CN101906485A - Primer set and kit for quickly detecting various melon viruses - Google Patents
Primer set and kit for quickly detecting various melon viruses Download PDFInfo
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Abstract
The invention relates to a primer set and a kit for quickly detecting various melon viruses. By applying specificity primer pairs SEQ ID NO.1-10 designed according to nucleotide conserved region sequences of 5 viruses, a multiple RT-PCR system is optimized in aspects such as primer concentration, Mg2+ concentration, Taq DNA polymerase concentration, dNTPs concentration, annealing temperature and the like which influence multiple RT-PCR (M-PCR) amplification, and the primer set and a kit capable of simultaneously detecting field samples complexly infected by five viruses CMV, SqMV, TMV, WMV and ZYMV from watermelon leaf tissues are established. The primer set and the kit for detecting complex infectious viruses of melons have the advantages of saving time, reducing cost and improving efficiency.
Description
Technical field
The invention belongs to the plant virology technical field, particularly relate to the primer sets and the test kit of the multiple melon viruses of a kind of rapid detection.
Background technology
China is one of major country of production of watermelon, and on average more than 1,800 ten thousand mu, cultivated area ranks first in the world annual growth of watermelon area.Wherein the Northwest is the important watermelon high-quality producing region of China.Virus disease is a kind of generally the generation and the very big disease of hazardness in watermelon production, and general time incidence rate is 10%～30%, and retransmitting the time can be up to more than 50%～80%.The big area of watermelon virus disease takes place, and causes a large amount of underproduction of watermelon, and quality descends, and will have a strong impact on high yield, stable yields, high-quality, high benefit and the melon grower's of watermelon enthusiasm for production.
The virus that infects watermelon mainly contains following 5 kinds: cucumber mosaic virus (Cucumber mosaicvirus, CMV), Flos Cucurbitae mosaic virus (Squash mosaic virus, SqMV), tobacco mosaic virus (TMV) (Tobaccomosaic virus, TMV), watermelon mosaic virus (Watermelon mosaic virus, WMV) and little zucchini yellow mosaic virus (Zucchini yellow mosaic virus, ZYMV), and in field virus multiplicity of infection can often take place.
At present, the detection method that is used for watermelon virus, biology, electron microscopic observation, serology, RT-PCR and nucleic acid hybridization are arranged, but because the biology detection cycle is long, the certain technical ability of Electronic Speculum manipulation require, be difficult for carrying out focusing on of great amount of samples, there is very big limitation in instrument expense height so biological method and Electronic Speculum detect in watermelon virus detects simultaneously.Although serological method has obtained widespread use, commercial antiserum(antisera) price is higher, and a kind of antiserum(antisera) can only detect a kind of virus, but also has certain problems such as false positive reaction.Reaction of substance RT-PCR (sRT-PCR) and detection method of nucleic acid hybridization can only detect a kind of virus, and mostly field watermelon virus is compound and infects, and will expend more time and reagent so detect with these two kinds of methods.For output and the quality that guarantees that watermelon is produced, accurately identify the watermelon virus disease, be badly in need of a kind of comparatively accurate, sensitive and viral fast detect primer and test kit in the watermelon production.
Summary of the invention
The present situation that this research takes place at Shaanxi Province's watermelon disease, utilization is right according to the Auele Specific Primer of 5 kinds of viral nucleotide conserved regions sequences Design, carry out the optimization of multiple RT-PCR system from aspects such as the primer concentration that influences multiple RT-PCR (M-PCR) amplification, Mg2+ concentration, Taq archaeal dna polymerase concentration, dNTPs concentration, annealing temperatures, foundation can detect compound primer sets and the test kit that infects the field sample of CMV, SqMV, TMV, WMV and 5 kinds of viruses of ZYMV simultaneously from the water melon leaf tissue.
