water stress and, in this regard, it is necessary to improve rice cultivars to tolerance to environmental stresses. In this research 154 recombinant inbred lines (F9) derived from a cross between Shah-Pasand and IR28 in three conditions (non-stress, osmotic stress -0.3 and -0.6 Mpa induced through polyethylene glycol-6000) were evaluated as a factorial experiment in randomized complete block design. In addition, for molecular polymorphism experiment, 110 SSR and EST-SSR markers were assessed on parents of population and among them, 41 markers identified which had proper polymorphism between two parents. The regression analysis between germination components and molecular markers revealed the most coefficient of determination were found in RM211 for allometric coefficient (17%) under non-stress, RMES10-1 for Plumule dry weight (18%) under -0.3 MPa; and RM273 for germination uniformity (22.7%) under -0.6 MPa. RM3496, RM452, and RMES6-1 in three conditions had the most number of significant relationships with six, three and eight traits, respectively, and they can be a suitable candidate for simultaneous improvement of several traits in breeding programs of marker-assisted selection. In addition, after the identification of significant markers associated with germination components, the closest genes to these markers were identified using bioinformatic analysis, and the analysis of their expression were performed by rice transcriptome database. According to the results, the maximum gene expression pattern under drought stress and under non-stress conditions were related to loci LOC_Os01g57220 and LOC_Os01g26039, respectively and this information could be applied in breeding programs.