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Advances in molecular marker techniques and their applications in plant sciences

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Abstract

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.

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Abbreviations

RFLP:

Restriction fragment length polymorphism

RAPD:

Random amplified polymorphic DNA

AP-PCR:

Arbitrarily primed-PCR

DAF:

DNA amplification fingerprinting

AFLP:

Amplified fragment length polymorphism

SSR:

Simple sequence repeats

SNP:

Single nucleotide polymorphism

SSCP:

Single strand conformation polymorphism

CAPS:

Cleaved amplified polymorphic sequence

SCAR:

Sequence characterized amplified region

RAMP:

Randomly amplified microsatellite polymorphisms

TRAP:

Target region amplification polymorphism

SRAP:

Sequence-related amplified polymorphism

IRAP:

Inter-retrotransposon amplified polymorphism

REMAP:

REtransposon-microsatellite amplified polymorphism

TD:

Transposable display

MITES:

Miniature inverted repeat transposable elements

IMP:

Inter-MITE polymorphism

S-SAP:

Sequence-specific amplification polymorphism

RBIP:

Retrotransposon-based insertion polymorphism

RAP-PCR:

RNA fingerprinting by arbitrarily primed PCR

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  1. B. V. Patel Pharmaceutical Education Research and Development (PERD) Centre, Thaltej-Gandhinagar Highway, Ahmadabad, 380054, India

    Milee Agarwal, Neeta Shrivastava & Harish Padh

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  1. Milee Agarwal
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  2. Neeta Shrivastava
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Correspondence to Harish Padh.

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Communicated by P. Kumar.

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Agarwal, M., Shrivastava, N. & Padh, H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27, 617–631 (2008). https://doi.org/10.1007/s00299-008-0507-z

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