Background

Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far.

Results

In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2–3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2–12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2–10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2–10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2–10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3′ end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines.

Conclusion

Among the 11 QTLs identified in this study, qLTG_sRDP2–10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2–10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2–10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2–10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.

中文翻译：

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水稻低温发芽率稳定表达QTL的候选基因（Oryza sativa L.）

背景

直播是水稻高效栽培技术。然而，现代水稻品种的低温发芽性（LTG）较差限制了其应用。识别LTG相关基因并进行分子育种是解决这一问题的根本途径。然而，迄今为止，很少有LTG QTL被精细定位和克隆。

结果

本研究对水稻多样性Panel 2中选取的375份水稻材料的LTG评价表明，群体内LTG变异较大，籼稻组的LTG显着高于粳稻组和澳大利亚组（p  < 0.01） ）。通过全基因组关联研究 (GWAS) 总共鉴定了 11 个 LTG QTL。其中，qLTG_sRDP2–3/qLTG_JAP-3、qLTG_AUS-3和qLTG_sRDP2–12是本研究首次报道的。10 号染色体上的 QTL qLTG_sRDP2–10a对 375 个水稻品种中的 LTG 变异贡献最大，并使用单片段替换系 (SSSL) 进行了进一步验证。qLTG_sRDP2–10a的存在可导致在 15 °C 低温下 LTG 增加 59.8%。qLTG_sRDP2-10a区域内基因的表达分析表明，LOC_Os10g22520和LOC_Os10g22484在高LTG系和低LTG系之间表现出差异表达。进一步的序列比对发现，高、低LTG株系之间LOC_Os10g22520的启动子区和内含子区存在插入和缺失序列差异， LOC_Os10g22484的3′端存在约6 kb的变异，表明两者的序列变异基因可能是其在高 LTG 系和低 LTG 系中表达差异的原因。

结论

在本研究鉴定的11个QTL中，qLTG_sRDP2-10a在其他三项使用不同种质在不同寒冷环境下的研究中也可以检测到。其巨大的效应和稳定的表达使得qLTG_sRDP2-10a在水稻育种中特别有价值。LOC_Os10g22484和LOC_Os10g22520这两个基因被认为是qLTG_sRDP2–10a的候选基因。我们的结果表明，整合 GWAS 和 SSSL 可以促进水稻复杂性状 QTL 的鉴定。qLTG_sRDP2-10a及其候选基因的鉴定为LTG基因克隆和水稻LTG分子育种提供了良好的资源。