Plant Cell Reports

, Volume 27, Issue 4, pp 617–631 | Cite as

Advances in molecular marker techniques and their applications in plant sciences

  • Milee Agarwal
  • Neeta Shrivastava
  • Harish PadhEmail author


Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena in plants. Since the entire plant kingdom cannot be covered under sequencing projects, molecular markers and their correlation to phenotypes provide us with requisite landmarks for elucidation of genetic variation. Genetic or DNA based marker techniques such as RFLP (restriction fragment length polymorphism), RAPD (random amplified polymorphic DNA), SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphism) are routinely being used in ecological, evolutionary, taxonomical, phylogenic and genetic studies of plant sciences. These techniques are well established and their advantages as well as limitations have been realized. In recent years, a new class of advanced techniques has emerged, primarily derived from combination of earlier basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques. The newer methods also incorporate modifications in the methodology of basic techniques to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. The advanced marker techniques also utilize newer class of DNA elements such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. The review details account of techniques used in identification of markers and their applicability in plant sciences.


Molecular marker CAPS REMAP SRAP Retrotransposon-based Plant sciences Agriculture 



Restriction fragment length polymorphism


Random amplified polymorphic DNA


Arbitrarily primed-PCR


DNA amplification fingerprinting


Amplified fragment length polymorphism


Simple sequence repeats


Single nucleotide polymorphism


Single strand conformation polymorphism


Cleaved amplified polymorphic sequence


Sequence characterized amplified region


Randomly amplified microsatellite polymorphisms


Target region amplification polymorphism


Sequence-related amplified polymorphism


Inter-retrotransposon amplified polymorphism


REtransposon-microsatellite amplified polymorphism


Transposable display


Miniature inverted repeat transposable elements


Inter-MITE polymorphism


Sequence-specific amplification polymorphism


Retrotransposon-based insertion polymorphism


RNA fingerprinting by arbitrarily primed PCR


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© Springer-Verlag 2008

Authors and Affiliations

  1. 1.B. V. Patel Pharmaceutical Education Research and Development (PERD) CentreAhmadabadIndia

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