Background

Rice (Oryza sativa L.) yield is seriously influenced by panicle exsertion (PE) and the uppermost internode (UI) through panicle enclosure or energy transport during grain-filling stages. We evaluated the traits of PE and UI of 205 rice accessions in two independent environments and performed genome-wide association (GWAS) to explore the key genes controlling PE and UI, which could be used to improve panicle enclosure in rice breeding.

Results

In this study, extensive genetic variation was found in both PE and UI among the 205 rice accessions, and 10.7% of accessions had panicle enclosure (PE/UI ≤ 0). Correlation analysis revealed that PE was significantly positively correlated with 1000-grain weight (1000-GW) but negatively correlated with heading date (HD), and UI was significantly positively correlated with HD but no significantly correlated with 1000-GW. A total of 22 and 24 quantitative trait loci (QTLs) were identified for PE and UI using GWAS, respectively. Eight loci for PE and nine loci for UI were simultaneously detected both in 2015 and in 2016, seven loci had adjacent physical positions between PE and UI, and ten loci for PE and seven loci for UI were located in previously reported QTLs. Further, we identified the CYP734A4 gene, encoding a cytochrome P450 monooxygenase, and the OsLIS-L1 gene, encoding a lissencephaly type-1-like protein, as causal genes for qPE14 and qUI14, and for qPE19, respectively. PE and UI were both significantly shorter in these two genes’ mutants than in WT. Allelic Hap.1/2/4 of CYP734A4 and Hap.1/2/4 of OsLIS-L1 increased PE, UI, PE/UI, and 1000-GW, but Hap.3 of CYP734A4 and Hap.3 of OsLIS-L1 reduced them. In addition, six candidate genes were also detected for four key novel loci, qPE16, qPE21, qUI1, and qUI18, that seemed to be related to PE and UI.

Conclusions

Our results provide new information on the genetic architecture of PE and UI in rice, confirming that the CYP734A4 and OsLIS-L1 genes participate in PE and UI regulation, which could improve our understanding of the regulatory mechanism of PE and UI for rice breeding in the future.

中文翻译：

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水稻（Oryza sativa L.）穗伸长与最上节间的全基因组关联分析。

背景

水稻（Oryza sativa L.）的产量受到穗膨化（PE）和最高穗节间（UI）的影响，该过程通过穗包裹或在灌浆期进行能量传递。我们在两个独立的环境中评估了205个水稻品种的PE和UI特性，并进行了全基因组关联（GWAS）探索控制PE和UI的关键基因，这些基因可用于改善水稻育种的穗套。

结果

在这项研究中，在205个水稻种质中，PE和UI均存在广泛的遗传变异，其中10.7％的种质具有穗套（PE / UI≤0）。相关分析表明，PE与千粒重（1000-GW）显着正相关，而与抽穗期（HD）负相关，UI与HD显着正相关，而与1000-GW无显着相关。使用GWAS分别为PE和UI鉴定了22个和24个定量性状基因座（QTL）。在2015年和2016年同时检测到8个PE基因座和9个UI基因座，其中7个基因座在PE和UI之间的物理位置相邻，而10个PE基因座和7个UI基因座位于先前报告的QTL中。此外，我们确定了CYP734A4基因，编码细胞色素P450单加氧酶，和OsLIS-L1基因，无脑回畸形类型1样，蛋白质作为因果基因编码qPE14和qUI14，以及用于qPE19分别。在这两个基因的突变体中，PE和UI均显着短于WT。CYP734A4的等位基因Hap.1 / 2/4和OsLIS -L1的等位基因Hap.1 / 2/4增加PE，UI，PE / UI和1000-GW，但CYP734A4的等位基因3和OsLIS-L1的Hap.3减少它们。此外，还检测到四个关键新基因座qPE16，qPE21，qUI1和qUI18的六个候选基因。，这似乎与PE和UI有关。

结论

我们的结果为水稻中PE和UI的遗传结构提供了新的信息，证实CYP734A4和OsLIS-L1基因参与PE和UI调控，这可以增进我们对PE和UI在水稻育种中的调控机制的了解。未来。