Molecular Markers are used in plant breeding to identify and select desirable traits in plants. theses markers or specific DNA sequences that can be used to track the inheritance of genes associated with particulate traits such as disease resistance yield and quality. by using molecular Markers plant breeders can more accurately select plants with desired traits and reduce the time and cost associated with traditional breeding methods. additional molecular Markers can be used to identify genetic diversity within a population which can help breeders develop new varieties that are adapted to specific environments or have improved performance under certain conditions overall molecular markers play a critical role in accelerating the development of a new plant varieties that meet the needs of farmers and consumers

Molecular markers are stretches of DNA that are located within the entire genome of an organism. Due to their stability, cost-effectiveness, and ease of use provide an enormously accepted tool for various applications such as molecular genetic diversity analysis, genome mapping, gene tagging, QTL mapping, and phylogenetic analysis. In the last three decades, a number of molecular marker techniques have been developed and exploited in different plant breeding-related techniques worldwide.

Although, the choice of the genetic marker will obviously depend on the targeted use, microsatellites, single nucleotide polymorphisms (SNPs), and genotyping by sequencing largely fulfill most of the consumer requirements. Further, modern transcriptomic approaches will lead to the high-density genetic or linkage map construction, identification of stress-responsive QTLs, identification of trait-specific QTLs, and breeding with other high throughput techniques. Therefore, DNA marker or molecular markers technology's success in bringing genetic improvement in crop plants would depend on the positive interaction between plant breeders and plant biotechnologists.

Molecular markers are commonly used to assess genetic variation in agronomic germplasm, analyze population structure, localize quantitative traits (QTL), or linkage mapping for gene mapping. The most interesting application of molecular markers is marker-assisted selection (MAS). Molecular marker technology enables plant breeders to select individual plants based on their marker pattern (genotype) rather than their observable traits (phenotype). This process is called marker assisted selection (MAS) or marker assisted breeding (MAB). Compared with traditional breeding programs, molecular markers can increase the efficiency and effectiveness of breeding programs. Molecular markers in the construction of linkage maps, they have numerous applications in plant breeding such as assessing the genetic variations within cultivars and germplasms. Molecular markers are one of the most powerful tools for studying genetic diversity. They are used in the study of phylogenetic relationships, selection of superior plants, and the study of similarities or differences between different specimens. Molecular markers are also used in germplasm management and marker-assisted selection (MAS) to increase the efficiency of germplasm breeding.