CN100558902C - Transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence and application thereof - Google Patents
Transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence and application thereof Download PDFInfo
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Abstract
The invention discloses a kind of transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence and application thereof, relate to the detection of transgene rape in the technical field of bioengineering.The present invention is a material with transgene rape kind Ms1Rf1, obtains exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence, and sequence is SEQ NO.1.Wherein the 1-330 bit base is identical with insertion carrier sequence, and the 331-1116 bit base does not have homology with the insertion carrier, is the rape genome sequence.The present invention has set up the event-specific qualitative and quantitative analysis method of transgene rape exogenous origin gene integrator incident Rf1, can be further used for setting up other event-specifics PCR detection method research of transgenic rape Ms 1 Rf1.
Description
Technical field
The present invention relates to the detection of transgene rape in the technical field of bioengineering, specifically, relate to exogenous insertion vector flanking sequence and the application thereof of a kind of transgene rape exogenous origin gene integrator incident Rf1.
Background technology
In recent years, genetically modified crops such as corn, soybean, cotton, rape and tomato are got permission plantation and production in a lot of countries, and what have is processed to food, feed or is used as foodstuff additive.Because the ecological safety and the edible safety of transgenic product are controversial always, more than 30 countries and regions are implemented transgenic product sign system in succession.
According to the sequence information of foreign gene in the transgenic product, the array mode of foreign gene on transgenic constructs, and the integration site of construct on genome can adopt the detection method of gene specific, carrier specificity and event-specific.
1, gene specific detection method
Because a large amount of transgene carriers used identical foreign gene, so gene specific detection method and be not suitable for the reality that current transgenic product continues to bring out.
2, carrier specificity detection method
The carrier specificity detection method is utilized the border sequence feature between the gene element, can effectively identify the different constructs that use similar gene element, and the characteristics that exist sequence information to obtain easily, is therefore used by Many researchers.But, may obtain the transformant of a more than different qualities by same construct, even may be transformed in the different species, and these transformants may not all pass through safety assessment.Therefore the carrier specificity detection method can not be discerned different transgenic strains, can not differentiate this transgenic strain and whether pass through safety assessment.
3, the detection method of event-specific
The basis that event-specific detects is that the integration site of transgenic constructs on genomic dna sequence has high degree of specificity, even identical carrier repeatedly transforms, the position of integration and integration site feature also are unrepeatable.Therefore, according to unrepeatable integration site characteristic sequence, the specific detection method of the incident of having developed.Compare with preceding two kinds of methods, event-specific detects has the highest specificity, the most suitable qualitative and detection by quantitative of doing transgenic product.But the complete information of transgenic constructs is difficult to obtain usually, and known sequence gene element may have suitable distance apart from the border, and in the process of integrating, complicated reorganization may take place between carrier and the genome, therefore, separate flanking sequence and become the key that event-specific detects.In February, 2000, European Union has subsidized Qpcrgmofood European Project project for this reason, and this project is now successfully separated a plurality of kind flanking sequences of acquisition and is used to set up the event-specific detection method.Current, the event-specific detection method has been used to transgenosis Roundup Ready soybean, the detection of a series of transgenosis commercialization kinds such as Mon810 maize.
Through retrieval, do not find any about transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence with utilize this sequence to set up the report that event-specific is qualitative, quantitative PCR (polymerase chain reaction) detects as yet to existing patent and other documents.
Summary of the invention
The objective of the invention is to overcome the deficiency that prior art exists in detecting transgene rape exogenous origin gene integrator incident Rf1 and transgene rape kind Ms1Rf1, a kind of transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence and application thereof are provided.
The object of the present invention is achieved like this:
The present invention is a material with transgene rape kind Ms1Rf1, utilize the GenomeWalker of Invitrogen company test kit to make up genomic library, and utilize primer: RB1:5 ' GGATCCCCCGATGAGCTAAGCTAGC 3 ' and RB2:5 ' GCTTGGACTATAATACCTGACTT6 3 ' and the joint primer that test kit provides, obtain Rf1 with round pcr (polymerase chain reaction) amplification and integrate incident right border sequence SEQ NO.1.
