The document discusses several strategies for removing selectable marker genes from transgenic plants while retaining the gene of interest: 1. Site-specific recombination-based strategies use recombinases like Cre/lox to excise the selectable marker gene flanked by recombinase recognition sites. 2. Transposon-based strategies use transposable elements like Ac/Ds to mobilize and separate the selectable marker from the gene of interest. 3. Homologous recombination-based strategies induce double-strand breaks that can be repaired through homologous recombination, replacing the selectable marker with the desired gene.

1. Chapter-6:Elimination selective marker
from trangenic plants
 Following the production of transgenic plants, the
selectable marker gene(s) used in the process are
redundant,and their retention may be undesirable.
 Several strategies can be used to remove selectable
markers from transgenic plants, while retaining the gene of
interest (GOI).
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2. The strategies that can be used to
remove selectable markers from transgenic
plants the following :
site-specific recombination based
Transposon based systems
Intrachromosomal recombination
system based
Transformation without selection
Co-transformation of a marker gene
Homologous recombination
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3. site-specific recombination
 site-specific recombination based method
in which the transformation cassette
comprises, in addition to the GOI, the
selectable marker flanked by specific
recombinase recognition sites.
 Microbial site-specific recombinases have
the ability to cleave DNA at specific sites
and ligate it to the cleaved DNA at a
second target sequence.
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4.  The excision of foreign DNA that is placed in
between recognition sites in a direct repeat
orientation has been used to eliminate
unwanted transgenic material from the nuclear
genome of plants.
 The most used recombination systems are:
Cre/lox from bacteriophage P1
 FLP/FRT from Saccharomyces cerevisiae and
R/RS from Zygosaccharomyces rouxii[.
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5.  These systems are belonging to the tyrosine recombinase
family .
 After the reaction, a recombination site (lox, FRTor RS) is
remaining in the genome and it could potentially serve as a
site for integrative recombination.
 However, re-insertion of the elimination fragment has not
been detected , probably because excision is an
intramolecular event, whereas integration needs
interaction between unlinked site and second, the excised
circle cannot replicate autonomously and is probably
rapidly lost in vivo
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6.  The site-specific recombination systems can be
divided in two categories according to the position of
the recombinase gene:
The recombinase gene and the selectable
marker are on a different vector and the
recombinase gene is delivered to the plant
containing the SMG by re-transformation or
by sexual crosses .
The selectable marker and the recombinase
genes are on the same vector between the
recombination sites
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7.  .
Figure :Removal of selectable marker genes through site specific recombinases.
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8.  In a second category of methods using site-specific
recombination, the selectable marker and the recombinase
genes are on the same vector between the recombination sites
 This system is often referred to as “auto-excision” or self-excision
.
 The auto-excision strategy is a versatile system that could be
applied in every species and that shows flexibility in spatial
and temporal control.
 The expression of the recombinase gene can be induced by either
external or intrinsic signals resulting in auto-excision of both the
recombinase and marker genes placed within the excision site
boundaries after their function is no longer needed.
 The control of excision is enabled by the regulated promoter used to
control the recombinase gene.
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9. Figure 4.
Site-specific recombinase based auto-excision systems.
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10. Limitation of both system
 they require a time-consuming and labor-intensive breeding step,
and
 they are only applicable to sexually reproducing species or some
species where the retransformation is available.An alternative
approach depends on the expression of the recombinase transiently
with a modified plant virus carrying the cregene (PVX-Cre); as well
as in kanamycin resistant tobacco with aTMV-Cre .This method can
be applied to vegetatively propagated and long life cycle plants, but
the lack of virus-based transformation system in these species is a
drawback that should be improved in the future.
 that Cre can catalyze recombination between certain naturally
occurring “pseudo-loxsites” that can be highly divergent from
the loxconsensus sequence.
 This toxic effect was also investigated in creexpressing transgenic
plants where a correlation was found between aberrant phenotypes
and constitutive creexpression
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12. 12

13. 13

14. Transposon based systems
 This an approach in which the selectable marker gene
is flanked by sequences recognized by a transposase,
so that when the cassette is introduced, the selectable
marker is mobilized to a new location in the genome,
thereby becoming separated from the GOI.
 Controlling elements may be grouped into families.The
members of each family may be divided into two classes:
autonomous elements or non-autonomous elements.
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15. 15

