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 the germination stage (called low-temperature germinability). To understand the molecular basis of one of these QTLs, qLTG3-1 (quantitative trait locus for low-temperature germinability on chromosome 3), map-based cloning was performed, and this QTL was shown to be encoded by a protein of unknown function. The QTL qLTG3-1 is strongly expressed in the embryo during seed germination. Before and during seed germination, specific localization of beta-glucuronidase staining in the tissues covering the embryo, which involved the epiblast covering the coleoptile and the aleurone layer of the seed coat, was observed. 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.natural variation ͉ QTLs ͉ seed germination T he control of seed dormancy and germination is important for the adaptability of plants, and germination under favorable environmental conditions is needed for their survival. Seed dormancy and germination is a complex trait influenced by many genes and environmental conditions (1). In addition, the plant hormones gibberellin and abscisic acid (ABA) play important roles in the expression of seed dormancy and germination (2, 3).Strong seedling vigor under low temperatures is an important objective of rice breeding programs in direct-seeding cultivation methods in temperate rice-growing areas, at high altitudes in tropical and subtropical areas, and in areas with a cold irrigation water supply where low temperature induces retardation of early seedling growth. Germinability (germination rate) and early seedling growth are major components of seedling vigor. A wide range of phenotypic variation of low-temperature germinability was found in rice cultivars. Quantitative trait loci (QTL) analysis for low temperature germinability revealed that many genes control this trait (4-6). However, the molecular functions of the genes for these QTLs have not been identified.A QTL mapping approach is effective to detect genes controlling traits involved in seed germination. Under several kinds of stress, such as temperature, NaCl, and osmotic pressure, germination is delayed or inhibited. QTLs for the speed of germination may be important for germination in general and may not be affected by any kind of stress (7,8). QTLs for the speed of germination collocated with those of ABA sensitivity a...