Maize (Zea mays L.) is a staple food for millions of people all over the world. Breeding for improved protein quality in maize began in the mid-1960s with the discovery of mutants, such as opaque-2. The homozygous o2 (opaque2) mutant causes a decrease in the production of endosperm alpha-zein protein and an increase in the proportion of non-zein proteins that naturally contain higher levels of lysine and tryptophan. Maize with improved protein quality due to its superiority in lysine and tryptophan content which occurred due to opaque-2 gene is referred to as QPM or Quality Protein Maize. As many negative effects of o2 modifying genes such as poor pest resistance starchy endosperm mutants came to know, breeders worked to identify genotypes that restore the vitreous endosperm phenotype in o2 background. The most effective o2 modifier genes provided the background for QPM. Marker-assisted selection (MAS) for QTLs in breeding could be undertaken in maize. The accuracy of QTL mapping can be improved by increasing population sizes and the number of testing environments, but these same techniques also improve conventional phenotypic selection. Therefore, MAS for polygenic traits is mainly restricted to situations where phenotypic selection cannot be easily implemented. The use of molecular markers offers great savings as it is not necessary to phenotypically screen the progeny for the desired character so we don’t have to wait for plant to reach certain maturity level but they can be screened at young stage also the number of backcross to elite parental lines can be reduced.