For solving the problems of the technologies described above, the invention provides a kind of primer sets of synchronous detection 2-5 kind melon viruses, this primer sets comprises 2-5 in following 5 pairs of primers to primer:
The 1st couple of primer: CMV-F (SEQ ID NO.1)/CMV-R (SEQ ID NO.2)
SEQ?ID?NO.1：5′-ATTGGTCGTCCCACTCTT-3′
SEQ?ID?NO.2：5′-TCGCCAAACATAGCAGAG-3′
The 2nd couple of primer: SqMV-F (SEQ ID NO.3)/SqMV-R (SEQ ID NO.4)
SEQ?ID?NO.3：5′-AGGCACATTTCGCAGTTC-3′
SEQ?ID?NO.4：5′-CGATGGTTGCCTTTATGT-3′
The 3rd couple of primer: TMV-F (SEQ ID NO.5)/TMV-R (SEQ ID NO.6)
SEQ?ID?NO.5：5′-GCCGACCCAATAGAGTTA-3′
SEQ?ID?NO.6：5′-GAGGTCCAAACTAAACCAGAAG-3′
The 4th couple of primer: WMV-F (SEQ ID NO.7)/WMV-R (SEQ ID NO.8)
SEQ?ID?NO.7：5′-CCAGTGGCAAAGGTGATA-3′
SEQ?ID?NO.8：5′-TGCTGCGTCTGAGAAATG-3′
The 5th couple of primer: ZYMV-F (SEQ ID NO.9)/ZYMV-R (SEQ ID NO.10)
SEQ?ID?NO.9：5′-GGAGCGGAAACAAGTGAA-3′
SEQ?ID?NO.10：5′-ACCTGCTCATTCCCATCC-3′。
Preferably, comprise 5 couples of primer SEQ ID NO.1-10 in the primer sets.
Wherein melon viruses is cucumber mosaic virus (CMV), Flos Cucurbitae mosaic virus (SqMV), tobacco mosaic virus (TMV) (TMV), watermelon mosaic virus (WMV) and little zucchini yellow mosaic virus (ZYMV).
The present invention also provides a kind of test kit of synchronous detection 2-5 kind melon viruses, and this test kit comprises 5 couples of primer SEQ ID NO.1-10.
5 pairs of primer concentration ratios in the mentioned reagent box are the 1st pair of primer: the 2nd pair of primer: the 3rd pair of primer: the 4th pair of primer: the 5th couple of primer=1.2-1.6: 0.8-1.2: 0.8-1.2: 0.8-1.2: 1.3-1.7, preferably, five pairs of primer concentration ratios are the 1st pair of primer: the 2nd pair of primer: the 3rd pair of primer: the 4th pair of primer: the 5th pair of primer=1: 1: 1: 1: 1.
In the mentioned reagent box, also wrap dNTPs, Taq archaeal dna polymerase, Mg
2+, the PCR damping fluid.Wherein dNTPs concentration is 0.10-0.6mmol/L; Taq archaeal dna polymerase concentration is 0.05-0.5U/ μ L; Mg
2+Concentration is 1.0-3.5mmol/L, and preferably dNTPs concentration is 0.4mmol/L, and Taq archaeal dna polymerase concentration is 0.20U/ μ L, Mg
2+Concentration is 3.0mmol/L, the PCR buffer concentration is 0.8 * to 1 *.
The primer sets of above-mentioned synchronous detection 2-5 kind melon viruses and the use of test kit are to use according to the method that comprises following steps:
1) extraction of virus total RNA:
Extract the virus total RNA in the Muskmelon leaf that infects 1-5 kind virus;
2) multiple RT-PCR:
Application SEQ ID NO.2,4,6,8,10 (1-5 is to reverse primer sequences in the primer) are carried out reverse transcription to virus total RNA and are prepared the cDNA template, use SEQ ID NO.1-10 (1-5 is to forward in the primer and reverse sequence) then the cDNA template is carried out multi-PRC reaction, get amplified production;
3) electrophoresis detection:
Amplified production is carried out agarose gel electrophoresis, obtain virogene amplified production band, judge the tobacco virus kind.
