For the introduction of low temperature germinability (LTG), seed longevity and accelerated coleoptile growth derived from foreign varieties to Japanese elite varieties to breed rice varieties for direct seeding culture in Japan, we tried to establish backcross breeding to introduce these traits with marker-assisted selection (MAS). The objectives of this study were to identify quantitative trait loci (QTLs) for LTG and seed longevity using backcross inbred lines derived from a cross between a japonica variety Nipponbare and an indica variety Kasalath in order to facilitate MAS of these traits. Five putative QTLs controlling LTG were detected on chromosomes 2, 4 and 11. A putative QTL with a large seed longevity effect was detected on chromosome 9. We bred a near isogenic line for coleoptile growth by a backcross between Kitaibuki as the recurrent parent and Arroz da Terra as the donor parent to have more rapid coleoptile growth and higher seedling establishment rate than Kitaibuki. From the above experimental data, we conclude that backcross breeding with MAS is effective to introduce genes for adaptability to direct seeding from foreign varieties in Japanese rice breeding programs.