Department of Biology, University of Central Arkansas, Conway, AR, 72035, USA.
Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.
Plant Mol Biol. 2020 May;103(1-2):113-128. doi: 10.1007/s11103-020-00978-0. Epub 2020 Feb 21.
Using a time-course RNA-seq analysis we identified transcriptomic changes during formation of nodule-like structures (NLS) in rice and compared rice RNA-seq dataset with a nodule transcriptome dataset in Medicago truncatula. Plant hormones can induce the formation of nodule-like structures (NLS) in plant roots even in the absence of bacteria. These structures can be induced in roots of both legumes and non-legumes. Moreover, nitrogen-fixing bacteria can recognize and colonize these root structures. Therefore, identifying the genetic switches controlling the NLS organogenesis program in crops, especially cereals, can have important agricultural implications. Our recent study evaluated the transcriptomic response occurring in rice roots during NLS formation, 7 days post-treatment (dpt) with auxin, 2,4-D. In this current study, we investigated the regulation of gene expression occurring in rice roots at different stages of NLS formation: early (1-dpt) and late (14-dpt). At 1-dpt and 14-dpt, we identified 1662 and 1986 differentially expressed genes (DEGs), respectively. Gene ontology enrichment analysis revealed that the dataset was enriched with genes involved in auxin response and signaling; and in anatomical structure development and morphogenesis. Next, we compared the gene expression profiles across the three time points (1-, 7-, and 14-dpt) and identified genes that were uniquely or commonly differentially expressed at all three time points. We compared our rice RNA-seq dataset with a nodule transcriptome dataset in Medicago truncatula. This analysis revealed there is some amount of overlap between the molecular mechanisms governing nodulation and NLS formation. We also identified that some key nodulation genes were not expressed in rice roots during NLS formation. We validated the expression pattern of several genes via reverse transcriptase polymerase chain reaction (RT-PCR). The DEGs identified in this dataset may serve as a useful resource for future studies to characterize the genetic pathways controlling NLS formation in cereals.
利用时间进程 RNA-seq 分析，我们鉴定了在水稻根结状结构（NLS）形成过程中的转录组变化，并将水稻 RNA-seq 数据集与 Medicago truncatula 的根瘤转录组数据集进行了比较。植物激素可以在没有细菌的情况下诱导植物根形成根结状结构（NLS）。这些结构可以在豆科植物和非豆科植物的根中诱导。此外，固氮细菌可以识别和定植这些根结构。因此，鉴定控制作物，尤其是谷类作物 NLS 器官发生程序的遗传开关具有重要的农业意义。我们最近的研究评估了在生长素 2,4-D 处理后 7 天（dpt），水稻根中发生的 NLS 形成过程中的转录组反应。在本研究中，我们研究了在 NLS 形成的不同阶段（早期 1-dpt 和晚期 14-dpt）中发生的基因表达调控。在 1-dpt 和 14-dpt 时，我们分别鉴定了 1662 个和 1986 个差异表达基因（DEGs）。基因本体富集分析表明，该数据集富含参与生长素反应和信号转导以及解剖结构发育和形态发生的基因。接下来，我们比较了三个时间点（1-dpt、7-dpt 和 14-dpt）的基因表达谱，并鉴定了在所有三个时间点均唯一或共同差异表达的基因。我们将我们的水稻 RNA-seq 数据集与 Medicago truncatula 的根瘤转录组数据集进行了比较。这项分析表明，调控结瘤和 NLS 形成的分子机制之间存在一定程度的重叠。我们还发现，一些关键的结瘤基因在 NLS 形成过程中不在水稻根中表达。我们通过反转录聚合酶链反应（RT-PCR）验证了几个基因的表达模式。本数据集鉴定的 DEGs 可能成为未来研究的有用资源，用于表征控制谷类作物 NLS 形成的遗传途径。
