"Molecular Marker: A Simplest Pathway To Go Inside GenomeAbstract: The application of molecular markers in genotyping and utilisation of DNApolymorphism is one of the most historic progress in the area of moleculargenetics. The existence of numerous kinds of molecular markers, and alterationsin their values, methodologies, uses and principle require vigilant concern inchoosing one or more of such procedures. In spite, we had several markers butstill, none of them are accessible that fulfils all of the necessities required byinvestigators. In this review, we will effort to feature principle regardingdifferent type of molecular marker or DNA fingerprinting markers like RFLP,RAPD, AFLP, ISSRs, SCARs, SRAP, STSs, CAPS, SSRs, SSCP, ESTs, TRAP,RAMP, SNPs, and DArT. A new class of progressive techniques has developed,mainly resulting from the combination of previous basic techniques. Progressivemarker techniques are likely to merge valuable features of numerous basictechniques. These newer methods also integrate alterations in the procedure ofbasic techniques to upsurge the understanding and resolution to identify geneticdiscontinuity and uniqueness.Keywords: Molecular markers, DNA Fingerprinting, RFLP, ISSR,RAPD, SSR, RAMP, EST, DArT.Introduction:Plant genetic resources use in conservation requires specific documentation oftheir accession. The intense progress in molecular biology in the last few yearshave provided researchers easy and valuable method in the preservation of PGR(plant genetic resources) with a variety of new procedures for easy andconsistent documentation of plant species. The development of DNA-basedmolecular markers has transformed the species identification methods (Botsteinet al. 1980). Usage of biotechnological tools like the PCR (Polymerase ChainReaction) and restriction enzymes in several mishmashes has been utilised toimprove several approaches of DNA fingerprinting. DNA molecular markersused in DNA fingerprinting arrays are alleles at particular loci at where there issequence differences or polymorphism present among genotypes that aretypically impartial in relationships of the phenotype. Thus it documentsuniqueness establishment for detailed individualization in examination validityin different plants species. Molecular markers contain biochemical likesecondary metabolites and enzymatic yields in plants and deoxyribonucleicacids and ribonucleic acids. Examination of secondary metabolites is limited toonly those plant life that yields an appropriate range of metabolites that can besimply studied and which can discriminate among varieties. These metabolitesthat are utilised as a molecular marker should be preferably impartial to environmental special effects or managing practices. Properties required forperfect DNA markers comprise co-dominant inheritance, numerous existencesin the genome, easy accessibility (availability), highly polymorphic nature,stress-free and fast assay, high reproducibility, and easy interchange of databetween different laboratories (Joshi et al. 1999). Hence, among the usedmolecular markers, DNA markers are more appropriate and ubiquitous toutmost of the living organisms.Hybridization-Based Molecular Markers:RFLP (Restriction Fragment Length Polymorphism) Among hybridization-based molecular marker, RFLP is the utmost widely used.In plant genome, it was first time used in 1975 to recognise DNA sequencepolymorphisms for genetic mapping study (Helentjaris et al. 1986). Theuniversal principal of RFLP technique (FIG 1) is to recognised restrictionenzymes site that exposes a configuration difference between DNA sequencesizes in individual organisms. Due to having insertion/deletion, point mutation,inversion, translocation and duplication in the genome that will always differ atonly a few nucleotides among two individuals of the similar species have almostalike genomes. Specific differences in the DNA sequences at the restrictionpositions can effect in the gain, or loss of a restriction site. Therefore, thebreakdown of DNA with restriction enzymes consequences in fragmentsproduction that’s number along with size can vary amongst individuals, populations, and species. Thus RFLP procedure based on probe-basedhybridization documentation of polymorphism is completed by following stepslike Isolation of DNA from plant material, restriction enzymes digestion, sizeidentification on a gel by using electrophoresis, transmission of DNA fragmentsover hybridization membrane, and hybridization of labeled SS (Single Stranded)markers probe to its single stranded DNA match on the filter. Such hybridisedprobe is further washed off, and the filter exposed to X-ray film to generate anautoradiogram. The bands noticeable on an autoradiogram signify the restrictionfragments of the digested DNA that comprise the sequences homologous to thecloned sequences which were used as the probe. RFLP study is a remarkablytrustworthy technique for DNA fingerprinting and for outlining geneticrelationship. The principal benefit of RFLP is that this method is robust andvoluntarily transferable between laboratories. However, the widespreadapplication of RFLP is limited due to several restrictions.Limitations using RFLP include prerequisite of high quantity 40-200 microgramDNA having good purity requiring large scale isolation which seems to betiresome and laborious, it totally depends on the construction of specificlibraries probe for the species, its polymorphism level is limited, and rare lociare identified per assay, envelopment of radioactivity, time consumingprocedure, laborious, and costly inclusive very lengthy procedure.This procedure has been extensively used in understanding genetic dissimilarity and phylogenetic relationships amongst populations, varieties and species(Wang and Tanksley 1989; Nakano et al. 1992; Wang et al. 1992; Zhang et al.1992; Doi et al. 1995). RFLP study also offers a valuable tool for calculating theextent of the genetic diversity between and within populations or species. (Caiet al. 1996) examined the genetic diversity study of three different naturalpopulations of CWR from different regions of the world by means of 15 probes.Huang et al. (1996) related 700 Chinese local lines from six distinctgeographical regions and specified that the Yunnan varieties had the maximumgenetic diversity. "