qLTG3-1 is a major quantitative trait locus (QTL) controlling tolerance to low-temperature at the seed germination stage (termed low-temperature germinability) in rice using a population derived from the cross between Italica Livorno from Italy and Hayamasari from Japan. Map-based cloning identified that qLTG3-1 encodes a protein of unknown function. The molecular identification of this major QTL could make it possible to identify allelic variation and favorable alleles for rice breeding programs. The present study examined the identification of qLTG3-1 alleles and their distribution among 62 landraces of Asian cultivated rice (Oryza sativa L.) collected from 19 different countries, termed the rice core collection. In the coding region, a single non-synonymous substitution and 3 in-frame insertion/deletion polymorphisms (indels) were detected. The almost completely conserved protein alignment of qLTG3-1 was also identified among 5 Oryza species, suggesting that the function of qLTG3-1 is critical for seed germination or for rice growth by pleiotropic effects of the gene. The functional nucleotide polymorphisms (FNPs), a 71-bp deletion found in Hayamasari and an amino acid substitution found in Nipponbare, was identified in varieties from Japan. These alleles with FNPs might be adapted to rice cultivation in specific local conditions. The present results may contribute to the utilization of favorable alleles of qLTG3-1 for the improvement of low-temperature germinability in rice breeding programs.