Transposons and Transposable Elements(TE) based Molecular markers

1. Transposons or mobile genetic elements are DNA sequences that displace within the genome, sometimes
creating or reversing mutations and altering the cell’s genetic identity and genome size.
• A major cause of variation in nearly all
genomes is provided by transposable
elements, or transposons.
• Present in the genomes of all life forms,
especially in plants.
• More than 50% of both human and maize
genomes are composed of transposon-
related sequences.

2. Potential Role of
Transposable
Elements
as Molecular
Markers
they cause
insertional
polymorphism
found in
almost every
living species
a large part of
the genome of
many species
consists of
transposons
Make up a determinant genetic
marker in areas such as DNA
fingerprinting, genetic mapping
and molecular phylogeny
cause
permanent
genomic
mutations such
as duplication,
deletion and
insertion
causes new
allele formation

3. • those that make cDNA copies from their RNA
transcripts and propagate to new sites
• Called as retroelements or retrotransposons
Class I type TE Class II type TE
• those that are able to propagate as DNA within
the genome
• Called as DNA type elements

4. location A
location B

6. LTR
Retrotransposons
Non - LTR
Retrotransposons
LTR LTR
RT & Integrase 5’ UTR 3’ UTR
Poly A tail
GAATTC
CTTAAG INVERTED
REPEATS

7. Inter Retrotransposon Amplified
Polymorphism (IRAP)
Sequence Specific Amplified
Polymorphism (SSAP)
Retrotransposon Microsatellite
Amplified Polymorphism (REMAP)
Inter Primer Binding Site
Amplification (iPBS)
Retrotransposon Based Insertional
Polymorphism (RBIP)
Transposable Element- Target
Region Amplified Polymorphism
(TE-TRAP)

8. REtrotransposon Microsatellite Amplified Polymorphism
(REMAP) (Kalendar et al., 1999)
Inter Retrotransposon Amplified Polymorphism
(IRAP)
To detect polymorphism in retrotransposon splices, marker systems generally rely on PCR amplification
between these conserved ends and some components of adjacent genomic DNA
• IRAP marker system products were generated
from two near retrotransposons and amplifying
region between two neighboring LTRs using
primers facing outward.
• Primers are designed using LTR region which
will anneal to dispersed members of
retrotransposons family.
Amplification based TE markers
• REMAP marker were generated using outward
facing primer from LTR and another from a
microsatellite sequence.
• Single primer from LTR and another from
microsatellite (GA)n (CT)n etc. are anchored at 3’
end.

9. Both marker systems do not require restriction enzyme to generate marker bands
Both markers are extremely polymorphic and used to determine intraspecific kinship for use
in genetic diversity studies

10. Retrotransposon Based Insertional Polymorphism (RBIP) (Flavell et al., 1998)
• A codominant marker which utilises PCR primers designed from the retrotransposon and its
flanking DNA to examine insertional polymorphisms for individual retrotransposons.
• More expensive and technically demanding
• RBIP requires information on the sequences of the 5’ and 3’ flanking regions of the retrotransposon
insertions
• Does not necessarily require a gel-based detection rather a simple dot hybridization assay can be
adapted for high throughput automated marker analysis

11. Sequence Specific Amplified Polymorphism (SSAP)
• It involves a PCR primer facing outward and
matching the 3’ end of a LTR in combination with
other an AFLP adapter primer.
• SSAP is a multiplex AFLP like approach
• In SSAP, two primers are designed to produce
amplification between RTs and adaptors ligated to
a restriction site (usually MseI or PstI)
• SSAP usually displays a higher level of
polymorphism as compared to AFLP
• Enables high quality visualization of insertions and
no. of bands formed are higher than IRAP and
REMAP
inter Primer Binding Site Amplification (iPBS)
• No need for sequence information to design IPBS
primers
• Primer Binding Sequence (PBS) is part of the
internal domain of retrotransposons
• RTs can be easily amplified using conservative PBS
primers and PCR amplification occurs between two
nested PBSs of two neighboring LTR-RTs
• Specific tRNA capture is useful for conservative PBS
sites for iPBS amplification method
(Waugh et al., 1997) (Kalendar et al., 2010)

12. Transposable Element- Target Region Amplified Polymorphism (TE-TRAP)
• TE-TRAP marker system is a modification of the conventional TRAP marker system
• TE-TRAP is a simple PCR-based marker technique
• It utilizes class 2 type TE (DNA type elements) as a fixed primer by obtaining sequence
information from superfamily and the arbitrary primer that target intron or exon regions with an
AT- or GC-rich core to amplify DNA fragments.

13. • Alzohairy, A. M., Gyulai, G., Mustafa, M. M., Edris, S., Sabir, J. S. M., Jansen, R. K., & Bahieldin, A. (2015).
Retrotransposon-based plant DNA barcoding. Plant DNA barcoding and phylogenetics, 91-105
• Regina, R. K. T. G. M., & Schulman, A. S. A. (1999). IRAP and REMAP: two new retrotransposon-based DNA
fingerprinting techniques. Theor Appl Genet, 98(704), 711
• Arvas, Y. E., Abed, M. M., Zaki, Q. A., Kocaçalışkan, İ., & Haji, E. K. (2021, May). The potential role of transposable
elements as molecular markers. In IOP Conference Series: Earth and Environmental Science (Vol. 761, No. 1, p.
012031). IOP Publishing
• Im, S., Kwon, S. J., Ryu, J., Jeong, S., Kim, J., Ahn, J. W., ... & Kang, S. Y. (2016). Development of a transposon-
based marker system for mutation breeding in sorghum (Sorghum bicolor L.). Genet Mol Res, 15(3), PMID-
27706735
• Flavell, A. J., Knox, M. R., Pearce, S. R., & Ellis, T. N. (1998). Retrotransposon‐based insertion polymorphisms
(RBIP) for high throughput marker analysis. The Plant Journal, 16(5), 643-650
• Kalendar, R., Flavell, A. J., Ellis, T. H. N., Sjakste, T., Moisy, C., & Schulman, A. H. (2011). Analysis of plant
diversity with retrotransposon-based molecular markers. Heredity, 106(4), 520-530.