN102242224A
CN102242224A CN2011101985079A CN201110198507A CN102242224A CN 102242224 A CN102242224 A CN 102242224A CN 2011101985079 A CN2011101985079 A CN 2011101985079A CN 201110198507 A CN201110198507 A CN 201110198507A CN 102242224 A CN102242224 A CN 102242224A
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tobacco
pcr
primer
tmv
pvy
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CN102242224B (en
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杨军
张俊祺
罗朝鹏
王燃
李锋
金立锋
宋纪真
林福呈
翟妞
周会娜
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Zhengzhou Tobacco Research Institute of CNTC
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Abstract

The invention discloses a method for synchronously detecting three kinds of viruses on tobacco through triple one-step method RT-PCR (Reverse Transcription Polymerase Chain Reaction). The method is characterized by being used for synchronously detecting TMV (Tobacco Mosaic Virus), PVY (Potato Virus Y) and CMV (Cucumber Mosaic Virus), the method comprises the following steps of screening and comparing conservation areas in a virus gene group, artificially screening and synthesizing specificity primers suitable for composite RT-PCR of three kinds of virus diseases; analyzing to obtain TMV, PVY and CMV infection tobacco leaf samples; and integrating enzymes and a buffer solution required by a reverse transcription and a PCR (Polymerase Chain Reaction), and establishing a method for compositely detecting the TMV, PCY and CMV infection of tobacco leaves based on one-step method RT-PCR through optimization of reaction conditions. The triple one-step method RT-PCR utilized by the invention has the advantages of simple and convenient operation, time and labor saving, reliable result and low cost; simultaneously, the probability of cross-contamination of samples in an operation process can be effectively reduced, and the monitoring on the TMV, PVY and CMV in tobacco agricultural production has wide application prospect.

Description

Triple single stage method RT-PCR detect the method for three kinds of viruses on the tobacco simultaneously
Technical field
The invention belongs to viral diseases of plants detection technique field, provide a kind of triple single stage method RT-PCR detect simultaneously the tobacco mosaic viruses disease ( Tobacco mosaic virus, TMV), tobacco potato Y virus ( Potato Y virus, PVY) and tobacco cucumber mosaic virus ( Cucumber mosaic virus, method CMV) is specifically related to the effective foundation of synthetic and this detection method that grows tobacco virus-specific nucleotide primer sequence at three.
Background technology
Tobacco mosaic viruses ( Tobacco mosaic virus, TMV), marmor upsilon ( Potato virus Y, PVY), cucumber mosaic virus ( Cucumber mosaic virus, CMV) host range is extensive, diversified economy crop and garden crops such as main harm tobacco, tomato, cucumber, potato.Its regional distribution is extremely wide, belongs to worldwide virus disease, and the crop production of different continents is the virus disease that causes of Ceng Yinqi and be subjected to heavy losses all.
More than three kinds of virus diseases be that important virus disease general, that harm is serious takes place on the tobacco, alleviate tobacco agriculture produce in the key of virus disease harm be that big area is promoted to cultivate and used virus-free strong sprout, enhances field management and take viral effectively prevention and control technical measures.It is a important step in the prevention and control technical measures that virus detects monitoring, has big, popular wide, the characteristics that control is difficult of harm at tobacco virus, sets up as early as possible as early as possible that detection technique is very necessary fast, accurately and efficiently.The method of land for growing field crops tobacco virus evaluation at present mainly contains conventional Biological Detection, immunology and molecular biology method, but all has in various degree defective and deficiency.Conventional Biological Detection wastes time and energy, and seroimmunity and molecular Biological Detection method are to preparing restriction and the expense costliness that the viral sample material requirements is higher, be subject to experiment condition.Usually in the molecular Biological Detection process of actual virus, TMV, PVY, CMV etc. identify that separately repetitive operation is more, and the cost of wasting time and energy is higher.Multiple RT-PCR (Multiplex reverse transcription polymerase chain reaction) is the primer that adds in a reverse transcription (RT) reaction more than 1 pair, at first the purpose viral nucleic acid is carried out reverse transcription, be the template of polymerase chain reaction (PCR) with a plurality of reverse transcription products of this stage synthetic (cDNA) then, the index amplification obtains a corresponding above virus causing disease authentication information.Because tobacco virus mostly is mixed infection, the symptom performance is complicated, it is bigger to utilize many kinds of single RT-PCR virus to carry out the workload that system detects, compare with the single RT-PCR of routine, multiple RT-PCR can detect multiple virus simultaneously or distinguish the not homophyletic system of virus, can improve detection efficiency significantly, reduce and detect cost, thereby the superiority of multiple RT-PCR in tobacco virus detects is more obvious.The key that detects the dual of two or more viruses or multiple RT-PCR technology simultaneously is to select suitable primer for use, under the prerequisite that guarantees primer specificity, avoids mutual interference the between the primer.
Multiple RT-PCR is divided into two operation stepss and carries out in actual application, at first the purpose viral nucleic acid is carried out reverse transcription (RT), is that template is carried out the corresponding virus causing disease authentication information of index amplification acquisition with reverse transcription product (cDNA) then.Two reactions steps and stage corresponding two different reaction systems, the influence factor of whole test is more, has also strengthened that test is polluted and the probability of artificial incorrect operation simultaneously.
 
