The process of developing new crop varieties through conventional breeding takes about 10 - 15 years and the invention of biotechnological tools like marker assisted selection (MAS) and genetic engineering made it possible to shorten the time period required (to 7 – 10 years) for developing new crop varieties.  Marker-assisted breeding enabled us to make remarkable improvement in the efficiency with which breeders can select plants with desirable combinations of genes. As a shortcut, plant breeders use marker-assisted selection (MAS) to select a particular trait during the process of breeding. Molecular markers are “genetic tag” that identifies a particular location in a genome that controls a specific phenotypic trait. The markers (segment of DNA) are located near the “candidate gene” and always co-segregate with the trait/gene of our interest which is called genetic linkage. This linkage helps scientists to predict whether a plant is harbouring the desired gene.

Construction of genetic linkage maps will help the scientists to learn where markers are located on a chromosome and how closely they are linked. This linkage map will help in detecting or mapping the QTL’s (quantitative trait loci) controlling the desired phenotypic trait or identifying markers linked to specific phenotypic trait. Using very detailed genetic maps, researchers can conclude whether the progeny is having the desired gene or just by analyzing the DNA extracted from the seedling. This helps to reduce the time involved in selecting the progeny by phenotype. Markers are also used to monitor introgression of desired genomic region from the donor parent into the recipient parent. This process can help us in precise transfer of many QTLs from several donors into a single recipient parent which is called as “QTL pyramiding”. 

Applications of molecular markers

• Assessment of genetic variability and characterization of germplasm
• Molecular fingerprinting of crop varieties
• Detection of monogenic and quantitative trait loci (QTL)
• Marker-assisted selection
• Identification of sequences of useful candidate genes