Aforesaid method can also comprise following steps:
4) interpretation of result
Gene in the band is carried out external the connection with plasmid, and the picking positive colony extracts the plasmid order-checking, and is relatively big or small with the PCR product of design, analyzes the homology of institute's calling sequence and reference sequences, judges the reliability of multiple RT-PCR detected result.
Material described in this method is used above-mentioned primer sets and test kit.
In the aforesaid method, in the multi-PRC reaction, annealing temperature is 46-51 ℃, and the extension time is 20s-90s, and cycle index is 25-45 time, and preferably, amplification condition is 51 ℃ of annealing temperatures, extends time 60s, cycle index 35 times.
Melon viruses is sick normal to be compound infecting, and this research is through repeatedly optimizing and the condition of groping has been set up the primer sets and the test kit of the multiplex PCR that detects five kinds of melon viruses simultaneously.The technology of using these primer sets and test kit has and saves time, reduces cost, raises the efficiency advantage in the detection of muskmelon multiplicity of infection virus.In the muskmelon cultivation and production, can be that quick, the accurate easy and economic again seedling that detects is with malicious situation, so that take effective prophylactico-therapeutic measures as early as possible, generation, minimizing financial loss, disease-resistant screening and the disease fashion forecasting in the field has crucial meaning to the control disease.Detecting multiple melon viruses disease does not at home simultaneously almost report.This technology is successful is applied to the compound synchronous detection that infects of field muskmelon disease.
Description of drawings
Use the multiple RT-PCR system of being set up to detect five kinds of single (sample 1, sample 2, sample 3, sample 4, sample 5) and blended melon viruses (sample 6) under Fig. 1 laboratory condition;
Fig. 2 is the electrophoresis detection result who detects the melon viruses (sample 1, sample 2, sample 3, sample 4, sample 5, sample 6) on the Yang Ling of Shaanxi Province, Hancheng, Liquan, Fufeng, thoughtful, 6 regional muskmelon samples of acrobatic skill
Embodiment
In order to understand the present invention, further specify the present invention with embodiment below, but do not limit the present invention.
Primer design and preparation
Go up CMV, SqMV, TMV, WMV and the ZYMV virus coat protein gene sequence (EF202597.1, DQ868881.1, DQ352454.1, DQ399708.1, AY611022.1) of login according to GenBank, use the special primer that Primier 5.0 primer-design softwares design these 5 kinds of viruses respectively.Because multiplex PCR requires to increase simultaneously a plurality of purpose fragments under same annealing temperature, therefore utilize software DNAMAN to calculate primer Tm value, a large amount of primers to design screen, select each consistent bar primer of Tm value, guarantee under same annealing temperature, to detect simultaneously WMV, CMV, SqMV, 5 kinds of cause of disease CMV-F of TMV and ZYMV (SEQ ID NO.1)/CMV-R (SEQ ID NO.2), SqMV-F (SEQ ID NO.3)/SqMV-R (SEQ ID NO.4), TMV-F (SEQ ID NO.5)/TMV-R (SEQ ID NO.6), WMV-F (SEQ ID NO.7) WMV-R (SEQ ID NO.8) and ZYMV-F (SEQ ID NO.9)/ZYMV-R (SEQ ID NO.10).The information of each primer is as shown in table 1 below:
The information of table 1 primer sequence SEQ ID NO.1-10
Above-mentioned primer is synthetic by match Parkson, Beijing company.
Used experiment material is as follows in the embodiments of the invention:
ZYMV, WMV, TMV, SqMV and 5 kinds of toxogens of CMV are inoculation reproduction on muskmelon respectively, is stored in-80 ℃ of refrigerators.The Taq box is an excellent brilliant biotechnology company limited product, and cloning vector pMD18-T simple vector, molecular biology bacterial strain material are available from the biological company limited of TaKaRa (Dalian).
