This document discusses methods for analyzing transgenic plants, including determining if a plant is transgenic and if transgenes are expressed. It describes established methods like PCR, Southern blots, and Northern blots. Southern blots are used to confirm transgene insertion into the genome by detecting fragments of different sizes after restriction enzyme digestion and gel electrophoresis. Northern blots detect RNA transcripts to confirm transgene expression. Proper experimental design and controls are important to avoid false positives and obtain conclusive evidence of stable transgene integration and expression.

1. Lecture 18, Chapter 11
Analysis of transgenic plants
part I
Mat Halter
3/27/12

2. Discussion questions
1. What are the established methods to determine if a plant is transgenic and
whether the transgene(s) is expressed?
2. In a Southern or northern blot, through what type of chemical bond does
the complementary probe bind to nucleic acid?
3. Nucleic acids and proteins are separated according to size in agarose and
sodium dodecyl sulfate–polyacrylamide gel electrophoreisis (SDS-PAGE)
gels, respectively. Why do both types of macromolecules migrate
toward the anode in an electrical current?
4. What is gene expression, and how can you measure it?
5. Explain why phenotypic data provide evidence of transformation but not
proof of a transformation event.
6. What factors are most important when designing a Southern blot
experiment to test for transgenic status?
Is my plant transgenic?

3. P
Visual
Selection T P
Antibiotic
Selection T P
Gene of
Interest T
LB RB
Visual Selection
(ex. OFP)
Antibiotic Selection
(ex. Hygromycin)

4. Fluorescent Proteins
http://en.wikipedia.org/wiki/File:FPbeachTsien.jpg

5. Visual selection using FPs
T+ T- T- T+

6. Antibiotic Selection
• When a mixture of transformed and
untransformed callus is placed on antibiotic
selection media, only the transformed callus
carrying the antibiotic selection cassette is
able to survive and grow.
• In most cases, the untransformed callus dies,
making it “easy” to select for callus carrying
the T-DNA.

7. Figure 9.3
Sometimes “escapes” occur– for kanamycin
resistance markers tissue is red—very stressed

8. Is my plant transgenic?
• Surviving selection—but remember that there can be
escapes. Need more proof besides surviving
selection.
• Reporter genes—better. But there must be a
reporter gene in the vector.
• All around easy test—PCR. But what if
Agrobacterium survives in low amounts in the T0
plants? Could give a false positive band. PCR is ok for
biolistics.
• Can do PCR on T1 plants or look at segregation of the
transgene.

9. GFP+Bt segregation
Using GFP screening to “see” Bt when the transgenes are linked. Nat Biotechnol 17:1125

10. Stable integration of transgene
• Transgene is permanently integrated into the
genome of the host plant.
• Transmitted to progeny (Tn plants) in
Mendelian fashion
• Need convincing proof of stable integration
• Multiple assays are possible—but most
researchers are best convinced by Southern
blot data.
Why all the mystique and skepticism?

11. Good reasons for doubt
• New methods don’t always work, but wishful
thinking takes over (see Chapter 10 section—
the Rush to Publish)
• Resilient Agrobacterium can linger
• The unexpected can be tricky.
• Others?

12. Molecular characterization of
transgenic plants
• PCR- Simplest and fastest method. Prone to false
positives.
• Southern Blot- Confirms insertion of the tDNA into the
genomic DNA of the target organism, as well as
provides insertion copy number.
• Northern Blot- Confirms the presence of RNA transcript
accumulation from the transgene of interest.
• Western Blot- Confirms presence of the PROTEIN
produced from the inserted transgene of interest.
• qRT-PCR- Provides a relative expression level for the
gene of interest—transcript—like Northern blot.

13. PCR and
DNA Gel Electrophoresis
PCR- Polymerase chain reaction, uses DNA primers to
amplify a target sequence of DNA, producing billions of
copies of identical DNA.
Gene cloning Molecular
analysis
(Confirmation of the presence
of a particular fragment of
DNA in a pool of DNA)

14. PCR analysis by gel electrophoresis
-
-
-
-
-
-
-
-
+
+
+
+

15. Gel electrophoresis
• The migration of DNA through an Agarose matrix using the
application of an electric field.
• Agarose, when solidified in a gelatin form, produces a thick
netting that allows small particles to move through it quickly,
while larger particles move more slowly.
• By moving particles of different size through the agarose gel,
they can be separated, with the small particles moving quickly
away from the slower moving large particles.
• This method is used to separate DNA fragments by size.

16. PCR analysis by gel electrophoresis
500 bp
750 bp
1000 bp
1500 bp-
+
Ladder Sample

17. PCR and False Positives
Genomic DNA
Transgenic plant produced from
Agrobacterium-mediated
transformation
• In T0 plants, Agrobacterium left over from the initial
transformation is still present in all tissues.
• Contamination of the genomic DNA with the initial transformation
vector that is still present in the agrobacterium can produce a PCR
band.

18. Southern Blot
• Southern blotting confirms the presence of
the gene of interest in the genomic DNA of
the target plant and avoids the pitfalls of
potential false positives.
• Steps
– Genomic DNA isolation
– Restriction enzyme digestion of genomic DNA
– Running digested DNA on agarose gel to separate
fragmented DNA by size.
– Transfer of separated DNA to nylon membrane
– Hybridization with radioactive DNA probe

19. Restriction Digestion of Genomic DNA
• Restriction digestion of genomic DNA produces a
streak on an agarose gel rather than a single band.
Why?