Summary of the invention
It is not enough and triple single stage method RT-PCR that provide detect the method for three kinds of important viruses on the tobaccos that purpose of the present invention just is being based on above-mentioned prior art.Design synthetic a pair of Auele Specific Primer respectively according to TMV, PVY, CMV genome sequence conservative region, integrate reverse transcription and PCR and react required enzyme and damping fluid, by reaction condition optimization, successfully set up based on single stage method RT-PCR and detected the method that tobacco leaf infects TMV, PVY, CMV simultaneously.The foundation of this technological method will provide a kind of sensitivity, quick, special and high-throughout method for the accurate detection of TMV, PVY, CMV in the tobacco agriculture production process.
The present invention seeks to be achieved through the following technical solutions: triple single stage method RT-PCR detect the method for tobacco mosaic viruses, marmor upsilon and cucumber mosaic virus.This method comprises screens conservative region in the comparison viral genome, and the synthetic screening is applicable to three kinds of compound RT-PCR Auele Specific Primers of virus disease; Analysis obtains TMV, PVY, CMV infects the tobacco leaf sample; Integrate reverse transcription and PCR and react required enzyme and damping fluid,, set up the method that infects TMV, PVY, CMV based on single stage method RT-PCR compound detection tobacco leaf by reaction condition optimization.
Concrete steps are as follows:
(1) three kind of virus-specific nucleotide primer design is with synthetic
Use DNAMAN6.0 software, TMV, PVY, each strain system of CMV virus, each regional isolate whole genome sequence that GenBank is included compare, determine the relative conservative region in the virus sequence, in selected conservative region, use Oligo 6.0 software design primers, and guarantee primer specificity by the BLAST analysis.Because multiplex PCR requires the right annealing temperature of each primer and primer approaching as far as possible, the size of amplicon also should be close as far as possible under the situation that agarose gel electrophoresis can significantly be distinguished simultaneously, so final selected TMV, PVY, each a pair of primer of CMV spend the RNase water dissolution to working concentration 10 μ M behind the synthetic.
TMV: upstream primer (TF1) 5 '-TGTGTGCAAAACTTACTTCCC-3 ';
Downstream primer (TR1) 5 '-AGGACAAAACATTTGCGTATG-3 ';
PVY: upstream primer (PF1) 5 '-ACTGTGATGAATGGGCTTATG-3 ';
Downstream primer (PR1) 5 '-GGCATATATGGTTCCTTTTTG-3 ';
CMV: upstream primer (C3F1) 5 '-GGCTTTCCAAGGTACCAGTAG-3 ';
Downstream primer (C3R1) 5 '-ATCGAGCTTGCCAATTACTAC-3 '.
(2) extraction of the total RNA of tobacco
