Mapping quantitative trait loci controlling low temperature germinability in rice (Oryza sativa L.)

Quantitative trait loci (QTLs) controlling low temperature germinability (LTG) in rice were identified using 98 backcross inbred lines (BILs) derived from a cross between a japonica variety Nipponbare and an indica variety Kasalath. Seeds of each BIL were stored at 30degreesC in a drying machine for 7 months to exclude the effects of seed dormancy. Then the germination rate at 15degreesC for 4 days was scored to represent the LTG. The LTG of Nipponbare and Kasalath was 17 and 61%, respectively, and that of the BILs ranged from 0 to 100%. Five putative QTLs, qLTG-2, qLTG-4-1, qLTG-4-2, qLTG-5 and qLTG-11, were detected on chromosome 2 (G1327: nearest marker locus), 4 (two regions, C946 and C513), 5 (11830) and chromosome 11 (G1465). In the case of qLTG-2, qLTG-4-1 and qLTG-11, Kasalath alleles increased the LTG, while Nipponbare alleles increased it in the case of qLTG-4-2 and qLTG-5. These QTLs explained 40.7% of the total phenotypic variation in the BC1F9 lines. Using chromosome segment substitution lines (SLs), the existence of qLTG-4-1 and qLTG-11 was confirmed and the effect of the Kasalath allele on qLTG-11 was more pronounced than that on qLTG-4-1. The effect of the Kasalath allele on qLTG-4-2, which suppressed the germination, was temporary and disappeared after 7 to 8 month's storage, suggesting that the disappearance was due to the breaking of seed dormancy and that qLTG-4-2 might control it. Kasalath allele in the case of qLTG-5 decreased the germination rate when the effect of dormancy was completely removed. Therefore, we concluded that qLTG-5 was involved in LTG but not in seed dormancy.