The feature of transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence is:
(1) the 1st to 330 bases derive from the exogenous insertion vector sequence;
(2) the 331st to 1116 bases derive from the rape genome sequence;
(3) origin the 331st to 1116 base coming from the 1st to 330 base of exogenous insertion vector and derive from the rape genome sequence formed rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence jointly.
The applied research of above-mentioned transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence:
(1) utilize this sequence signature to design the event-specific qualitative PCR detection method of transgene rape exogenous origin gene integrator incident Rf1;
(2) utilize this sequence signature to design the event-specific quantitative PCR detecting method of transgene rape exogenous origin gene integrator incident Rf1;
(3) utilize this sequence signature to design the strain specificity qualitative PCR detection method of transgene rape kind Ms1Rf1;
(4) utilize this sequence signature to design the strain specificity quantitative PCR detecting method of transgene rape kind Ms1Rf1.
Compared with prior art, the advantage and the effect that have of the present invention is as follows:
1, the present invention checks order first and announces transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence.
2, the present invention analyzes and confirms the source of different bases in the transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence first, and the joint site of definite exogenous insertion vector sequence and rape genome sequence.
3, the sequence signature that utilizes the present invention to find is set up qualitative, the quantitative PCR detecting method of event-specific of transgene rape exogenous origin gene integrator incident Rf1 and transgene rape kind Ms1Rf1.
4, the present invention is applicable to the aspects such as other event-specifics PCR detection method of setting up transgene rape exogenous origin gene integrator incident Rf1 and transgene rape kind Ms1Rf1.
Description of drawings
Fig. 1-transgene rape exogenous origin gene integrator incident Rf1 right margin binding site, its binding site characteristic sequence.
Fig. 2-transgene rape exogenous origin gene integrator incident Rf1 specificity qualitative PCR amplification,
Wherein:
M-molecular weight Marker;
1-transgenic rape Ms 8 Rf3 genomic dna template;
2-transgenic rape Ms 1 Rf1 genomic dna template;
3-transgenic rape Ms 1 Rf2 genomic dna template;
4-transgene rape Oxy-235 genomic dna template;
5-transgene rape T45 genomic dna template;
6-transgene rape Topas 19/2 genomic dna template;
7-transgene rape RT45 genomic dna template:
Oily 821 templates in the 8-non-transgenic rape.
Fig. 3-transgene rape exogenous origin gene integrator incident Rf1 specificity quantitative pcr amplification.
Embodiment
1, the pcr amplification of transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence
Earlier 20%SDS is preheating to 65 ℃, gets 15ml SDS extracting buffer (0.1TrisHCl, 0.05MEDTA, 1M NaCl pH8.0) and join the 50ml centrifuge tube, add 2.5 μ l beta-mercaptoethanols again, mixing; Blade about liquid nitrogen grinding 3g goes to 50ml with powder and contains in the 50ml centrifuge tube of extracting buffer, and the mixing that vibrates on vibrator adds the 20%SDS of 2ml preheating, mixing, and 65 ℃ of water-baths at least 30 minutes will be shaken test tube therebetween gently; After the water-bath, rapidly centrifuge tube is placed on ice, add 3ml 3M KAc, mixing was placed 30 minutes on ice; 4 ℃ of centrifugal 5min of 5000g; Supernatant is transferred in the new 50ml centrifuge tube, added the Virahol of 2/3 volume, mixing is placed more than the 30min for-20 ℃; 6000g, 4 ℃ of centrifugal 15min outwell supernatant, wash one time with 75% ethanol, and the ultrapure water dissolving DNA is used in vacuum-drying, after the dissolving, solution is transferred in the centrifuge tube of 15ml; Add Proteinase K by 1% of DNA volume of dissolution, 55 ℃ of water-bath 30min; Add equal-volume phenol, mixing, jog 30min, the centrifugal 10min of 8000g; Shift supernatant to new tube, add isopyknic phenol-chloroform-primary isoamyl alcohol (25: 24: 1), jog 20min, the centrifugal 15min of 8000g; Shift supernatant to new tube, add isopyknic chloroform-primary isoamyl alcohol (24: 1), jog 20min, the centrifugal 15min of 8000g; Draw supernatant, every pipe adds 5 μ l RNase, mixing, 37 ℃ of water-bath 1hr degradation of rna; With isopyknic phenol extracting once, jog 20min, the centrifugal 15min of 8000g; Shift supernatant to new centrifuge tube, add isopyknic chloroform-primary isoamyl alcohol (24: 1), jog 20min, the centrifugal 15min of 8000g; Suct and reset and add into 1/10 volume 3M NaAC, mixing adds the equal-volume Virahol, places 30min, deposit D NA for-20 ℃; 6000g, 4 ℃ of centrifugal 15min outwell supernatant, wash 2 times with 75% ethanol, centrifugally remove 75% ethanol, vacuum-drying; After the drying, standby with the ultrapure water dissolving DNA.