Serodiagnosis test kit check and analysis virus infection tobacco sample at first, the tobacco sample that finds TMV, PVY, CMV to infect by serological method.Get classical symptom tobacco leaf 50mg, grinding powder in the liquid nitrogen extracts the total RNA of tobacco, and extract product is dissolved in 50 μ l not to be had in the distilled water of RNA enzyme pollution, and-20 ℃ of storages are standby.
(3) triple single stage method RT-PCR detect the foundation of three kinds of viral reaction conditionss simultaneously
The system factor is groped and adjusted to this test repeatedly by a plurality of gradient trial tests, finally obtained to make the top condition of selected 3 pairs of primers normal reaction in same RT-PCR reaction tubes.Reaction system through optimization: 10 * PCR Buffer, 7.5 μ l; Mg 2+(25mM) 6 μ l; DNTP(2.5mM each) 4 μ l; Taq enzyme 4U; AMV ThermoScript II 5U; Ribonuclease Inhibitor 10U; Each 2 μ l of TMV upstream and downstream primer, each 2 μ l of CMV upstream and downstream primer, each 3 μ l of PVY upstream and downstream primer; Each 500ng of RNA; Go RNase water to complement to 50 μ l.Reaction conditions: 42 ℃ of reverse transcription 30min, 95 ℃ of heat inactivation 5min; 94 ℃ of sex change 30sec, 52 ℃ of annealing 30sec, 72 ℃ are extended 70sec, 30 circulations; 72 ℃ are replenished extension 10min, and amplified production is got 5 ~ 10 μ l electrophoresis detection in 1% sepharose.The enzyme that this experiment RT-PCR uses is all available from TaKaRa company.
In the present invention, use Agdia company's T MV, PVY, CMV diagnostic kit PathoScreen in the step (2) RTMV, PathoScreen RPVY, PathoScreen RCMV check and analysis virus tobacco sample, the tobacco sample that finds TMV, PVY, CMV to infect by serological method; Adopt RNeasy Plant Mini test kit to extract the total RNA of tobacco.
Triple single stage method RT-PCR reaction of the present invention, have easy and simple to handle, time saving and energy saving, reliable results, advantage with low cost, simultaneously can effectively reduce the possibility that causes the sample crossed contamination in the operating process, the monitoring of TMV, PVY, CMV is with a wide range of applications in producing for tobacco agriculture.
The present invention changes the defective in the multiple RT-PCR actual application, solved long, problem such as sensitivity is low of tobacco virus detection method cycle, utilizing single RT-PCR to detect on the basis of TMV, PVY, CMV, design synthetic Auele Specific Primer respectively according to TMV, PVY, CMV genome sequence conservative region, integrate reverse transcription and PCR and react required enzyme and damping fluid, by reaction condition optimization, a cover triple single stage method RT-PCR methods of three kinds of virus diseases of rapid detection have simultaneously successfully been set up.Compare with multiple RT-PCR than single RT-PCR, triple single stage method RT-PCR detection methods of being set up can a step detect TMV, PVY, CMV virus causing disease simultaneously, detect easier, can reduce pollute and reaction in influence factor, and shortened detection time greatly.
 
