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Protocols in ecological and environmental plant physiology


Article << Previous     |     Next >>   Contents Vol 41(8)

Retrotransposon-based molecular markers for assessment of genomic diversity

Ahmed M. Alzohairy A, Gábor Gyulai B, Mohamed F. Ramadan C, Sherif Edris D E F, Jamal S. M. Sabir D, Robert K. Jansen D G, Hala F. Eissa H I and Ahmed Bahieldin D F J

A Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt.
B Institute of Genetics and Biotechnology, St. István University, Gödöllő, H-2103, Hungary.
C Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
D King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia.
E Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia.
F Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt.
G Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
H Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
I Faculty of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt.
J Corresponding author: Email: bahieldin55@gmail.com

Functional Plant Biology 41(8) 781-789 http://dx.doi.org/10.1071/FP13351
Submitted: 6 December 2013  Accepted: 19 February 2014   Published: 9 April 2014

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Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in ‘repeat seas’ or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).

Additional keywords: IPBS, IRAP, molecular markers, RBIP, REMAP, retrotransposon, SSAP.


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