Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)
Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)
复制标题
水稻穗外伸和最上部节间的全基因组关联分析（Oryza sativa L.）
DOI：
10.1186/s12284-019-0330-x
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发表时间：
2019
期刊：
影响因子：
5.5
通讯作者：
Jinping Cheng
中科院分区：
文献类型：
--
作者：
Chengfang Zhan;Jiaxiao Hu;Qiao Pang;Bin Yang;Yanhao Cheng;Enshun Xu;Peiwen Zhu;Yingyi Li;Hongsheng Zhang;Jinping Cheng
研究背景水稻（Oryza sativa L.）穗伸出度（PE）和最上部节间（UI）通过穗围合或灌浆期能量运输对产量产生严重影响。本研究以205份水稻材料为材料，在两个独立的环境中对穗长和穗长进行了分析，并进行了全基因组关联分析（GWAS），以寻找控制穗长和穗长的关键基因，为水稻育种提供参考。有10.7%的材料发生了包穗现象（PE/UI ≤ 0）。相关分析表明，PE与千粒重呈显著正相关，与抽穗期呈显著负相关; UI与抽穗期呈显著正相关，与千粒重相关不显著。利用GWAS分别检测到22个和24个影响PE和UI的数量性状位点（QTL）。在2015年和2016年同时检测到8个PE位点和9个UI位点，其中7个位点位于PE和UI之间，另外10个PE位点和7个UI位点位于先前报道的QTL中。此外，我们确定了CYP 734 A4基因，编码细胞色素P450单加氧酶，和OsLIS-L1基因，编码无脑1型样蛋白，作为致病基因qPE 14和qUI 14，和qPE 19，分别。PE和UI在这两个基因突变体中均显著短于WT。CYP 734 A4等位基因Hap.1/2/4和OsLIS-L1等位基因Hap.1/2/4使PE、UI、PE/UI和1000-GW增加，而CYP 734 A4等位基因Hap.3和OsLIS-L1等位基因Hap.3使其减少。此外，还检测到了4个与PE和UI相关的关键新位点（qPE 16、qPE 21、qUI 1和qUI 18）的6个候选基因。结论本研究为水稻PE和UI的遗传结构提供了新的信息，证实了CYP 734 A4和OsLIS-L1基因参与PE和UI的调控，这将有助于我们进一步了解PE和UI的调控机制，为今后的水稻育种提供参考。
BackgroundRice (Oryza sativaL.) 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.ResultsIn 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 theCYP734A4gene, encoding a cytochrome P450 monooxygenase, and theOsLIS-L1gene, encoding a lissencephaly type-1-like protein, as causal genes forqPE14andqUI14, and forqPE19, respectively. PE and UI were both significantly shorter in these two genes’ mutants than in WT. Allelic Hap.1/2/4 ofCYP734A4and Hap.1/2/4 ofOsLIS-L1increased PE, UI, PE/UI, and 1000-GW, but Hap.3 ofCYP734A4and Hap.3 ofOsLIS-L1reduced them. In addition, six candidate genes were also detected for four key novel loci,qPE16,qPE21,qUI1, andqUI18, that seemed to be related to PE and UI.ConclusionsOur results provide new information on the genetic architecture of PE and UI in rice, confirming that theCYP734A4andOsLIS-L1genes 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.