Background

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.

Results

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).

Conclusions

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.

中文翻译：

---

新型qLTG3-1等位基因在野生稻米中的低温萌发特性

背景

稻米（Oryza sativa L.）通常对低温敏感，在使用直接播种的生产系统中，低温发芽性（LTG）是理想的特性。此前，的QTL，qLTG1和qLTG3，该控制LTG，使用BC被映射₄ ˚F ₈人口，其是韩国良种华和的横野生稻（IRGC 105491）。我们有特点和分析的QTL之间的相互作用，通过跨越TR20具有野生稻的等位基因qLTG1和qLTG3在华的背景下，与华城，开发一个F ₂群体。

结果

在F ₂植物既qLTG1和qLTG3从等位基因的野生稻具有较高的LTG的分数，比只用植物qLTG1或qLTG3。没有观察到qLTG1和qLTG3之间的显着相互作用，表明它们可能通过不同的途径调节LTG。根据其位置，qLTG3似乎与已知控制LTG的主要QTL qLTG3-1等位基因。为了研究控制LTG的两个亲本之间的遗传差异，我们比较了它们的qLTG3-1序列。在该编码区中，在华城和红景天之间鉴定出导致氨基酸变化的三个序列变异。其中，先前没有报道在第62个氨基酸位点的非同义取代。为了解亲本之间LTG变异的原因，我们对qLTG3-1的三个序列变异进行了基因分型，这些变异在98个亚洲栽培稻种（水稻）中鉴定出。根据三个变异和一个71 bp的缺失，将98个登录号分为5个单倍型。比较了单倍型和单倍型5（O。rufipogon）之间的平均低温发芽率-型）的发芽率明显高于单倍型2（日本晴型）和单倍型3（Italica Livorno-型）。

结论

的普通野生稻qLTG3-1等位基因可以用于LTG在稻育种计划的改善。近等基因系窝藏既qLTG1和qLTG3-1从等位基因普通野生稻，显示出更高的LTG分数比使用近等基因系qLTG1或qLTG3-1单独，并且两个的QTL经由不同途径调节LTG。据我们所知，这是第一个检测新的qLTG3-1等位基因并在接近等基因背景下分析两个LTG QTL相互作用的报告。