Utilizing the GenomeWalker of Invitogen company test kit, is material with rape Ms 1 Rf1 genomic dna, and the method that provides according to test kit makes up rape Ms 1 Rf1 genomic library.
The synthetic primer sequence is as follows: RB1:5 ' GGATCCCCCGATGAGCTAAGCTAGC 3 ' and RB2:5 ' GCTTGGACTATAATACCTGACTTG 3 '.
With the Ms1Rf1 genomic library is template, and the joint primer AP1 and the RB1 that utilize test kit to provide carry out pcr amplification.In the 50ul reaction system, get Ms1Rf1 genomic library DNA 1ul, other each component final concentrations are KOD Plus Buffer 1x, every kind of 200uM of dNTPs, MgSO
41mM, each 100nM of primer, KOD Plus enzyme 1u.Reaction conditions is, 94 ℃ of pre-sex change in 2 minutes, 94 ℃ 15 seconds, 68 ℃ 3 minutes, circulate 68 ℃ of insulations 7 minutes 45 times.Get 1ul PCR product, 50 times of dilute with waters are therefrom got 1ul as second template of taking turns PCR.Second to take turns reaction be primer with AP2 and the RB2 that test kit provides, and reaction system is identical with the first round.Reaction conditions is, 94 ℃ of pre-sex change in 2 minutes, 94 ℃ 15 seconds, 68 ℃ 3 minutes, circulate 68 ℃ of insulations 7 minutes 25 times.The agarose electrophoresis DNA isolation, the EB evaluation of dyeing.
With the QIAquick PCR Purification Kit of QIAGEN company purified pcr product.
PZero2 (Invitrogen) carrier that PCR product and EcoRV enzyme are cut is connected.Linked system: DNA mixture 22 μ l; 2.5 μ l 10 * T4DNA Ligase Buffer with 1mM ATP; 0.5 μ lT4 DNA Ligase (NEB).22 ℃ connect 1hr at least.
The method that provides according to " molecular cloning experiment guide " prepares intestinal bacteria TOP10 (Invitrogen) competent cell, and transforms to connect product.The picking mono-clonal carries out bacterium colony PCR with the mutational site special primer and detects recon.With the clone's enlarged culturing that filters out, prepare plasmid in a small amount, enzyme is cut checking.
Send the order-checking of order-checking company with the clone who filters out.With the sequence information that obtains, the Blastn software that utilizes NCBI to provide is analyzed the source of different piece sequence, thereby judges the binding site of genome and carrier.
2, application method
1) utilizes the event-specific qualitative PCR detection method that sequences Design transgene rape exogenous origin gene integrator incident Rf1 and transgene rape kind Ms1Rf1 are provided among the present invention
The synthetic primer sequence is as follows: Rf1RG:5 ' GGTGACTACACGCGACTCAT 3 ' and Rf1RV:5 ' AGACCTCAATTGCGAGCTTTCTAAT 3 '.