20. Example: EcoRI
• What is the probability of a sequence of DNA in a plant
genome having the sequence of bases corresponding to an
EcoRI cut site?
• Each site can be 4 possible bases (A, T, C, or G), and the EcoRI
enzyme requires 6 sites (GAATTC)
• The probability of finding a random site in a genome that
happens to have the sequence GAATTC can be calculated:
1⁄4 x 1⁄4 x 1⁄4 x 1⁄4 x 1⁄4 x 1⁄4 = 1⁄4096
• Probability states that there will be an EcoRI cut site once
every 4096 bases, purely by chance.

21. EcoRI example, cont.
• The Arabidopsis thaliana genome is roughly 157,000,000 base
pairs in size.
157,000,000⁄4096 = 38,330
• Though this value is only based on probability, and therefore
may not be the TRUE number of EcoRI cut sites in this
genome, it can still accurately be assumed that there are A
LOT of cut sites.
• If restriction digested with EcoRI, the arabidopsis genome
would be cut into tens of thousands of pieces, all of unique
size.
• This is why when you run a sample of digested genomic DNA,
you see a streak, rather than a band. The streak shows all
sizes of DNA produced by the random assortment of cut sites
within the genome.

22. Digested Genomic
• Essentially, every known
restriction enzyme will have cut
sites in a plant genome.
• How can enzyme selection be
used to detect copies of an
inserted transgene?
LB RB
DNA Probe
EcoRI Site
• Single cutting enzymes can be
designed into the T-DNA before
transformation that will enable
proper digestion of the genome as
well as a single cut within the T-
DNA.

23. Southern Blotting
Isolated genomic DNA from transgenic plant
Restriction enzyme digest
+
-
Gel electrophoresis

24. Southern Blotting
Transfer separated DNA from agarose gel to nylon
membrane
Agarose Gel Nylon Membrane

26. Southern Blotting
• The DNA probe is designed to be
complimentary to your gene of
interest.
•It is synthesized using radioactive
phosphorus, which emits a
detectable signal.
•The complimentary probe will
bind (by hydrogen bonding) only
to your gene of interest because of
the high sequence specificity.
Hybridizing the DNA probe

27. Southern Blotting
Lane 1- Ladder
Lane 2- Negative Control
Lanes 3-8- Experimental Events
• Bands at different places
from event to event indicate
insertion at different places
in the genome.
• The number of bands in
each well indicates how
many insertions there were
in each event.
The Final product

28. Why is a single cut within the T-DNA
necessary?
LB RB RBLB RB
EcoRI Site EcoRI Site
If there is no EcoRI site within the tDNA, after digestion with
EcoRI these two insertion sites will be indistinguishable from
one another after electrophoresis and probing.
Cutting within the T-DNA is necessary to distinguish each
and every insertion event. This is VERY important.

29. Restriction enzyme selection for
Southern blotting

30. Southern blot analysis of transgenic plants with an orange fluorescent protein
Southern analysis of mOrange plants genomic DNA.
A. Genomic DNA digested with BamHI, electrophoresed on 1% agarose
Arabidopsis Lane 1. 21-12-3-3
Lane 2. 21-12-6-1
Lane 3. 21-12-6-6
Lane 4. 21-12-7
Lane 5. 21-12-29
Lane 6. 21-12-34
Lane 7. ‘Columbia’
Tobacco Lane 1. 21-12-2-7
Lane 2. 21-12-5-5
Lane 3. 21-12-5-8
Lane 4. 21-12-6-6
Lane 5. 21-12-8-7
Lane 6. ‘Xanthi’
plasmid pMDC32-mOrange (21-12) BamHI digest
B. Transferred to nylon membrane. Hybridization to 32-P labeled probe of mOrange coding sequence. Exposed to
phosphor screen 3 weeks.
1.4
1.55
2
3
4
6
8
10
(Kb)
1
Arabidopsis Tobacco
1 3 42 5 6 7
plasmid
1 3 42 5 6
Arabidopsis Tobacco
1 3 42 5 6 7
plasmid
1 3 42 5 6
llg2007-05-02Sgel3mOrange.tif
llg2007-06-26SmOrange3wk.tif
What’s wrong?

31. Northern Blot
• Confirms the presence of mRNA transcripts
transcribed from the gene of interest in the
target organism.
• Extremely similar to the Southern blot, but
detects RNA instead of DNA.
• Steps:
– Isolation of RNA
– Running RNA on agarose gel to separate by size
– Transfer separated RNA from gel to membrane
– Hybridize a radioactive DNA probe to the RNA on the
membrane
Sound familiar?

32. Northern Blot
RNA loading controls
are necessary to
ensure an equal
amount of RNA is
loaded in each well.
No digestion
necessary… why is
this?

33. Discussion questions
1. What are the established methods to determine if a plant is transgenic and
whether the transgene(s) is expressed?
2. In a Southern or northern blot, through what type of chemical bond does
the complementary probe bind to nucleic acid?
3. Nucleic acids and proteins are separated according to size in agarose and
sodium dodecyl sulfate–polyacrylamide gel electrophoreisis (SDS-PAGE)
gels, respectively. Why do both types of macromolecules migrate
toward the anode in an electrical current?
4. What is gene expression, and how can you measure it?
5. Explain why phenotypic data provide evidence of transformation but not
proof of a transformation event.
6. What factors are most important when designing a Southern blot
experiment to test for transgenic status?