Description of drawings
PVY, the TMV of the triple single stage method RT-PCR reaction systems of Fig. 1, the electrophoresis detection result of CMV viral sample
Wherein: M is DNA marker, and the 1-4 swimming lane is respectively single PVY single stage method RT-PCR product, single TMV single stage method RT-PCR product, single CMV single stage method RT-PCR product, triple single stage method RT-PCR product.
 
Embodiment
The present invention is described further below with reference to embodiment, but does not limit the present invention.
Embodiment 1:
(1) uses DNAMAN6.0 software, TMV, PVY, each strain system of CMV virus, each regional isolate whole genome sequence that GenBank is included compare, determine the relative conservative region in the virus sequence, in selected conservative region, use Oligo 6.0 software design primers, and guarantee primer specificity by the BLAST analysis.Because multiplex PCR requires the right annealing temperature of each primer and primer approaching as far as possible, the size of amplicon also should be close as far as possible under the situation that agarose gel electrophoresis can significantly be distinguished simultaneously, so final selected TMV, PVY, each a pair of primer of CMV spend the RNase water dissolution to working concentration 10 μ M behind the synthetic.
TMV: upstream primer (TF1) 5 '-TGTGTGCAAAACTTACTTCCC-3 ';
Downstream primer (TR1) 5 '-AGGACAAAACATTTGCGTATG-3 ';
PVY: upstream primer (PF1) 5 '-ACTGTGATGAATGGGCTTATG-3 ';
Downstream primer (PR1) 5 '-GGCATATATGGTTCCTTTTTG-3 ';
CMV: upstream primer (C3F1) 5 '-GGCTTTCCAAGGTACCAGTAG-3 ';
Downstream primer (C3R1) 5 '-ATCGAGCTTGCCAATTACTAC-3 '.
 
(2) serodiagnosis test kit PathoScreen at first RTMV, PathoScreen RPVY, PathoScreen RThe virus infection tobacco sample that gather in cigarette district, CMV check and analysis land for growing field crops, the tobacco sample that finds TMV, PVY, CMV to infect by serological method.Get classical symptom tobacco leaf 50mg, grinding powder in the liquid nitrogen adopts the Shanghai RNeasy Plant Mini of bio-engineering corporation test kit to extract the total RNA of tobacco, and extract product is dissolved in 50 μ l not to be had in the distilled water of RNA enzyme pollution, and-20 ℃ of storages are standby.
(3) foundation of triple single stage method RT-PCR reaction conditionss
Reaction system through optimization: 10 * PCR Buffer, 7.5 μ l; Mg 2+(25mM) 6 μ l; DNTP(2.5mM each) 4 μ l; Taq enzyme 4U; AMV ThermoScript II 5U; Ribonuclease Inhibitor 10U; Each 2 μ l of TMV upstream and downstream primer, each 2 μ l of CMV upstream and downstream primer, each 3 μ l of PVY upstream and downstream primer; Each 500ng of RNA; Go RNase water to complement to 50 μ l.Reaction conditions: 42 ℃ of reverse transcription 30min, 95 ℃ of heat inactivation 5min; 94 ℃ of sex change 30sec, 52 ℃ of annealing 30sec, 72 ℃ are extended 70sec, 30 circulations; 72 ℃ are replenished extension 10min, and amplified production is got 5-10 μ l electrophoresis detection in 1% sepharose.
 
Embodiment 2:
(1) uses DNAMAN6.0 software, TMV, PVY, each strain system of CMV virus, each regional isolate whole genome sequence that GenBank is included compare, determine the relative conservative region in the virus sequence, in selected conservative region, use Oligo 6.0 software design primers, and guarantee primer specificity by the BLAST analysis.Because multiplex PCR requires the right annealing temperature of each primer and primer approaching as far as possible, the size of amplicon also should be close as far as possible under the situation that agarose gel electrophoresis can significantly be distinguished simultaneously, so final selected TMV, PVY, each a pair of primer of CMV (primer is with embodiment 1) spend the RNase water dissolution to working concentration 10 μ M behind the synthetic.
(2) TMV, PVY, the CMV virus causing disease that utilizes this laboratory to preserve inoculated 6-8 leaf phase tobacco (non-homophyletic tobacco) respectively separately, treat that viral symptom shows and gather the morbidity tobacco sample when obvious, get three kinds of classical symptom morbidity balanced mix 60mg, grinding powder in the liquid nitrogen, adopt the Shanghai RNeasy Plant Mini of bio-engineering corporation test kit to extract the total RNA of tobacco, extract product is dissolved in 50 μ l not to be had in the distilled water of RNA enzyme pollution, and-20 ℃ of storages are standby.
(3) foundation of triple single stage method RT-PCR reaction conditionss
Reaction system through optimization: 10 * PCR Buffer, 7.5 μ l; Mg 2+(25mM) 6 μ l; DNTP(2.5mM each) 4 μ l; Taq enzyme 4U; AMV ThermoScript II 5U; Ribonuclease Inhibitor 10U; Each 2 μ l of TMV upstream and downstream primer, each 2 μ l of CMV upstream and downstream primer, each 3 μ l of PVY upstream and downstream primer; Each 500ng of RNA; Go RNase water to complement to 50 μ l.Reaction conditions: 42 ℃ of reverse transcription 30min, 95 ℃ of heat inactivation 5min; 94 ℃ of sex change 30sec, 52 ℃ of annealing 30sec, 72 ℃ are extended 70sec, 30 circulations; 72 ℃ are replenished extension 10min, and amplified production is got 5-10 μ l electrophoresis detection in 1% sepharose.
 
