Characterization of a New qLTG3–1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon

Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production systems that use direct-seeding, low-temperature germinability (LTG) is a desired trait. Previously, the QTLs, qLTG1 and qLTG3, that control LTG, were mapped using the BC4F8 population, which is a cross of Korean elite cultivar Hwaseong and O. rufipogon (IRGC 105491). We have characterized and analyzed the interaction between the two QTLs, by crossing TR20 that has O. rufipogon alleles at qLTG1 and qLTG3 in a Hwaseong background, with Hwaseong, to develop an F2 population. The F2 plants with both qLTG1 and qLTG3 alleles from O. rufipogon showed higher LTG scores, than the plants with only qLTG1 or qLTG3. No significant interaction between the qLTG1 and qLTG3 was observed, indicating that they may regulate LTG via different pathways. Based on its location, qLTG3 appears to be allelic with qLTG3–1, a major QTL known to control LTG. To investigate the genetic differences between the two parents, that were controlling LTG, we compared their qLTG3–1 sequences. In the coding region, three sequence variations leading to amino acid changes were identified between the Hwaseong and O. rufipogon. Of these, a non-synonymous substitution at the 62nd amino acid site, had not previously been reported. To understand the cause of the LTG variations between the parents, we genotyped three sequence variations of qLTG3–1, that were identified in 98 Asian cultivated rice accessions (Oryza sativa L.). The 98 accessions were classified into 5 haplotypes, based on three variations and a 71-bp deletion. Mean low-temperature germination rates were compared among the haplotypes, and haplotype 5 (O. rufipogon-type) showed a significantly higher germination rate than haplotype 2 (Nipponbare-type), and haplotype 3 (Italica Livorno-type). The O. rufipogon qLTG3–1 allele can be utilized for the improvement of LTG in rice breeding programs. Nearly isogenic lines harboring both qLTG1 and qLTG3–1 alleles from O. rufipogon, showed higher LTG scores than the NILs with qLTG1 or qLTG3–1 alone, and the two QTLs regulate LTG via different pathways. To our knowledge, this is the first report to detect a new qLTG3–1 allele and analyze the interaction of the two LTG QTLs in a nearly isogenic background.