Get transgene rape kind Ms8Rf3 respectively, Ms1Rf1, Ms1Rf2, Oxy-235, T45, Topas 19/2, GT73; Oil 821 in the non-transgenic rape variety, and Arabidopis thaliana, Chinese cabbage, wild cabbage, leaf mustard, soybean, paddy rice, corn, cotton genomic dna are template, utilize Rf1RG and Rf1RV combination of primers to carry out pcr amplification respectively.In the 25ul reaction system, be template with 100ng different sources genomic dna, other each component final concentrations are PCR Buffer 1x (containing 10mM Tris.HCl pH8.3, KCl 50mM), every kind of 200uM of dNTPs, MgCl
22.5mM, each 250nM of primer, Hot Start Taq enzyme 1u.Reaction conditions is, 94 ℃ of pre-sex change in 2 minutes, 94 ℃ 15 seconds, 60 ℃ 30 seconds, 72 ℃ 30 seconds, circulate 72 ℃ of insulations 2 minutes 35 times.The PCR product separates with agarose gel electrophoresis, and EB dyeing back identifies whether there is amplified production.
2) utilize the event-specific quantitative PCR detecting method that sequences Design transgene rape exogenous origin gene integrator incident Rf1 and transgene rape kind Ms1Rf1 are provided among the present invention
Synthetic TaqMan probe sequence is as follows: Rf1RP:5 ' FAM-CATCCTCACCCAGTCAGCATCATCAC-TAMRA 3 '.
Primer, probe combinations at exogenous origin gene integrator incident Rf1 are used to the quantitative fluorescent PCR analysis.The quantitative fluorescent PCR analysis is carried out on MJR DNA Engine Opticon 2 Continuous FluorescenceDetector, and detection and analysis software are Opticon Monitor 2 Version 2.02.
Exogenous origin gene integrator incident Rf1 detection by quantitative reaction volume 20ul contains template DNA 100ng, and other component concentrations are: and TaqMan Buffer 1x (50mM KCl, 10mM.Tris-HCl, 10mM EDTA, pH8.3), MgCl
23.5mM, primer Rf1RG and RF1RV 600uM, probe Rf1RP 300uM, each 300uM of dATP dCTPdGTP, dUTP 600uM, Amperase Uracil N-glycosylase (UNG) 0.2u, AmpliTaq Gold 1.25u.
The TaqMan reaction conditions is: after 50 ℃ of 2 minutes and 95 ℃ of pre-sex change in 10 minutes, carry out 50 PCR circulations: 95 ℃ of sex change in 15 seconds, plate is read in 60 ℃ of annealing in 1 minute and extending.
Result according to typical curve is optimized utilizes the PCR reaction conditions identical with setting up typical curve, is with reference to the amount of measuring Ms1Rf1 genomic dna in the mixed rape DNA sample that contains the Ms1Rf1 genomic dna with the typical curve.Getting the 100ng genomic dna is template, utilizes the different content standard model to do typical curve, according to the typical curve that obtains and the Ct value of transgenosis sample, calculates the quality of Ms1Rf1 genomic dna, thereby calculates the content of Ms1Rf1 in sample.All fluorescent quantitation reactions all repeat 3 times.
3. experimental result
1) pcr amplification and the sequencing analysis of transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence
Utilize AP1/RB1 and AP2/RB2 combination of primers, the GenomeWalker library that makes up with the Ms1Rf1 genomic dna is a template, and successfully amplification obtains the 1116bp amplified production.To PCR product order-checking, and analyze through Blastn, find wherein 330 base pairs and different sources carrier sequence homology, its right margin tumor-necrosis factor glycoproteins is lost, and all the other 786 base pairs and Chinese cabbage genome sequence homology are considered to the rape genome sequence.Concrete transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence is seen SEQNO.1.
According to above analysis, the sequence that the present invention separates acquisition comprises transgene rape exogenous origin gene integrator incident Rf1 right margin binding site, and its binding site characteristic sequence as shown in Figure 1.
