Genetic markers have always been useful tools for characterization of germplasm in plant genetic resources as they help in understanding the variability present within and between populations and individuals belonging to a species. Knowledge on genetic variation provides useful insights into taxonomy, mapping and phylogeny of plant species.
Each individual has a unique genome when observed at the nucleotide sequence level. Thus, the molecular markers derived from DNA molecule become extremely useful with high information content, and have an added advantage of unlimited supply. A wide variety of techniques to visualize DNA sequence polymorphisms have been developed in the past few years such as RFLP, RAPD, ISSR, STMS, AFLP, and SAMPL.
Advantages:
Generating molecular markers at the DNA level as compared to using morphological characters or allozymes as genetic markers, has several advantages:
- Heritable
- Easy to score
- Free from developmental and environmental influence
- Detectable in all tissues
- Insensitive to epstatic or pleiotropic interactions Provide a choice of codominant (simultaneous detection of various alleles) or dominant (does not convey any allelic information) markers.
Types:
Variations at DNA level can be studied by various means; the most direct strategy is the determination of nucleotide sequence. DNA sequencing provides a highly reproducible and informative analysis of data, and can be adapted to different levels of discriminatory potential by choosing appropriate regions of the genome. Unfortunately, DNA sequencing is comparatively difficult/laborious as well as expensive (though fluorescence technology has made the process faster and easier, the sequencing equipment is still expensive). Several alternative means for evaluating DNA sequence variation have been derived. The most prevalent among these techniques for plants is DNA profiling or fingerprinting which is a multi-locus approach of visualizing DNA polymorphisms.
Many different DNA based molecular techniques have been employed to provide polymorphic markers for the direct evaluation at genome level. They constitute a toolbox, from which ‘implements’ may be selected to address problems in required fields. One may feel overwhelmed by the number of different DNA markers currently available. Most molecular markers fall into one of two basic categories that use either hybridization technique or are based on Polymerase Chain Reaction (PCR).
Applications:
Short term applications:
- Identification and discrimination of genotypes
- Cultivar identification
- Germplam analysis
- Taxonomical status evaluation
- Selection of parents for breeding programmes
Long term applications: - Generation of linkage maps
- Tagging of simple and compound traits
- Synteny mapping
- Marker-assisted selection for breeding
