Plant Breeding has utilized a wide range of techniques and methods to improve the quality and quantity of plants. The molecular markers are the tools that have provided a new perspective for plant breeding advancements. This article has reviewed the various advantages and uses of molecular markers and the utilization of the high potential of natural polymorphisms within communities, combined with the abilities of conventional plant breeding methods. The marker attributes are not subject to environmental influence and their high frequency of these markers in their number, high structural diversity are as part of their benefits in identifying identities, determining the genetic diversity of species and studying relationship between populations. They may aid in discovering more information about protecting and maintaining genetic stock collections, identifying varieties, determining genes with chromosomal location and the number of genes controlling traits. Genome sequencing, the preparation of physical and genetic maps, genomic fingerprinting of plants are some of the other applications of this tool in plant breeding. The high efficiency of selection with the help of markers in selection of genotypes has been emphasized as the parent of crosses and selection with the help of a marker in breeding programs and genomic selection. New technologies offers new opportunities to shape genetic variation in the improvement of specific plant breeding programs. Nowadays development of next-generation sequencing technology, genome sequencing and high throughput approaches for markers have facilitated EST-derived simple sequence repeat (EST-SSR) marker development as well as single nucleotide polymorphism (SNP) marker. These markers can be successfully employed in accelerating research and plant breeding programs.

In a breeding program, it is important to find out information about the genes action, because knowledge in this field could help the researchers in their crossing programs and realizing effective selection. In this study, breeding values of different agronomic traits in oriental tobacco were predicted using the best linear unbiased prediction (BLUP) procedure. For this purpose, 89 tobacco genotypes were evaluated in a randomized complete block design with three replications under normal (without broomrape) and stress (with broomrape) conditions at Urmia Tobacco Research Centre, during two successive years. Broomrape stress was applied by mixing 0.06 gr broomrape seed with soil in pots. C.H.T.209.12e × F.K.40-1 genotype had high yield under both normal and broomrape stress conditions and was one of the desirable genotypes in terms of yield tolerance and stability index. The Rustica genotype was the best genotype in terms of the breeding value of most of studied traits in both normal and broomrape stress conditions. The result from cluster analysis based on the breeding values of the studied traits showed that, tobacco genotypes were divided into 6 and 5 groups in normal and broomrape stress conditions, respectively; but the distribution of genotypes within the groups was different depending on the conditions. The highest heritability was observed for root fresh weight under normal condition and for leaf fresh weight under broomrape stress conditionss. The results showed that a genotype with good phenotypic performance may have low breeding value. Therefore, considering breeding value information along with phenotypic mean of traits can increase the efficiency of breeding programs.