Since rice needs more water to grow than other cereals, therefore it would be more vulnerable to
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.