2) utilize the event-specific qualitative PCR detection method that sequences Design transgene rape exogenous origin gene integrator incident Rf1 and transgene rape kind Ms1Rf1 are provided among the present invention
With different sources transgene rape, non-transgenic rape genomic dna is template, utilizes exogenous origin gene integrator incident Rf1 Auele Specific Primer combination Rf1RG and Rf1RV, carries out pcr amplification, result such as Fig. 2.Have only the Ms1Rf1 genomic dna can amplify special PCR product, and other transgenosiss and non-transgenic rape DNA all there are not amplified production can be observed when doing template, comprise the Ms8Rf3 kind with similar gene element and sequence.Be template with other non-rape plant genome DNAs simultaneously, also do not have the visible pcr amplification product.Therefore, we think that this combination of primers has good specificity, are suitable for the detection of event-specific.
3) utilize the event-specific quantitative PCR detecting method that sequences Design transgene rape exogenous origin gene integrator incident Rf1 and transgene rape kind Ms1Rf1 are provided among the present invention
According to the gradient dilution template, the fluorescence curve information that repeats to obtain for 3 times is established at the specificity fluorescent quantitative PCR reaction normal curve of exogenous origin gene integrator incident Rf1, as shown in Figure 3, and its R
2Value is 0.998, shows that the copy number of foreign gene and fluorescence intensity all have good corresponding relation, are suitable for the accurate quantification of foreign gene.
In order to verify the accuracy of the quantivative approach of setting up in this research, we have used the genomic dna that extracts from standard transgenic rape Ms 1 Rf1 product to be diluted to certain content with non-transgenic rape genomic dna, and do contrast with the same amount genomic dna that does not contain transgenic rape Ms 1 Rf1 genomic dna, template as the real-time fluorescence quantitative PCR reaction, and, calculate the content of transgene rape Ms1Rf1 genomic dna in the different samples according to the typical curve that the same terms obtains down.
With the non-transgenic rape genomic dna that do not contain transgenic rape Ms 1 Rf1 is template, does not have amplified production to be detected.For mixed laboratory sample, detect with setting up exogenous origin gene integrator incident Rf1 specificity fluorescent quantitative detecting method in this research, all very approaching with theoretical value, error is less than 15%.
Above result as can be seen, the present invention has been for the quantitative detecting analysis of transgene rape incident Rf1 and transgenic rape Ms 1 Rf1 provides based on simple, measuring method reliably, can be used for the mixed product transgene rape exogenous origin gene integrator incident Rf1 of different sources, different content and transgene rape kind Ms1Rf1 quantitatively.The present invention provides a kind of useful reference for transgenosis sign, provides necessary means to the control of transgenic product.
Sequence table
＜110〉Inst. of Oil Crops, Chinese Academy of Agriculture
＜120〉transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence and application thereof
<160>1
<210>1
<211>1116
<212>DNA
＜213〉rape (Brassica napus cv.Ms1Rf1)
<400>
gcttggacta?taatacctga?cttgttattt?tatcaataaa?tatttaaact?atatttcttt 60
caagatggga?attaacatct?acaaattgcc?ttttcttatc?gaccatgtac?gtaagcgctt 120
acgtttttgg?tggacccttg?aggaaactgg?tagctgttgt?gggcctgtgg?tctcaagatg 180
gatcattaat?ttccaccttc?acctacgatg?gggggcatcg?caccggtgag?taatattgta 240
cggctaagag?cgaatttggc?ctgtagacct?caattgcgag?ctttctaatt?tcaaactatt 300
cgggcctaac?ttttggtgtg?atgatgctga?ctgggtgagg?atgatgagtc?gcgtgtagtc 360
accggaaaag?atggaaaagg?gttcttcgcc?tgctacatct?tgacctccct?tagccctcgt 420
cacaagggtc?acacctatat?cgggtactcc?ttctactttc?tcttccctat?gatctgtcct 480