Take the Muskmelon leaf of 6 sample: ZYMV, WMV, TMV, SqMV, CMV and 5 kinds of virus mixed infections respectively, the sample label is: sample 1, sample 2, sample 3, sample 4, sample 5, sample 6.
The extraction of virus total RNA
Each 0.5g of Muskmelon leaf (being labeled as sample 2, sample 3, sample 4, sample 5, sample 6 respectively) that takes by weighing ZYMV, WMV, TMV, SqMV, CMV and 5 kinds of virus mixed infections respectively puts into-80 ℃ of dark mortars that freeze and adds liquid nitrogen and fully grind, be transferred to rapidly in the aseptic 1.5mLeppendorf pipe of no RNase, add 500 μ L phenol/chloroform (1: 1) and 500 μ L RNA extraction buffer (Tris-HCl20mmol/L, SDS1%, NaCl 200mmol/L, EDTA50mmol/L), 2min fully vibrates, 4 ℃, 12, the centrifugal 5min of 000g.Supernatant with the equal-volume phenol/chloroform again extracting once, 4 ℃, 12, the centrifugal 5min of 000g.Supernatant adds equal-volume 4M LiCl, more than 4 ℃ of precipitation 4h, and in 4 ℃, 12, the centrifugal 15min of 000g.Abandon supernatant liquor, precipitation is with 70% precooled ethanol washed twice, and it is standby to be dissolved among the ddH2O of 30 μ L DEPC processing-20 ℃ of preservations after the thorough drying.With the total negative contrast of RNA of health tobacco (being labeled as sample 1), extracting method is the same simultaneously.
Reverse transcription (RT) reaction
Total RNA to every kind of virus carries out reverse transcription reaction respectively.With synthetic each viral cDNA first chain of M-MLV ThermoScript II reverse transcription.25 μ LRT reaction systems are as follows: the total RNA of 2 μ L, 1 μ L virus special reverse primer (10 μ mol/L), 7 μ LDEPC-H
2O, 70 ℃ of sex change 5min put 5min on ice rapidly; Add 5 μ L, 5 * RT buffer again, 5 μ LdNTP (2.5mmol/L each), 0.5 μ LRNase inhibitor (40U/ μ L) and 1 μ L M-MLV ThermoScript II (200U/ μ L), centrifugal after, 42 ℃ of water-bath 1h, 95 ℃ of deactivation 5min put stand-by on ice.
The PCR reaction
25 μ L PCR standard reaction systems: 12.3 μ L ddH2O, 2.5 μ L, 10 * PCR buffer[750mmol/LTris-HCl (pH 8.8), 200mmol/L (NH4)
2SO
4, 0.1%Tween 20], 2 μ L25mmol/LMgCl
2, 2 μ LdNTP (2.5m mol/L each), 2 μ L forwards and reverse primer mixture (each 10 μ mol/L), 0.2 μ LTaq archaeal dna polymerase (5U/ μ L) and 2 μ L RT products.PCR reaction cycle parameter: 94 ℃ of pre-sex change 3min; 94 ℃ of sex change 45s, 46 ℃ of annealing 45s, 72 ℃ are extended 1min, circulate 30 times; Last 72 ℃ stop compensation extension 10min.Get 5 μ LPCR products relatively through 2% agarose gel electrophoresis analysis.
Electrophoresis detection
Get 5 μ L PCR reaction product and carry out 2% agarose gel electrophoresis, in 0.5 * TAE buffered environment, 110V voltage stabilizing electrophoresis 40min, observe with gel imaging system then and the record result, obtain 5 specific bands respectively, obtain the amplimer band position of every kind of virus, referring to the Fig. 1 in the Figure of description.