Embodiment 3:
(1) uses DNAMAN6.0 software, TMV, PVY, each strain system of CMV virus, each regional isolate whole genome sequence that GenBank is included compare, determine the relative conservative region in the virus sequence, in selected conservative region, use Oligo 6.0 software design primers, and guarantee primer specificity by the BLAST analysis.Because multiplex PCR requires the right annealing temperature of each primer and primer approaching as far as possible, the size of amplicon also should be close as far as possible under the situation that agarose gel electrophoresis can significantly be distinguished simultaneously, so final selected TMV, PVY, each a pair of primer of CMV (primer is with embodiment 1) spend the RNase water dissolution to working concentration 10 μ M behind the synthetic.
(2) TMV, PVY, the CMV virus causing disease that utilizes this laboratory to preserve successively inoculated 8-10 leaf phase tobacco (homophyletic tobacco), treat that viral symptom shows and gather the morbidity tobacco sample when obvious, get classical symptom morbidity tobacco leaf 50mg, grinding powder in the liquid nitrogen, adopt the Shanghai RNeasy Plant Mini of bio-engineering corporation test kit to extract the total RNA of tobacco, extract product is dissolved in 50 μ l not to be had in the distilled water of RNA enzyme pollution, and-20 ℃ of storages are standby.
(3) foundation of triple single stage method RT-PCR reaction conditionss
Reaction system through optimization: 10 * PCR Buffer, 7.5 μ l; Mg 2+(25mM) 6 μ l; DNTP(2.5mM each) 4 μ l; Taq enzyme 4U; AMV ThermoScript II 5U; Ribonuclease Inhibitor 10U; Each 2 μ l of TMV upstream and downstream primer, each 2 μ l of CMV upstream and downstream primer, each 3 μ l of PVY upstream and downstream primer; Each 500ng of RNA; Go RNase water to complement to 50 μ l.Reaction conditions: 42 ℃ of reverse transcription 30min, 95 ℃ of heat inactivation 5min; 94 ℃ of sex change 30sec, 52 ℃ of annealing 30sec, 72 ℃ are extended 70sec, 30 circulations; 72 ℃ are replenished extension 10min, and amplified production is got 5-10 μ l electrophoresis detection in 1% sepharose.

Claims (5)