tctttccaaa?tcctcgaaac?agaggatcat?gttctgttat?gaagttaccg?atctgaaatg 540
aactgatgct?tgtctgatca?aattggctac?tccctcttgg?tcaaatctga?atttagactt 600
caagatgttg?ctttactgct?gaaattggtt?aagtaacggt?ttggtattac?aggttcacgg 660
ttaacccaaa?gcggagaata?aggcagcaca?atggagagat?aaggagtggt?gcatttagaa 720
ctaagaagaa?acgtccttgg?gaaatggtcc?tctgtatctt?tggtttccct?accaacgtct 780
ctgcccttca?ggttcccttt?gatcttcgat?accgcccaag?cttcagtctt?tataataata 840
atcaccaatt?cctggctaaa?gctccttgct?ttcttgtcct?ctgtgcagtt?tggagtgggc 900
ttggcagcat?cccagagaat?ctcggtgcag?tggcgagaag?ctgctgctgc?tttaaatctt 960
ctctggactt?gcaacgcaga?atcagctgcc?taacccattg?cttacctcag?cctggattag?1020
ttaagaagat?aaagctctgg?tgtggttaag?ctgagaatcg?ttaaattacg?gactacgtat?1080
tctctcggtg?cttgtgacag?cttgaaacct?gtgaag 1116
Claims (2)
1, a kind of transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence is characterized in that:
(1) the 1st to 330 base derives from the exogenous insertion vector sequence among the SEQ.ID.NO.1;
(2) the 331st to 1116 base derives from the rape genome sequence among the SEQ.ID.NO.1;
(3) origin comes from the 1st to 330 base of exogenous insertion vector and derives from the common dna sequence dna of forming of the 331st to 1116 base of rape genome sequence, is transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence.
2, by the application of the described a kind of transgene rape exogenous origin gene integrator incident Rf1 exogenous insertion vector flanking sequence of claim 1, it is characterized in that:
(1) utilize this sequence signature to design the event-specific qualitative PCR detection method of transgene rape exogenous origin gene integrator incident Rf1;
(2) utilize this sequence signature to design the event-specific quantitative PCR detecting method of transgene rape exogenous origin gene integrator incident Rf1;
(3) utilize this sequence signature to design the strain specificity qualitative PCR detection method of transgene rape kind Ms1Rf1;
(4) utilize this sequence signature to design the strain specificity quantitative PCR detecting method of transgene rape kind Ms1Rf1.
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| WO2012075429A1 (en) | 2010-12-03 | 2012-06-07 | Dow Agrosciences Llc | Stacked herbicide tolerance event 8291.45.36.2, related transgenic soybean lines, and detection thereof |
| EP3382028A1 (en) | 2010-12-03 | 2018-10-03 | Dow AgroSciences LLC | Stacked herbicide tolerance event 8264.44.06.1, related transgenic soybean lines, and detection thereof |
| CN102212540B (en) * | 2011-03-31 | 2013-03-20 | 中华人民共和国上海出入境检验检疫局 | Standard molecule simultaneously adapting to specificity detection on seven transgene rape strains |
| TW201317353A (en) | 2011-07-13 | 2013-05-01 | Dow Agrosciences Llc | Stacked herbicide tolerance event 8264.42.32.1, related transgenic soybean lines, and detection thereof |
| CN102888398B (en) * | 2011-07-22 | 2014-03-05 | 中国农业科学院生物技术研究所 | Flanking sequence of exogenous insertion fragment of transgenic rice variety Bar68-1 and application thereof |
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| CN1420181A (en) * | 2002-10-11 | 2003-05-28 | 覃文 | Probe sequence and kit for real time fluorescence PCR detection of transgenic rapeseed |
| CN1480538A (en) * | 2002-09-04 | 2004-03-10 | 中华人民共和国上海出入境检验检疫局 | Quantitative measuring transgene component in transgene rapeseed and processed product |
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| CN1480538A (en) * | 2002-09-04 | 2004-03-10 | 中华人民共和国上海出入境检验检疫局 | Quantitative measuring transgene component in transgene rapeseed and processed product |
| CN1420181A (en) * | 2002-10-11 | 2003-05-28 | 覃文 | Probe sequence and kit for real time fluorescence PCR detection of transgenic rapeseed |
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| Title |
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| 中国转基因油菜的环境安全性分析. 卢长明等.农业生物科技学报，第13卷第3期. 2005 * |
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