Professional Documents
Culture Documents
Ingham Et Al 2018 Quantitative Real Time PCR Assay For Determining Transgene Copy Number in Transformed Plants
Ingham Et Al 2018 Quantitative Real Time PCR Assay For Determining Transgene Copy Number in Transformed Plants
David J. Ingham, Sandra INTRODUCTION ues are determined during the logarith-
Beer, Stephanie Money, and mic phase of amplification, PCR
Geneviève Hansen Efficient transformation procedures reagents are nonlimiting, and reactions
for plants necessitate the development will be most efficient (2). Therefore,
Syngenta, Research Triangle of rapid assays for the analysis of the use of real-time (kinetic) detection
Park, NC, USA putative transformants. To determine techniques both simplifies and increas-
whether the insertion of the transgene is es the accuracy of quantitative PCR as-
simple (one copy) or complex (multiple says (reviewed in Reference 2).
and truncated copies), scientists have In the assay described here, we use
traditionally relied on labor-intensive duplexed TaqMan reactions to accu-
nucleic acid blotting techniques (South- rately quantitate the level of a transgene
ern blots) (16). To overcome this limita- relative to an endogenous calibrator
tion, we have developed an assay for gene. This relative quantitation ap-
transgene insertion characterization that proach provides a simplified, accurate
utilizes the speed, throughput, and alternative to using standard curves and
quantitative accuracy of the fluorogenic absolute quantitation. Because the en-
5′-nuclease assay known as TaqMan dogenous calibrator sequence remains
(Applied Biosystems, Foster City, CA, constant relative to total genomic DNA,
USA) (4,7,8,10,12). any variation in the relative level of the
The TaqMan assay is a real-time transgene to the endogenous gene is in-
ABSTRACT PCR detection technique in which the dicative of a difference in copy number.
accumulation of PCR product is moni- As shown in Figure 1, 2-fold differ-
The development of transgenic events tored directly during the progress of the ences in copy number are easily distin-
can be limited by many factors. These in- reaction. The details of the TaqMan as- guished using TaqMan technology. The
clude expression levels, insert stability and say have been described previously TaqMan copy number assay allows the
inheritance, and the identification of simple (4,8,10,12). Degradation of target-spe- screening of hundreds of plants with
insertion events. All of the factors can be re- cific probe molecules by the 5′ to 3′ ex- greater accuracy within hours as com-
lated to the copy number of the transgene. onuclease activity of Taq DNA poly- pared to weeks using conventional
Traditionally, copy number has been deter- merase during each cycle of methods. This allows greater numbers
mined by laborious blotting techniques. We amplification produces an accumula- of independent transformation events to
have developed an alternative approach tion of fluorescence. Increased levels of be screened for desired traits in shorter
that utilizes the fluorogenic 5′ nuclease fluorescence are directly related to the time and at significant cost savings.
(TaqMan) assay to quantitatively deter- accumulation of PCR product and are Advantages and limitations of the Taq-
mine transgene copy level in plants. Using detected during each cycle of amplifi- Man assay over conventional proce-
this assay, hundreds of samples can be ana- cation through the use of specialized in- dures are also discussed.
lyzed per day in contrast to the low through- strumentation (ABI PRISM 7700; Ap-
put encountered with traditional methods. plied Biosystems, Foster City, CA,
To develop the TaqMan copy number assay, USA). Cycle thresholds (Ct) are as- MATERIALS AND METHODS
we chose to utilize our highly efficient signed automatically to each sample
Agrobacterium-mediated transformation according to the cycle at which the flu- Plant Material
system of maize. This transformation proce- orescence exceeds a specific level
dure generates predominantly low copy above background (Figure 1). Samples Transgenic maize plants from the in-
number insertion events, which simplified with higher levels of template at the be- bred line A188 were obtained via
assay development. We have also successful ginning of the reaction will amplify to Agrobacterium-mediated transforma-
applied this assay to other crops and trans- detectable levels more quickly and tion. The selectable marker phospho-
formation systems. yield a lower Ct. Because threshold val- mannose isomerase (pmi) under the
TaqMan Reactions
Figure 3. Southern blot showing the correlation of TaqMan copy number assay data with Southern
analysis. (A) Graphic representation of the putative insertion event (not to scale). Open box indicates the
Agrobacterium insertion cassette with left (LB) and right (RB) borders represented by hatched boxes.
The position of the pmi gene is indicated by the filled arrow. Flanking plant genomic sequences are indi-
cated by the solid lines. Positions of EcoRV restriction sites are indicated above the T-DNA insert and at
an unknown position in the genomic DNA flanking the insert. The fragment used to generate pmi-spe-
cific probes is indicated by the speckle-filled box below the pmi gene. (B) As described in Materials and
Methods, DNA samples from 16 single-copy events as determined by TaqMan copy number assay were
digested with EcoRV, fractionated by agarose gel electrophoresis, blotted to nylon, and probed with a
pmi-specific probe. Results confirm all 16 events as single copy for the pmi transgene. Position of mole-
cular weight size markers is indicated to the left of the figure.