Molecular mapping is a technique used to locate the markers in the genome. The marker is feature of nucleotide in the genome. The technique facilitates to hasten the transfer of desirable genes between varieties and to identify the novel genes from wild species in to the cultivated crops. These molecular markers are method of analysis such as hybridization based molecular marker and PCR based molecular marker.
The technique is based on principle of hybridization between two complementary DNA molecules. Restriction fragment length polymerase (RFLP) is one, widely used hybridization based molecular marker. The genomic DNA is fragmented into small fragments withrestriction enzyme/s. The restricted fragment blotted on nylon/ nitrocellulose membrane from DNA resolved on agarose gel. The immobilized DNA fragments were hybridized with labeled probe (s). The labeled probed that hybridizes with one/more of the blotted DNA sample, thus revealing a unique blotting pattern characteristic to a specific genotype at specific loci. The amplified RFLP product resolved in agarose/polyacrylamide gel electrophoresis and based on banding pattern presence/ absence of a characters or similarity between genotypes can be studied.
PCR is a molecular biology technique for enzymatically replicating small quantity of DNA without using a living organism. Here an oligonucleotide fragment of 20-24 nucleotides (primer) designed. The primer can anneal and amplify a specific DNA fragment (site directed PCR markers) such as EST, CAPS, SSR, SCAR, STSs or primers can amplify the random region in the genome (arbitrary /semi arbitrary primed based PCR) such as AP-PCR, DAF, RAPD, AFLP and ISSR.