The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The “green revolution” gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene. We identified a PH-related quantitative trait locus, qCL1.2,from wild riceusing a set of chromosome segment substitution lines. qCL1.2encodesa novel allele of SD1 gene. The wild allele of SD1 is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the SD1 gene were performed using 2822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated japonica and indica rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increasesunderstanding of the rice SD1 gene and provides additional evidence of this gene’s selection during rice domestication. Our findings provide evidence thatSD1 gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.

中文翻译：

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qCL1.2的鉴定和遗传分析，qCL1.2是来自野生稻（Oryza rufipogon）的“绿色革命”基因SD1的新等位基因，可提高株高。

从野生稻中收获在水稻种植过程中丢失的新等位基因对于水稻育种和进化研究可能非常重要。株高（PH）是水稻驯化过程中人工选择的目标，仍然是现代育种的目标。在过去的几十年中，“绿色革命”基因半矮1（SD1）得到了充分的文献证明和使用，来自野生稻的等位基因可能为该基因的功能和进化提供新的见识。我们使用一组染色体片段替代品系从野生稻中鉴定出与PH相关的数量性状基因座qCL1.2。qCL1.2编码SD1基因的新等位基因。SD1的野生等位基因是一个显性位点，可通过调节赤霉素生物合成和信号转导中涉及的基因的表达水平来显着提高水稻节间长度。使用2822个水稻地方品种对SD1基因进行核苷酸多样性和单倍型网络分析。先前报道的两个功能核苷酸多态性清楚地区分了粳稻和in稻。但是，它们与PH选择无关。水稻驯化过程中，编码区（而非启动子区）中的其他新功能核苷酸多态性参与了PH选择。我们的研究增加了对水稻SD1基因的了解，并为水稻驯化过程中该基因的选择提供了更多证据。我们的发现提供了证据，表明来自野生稻的SD1基因可提高株高，并且在栽培稻分化过程中人为选择了该基因的新功能核苷酸多态性。先前报道的两个功能核苷酸多态性清楚地区分了粳稻和in稻。但是，它们与PH选择无关。水稻驯化过程中，编码区（而非启动子区）中的其他新功能核苷酸多态性参与了PH选择。我们的研究增加了对水稻SD1基因的了解，并为水稻驯化过程中该基因的选择提供了更多证据。我们的发现提供了证据，表明来自野生稻的SD1基因可提高株高，并且在栽培稻分化过程中人为选择了该基因的新功能核苷酸多态性。先前报道的两个功能核苷酸多态性清楚地区分了粳稻和in稻。但是，它们与PH选择无关。水稻驯化过程中，编码区（而非启动子区）中的其他新功能核苷酸多态性参与了PH选择。我们的研究增加了对水稻SD1基因的了解，并为水稻驯化过程中该基因的选择提供了更多证据。我们的发现提供了证据，表明来自野生稻的SD1基因可提高株高，并且在栽培稻分化过程中人为选择了该基因的新功能核苷酸多态性。水稻驯化过程中，编码区（而非启动子区）中的其他新功能核苷酸多态性参与了PH选择。我们的研究增加了对水稻SD1基因的了解，并为水稻驯化过程中该基因的选择提供了更多证据。我们的发现提供了证据，表明来自野生稻的SD1基因可提高株高，并且在栽培稻分化过程中人为选择了该基因的新功能核苷酸多态性。水稻驯化过程中，编码区（而非启动子区）中的其他新功能核苷酸多态性参与了PH选择。我们的研究增加了对水稻SD1基因的了解，并为水稻驯化过程中该基因的选择提供了更多证据。我们的发现提供了证据，表明来自野生稻的SD1基因可提高株高，并且在栽培稻分化过程中人为选择了该基因的新功能核苷酸多态性。