The extraction of virus total RNA
Respectively to from Shaanxi Yang Ling, the Hancheng, Liquan, the Fufeng, thoughtful and Muskmelon flower leaf disease samples six places of acrobatic skill (are labeled as sample 1 respectively, sample 2, sample 3, sample 4, sample 5, sample 6) each 0.5g puts into-80 ℃ of dark mortars that freeze and adds liquid nitrogen and fully grind, be transferred to rapidly in the aseptic 1.5mLeppendorf pipe of no RNase, add 500 μ L phenol/chloroform (1: 1) and 500 μ LRNA extraction buffer (Tris-HCl 20mmol/L, SDS1%, NaCl 200mmol/L, EDTA50mmol/L), 2min fully vibrates, 4 ℃, 12, the centrifugal 5min of 000g.Supernatant with the equal-volume phenol/chloroform again extracting once, 4 ℃, 12, the centrifugal 5min of 000g.Supernatant adds equal-volume 4M LiCl, more than 4 ℃ of precipitation 4h, and in 4 ℃, 12, the centrifugal 15min of 000g.Abandon supernatant liquor, precipitation is with 70% precooled ethanol washed twice, and it is standby to be dissolved among the ddH2O of 30 μ L DEPC processing-20 ℃ of preservations after the thorough drying.
Multiple reverse transcription (RT) reaction
Total RNA to each viral sample carries out reverse transcription reaction respectively.With synthetic each viral cDNA first chain of M-MLV ThermoScript II reverse transcription.25 μ L RT reaction systems are as follows: the total RNA of 15 μ L, the special reverse primer mixture of 5 kinds of viruses of 2 μ L (each 10 μ mol/L), 7 μ L DEPC-H
2O, 70 ℃ of sex change 5min put 5min on ice rapidly; Add 5 μ L, 5 * RT buffer again, 5 μ LdNTP (2.5mmol/L each), 0.5 μ LRNase inhibitor (40U/ μ L) and 1 μ L M-MLV ThermoScript II (200U/ μ L), centrifugal after, 42 ℃ of water-bath 1h, 95 ℃ of deactivation 5min put stand-by on ice.
Multi-PRC reaction
25 μ L PCR standard reaction systems: 12.3 μ L ddH2O, 2.5 μ L, 10 * PCR buffer[750mmol/LTris-HCl (pH 8.8), 200mmol/L (NH4)
2S O
4, 0.1%Tween 20], 3 μ LMgCl
2(25mmol/L), 4 μ LdNTP (each 2.5m mol/L), 5 couples of each 0.4 μ L of Auele Specific Primer (each 10 μ mol/L), 0.2 μ L Taq archaeal dna polymerase (5U/ μ L) and 2 μ L RT products.PCR reaction cycle parameter: 94 ℃ of pre-sex change 3min; 94 ℃ of sex change 45s, 46 ℃ of annealing 45s, 72 ℃ are extended 1min, circulate 30 times; Last 72 ℃ stop compensation extension 10min.Get 5 μ LPCR products relatively through 2% agarose gel electrophoresis analysis.
Electrophoresis detection
Get 5 μ L PCR reaction product and carry out 2% agarose gel electrophoresis, in 0.5 * TAE buffered environment, 110V voltage stabilizing electrophoresis 40min, observe with gel imaging system then and the record result, obtain 5 specific bands respectively, obtain the amplimer band position of every kind of virus, referring to the Fig. 2 in the Figure of description.
The sequential analysis of PCR product
ZYMV, WMV, TMV, SqMV and the CMV band through the multiplex PCR amplification reclaimed in rubber tapping, carries out external the connection with pMD18-T simple vector, and the picking positive colony extracts the plasmid order-checking.Sequencing result shows, the amplified production of ZYMV, WMV, TMV, SqMV and CMV is made up of 542,485,410,354,293 Nucleotide respectively, identical with the PCR product size of design, be respectively the partial sequence of ZYMV, WMV, TMV, SqMV and CMVCP gene.Sequence homology analysis is the result show, the homology of institute's calling sequence and reference sequences reaches 98.63%, 99.24%, 99.91%, 98.32 and 99.02% respectively.Proved the reliability of multiplex PCR detected result.