1. triple single stage method RT-PCR detect the method for three kinds of viruses on the tobacco simultaneously, it is characterized in that: be the method that detects tobacco mosaic viruses, marmor upsilon and cucumber mosaic virus simultaneously, this method comprises screens conservative region in the comparison viral genome, and artificial screening is synthetic to be applicable to three kinds of compound RT-PCR Auele Specific Primers of virus disease; Analysis obtains TMV, PVY, CMV infects the tobacco leaf sample; Integrate reverse transcription and PCR and react required enzyme and damping fluid,, set up the method that infects TMV, PVY, CMV based on single stage method RT-PCR compound detection tobacco leaf by reaction condition optimization.
2. triple single stage method RT-PCR according to claim 1 detect the method for three kinds of viruses on the tobacco simultaneously, and concrete steps are as follows:
(1) three kind of virus-specific nucleotide primer design is with synthetic
Use DNAMAN6.0 software, TMV, PVY, each strain system of CMV virus, each regional isolate whole genome sequence that GenBank is included compare, determine the relative conservative region in the virus sequence, in selected conservative region, use Oligo 6.0 software design primers, and guarantee primer specificity by the BLAST analysis; Because multiplex PCR requires the right annealing temperature of each primer and primer approaching as far as possible, the size of amplicon also should be close as far as possible under the situation that agarose gel electrophoresis can significantly be distinguished simultaneously, so final selected TMV, PVY, each a pair of primer of CMV spend the RNase water dissolution to working concentration 10 μ M behind the synthetic;
TMV: upstream primer (TF1) 5 '-TGTGTGCAAAACTTACTTCCC-3 '
Downstream primer (TR1) 5 '-AGGACAAAACATTTGCGTATG-3 '
PVY: upstream primer (PF1) 5 '-ACTGTGATGAATGGGCTTATG-3 '
Downstream primer (PR1) 5 '-GGCATATATGGTTCCTTTTTG-3 '
CMV: upstream primer (C3F1) 5 '-GGCTTTCCAAGGTACCAGTAG-3 '
Downstream primer (C3R1) 5 '-ATCGAGCTTGCCAATTACTAC-3 '
(2) extraction of the total RNA of tobacco
Serodiagnosis test kit check and analysis virus infection tobacco sample at first, the tobacco sample that finds TMV, PVY, CMV to infect by serological method, get classical symptom tobacco leaf 50mg, grinding powder in the liquid nitrogen, extract the total RNA of tobacco, extract product is dissolved in 50 μ l not to be had in the distilled water of RNA enzyme pollution, and-20 ℃ of storages are standby;
(3) triple single stage method RT-PCR detect the foundation of three kinds of viral reaction conditionss simultaneously
The system factor is groped and adjusted to this test repeatedly by a plurality of gradient trial tests, finally obtained to make the top condition of selected 3 pairs of primers normal reaction in same RT-PCR reaction tubes, through the reaction system of optimizing is: 10 * PCR Buffer, 7.5 μ l; Mg 2+(25mM) 6 μ l; DNTP(2.5mM each) 4 μ l; Taq enzyme 4U; AMV ThermoScript II 5U; Ribonuclease Inhibitor 10U; Each 2 μ l of TMV upstream and downstream primer, each 2 μ l of CMV upstream and downstream primer, each 3 μ l of PVY upstream and downstream primer; Each 500ng of RNA; Go RNase water to complement to 50 μ l; Reaction conditions: 42 ℃ of reverse transcription 30min, 95 ℃ of heat inactivation 5min; 94 ℃ of sex change 30sec, 52 ℃ of annealing 30sec, 72 ℃ are extended 70sec, 30 circulations; 72 ℃ are replenished extension 10min, and amplified production is got 5-10 μ l electrophoresis detection in 1% sepharose.
3. triple single stage method RT-PCR according to claim 2 detect the method for three kinds of viruses on the tobacco simultaneously, it is characterized in that: use Agdia company's T MV, PVY, CMV diagnostic kit PathoScreen in the step (2) RTMV, PathoScreen RPVY, PathoScreen RCMV check and analysis virus tobacco sample, the tobacco sample that finds TMV, PVY, CMV to infect by serological method.
4. triple single stage method RT-PCR according to claim 2 detect the method for three kinds of viruses on the tobacco simultaneously, it is characterized in that: adopt RNeasy Plant Mini test kit to extract the total RNA of tobacco in step (2).
5. triple according to claim 1 single stage method RT-PCR detect the method the primer of three kinds of viruses on the tobacco simultaneously, and it is characterized in that: described Auele Specific Primer is:
TMV: upstream primer (TF1) 5 '-TGTGTGCAAAACTTACTTCCC-3 '
Downstream primer (TR1) 5 '-AGGACAAAACATTTGCGTATG-3 '
PVY: upstream primer (PF1) 5 '-ACTGTGATGAATGGGCTTATG-3 '
Downstream primer (PR1) 5 '-GGCATATATGGTTCCTTTTTG-3 '
CMV: upstream primer (C3F1) 5 '-GGCTTTCCAAGGTACCAGTAG-3 '
Downstream primer (C3R1) 5 '-ATCGAGCTTGCCAATTACTAC-3 '.
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