Quantitative trait loci (QTL) affecting the germination rate, coleoptile length, and shoot dry weight were analyzed under submerged and low temperature conditions using inbred lines derived from crossing the rice cultivars Ouu 365 and Arroz da Terra. The QTIs that increased the germination rate and shoot dry weight by Arroz da Terra allele were detected on the same region of chromosome 3, where the low temperature germinability gene, qLTG3-1, localized, suggesting that greater germinability might lead to increased shoot growth in paddy fields. The QTLs that increased the coleoptile length by Ouu 365 and Arroz da Terra alleles were detected on chromosome 8 and 11, respectively. The analysis of the known germinability genes suggested that functional allele of qLTG3-1 increased germination rates of the inbred lines. However, Rc which induced red pigmentation in pericarp declined the germination rates of the lines with functional qLTG3-1.