16.  Autonomous elements have the ability to transpose whereas
the non-autonomous elements are stable (but can transpose
with the aid of an autonomous element through trans-
activation)
 Two mutations:
 dissociation (Ds) : The Ds element is
located on chromosome 9and it has the
effect of causing chromosome breakage
at a point on the chromosome adjacent
to its location
activator (Ac):Ac is capable of autonomous
move ment, but Ds moves only in the
presence of Ac.
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17. 17

18.  Transposable elements (e.g. Ac/Ds from maize) can mediate
repositioning of genetic material in the plant genome.
The Ac/Dstransposable element system has been used for relocation
and elimination of a selectable marker in tomato and rice].
Transposable elements can be excised from the genome after the
expression of the transposase; they can either re-insert or not (Fig.
2).Taking into account these options, two approaches can be
followed. In the first one, if one counts on re-insertion of the
transposon, the gene of interest (GOI) is placed on the transposable
element.Thus, the GOI will be excised and can be reinserted in a
locus that is not linked to the locus in which the selectable marker
gene is located; they can be segregated in the next generation
[47, 49]. In a second approach, one relies on the fact that the
transposon will not be re-inserted [50].An example of such a
system is the one described by Ebinuma et al. [51], in which
the iptselectable marker gene was inserted in an Acderivative.
However, marker-free transgenic pl
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19. Fig:Transposon-mediated repositioning of the
SMG
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22. 22

23. Draw backs:
 The transposition efficiency is variable in different species.
 The method is labor intensive and time consuming
because it requires crossing transgenic plants and the
selection of the progeny
 The method shows low efficiency of marker gene
elimination because of the tendency of transposable
elements to reinsert in positions genetically linked to the
original position.
 The systems are the genomic instability of transgenic plants
because of the continuous presence of heterologous transposons
and the generation of mutations because of insertion and excision
cycles. Transposition can induce genome rearrangements, including
deletions, inverted duplications, inversions, and translocations
 The system cannot be used for sterile plants and
vegetative propagated species and is impractical for plants
with a long life cycle.
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25. 25

26. Transformation without selection
 The most straightforward method to obtain marker-free plants is to
transform without any selectable marker gene.
 However, most of the transformation protocols described are inefficient
and just few cells integrate the foreign DNA. Nonetheless, some groups
have studied the feasibility to obtain transgenic plants omitting
selection.
 De Buck et al. failed to obtain any transgenic plants
when Arabidopsisroots were transformed via A. tumefaciensand shoots
regenerated on non-selective media. However, in tobacco protoplast
transformation, these authors obtained a total transformation
frequency of 18%.Transformation protocols have important influence
on these and other results. For example, in a study
where Arabidopsiswas transformed by the floral dip protocol and
seedlings were grown on non-selective media, transgenic plants could
be obtained with an efficiency of 3.5%
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27. Co-transformation of a marker gene
 The SMG and the gene of interest can be delivered
by:
(i) twodifferent Agrobacteriumstrains each
containing a binary plasmid carrying a single
T-DNA region
(ii) a single Agrobacteriumstrain, either
containing one plasmid with two separate T-
DNAs (Fig. 1C) [or
(iii) containing two separate plasmids each
containing a T-DNA
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28.  co-transformation can be achieved by particle co-
bombardment .
 The co-transformation strategy is limited
because :
co-integration of both T-DNAs at the same
genomic locus is frequently observed leading
to linkage between the marker and the
transgene, which makes their segregation
impossible.
This phenomenon has even more frequently
been observed with particle bombardment-
mediated transformation.
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29. The methods cannot be applied to
sterile plants and vegetatively
propagated species, and are not
practical in plants with a long life
cycle such as trees
The approach requires the generation
of many transformants (to find unlinked
marker genes and genes-of-interest) and
 Crossing steps (to remove the marker
gene) making it a labor intensive work.
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31. 31

32. Homologous recombination
 This method is based the DNA repair machinery of plant
cells. Indeed, efficient repair of double-strand breaks (DSBs)
is important for survival of all organisms.
 DSBs can be repaired via :
homologous recombination (HR) or
non-homologous end-joining (NHEJ) .
 The ratio of HR to NHEJ events increases if homologous
sequences near the brake are available .
 During the repair process the gene can be converted or
deleted.
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