Method of the present invention is described by specific embodiment.Those skilled in the art can use for reference links such as content appropriate change raw material of the present invention, processing condition and realize corresponding other purpose, its relevant change does not all break away from content of the present invention, all similar replacements and change will become apparent to those skilled in the art that and all be regarded as comprising within the scope of the present invention.
Claims (9)
1. the primer sets of a synchronous detection 2-5 kind melon viruses, this primer sets comprise 2-5 in following 5 pairs of primers to primer:
The 1st couple of primer: CMV-F (SEQ ID NO.1)/CMV-R (SEQ ID NO.2)
SEQ?ID?NO.1：5′-ATTGGTCGTCCCACTCTT-3′
SEQ?ID?NO.2：5′-TCGCCAAACATAGCAGAG-3′
The 2nd couple of primer: SqMV-F (SEQ ID NO.3)/SqMV-R (SEQ ID NO.4)
SEQ?ID?NO.3：5′-AGGCACATTTCGCAGTTC-3′
SEQ?ID?NO.4：5′-CGATGGTTGCCTTTATGT-3′
The 3rd couple of primer: TMV-F (SEQ ID NO.5)/TMV-R (SEQ ID NO.6)
SEQ?ID?NO.5：5′-GCCGACCCAATAGAGTTA-3′
SEQ?ID?NO.6：5′-GAGGTCCAAACTAAACCAGAAG-3′
The 4th couple of primer: WMV-F (SEQ ID NO.7)/WMV-R (SEQ ID NO.8)
SEQ?ID?NO.7：5′-CCAGTGGCAAAGGTGATA-3′
SEQ?ID?NO.8：5′-TGCTGCGTCTGAGAAATG-3′
The 5th couple of primer: ZYMV-F (SEQ ID NO.9)/ZYMV-R (SEQ ID NO.10)
SEQ?ID?NO.9：5′-GGAGCGGAAACAAGTGAA-3′
SEQ?ID?NO.10：5′-ACCTGCTCATTCCCATCC-3′。
2. primer sets according to claim 1 comprises 5 couples of primer SEQ IDNO.1-10 in this primer sets.
3. primer sets according to claim 1 and 2, wherein melon viruses is cucumber mosaic virus (CMV), Flos Cucurbitae mosaic virus (SqMV), tobacco mosaic virus (TMV) (TMV), watermelon mosaic virus (WMV) and little zucchini yellow mosaic virus (ZYMV).
4. the test kit of a synchronous detection 2-5 kind melon viruses, this test kit comprises 5 couples of primer SEQ IDNO.1-10.
5. test kit according to claim 4, wherein 5 pairs of primer concentration ratios are the 1st pair of primer: the 2nd pair of primer: the 3rd pair of primer: the 4th pair of primer: the 5th couple of primer=1.2-1.6: 0.8-1.2: 0.8-1.2: 0.8-1.2: 1.3-1.7.
6. test kit according to claim 5, wherein 5 pairs of primer concentration ratios are the 1st pair of primer: the 2nd pair of primer: the 3rd pair of primer: the 4th pair of primer: the 5th pair of primer=1: 1: 1: 1: 1.
7. test kit according to claim 4 wherein also wraps dNTPs, Taq archaeal dna polymerase, Mg
2+, the PCR damping fluid.
8. test kit according to claim 7, wherein dNTPs concentration is that 0.10-0.6mmol/L TaqDNA polymerase concentration is 0.05-0.5U/ μ L; Mg
2+Concentration is 1.0-3.5mmol/L.
9. according to claim 7 or 8 described test kits, wherein dNTPs concentration is 0.4mmol/L, and Taq archaeal dna polymerase concentration is 0.20U/ μ L, Mg
2+Concentration is 3.0mmol/L, the PCR buffer concentration is 0.8 * to 1 *.
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