Tolerance to abiotic stress is an important agronomic trait in crops and is controlled by many genes, which are called quantitative trait loci (QTLs). Identification of these QTLs will contribute not only to the understanding of plant biology but also for plant breeding to achieve stable crop production around the world. Previously, we mapped three QTLs controlling low temperature tolerance at germination stage (called low temperature germinability). To understand the molecular basis of low temperature germinability, the most effective QTL, qLTG3-1 (quantitative trait locus for low temperature germinability on chromosome 3), was cloned by map-based cloning strategy. qLTG3-1 is strongly expressed in the embryo during seed germination. Prior to and during seed germination, specific localization of GUS staining in the tissues covering the embryo, which involved the epiblast covering the coleoptile and the aleurone layer of the seed coat, was observed in the promoter-GUS experiment. Expression of qLTG3-1 was tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. These phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants. However, qLTG3-1 encods a protein of unknown function. In this study, microarray analysis was performed to elucidate the molecular function of qLTG3-1.