Morphological characterization is the first step in description and classification of the germplasm. But biochemical markers like isozymes, resistance to chemicals and seed storage proteins are also being used for genotyping studies in plant breeding. Now days, molecular markers are the markers of attention for advanced research. These can be classified into two categories including non-Polymerase Chain Reaction (PCR) based techniques and PCR-based techniques. Several new array chip techniques that utilize DNA hybridization coupled with labeled nucleotides and Next-Generation sequencing techniques have also been developed. The techniques that are promising for plant genotyping are the Restriction fragment length polymorphism (RFLP), Amplified Fragment Length Polymorphism (AFLP), Random Amplified Polymorphic DNA (RAPD), Microsatellites or Simple Sequence Repeat (SSR), and Single Nucleotide Polymorphism (SNP). The choice of a molecular marker technique depends upon the reliability, ease of analysis and level of polymorphisms. The merger of genetics and genomics has unraveled the new insights by defining various metabolic, regulatory and developmental pathways, but rigorous investigations still need to be completed.
