Hybridization-Based Markers

  • B. D. Singh
  • A. K. Singh


Qualitative traits have long been used for genetic studies, including the preparation of linkage maps. They were also used as markers to identify genomic regions involved in the control of quantitative traits. Their usefulness as markers prompted the search for other more abundant, easily detectable and stable characteristics leading to the development of protein-based and, finally, DNA-based markers. In the current parlance, morphological and protein-based markers are called classical markers, while DNA markers are referred to as molecular markers. DNA-based markers represent variation in genomic DNA sequences of different individuals. Restriction fragment length polymorphism (RFLP) was the first DNA marker, but it was technically demanding and required considerable time for marker genotyping. Therefore, efforts were made to develop more user-friendly marker systems; as a result, several different marker systems like RAPDs, DAF, AFLP, SCAR, SSR, etc. were developed. DNA marker systems have been classified on the basis of different criteria, such as chronology of their development, genomic location and functional significance, and the method of marker detection. On the basis of detection method, the DNA markers are classified into three groups, viz., hybridization-based, PCR-based, and sequence-based markers. The marker systems RFLP, diversity array technology (DArT), variable number of tandem repeats (VNTRs), single-feature polymorphism (SFP), and restriction-site-associated DNA (RAD) markers are detected by DNA:DNA hybridization. This chapter is devoted to the discussion of these hybridization-based marker systems, their salient features, as well as the advantages and limitations of these marker systems.


Restriction Fragment Length Polymorphism Amplify Fragment Length Polymorphism Functional Marker Target Region Amplification Polymorphism Restriction Fragment Length Polymorphism Marker 
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© Author(s) 2015

Authors and Affiliations

  • B. D. Singh
    • 1
  • A. K. Singh
    • 2
  1. 1.School of BiotechnologyBanaras Hindu UniversityVaranasiIndia
  2. 2.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia

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